0s autopkgtest [23:30:55]: starting date and time: 2025-03-15 23:30:55+0000
  0s autopkgtest [23:30:55]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [23:30:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rfujrehb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade trinityrnaseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-5.secgroup --name adt-plucky-amd64-trinityrnaseq-20250315-233054-juju-7f2275-prod-proposed-migration-environment-2-f4af3eb7-81b6-4cd4-bb96-bbab953f2788 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 98s autopkgtest [23:32:33]: testbed dpkg architecture: amd64
 98s autopkgtest [23:32:33]: testbed apt version: 2.9.31ubuntu1
 98s autopkgtest [23:32:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 99s autopkgtest [23:32:34]: testbed release detected to be: None
 99s autopkgtest [23:32:34]: updating testbed package index (apt update)
100s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
100s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
100s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
100s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
100s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB]
100s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB]
100s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB]
100s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB]
100s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB]
100s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B]
100s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B]
100s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB]
100s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB]
100s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB]
100s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B]
100s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB]
100s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B]
101s Fetched 1265 kB in 1s (1447 kB/s)
102s Reading package lists...
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
103s Calculating upgrade...
103s Calculating upgrade...
103s The following package was automatically installed and is no longer required:
103s   libnl-genl-3-200
103s Use 'sudo apt autoremove' to remove it.
104s The following NEW packages will be installed:
104s   bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10
104s   linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic
104s   linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic
104s   linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids
104s The following packages will be upgraded:
104s   apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu
104s   cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base
104s   gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools
104s   initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0
104s   libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1
104s   libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0
104s   libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1
104s   libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64
104s   libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6
104s   libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200
104s   libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib
104s   libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2
104s   libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0
104s   libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2
104s   linux-firmware linux-generic linux-headers-generic linux-headers-virtual
104s   linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common
104s   linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term
104s   parted pci.ids pciutils pinentry-curses python-apt-common python3
104s   python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi
104s   python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal
104s   python3-newt python3-rpds-py python3-systemd python3-yaml python3.13
104s   python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd
104s   systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd
104s   ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail
104s   xz-utils
104s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded.
104s Need to get 829 MB of archives.
104s After this operation, 325 MB of additional disk space will be used.
104s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB]
104s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB]
104s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB]
104s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB]
104s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB]
104s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB]
104s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB]
105s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB]
105s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB]
105s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB]
105s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB]
105s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB]
105s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB]
105s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB]
105s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB]
105s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB]
105s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB]
105s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB]
105s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB]
105s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB]
105s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB]
105s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB]
105s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB]
105s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB]
105s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB]
105s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB]
105s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B]
105s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB]
105s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB]
105s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB]
105s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB]
105s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB]
105s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB]
105s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB]
105s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB]
105s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB]
105s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB]
105s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB]
105s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB]
105s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB]
105s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB]
105s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB]
105s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB]
105s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB]
105s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB]
105s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB]
105s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB]
105s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB]
105s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB]
105s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB]
105s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B]
105s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB]
105s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB]
105s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB]
105s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB]
105s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB]
106s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB]
106s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B]
106s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB]
106s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB]
106s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB]
106s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB]
106s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB]
106s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB]
106s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB]
106s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB]
106s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB]
106s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB]
106s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB]
106s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB]
106s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB]
106s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB]
106s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB]
106s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB]
106s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB]
106s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB]
106s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB]
106s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB]
106s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB]
106s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB]
106s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB]
106s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB]
106s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB]
106s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB]
106s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB]
106s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB]
106s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB]
106s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB]
106s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB]
106s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB]
106s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB]
106s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB]
106s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B]
106s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB]
106s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB]
106s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB]
106s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB]
106s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
106s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB]
106s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB]
106s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB]
106s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB]
107s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB]
107s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB]
107s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB]
107s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB]
107s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB]
107s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB]
107s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB]
127s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B]
127s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB]
127s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB]
127s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB]
127s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB]
127s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB]
127s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB]
127s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB]
128s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB]
129s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB]
133s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B]
133s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB]
133s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B]
133s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB]
133s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B]
133s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB]
133s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB]
133s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB]
133s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB]
134s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB]
134s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B]
134s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB]
134s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB]
134s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB]
134s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB]
134s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB]
134s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB]
134s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B]
134s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB]
134s Preconfiguring packages ...
134s Fetched 829 MB in 30s (27.5 MB/s)
135s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109140 files and directories currently installed.)
135s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ...
135s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ...
135s Setting up ncurses-bin (6.5+20250216-2) ...
135s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109140 files and directories currently installed.)
135s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ...
135s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
135s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ...
135s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
135s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ...
135s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
135s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ...
135s Checking for services that may need to be restarted...
135s Checking init scripts...
135s Checking for services that may need to be restarted...
135s Checking init scripts...
136s Stopping some services possibly affected by the upgrade (will be restarted later):
136s   cron: stopping...done.
136s 
136s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
136s Setting up libc6:amd64 (2.41-1ubuntu1) ...
136s Checking for services that may need to be restarted...
136s Checking init scripts...
136s Restarting services possibly affected by the upgrade:
136s   cron: restarting...done.
136s 
136s Services restarted successfully.
136s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109141 files and directories currently installed.)
136s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ...
136s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ...
136s Setting up libc-bin (2.41-1ubuntu1) ...
136s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109141 files and directories currently installed.)
136s Preparing to unpack .../linux-libc-dev_6.14.0-10.10_amd64.deb ...
136s Unpacking linux-libc-dev:amd64 (6.14.0-10.10) over (6.12.0-16.16) ...
137s Preparing to unpack .../libatomic1_15-20250222-0ubuntu1_amd64.deb ...
137s Unpacking libatomic1:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ...
137s Preparing to unpack .../gcc-15-base_15-20250222-0ubuntu1_amd64.deb ...
137s Unpacking gcc-15-base:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ...
137s Setting up gcc-15-base:amd64 (15-20250222-0ubuntu1) ...
137s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
137s Preparing to unpack .../libgcc-s1_15-20250222-0ubuntu1_amd64.deb ...
137s Unpacking libgcc-s1:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ...
137s Setting up libgcc-s1:amd64 (15-20250222-0ubuntu1) ...
137s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
137s Preparing to unpack .../libstdc++6_15-20250222-0ubuntu1_amd64.deb ...
137s Unpacking libstdc++6:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ...
137s Setting up libstdc++6:amd64 (15-20250222-0ubuntu1) ...
137s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
137s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ...
137s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ...
137s Setting up ncurses-base (6.5+20250216-2) ...
137s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
137s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ...
137s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ...
138s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ...
138s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ...
138s Setting up liblz4-1:amd64 (1.10.0-4) ...
138s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
138s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ...
138s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ...
138s Setting up liblzma5:amd64 (5.6.4-1) ...
138s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
138s Preparing to unpack .../libsystemd0_257.3-1ubuntu3_amd64.deb ...
138s Unpacking libsystemd0:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Setting up libsystemd0:amd64 (257.3-1ubuntu3) ...
138s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
138s Preparing to unpack .../libnss-systemd_257.3-1ubuntu3_amd64.deb ...
138s Unpacking libnss-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Preparing to unpack .../systemd-sysv_257.3-1ubuntu3_amd64.deb ...
138s Unpacking systemd-sysv (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Preparing to unpack .../systemd-resolved_257.3-1ubuntu3_amd64.deb ...
138s Unpacking systemd-resolved (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Preparing to unpack .../libpam-systemd_257.3-1ubuntu3_amd64.deb ...
138s Unpacking libpam-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Preparing to unpack .../libsystemd-shared_257.3-1ubuntu3_amd64.deb ...
138s Unpacking libsystemd-shared:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
138s Setting up libsystemd-shared:amd64 (257.3-1ubuntu3) ...
139s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
139s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ...
139s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
139s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ...
139s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
139s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ...
139s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
139s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ...
139s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
139s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ...
139s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ...
139s Setting up libudev1:amd64 (257.3-1ubuntu3) ...
139s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
139s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ...
139s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ...
139s Setting up libaudit-common (1:4.0.2-2ubuntu2) ...
139s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
139s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ...
139s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ...
139s Setting up libcap-ng0:amd64 (0.8.5-4build1) ...
139s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
139s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ...
139s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ...
139s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ...
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
140s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu6_amd64.deb ...
140s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu6) over (2.5.5-1ubuntu5) ...
140s Setting up libseccomp2:amd64 (2.5.5-1ubuntu6) ...
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
140s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ...
140s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ...
140s Setting up libselinux1:amd64 (3.7-3ubuntu3) ...
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
140s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ...
140s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ...
140s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ...
140s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ...
140s Setting up libapt-pkg7.0:amd64 (2.9.33) ...
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
140s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ...
140s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ...
140s Setting up apt (2.9.33) ...
141s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
141s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ...
141s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ...
141s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ...
141s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ...
141s Setting up python3-minimal (3.13.2-2) ...
141s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
141s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ...
141s Unpacking python3 (3.13.2-2) over (3.13.2-1) ...
141s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ...
141s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ...
141s Preparing to unpack .../2-media-types_13.0.0_all.deb ...
141s Unpacking media-types (13.0.0) over (12.0.0) ...
141s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ...
141s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ...
141s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ...
141s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ...
141s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ...
141s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ...
141s Setting up libtinfo6:amd64 (6.5+20250216-2) ...
141s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109146 files and directories currently installed.)
141s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ...
141s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ...
141s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ...
142s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ...
142s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ...
142s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ...
142s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ...
142s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ...
142s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ...
142s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ...
142s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ...
142s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ...
142s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ...
142s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ...
142s Selecting previously unselected package libdebuginfod-common.
142s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ...
142s Unpacking libdebuginfod-common (0.192-4) ...
142s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ...
142s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ...
142s Setting up libsemanage-common (3.7-2.1build1) ...
142s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109155 files and directories currently installed.)
142s Preparing to unpack .../libsemanage2_3.7-2.1build1_amd64.deb ...
142s Unpacking libsemanage2:amd64 (3.7-2.1build1) over (3.7-2.1) ...
142s Setting up libsemanage2:amd64 (3.7-2.1build1) ...
142s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109155 files and directories currently installed.)
142s Preparing to unpack .../libassuan9_3.0.2-2_amd64.deb ...
142s Unpacking libassuan9:amd64 (3.0.2-2) over (3.0.1-2) ...
142s Setting up libassuan9:amd64 (3.0.2-2) ...
143s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109155 files and directories currently installed.)
143s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ...
143s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ...
143s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ...
143s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ...
143s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ...
143s Unpacking libglib2.0-0t64:amd64 (2.84.0-1) over (2.83.5-1) ...
143s Preparing to unpack .../03-libgirepository-1.0-1_1.83.4-1_amd64.deb ...
143s Unpacking libgirepository-1.0-1:amd64 (1.83.4-1) over (1.82.0-4) ...
143s Preparing to unpack .../04-libestr0_0.1.11-2_amd64.deb ...
143s Unpacking libestr0:amd64 (0.1.11-2) over (0.1.11-1build1) ...
143s Preparing to unpack .../05-libglib2.0-data_2.84.0-1_all.deb ...
143s Unpacking libglib2.0-data (2.84.0-1) over (2.83.5-1) ...
143s Preparing to unpack .../06-python3-newt_0.52.24-4ubuntu2_amd64.deb ...
143s Unpacking python3-newt:amd64 (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ...
143s Preparing to unpack .../07-libnewt0.52_0.52.24-4ubuntu2_amd64.deb ...
143s Unpacking libnewt0.52:amd64 (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ...
143s Preparing to unpack .../08-libxml2_2.12.7+dfsg+really2.9.14-0.2ubuntu5_amd64.deb ...
143s Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) over (2.12.7+dfsg+really2.9.14-0.2ubuntu4) ...
143s Preparing to unpack .../09-python-apt-common_2.9.9build1_all.deb ...
143s Unpacking python-apt-common (2.9.9build1) over (2.9.9) ...
143s Preparing to unpack .../10-python3-apt_2.9.9build1_amd64.deb ...
143s Unpacking python3-apt (2.9.9build1) over (2.9.9) ...
143s Preparing to unpack .../11-python3-cffi-backend_1.17.1-2build2_amd64.deb ...
143s Unpacking python3-cffi-backend:amd64 (1.17.1-2build2) over (1.17.1-2build1) ...
143s Preparing to unpack .../12-python3-dbus_1.3.2-5build5_amd64.deb ...
143s Unpacking python3-dbus (1.3.2-5build5) over (1.3.2-5build4) ...
143s Preparing to unpack .../13-python3-gi_3.50.0-4build1_amd64.deb ...
144s Unpacking python3-gi (3.50.0-4build1) over (3.50.0-4) ...
144s Preparing to unpack .../14-python3-yaml_6.0.2-1build2_amd64.deb ...
144s Unpacking python3-yaml (6.0.2-1build2) over (6.0.2-1build1) ...
144s Preparing to unpack .../15-rsyslog_8.2412.0-2ubuntu2_amd64.deb ...
144s Unpacking rsyslog (8.2412.0-2ubuntu2) over (8.2412.0-2ubuntu1) ...
144s Preparing to unpack .../16-whiptail_0.52.24-4ubuntu2_amd64.deb ...
144s Unpacking whiptail (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ...
144s Preparing to unpack .../17-ubuntu-minimal_1.549_amd64.deb ...
144s Unpacking ubuntu-minimal (1.549) over (1.548) ...
144s Preparing to unpack .../18-apparmor_4.1.0~beta5-0ubuntu8_amd64.deb ...
145s Unpacking apparmor (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ...
145s Preparing to unpack .../19-dosfstools_4.2-1.2_amd64.deb ...
145s Unpacking dosfstools (4.2-1.2) over (4.2-1.1build1) ...
145s Preparing to unpack .../20-libnl-genl-3-200_3.7.0-1_amd64.deb ...
145s Unpacking libnl-genl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ...
145s Preparing to unpack .../21-libnl-route-3-200_3.7.0-1_amd64.deb ...
145s Unpacking libnl-route-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ...
145s Preparing to unpack .../22-libnl-3-200_3.7.0-1_amd64.deb ...
145s Unpacking libnl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ...
145s Preparing to unpack .../23-parted_3.6-5_amd64.deb ...
145s Unpacking parted (3.6-5) over (3.6-4build1) ...
145s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ...
145s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64'
145s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64'
145s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ...
145s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ...
145s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ...
145s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ...
145s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ...
145s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ...
145s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ...
145s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ...
145s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
145s Preparing to unpack .../29-xz-utils_5.6.4-1_amd64.deb ...
145s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ...
145s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ...
145s Unpacking ubuntu-standard (1.549) over (1.548) ...
145s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ...
145s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ...
146s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ...
146s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ...
146s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ...
146s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ...
146s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ...
146s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ...
146s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ...
146s Preparing to unpack .../39-hwdata_0.393-3_all.deb ...
146s Unpacking hwdata (0.393-3) over (0.392-1) ...
146s Selecting previously unselected package pnp.ids.
146s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ...
146s Unpacking pnp.ids (0.393-3) ...
146s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ...
146s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ...
146s Selecting previously unselected package bpftool.
146s Preparing to unpack .../42-bpftool_7.6.0+6.14.0-10.10_amd64.deb ...
146s Unpacking bpftool (7.6.0+6.14.0-10.10) ...
146s Preparing to unpack .../43-python3-markupsafe_2.1.5-1build4_amd64.deb ...
146s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ...
146s Preparing to unpack .../44-python3-jinja2_3.1.5-2ubuntu1_all.deb ...
146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
146s Preparing to unpack .../45-cloud-init-base_25.1-0ubuntu3_all.deb ...
146s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ...
147s Preparing to unpack .../46-libbrotli1_1.1.0-2build4_amd64.deb ...
147s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ...
147s Preparing to unpack .../47-curl_8.12.1-3ubuntu1_amd64.deb ...
147s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ...
147s Preparing to unpack .../48-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ...
147s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ...
147s Preparing to unpack .../49-exfatprogs_1.2.8-1_amd64.deb ...
147s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ...
147s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ...
147s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ...
147s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ...
147s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ...
147s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ...
147s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ...
147s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ...
147s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ...
147s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ...
147s Unpacking htop (3.4.0-2) over (3.3.0-5) ...
147s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ...
147s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ...
151s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ...
151s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ...
151s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ...
151s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ...
151s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ...
151s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ...
151s Selecting previously unselected package libdebuginfod1t64:amd64.
151s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ...
151s Unpacking libdebuginfod1t64:amd64 (0.192-4) ...
151s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ...
151s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ...
151s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ...
151s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ...
151s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ...
151s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ...
151s Selecting previously unselected package linux-modules-6.14.0-10-generic.
151s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ...
151s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ...
151s Selecting previously unselected package linux-image-6.14.0-10-generic.
151s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ...
151s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ...
151s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic.
151s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ...
151s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ...
153s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ...
153s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ...
153s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ...
153s Unpacking linux-image-generic (6.14.0-10.10) over (6.12.0-16.16+2) ...
153s Preparing to unpack .../68-linux-virtual_6.14.0-10.10_amd64.deb ...
153s Unpacking linux-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ...
153s Preparing to unpack .../69-linux-image-virtual_6.14.0-10.10_amd64.deb ...
153s Unpacking linux-image-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ...
153s Preparing to unpack .../70-linux-headers-virtual_6.14.0-10.10_amd64.deb ...
153s Unpacking linux-headers-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ...
153s Selecting previously unselected package linux-headers-6.14.0-10.
153s Preparing to unpack .../71-linux-headers-6.14.0-10_6.14.0-10.10_all.deb ...
153s Unpacking linux-headers-6.14.0-10 (6.14.0-10.10) ...
155s Selecting previously unselected package linux-headers-6.14.0-10-generic.
155s Preparing to unpack .../72-linux-headers-6.14.0-10-generic_6.14.0-10.10_amd64.deb ...
155s Unpacking linux-headers-6.14.0-10-generic (6.14.0-10.10) ...
157s Preparing to unpack .../73-linux-headers-generic_6.14.0-10.10_amd64.deb ...
157s Unpacking linux-headers-generic (6.14.0-10.10) over (6.12.0-16.16+2) ...
157s Selecting previously unselected package linux-perf.
157s Preparing to unpack .../74-linux-perf_6.14.0-10.10_amd64.deb ...
157s Unpacking linux-perf (6.14.0-10.10) ...
157s Selecting previously unselected package linux-tools-6.14.0-10.
157s Preparing to unpack .../75-linux-tools-6.14.0-10_6.14.0-10.10_amd64.deb ...
157s Unpacking linux-tools-6.14.0-10 (6.14.0-10.10) ...
157s Selecting previously unselected package linux-tools-6.14.0-10-generic.
157s Preparing to unpack .../76-linux-tools-6.14.0-10-generic_6.14.0-10.10_amd64.deb ...
157s Unpacking linux-tools-6.14.0-10-generic (6.14.0-10.10) ...
157s Preparing to unpack .../77-pinentry-curses_1.3.1-2ubuntu3_amd64.deb ...
157s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
157s Preparing to unpack .../78-python3-lazr.uri_1.0.6-6_all.deb ...
157s Unpacking python3-lazr.uri (1.0.6-6) over (1.0.6-5) ...
157s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ...
158s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ...
158s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ...
158s Unpacking python3-systemd (235-1build6) over (235-1build5) ...
158s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ...
158s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ...
158s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ...
158s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ...
158s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ...
158s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ...
158s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ...
158s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ...
158s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ...
158s Setting up media-types (13.0.0) ...
158s Installing new version of config file /etc/mime.types ...
158s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ...
158s Setting up ubuntu-kernel-accessories (1.549) ...
158s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ...
158s Setting up pci.ids (0.0~2025.03.09-1) ...
158s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ...
158s Setting up apt-utils (2.9.33) ...
158s Setting up libdebuginfod-common (0.192-4) ...
158s Setting up exfatprogs (1.2.8-1) ...
158s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ...
158s Setting up bpftool (7.6.0+6.14.0-10.10) ...
158s Setting up libestr0:amd64 (0.1.11-2) ...
158s Setting up libbrotli1:amd64 (1.1.0-2build4) ...
158s Setting up libsqlite3-0:amd64 (3.46.1-2) ...
158s Setting up dosfstools (4.2-1.2) ...
158s Setting up rsyslog (8.2412.0-2ubuntu2) ...
158s info: The user `syslog' is already a member of `adm'.
159s Setting up binutils-common:amd64 (2.44-3ubuntu1) ...
159s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ...
159s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ...
159s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ...
159s Setting up systemd (257.3-1ubuntu3) ...
159s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.

159s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'.

160s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.

160s Setting up libparted2t64:amd64 (3.6-5) ...
160s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64'
160s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64'
160s Setting up linux-headers-generic (6.14.0-10.10) ...
160s Setting up libjemalloc2:amd64 (5.3.0-3) ...
160s Setting up locales (2.41-1ubuntu1) ...
160s Installing new version of config file /etc/locale.alias ...
161s Generating locales (this might take a while)...
163s   en_US.UTF-8... done
163s Generation complete.
163s Setting up libsframe1:amd64 (2.44-3ubuntu1) ...
163s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ...
163s Setting up apparmor (4.1.0~beta5-0ubuntu8) ...
163s Installing new version of config file /etc/apparmor.d/fusermount3 ...
163s Installing new version of config file /etc/apparmor.d/lsusb ...
163s Installing new version of config file /etc/apparmor.d/openvpn ...
164s Reloading AppArmor profiles 
166s Setting up libftdi1-2:amd64 (1.5-8build1) ...
166s Setting up libglib2.0-data (2.84.0-1) ...
166s Setting up systemd-cryptsetup (257.3-1ubuntu3) ...
166s Setting up libncurses6:amd64 (6.5+20250216-2) ...
166s Setting up strace (6.13+ds-1ubuntu1) ...
166s Setting up xz-utils (5.6.4-1) ...
166s Setting up systemd-timesyncd (257.3-1ubuntu3) ...
166s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it.
166s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ...
166s Setting up udev (257.3-1ubuntu3) ...
167s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ...
169s Setting up libncursesw6:amd64 (6.5+20250216-2) ...
169s Setting up libpci3:amd64 (1:3.13.0-2) ...
169s Setting up whiptail (0.52.24-4ubuntu2) ...
169s Setting up python-apt-common (2.9.9build1) ...
169s Setting up pnp.ids (0.393-3) ...
169s Setting up libnl-3-200:amd64 (3.7.0-1) ...
169s Setting up python3.13-minimal (3.13.2-2) ...
170s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ...
170s Setting up libbinutils:amd64 (2.44-3ubuntu1) ...
170s Setting up libc-dev-bin (2.41-1ubuntu1) ...
170s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ...
170s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ...
170s Setting up rsync (3.4.1+ds1-3) ...
171s rsync.service is a disabled or a static unit not running, not starting it.
171s Setting up python3.13-gdbm (3.13.2-2) ...
171s Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
171s Setting up systemd-resolved (257.3-1ubuntu3) ...
171s Setting up initramfs-tools-bin (0.146ubuntu1) ...
171s Setting up ncurses-term (6.5+20250216-2) ...
171s Setting up libctf0:amd64 (2.44-3ubuntu1) ...
171s Setting up libpython3.13:amd64 (3.13.2-2) ...
171s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
172s Setting up libdebuginfod1t64:amd64 (0.192-4) ...
172s Setting up systemd-sysv (257.3-1ubuntu3) ...
172s Setting up linux-headers-virtual (6.14.0-10.10) ...
172s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ...
172s Setting up python3.13 (3.13.2-2) ...
172s Setting up htop (3.4.0-2) ...
172s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ...
175s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic
175s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic
175s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic
175s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic
175s Setting up parted (3.6-5) ...
175s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ...
175s Setting up python3 (3.13.2-2) ...
175s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ...
175s Setting up python3-markupsafe (2.1.5-1build4) ...
176s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ...
178s Setting up libnl-route-3-200:amd64 (3.7.0-1) ...
178s Setting up hwdata (0.393-3) ...
178s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
178s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ...
178s No schema files found: doing nothing.
178s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ...
178s Setting up linux-perf (6.14.0-10.10) ...
178s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ...
178s Setting up pciutils (1:3.13.0-2) ...
178s Setting up python3-rpds-py (0.21.0-2ubuntu2) ...
178s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ...
178s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ...
178s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ...
178s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ...
178s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ...
178s Setting up curl (8.12.1-3ubuntu1) ...
178s Setting up linux-image-virtual (6.14.0-10.10) ...
178s Setting up initramfs-tools-core (0.146ubuntu1) ...
178s Setting up linux-tools-common (6.14.0-10.10) ...
178s Setting up python3-systemd (235-1build6) ...
179s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ...
179s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ...
179s Setting up linux-image-generic (6.14.0-10.10) ...
179s Setting up python3-dbus (1.3.2-5build5) ...
179s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ...
179s Setting up initramfs-tools (0.146ubuntu1) ...
179s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ...
179s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ...
179s update-initramfs: deferring update (trigger activated)
179s Setting up linux-generic (6.14.0-10.10) ...
179s Setting up ubuntu-minimal (1.549) ...
179s Setting up python3-apt (2.9.9build1) ...
179s Setting up python3-bcrypt (4.2.0-2.1build1) ...
179s Setting up python3-yaml (6.0.2-1build2) ...
179s Setting up libfwupd3:amd64 (2.0.6-4) ...
179s Setting up python3-lazr.uri (1.0.6-6) ...
179s Setting up binutils (2.44-3ubuntu1) ...
179s Setting up ubuntu-standard (1.549) ...
179s Setting up cloud-init-base (25.1-0ubuntu3) ...
181s Setting up linux-virtual (6.14.0-10.10) ...
181s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ...
181s Setting up python3-gi (3.50.0-4build1) ...
181s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ...
181s Setting up fwupd (2.0.6-4) ...
182s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
182s fwupd.service is a disabled or a static unit not running, not starting it.
182s Setting up cloud-init (25.1-0ubuntu3) ...
182s Processing triggers for man-db (2.13.0-1) ...
184s Processing triggers for dbus (1.16.2-1ubuntu1) ...
184s Processing triggers for shared-mime-info (2.4-5) ...
184s Warning: program compiled against libxml 212 using older 209
184s Processing triggers for libc-bin (2.41-1ubuntu1) ...
184s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ...
184s /etc/kernel/postinst.d/initramfs-tools:
184s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic
184s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
196s /etc/kernel/postinst.d/zz-update-grub:
196s Sourcing file `/etc/default/grub'
196s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
196s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
196s Generating grub configuration file ...
196s Found linux image: /boot/vmlinuz-6.14.0-10-generic
196s Found initrd image: /boot/initrd.img-6.14.0-10-generic
196s Found linux image: /boot/vmlinuz-6.12.0-16-generic
196s Found initrd image: /boot/initrd.img-6.12.0-16-generic
196s Found linux image: /boot/vmlinuz-6.11.0-8-generic
196s Found initrd image: /boot/initrd.img-6.11.0-8-generic
197s Warning: os-prober will not be executed to detect other bootable partitions.
197s Systems on them will not be added to the GRUB boot configuration.
197s Check GRUB_DISABLE_OS_PROBER documentation entry.
197s Adding boot menu entry for UEFI Firmware Settings ...
197s done
197s Processing triggers for initramfs-tools (0.146ubuntu1) ...
197s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic
197s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
210s Reading package lists...
210s Building dependency tree...
210s Reading state information...
210s Solving dependencies...
210s The following packages will be REMOVED:
210s   libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib*
210s   libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
210s   linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic*
210s   linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic*
210s   linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic*
210s   linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8*
210s   linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16*
210s   linux-tools-6.12.0-16-generic*
211s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
211s After this operation, 545 MB disk space will be freed.
211s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 148643 files and directories currently installed.)
211s Removing libnl-genl-3-200:amd64 (3.7.0-1) ...
211s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
211s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
211s Removing libpython3.12t64:amd64 (3.12.9-1) ...
211s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ...
211s Removing libnsl2:amd64 (1.3.0-3build3) ...
211s Removing libpython3.12-minimal:amd64 (3.12.9-1) ...
211s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
212s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
214s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ...
215s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ...
217s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
218s /etc/kernel/postrm.d/initramfs-tools:
218s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
218s /etc/kernel/postrm.d/zz-update-grub:
218s Sourcing file `/etc/default/grub'
218s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
218s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
218s Generating grub configuration file ...
218s Found linux image: /boot/vmlinuz-6.14.0-10-generic
218s Found initrd image: /boot/initrd.img-6.14.0-10-generic
218s Found linux image: /boot/vmlinuz-6.12.0-16-generic
218s Found initrd image: /boot/initrd.img-6.12.0-16-generic
219s Warning: os-prober will not be executed to detect other bootable partitions.
219s Systems on them will not be added to the GRUB boot configuration.
219s Check GRUB_DISABLE_OS_PROBER documentation entry.
219s Adding boot menu entry for UEFI Firmware Settings ...
219s done
219s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ...
219s W: Removing the running kernel
219s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
219s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
219s /etc/kernel/postrm.d/initramfs-tools:
219s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic
219s /etc/kernel/postrm.d/zz-update-grub:
219s Sourcing file `/etc/default/grub'
219s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
219s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
219s Generating grub configuration file ...
219s Found linux image: /boot/vmlinuz-6.14.0-10-generic
219s Found initrd image: /boot/initrd.img-6.14.0-10-generic
219s Warning: os-prober will not be executed to detect other bootable partitions.
219s Systems on them will not be added to the GRUB boot configuration.
219s Check GRUB_DISABLE_OS_PROBER documentation entry.
219s Adding boot menu entry for UEFI Firmware Settings ...
219s done
219s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
220s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ...
222s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ...
222s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ...
222s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ...
222s Processing triggers for libc-bin (2.41-1ubuntu1) ...
222s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 76972 files and directories currently installed.)
222s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
222s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ...
222s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ...
222s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ...
222s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed
222s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
222s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ...
222s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty
222s autopkgtest [23:34:37]: upgrading testbed (apt dist-upgrade and autopurge)
223s Reading package lists...
223s Building dependency tree...
223s Reading state information...
223s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
224s Starting 2 pkgProblemResolver with broken count: 0
224s Done
224s Entering ResolveByKeep
224s 
225s Calculating upgrade...
225s The following packages will be upgraded:
225s   libc-bin libc-dev-bin libc6 libc6-dev locales
225s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
225s Need to get 10.5 MB of archives.
225s After this operation, 1024 B of additional disk space will be used.
225s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB]
226s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB]
226s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB]
226s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB]
226s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB]
226s Preconfiguring packages ...
226s Fetched 10.5 MB in 1s (8359 kB/s)
227s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 76968 files and directories currently installed.)
227s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ...
227s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
227s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ...
227s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
227s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ...
227s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
227s Setting up libc6:amd64 (2.41-1ubuntu2) ...
227s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 76968 files and directories currently installed.)
227s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ...
227s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
227s Setting up libc-bin (2.41-1ubuntu2) ...
228s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 76968 files and directories currently installed.)
228s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
228s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
228s Setting up locales (2.41-1ubuntu2) ...
229s Generating locales (this might take a while)...
230s   en_US.UTF-8... done
230s Generation complete.
230s Setting up libc-dev-bin (2.41-1ubuntu2) ...
230s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ...
230s Processing triggers for man-db (2.13.0-1) ...
231s Processing triggers for systemd (257.3-1ubuntu3) ...
232s Reading package lists...
233s Building dependency tree...
233s Reading state information...
233s Starting pkgProblemResolver with broken count: 0
233s Starting 2 pkgProblemResolver with broken count: 0
233s Done
233s Solving dependencies...
234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
234s autopkgtest [23:34:49]: rebooting testbed after setup commands that affected boot
257s autopkgtest [23:35:12]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025
261s autopkgtest [23:35:16]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq
275s Get:1 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.2+dfsg-1 (dsc) [2605 B]
275s Get:2 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.2+dfsg-1 (tar) [305 MB]
275s Get:3 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.2+dfsg-1 (diff) [38.9 kB]
275s gpgv: Signature made Wed Aug 21 22:00:38 2024 UTC
275s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
275s gpgv: Can't check signature: No public key
275s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.2+dfsg-1.dsc: no acceptable signature found
280s autopkgtest [23:35:35]: testing package trinityrnaseq version 2.15.2+dfsg-1
281s autopkgtest [23:35:36]: build not needed
298s autopkgtest [23:35:53]: test run-tests: preparing testbed
299s Reading package lists...
299s Building dependency tree...
299s Reading state information...
300s Starting pkgProblemResolver with broken count: 0
300s Starting 2 pkgProblemResolver with broken count: 0
300s Done
301s The following NEW packages will be installed:
301s   adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2
301s   ca-certificates-java dconf-gsettings-backend dconf-service default-jre
301s   default-jre-headless fontconfig fontconfig-config fonts-dejavu-core
301s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
301s   fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2 jaligner
301s   java-common javascript-common jellyfish junit4 kallisto libapache-pom-java
301s   libasan8 libasound2-data libasound2t64 libatinject-jsr330-api-java
301s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
301s   libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java
301s   libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0
301s   libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.83-dev
301s   libcairo-gobject2 libcairo2 libclone-perl libcolord2
301s   libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java
301s   libcommons-collections4-java libcommons-compress-java libcommons-io-java
301s   libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java
301s   libcommons-math3-java libcommons-parent-java libcups2t64 libdatrie1
301s   libdconf1 libdeflate0 libdrm-intel1 libencode-locale-perl libepoxy0
301s   liberror-prone-java libezmorph-java libfile-listing-perl libfontconfig1
301s   libfreemarker-java libgatk-native-bindings-java libgbm1 libgcc-14-dev
301s   libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5
301s   libgif7 libgkl-java libgl1 libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0
301s   libgomp1 libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
301s   libguava-java libhamcrest-java libharfbuzz0b libhtml-parser-perl
301s   libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2
301s   libhtsjdk-java libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
301s   libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0
301s   libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libitm1
301s   libjaxen-java libjbig0 libjbzip2-java libjellyfish-2.0-2 libjoptsimple-java
301s   libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3
301s   libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
301s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax
301s   libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify
301s   libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker
301s   libjs-underscore libjson-java libjsr305-java libjung-free-java liblapack3
301s   liblcms2-2 liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0
301s   liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16
301s   libmbedtls21 libmbedx509-7 libmongodb-java libncbi-ngs3 libncbi-vdb3
301s   libnet-http-perl libnet-ssleay-perl libngs-java libngs-jni libpango-1.0-0
301s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0
301s   libpcsclite1 libpicard-java libpixman-1-0 libprotobuf32t64 libquadmath0
301s   librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni
301s   libsnappy1v5 libstaden-read14t64 libstdc++-14-dev libtbb12 libtbbbind-2-5
301s   libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl
301s   libtk8.6 libtry-tiny-perl libtsan2 libubsan1 liburi-perl libvulkan1
301s   libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0
301s   libwebp7 libwww-perl libwww-robotrules-perl libx11-xcb1 libxcb-dri3-0
301s   libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0
301s   libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1
301s   libxerces2-java libxfixes3 libxft2 libxi6 libxinerama1
301s   libxml-commons-external-java libxml-commons-resolver1.1-java libxom-java
301s   libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1
301s   littler mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data
301s   node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre
301s   openjdk-21-jre-headless pandoc pandoc-data parafly perl-openssl-defaults
301s   python3-hisat2 python3-htseq python3-numpy python3-numpy-dev python3-pysam
301s   r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase
301s   r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
301s   r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2
301s   r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase
301s   r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata
301s   r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
301s   r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-keggrest r-bioc-limma
301s   r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rsamtools
301s   r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
301s   r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils
301s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-argparse r-cran-askpass
301s   r-cran-backports r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-bit
301s   r-cran-bit64 r-cran-bitops r-cran-blob r-cran-broom r-cran-bslib
301s   r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli r-cran-clipr
301s   r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-commonmark
301s   r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table
301s   r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dtplyr
301s   r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
301s   r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython
301s   r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
301s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
301s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
301s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
301s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
301s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
301s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
301s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
301s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
301s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
301s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
301s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
301s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
301s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
301s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
301s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
301s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
301s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
301s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
301s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
301s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
301s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
301s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
301s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
301s   subread trimmomatic trinityrnaseq trinityrnaseq-examples unzip x11-common
301s   xdg-utils zip zlib1g-dev
301s 0 upgraded, 452 newly installed, 0 to remove and 0 not upgraded.
301s Need to get 883 MB of archives.
301s After this operation, 2133 MB of additional disk space will be used.
301s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB]
301s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB]
301s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB]
301s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB]
301s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB]
302s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [8004 B]
302s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
302s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
302s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB]
302s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
302s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
302s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
302s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
302s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
302s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [161 kB]
302s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.17.5+ds-3ubuntu1 [54.0 kB]
302s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB]
302s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 48.0-1 [578 kB]
302s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.55.90-1 [9072 B]
302s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB]
302s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.1ubuntu2 [287 kB]
302s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1ubuntu2 [323 kB]
302s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1ubuntu2 [278 kB]
302s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libprotobuf32t64 amd64 3.21.12-10build2 [959 kB]
302s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 berkeley-express amd64 1.5.3+dfsg-3build5 [210 kB]
302s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB]
302s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-5 [39.8 kB]
302s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-5 [28.4 kB]
302s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [22.7 kB]
302s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B]
302s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
302s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.1-1 [26.6 kB]
302s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.6+7-1 [46.4 MB]
303s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
303s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.55.90-1 [55.3 kB]
303s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB]
303s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.55.90-1 [91.1 kB]
303s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.55.90-1 [69.0 kB]
303s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
303s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
303s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB]
303s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB]
303s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
303s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
303s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
303s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
303s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
303s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB]
303s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-3 [155 kB]
303s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-16ubuntu1 [30.9 kB]
303s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-16ubuntu1 [23.6 kB]
303s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-16ubuntu1 [27.5 kB]
303s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB]
303s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB]
303s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
303s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
303s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB]
303s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
303s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
303s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
303s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB]
303s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB]
303s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB]
303s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB]
304s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.1-3 [10.9 kB]
304s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.1-3 [6168 B]
304s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [6642 B]
304s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB]
304s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB]
304s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B]
304s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B]
304s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB]
304s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.48-3ubuntu1 [1424 kB]
304s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.48-3ubuntu1 [3169 kB]
304s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB]
304s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B]
304s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B]
304s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB]
304s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B]
304s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB]
304s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B]
304s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB]
304s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.123-1 [68.8 kB]
304s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB]
304s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B]
304s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B]
304s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 25.0.1-2ubuntu1 [12.1 MB]
304s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB]
304s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 25.0.1-2ubuntu1 [33.4 kB]
304s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB]
304s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 25.0.1-2ubuntu1 [35.7 kB]
304s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 25.0.1-2ubuntu1 [146 kB]
304s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB]
304s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB]
304s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.13-1build1 [21.1 kB]
304s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.13-1build1 [437 kB]
304s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libgif7 amd64 5.2.2-1ubuntu2 [36.0 kB]
304s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
304s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.5-1 [13.0 kB]
304s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre amd64 21.0.6+7-1 [219 kB]
304s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre amd64 2:1.21-76 [918 B]
304s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
305s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
305s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
305s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 hisat2 amd64 2.2.1-5 [3889 kB]
305s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB]
305s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 javascript-common all 12 [5216 B]
305s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB]
305s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB]
305s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjellyfish-2.0-2 amd64 2.3.1-4build1 [71.9 kB]
305s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 jellyfish amd64 2.3.1-4build1 [845 kB]
305s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhamcrest-java all 2.2-2 [117 kB]
305s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 junit4 all 4.13.2-5 [348 kB]
305s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 kallisto amd64 0.48.0+dfsg-4build1 [273 kB]
305s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B]
305s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB]
305s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B]
305s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
305s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang3-java all 3.17.0-1 [603 kB]
305s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfreemarker-java all 2.3.32-2 [1542 kB]
305s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB]
305s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjoptsimple-java all 5.0.4-7 [73.2 kB]
306s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB]
306s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB]
306s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB]
306s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB]
306s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB]
306s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB]
306s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 libslf4j-java all 1.7.32-1 [141 kB]
306s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB]
306s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
306s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB]
306s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB]
306s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB]
306s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB]
306s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB]
306s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB]
306s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB]
306s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB]
306s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB]
306s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu2 [10.7 MB]
307s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-dev amd64 1.83.0.2ubuntu1 [4468 B]
307s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.1ubuntu2 [260 kB]
307s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libclone-perl amd64 0.47-1 [10.7 kB]
307s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-collections3-java all 3.2.2-3 [526 kB]
307s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-beanutils-java all 1.9.4-2 [228 kB]
307s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-collections4-java all 4.4-2 [670 kB]
307s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.18.0-1 [477 kB]
307s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB]
307s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB]
307s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-math3-java all 3.6.1-4 [2029 kB]
307s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB]
307s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-12 [27.0 kB]
307s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
307s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
307s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 libezmorph-java all 1.0.6-4 [76.0 kB]
307s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB]
307s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB]
307s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB]
307s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B]
307s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB]
307s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjaxen-java all 1.1.6-5 [213 kB]
307s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
307s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB]
307s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxerces2-java all 2.12.2-1 [1430 kB]
307s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libxom-java all 1.3.9-1 [174 kB]
307s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjson-java all 3.1.0+dfsg-2 [141 kB]
307s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB]
307s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB]
307s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB]
307s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [67.7 kB]
307s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1409 kB]
307s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7.1ubuntu1 [165 kB]
307s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-jni amd64 3.0.9+dfsg-7.1ubuntu1 [4842 B]
307s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-java amd64 3.0.9+dfsg-7.1ubuntu1 [91.1 kB]
307s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 librhino-java all 1.7.15-1 [1354 kB]
308s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB]
308s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-jni amd64 1.1.10.7-1 [6786 B]
308s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-java all 1.1.10.7-1 [83.6 kB]
308s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1829 kB]
308s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB]
308s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tagset-perl all 3.24-1 [14.1 kB]
308s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 liburi-perl all 5.30-1 [94.4 kB]
308s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-parser-perl amd64 3.83-1build1 [86.2 kB]
308s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tree-perl all 5.07-3 [200 kB]
308s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-html-perl all 1.004-3 [15.9 kB]
308s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB]
308s Get:188 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-message-perl all 7.00-2ubuntu1 [75.9 kB]
308s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB]
308s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB]
308s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB]
308s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
308s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 perl-openssl-defaults amd64 7build3 [6626 B]
308s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-ssleay-perl amd64 1.94-3 [318 kB]
308s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-socket-ssl-perl all 2.089-1 [200 kB]
308s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
308s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
308s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
308s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-d3 all 3.5.17-4 [132 kB]
308s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
308s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
308s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
308s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
308s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
308s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
308s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
308s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
308s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
308s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
308s Get:210 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
308s Get:211 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB]
308s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjung-free-java all 2.1.1-3 [1478 kB]
309s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.7-1 [196 kB]
309s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-http-perl all 6.23-1 [22.3 kB]
309s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 libtry-tiny-perl all 0.32-1 [21.2 kB]
309s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB]
309s Get:217 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-perl all 6.78-1 [139 kB]
309s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-protocol-https-perl all 6.14-1 [9040 B]
309s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
309s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
309s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpicard-java all 3.3.0+dfsg-2 [1765 kB]
309s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
309s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 libstaden-read14t64 amd64 1.15.0-1.1build2 [251 kB]
309s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbbind-2-5 amd64 2022.0.0-2 [15.8 kB]
309s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbmalloc2 amd64 2022.0.0-2 [55.7 kB]
309s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbb12 amd64 2022.0.0-2 [103 kB]
309s Get:227 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB]
309s Get:228 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
309s Get:229 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
309s Get:230 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB]
309s Get:231 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
309s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB]
309s Get:233 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
309s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
309s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB]
310s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB]
310s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B]
310s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB]
310s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB]
310s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
310s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
310s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB]
310s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
310s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc amd64 3.1.11.1+ds-2 [27.2 MB]
311s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 parafly amd64 0.1.0-5 [17.4 kB]
311s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hisat2 all 2.2.1-5 [12.7 kB]
311s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB]
311s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-htseq amd64 2.0.9+dfsg-1build2 [354 kB]
311s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
311s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
311s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
311s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-iranges amd64 2.40.1-2 [2310 kB]
311s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB]
311s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
311s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.6.0-1-1ubuntu2 [501 kB]
311s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB]
311s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
311s Get:258 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
311s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
311s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
311s Get:261 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
311s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
312s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
312s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
312s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
312s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
312s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB]
312s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
312s Get:269 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 6.2.1+dfsg-1ubuntu1 [197 kB]
312s Get:270 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
312s Get:271 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
312s Get:272 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
312s Get:273 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
312s Get:274 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
312s Get:275 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
312s Get:276 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
312s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
312s Get:278 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
312s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
312s Get:280 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
312s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
312s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
312s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
312s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
312s Get:285 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
312s Get:286 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-2 [183 kB]
313s Get:287 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
313s Get:288 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml amd64 3.99-0.18-1 [1748 kB]
313s Get:289 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
313s Get:290 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB]
313s Get:291 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB]
313s Get:292 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
313s Get:293 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
313s Get:294 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
313s Get:295 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB]
313s Get:296 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
313s Get:297 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
313s Get:298 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
313s Get:299 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB]
313s Get:300 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB]
313s Get:301 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB]
313s Get:302 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
313s Get:303 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
313s Get:304 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbplyr all 2.5.0+dfsg-1 [1233 kB]
313s Get:305 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB]
313s Get:306 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocfilecache all 2.14.0+dfsg-2 [300 kB]
314s Get:307 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB]
314s Get:308 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
314s Get:309 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
314s Get:310 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
314s Get:311 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
314s Get:312 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
314s Get:313 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB]
314s Get:314 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
314s Get:315 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
314s Get:316 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB]
314s Get:317 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
314s Get:318 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
314s Get:319 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB]
314s Get:320 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr2 all 1.1.1-1 [752 kB]
314s Get:321 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB]
314s Get:322 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml2 amd64 1.3.7-1 [334 kB]
314s Get:323 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biomart all 2.62.1+dfsg-1 [444 kB]
314s Get:324 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
314s Get:325 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB]
314s Get:326 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
314s Get:327 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
314s Get:328 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB]
314s Get:329 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
314s Get:330 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-1 [1392 kB]
314s Get:331 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
314s Get:332 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
314s Get:333 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
314s Get:334 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-locfit amd64 1.5-9.12-1 [552 kB]
314s Get:335 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
314s Get:336 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
314s Get:337 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB]
314s Get:338 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB]
314s Get:339 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB]
314s Get:340 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
314s Get:341 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
314s Get:342 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB]
314s Get:343 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB]
314s Get:344 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
314s Get:345 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB]
314s Get:346 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB]
315s Get:347 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
315s Get:348 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
315s Get:349 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB]
315s Get:350 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.2.3-1-1 [864 kB]
315s Get:351 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-deseq2 amd64 1.46.0+dfsg-2 [1250 kB]
315s Get:352 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hwriter all 1.3.2.1-1 [106 kB]
315s Get:353 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
315s Get:354 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB]
315s Get:355 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB]
315s Get:356 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
315s Get:357 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-geneplotter all 1.84.0+dfsg-2 [1508 kB]
315s Get:358 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB]
315s Get:359 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genefilter amd64 1.88.0-2 [1243 kB]
315s Get:360 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dexseq all 1.52.0+dfsg-2 [453 kB]
315s Get:361 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-limma amd64 3.62.2+dfsg-1 [1969 kB]
315s Get:362 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-edger amd64 4.4.2+dfsg-1 [1120 kB]
315s Get:363 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB]
315s Get:364 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
315s Get:365 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB]
315s Get:366 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
315s Get:367 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
315s Get:368 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rtracklayer amd64 1.66.0-2 [5227 kB]
316s Get:369 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB]
316s Get:370 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-txdbmaker all 1.2.1+ds-2 [875 kB]
316s Get:371 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genelendatabase all 1.42.0-3 [100 MB]
320s Get:372 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-go.db all 3.20.0-2 [16.5 MB]
320s Get:373 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biasedurn amd64 2.0.12-1 [290 kB]
320s Get:374 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-goseq all 1.58.0-2 [1911 kB]
321s Get:375 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
321s Get:376 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB]
321s Get:377 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-qvalue all 2.38.0-2 [2811 kB]
321s Get:378 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-findpython all 1.0.9-1 [25.3 kB]
321s Get:379 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-argparse all 2.2.5+dfsg-1 [143 kB]
321s Get:380 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB]
321s Get:381 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB]
321s Get:382 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB]
321s Get:383 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
321s Get:384 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
321s Get:385 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
321s Get:386 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
321s Get:387 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bslib all 0.8.0+dfsg-1 [4294 kB]
321s Get:388 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
321s Get:389 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
321s Get:390 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
321s Get:391 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB]
321s Get:392 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB]
321s Get:393 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB]
321s Get:394 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.8.1-1 [579 kB]
321s Get:395 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.2-2 [137 kB]
321s Get:396 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB]
321s Get:397 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB]
321s Get:398 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dtplyr all 1.3.1-1 [364 kB]
321s Get:399 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB]
321s Get:400 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB]
321s Get:401 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastcluster amd64 1.2.6-2 [197 kB]
321s Get:402 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
321s Get:403 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB]
321s Get:404 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gargle all 1.5.2-1 [737 kB]
321s Get:405 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB]
322s Get:406 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB]
322s Get:407 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googledrive all 2.1.1-3 [1238 kB]
322s Get:408 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ids all 1.0.1-2 [124 kB]
322s Get:409 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB]
322s Get:410 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googlesheets4 all 1.1.1-1 [520 kB]
322s Get:411 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gridextra all 2.3-3build1 [1024 kB]
322s Get:412 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-goplot all 1.0.2-2 [2427 kB]
322s Get:413 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB]
322s Get:414 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB]
322s Get:415 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB]
322s Get:416 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB]
322s Get:417 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.51+dfsg-1 [574 kB]
322s Get:418 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
322s Get:419 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
322s Get:420 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
322s Get:421 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
322s Get:422 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kernsmooth amd64 2.23-26-1 [94.5 kB]
322s Get:423 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
322s Get:424 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB]
322s Get:425 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB]
322s Get:426 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB]
323s Get:427 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB]
323s Get:428 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-systemfonts amd64 1.2.1-1 [347 kB]
323s Get:429 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-textshaping amd64 0.3.7-2 [95.5 kB]
323s Get:430 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ragg amd64 1.3.3-1 [510 kB]
323s Get:431 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readxl amd64 1.4.4-1 [360 kB]
323s Get:432 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tinytex all 0.56-1 [148 kB]
323s Get:433 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-modernizr all 3.13.0-0.1 [101 kB]
323s Get:434 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
323s Get:435 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
323s Get:436 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
323s Get:437 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rmarkdown all 2.29+dfsg-1 [1501 kB]
323s Get:438 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rstudioapi all 0.17.1-1 [299 kB]
323s Get:439 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reprex all 2.1.1-1 [468 kB]
323s Get:440 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-selectr all 0.4-2-2build1 [416 kB]
323s Get:441 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rvest all 1.0.4-1 [298 kB]
323s Get:442 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyverse all 2.0.0+dfsg-2 [85.2 kB]
323s Get:443 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie amd64 1.3.1-3 [1562 kB]
323s Get:444 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB]
323s Get:445 http://ftpmaster.internal/ubuntu plucky/universe amd64 rsem amd64 1.3.3+dfsg-3build1 [36.1 MB]
324s Get:446 http://ftpmaster.internal/ubuntu plucky/universe amd64 salmon amd64 1.10.2+ds1-1build2 [3308 kB]
324s Get:447 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB]
324s Get:448 http://ftpmaster.internal/ubuntu plucky/universe amd64 subread amd64 2.0.7+dfsg-1 [552 kB]
324s Get:449 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB]
324s Get:450 http://ftpmaster.internal/ubuntu plucky/universe amd64 trimmomatic all 0.39+dfsg-2 [758 kB]
324s Get:451 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq amd64 2.15.2+dfsg-1 [1779 kB]
324s Get:452 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq-examples amd64 2.15.2+dfsg-1 [299 MB]
334s Preconfiguring packages ...
334s Fetched 883 MB in 32s (27.4 MB/s)
334s Selecting previously unselected package python3-numpy-dev:amd64.
334s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 76968 files and directories currently installed.)
334s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ...
334s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ...
334s Selecting previously unselected package libblas3:amd64.
334s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ...
334s Unpacking libblas3:amd64 (3.12.1-2) ...
334s Selecting previously unselected package libgfortran5:amd64.
334s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ...
334s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ...
334s Selecting previously unselected package liblapack3:amd64.
334s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ...
334s Unpacking liblapack3:amd64 (3.12.1-2) ...
334s Selecting previously unselected package python3-numpy.
334s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ...
334s Unpacking python3-numpy (1:2.2.3+ds-5) ...
335s Selecting previously unselected package libgdk-pixbuf2.0-common.
335s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.42.12+dfsg-2_all.deb ...
335s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
335s Selecting previously unselected package libjpeg-turbo8:amd64.
335s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ...
335s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
335s Selecting previously unselected package libjpeg8:amd64.
335s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ...
335s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
335s Selecting previously unselected package libdeflate0:amd64.
335s Preparing to unpack .../008-libdeflate0_1.23-1_amd64.deb ...
335s Unpacking libdeflate0:amd64 (1.23-1) ...
335s Selecting previously unselected package libjbig0:amd64.
335s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
335s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
335s Selecting previously unselected package liblerc4:amd64.
335s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ...
335s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
335s Selecting previously unselected package libsharpyuv0:amd64.
335s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_amd64.deb ...
335s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ...
335s Selecting previously unselected package libwebp7:amd64.
335s Preparing to unpack .../012-libwebp7_1.5.0-0.1_amd64.deb ...
335s Unpacking libwebp7:amd64 (1.5.0-0.1) ...
335s Selecting previously unselected package libtiff6:amd64.
335s Preparing to unpack .../013-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ...
335s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
335s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64.
335s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.42.12+dfsg-2_amd64.deb ...
335s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ...
335s Selecting previously unselected package gtk-update-icon-cache.
335s Preparing to unpack .../015-gtk-update-icon-cache_4.17.5+ds-3ubuntu1_amd64.deb ...
335s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
335s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed.
335s Unpacking gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
335s Selecting previously unselected package hicolor-icon-theme.
335s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ...
335s Unpacking hicolor-icon-theme (0.18-2) ...
335s Selecting previously unselected package adwaita-icon-theme.
335s Preparing to unpack .../017-adwaita-icon-theme_48.0-1_all.deb ...
335s Unpacking adwaita-icon-theme (48.0-1) ...
335s Selecting previously unselected package at-spi2-common.
335s Preparing to unpack .../018-at-spi2-common_2.55.90-1_all.deb ...
335s Unpacking at-spi2-common (2.55.90-1) ...
335s Selecting previously unselected package libbamtools2.5.2:amd64.
335s Preparing to unpack .../019-libbamtools2.5.2_2.5.2+dfsg-6build1_amd64.deb ...
335s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ...
335s Selecting previously unselected package libboost-filesystem1.83.0:amd64.
335s Preparing to unpack .../020-libboost-filesystem1.83.0_1.83.0-4.1ubuntu2_amd64.deb ...
335s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
335s Selecting previously unselected package libboost-program-options1.83.0:amd64.
336s Preparing to unpack .../021-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_amd64.deb ...
336s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
336s Selecting previously unselected package libboost-thread1.83.0:amd64.
336s Preparing to unpack .../022-libboost-thread1.83.0_1.83.0-4.1ubuntu2_amd64.deb ...
336s Unpacking libboost-thread1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
336s Selecting previously unselected package libprotobuf32t64:amd64.
336s Preparing to unpack .../023-libprotobuf32t64_3.21.12-10build2_amd64.deb ...
336s Unpacking libprotobuf32t64:amd64 (3.21.12-10build2) ...
336s Selecting previously unselected package berkeley-express.
336s Preparing to unpack .../024-berkeley-express_1.5.3+dfsg-3build5_amd64.deb ...
336s Unpacking berkeley-express (1.5.3+dfsg-3build5) ...
336s Selecting previously unselected package ca-certificates-java.
336s Preparing to unpack .../025-ca-certificates-java_20240118_all.deb ...
336s Unpacking ca-certificates-java (20240118) ...
336s Selecting previously unselected package libdconf1:amd64.
336s Preparing to unpack .../026-libdconf1_0.40.0-5_amd64.deb ...
336s Unpacking libdconf1:amd64 (0.40.0-5) ...
336s Selecting previously unselected package dconf-service.
336s Preparing to unpack .../027-dconf-service_0.40.0-5_amd64.deb ...
336s Unpacking dconf-service (0.40.0-5) ...
336s Selecting previously unselected package dconf-gsettings-backend:amd64.
336s Preparing to unpack .../028-dconf-gsettings-backend_0.40.0-5_amd64.deb ...
336s Unpacking dconf-gsettings-backend:amd64 (0.40.0-5) ...
336s Selecting previously unselected package java-common.
336s Preparing to unpack .../029-java-common_0.76_all.deb ...
336s Unpacking java-common (0.76) ...
336s Selecting previously unselected package liblcms2-2:amd64.
336s Preparing to unpack .../030-liblcms2-2_2.16-2_amd64.deb ...
336s Unpacking liblcms2-2:amd64 (2.16-2) ...
336s Selecting previously unselected package libpcsclite1:amd64.
336s Preparing to unpack .../031-libpcsclite1_2.3.1-1_amd64.deb ...
336s Unpacking libpcsclite1:amd64 (2.3.1-1) ...
336s Selecting previously unselected package openjdk-21-jre-headless:amd64.
336s Preparing to unpack .../032-openjdk-21-jre-headless_21.0.6+7-1_amd64.deb ...
336s Unpacking openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
337s Selecting previously unselected package default-jre-headless.
337s Preparing to unpack .../033-default-jre-headless_2%3a1.21-76_amd64.deb ...
337s Unpacking default-jre-headless (2:1.21-76) ...
337s Selecting previously unselected package libatk1.0-0t64:amd64.
337s Preparing to unpack .../034-libatk1.0-0t64_2.55.90-1_amd64.deb ...
337s Unpacking libatk1.0-0t64:amd64 (2.55.90-1) ...
337s Selecting previously unselected package libxi6:amd64.
337s Preparing to unpack .../035-libxi6_2%3a1.8.2-1_amd64.deb ...
337s Unpacking libxi6:amd64 (2:1.8.2-1) ...
337s Selecting previously unselected package libatspi2.0-0t64:amd64.
337s Preparing to unpack .../036-libatspi2.0-0t64_2.55.90-1_amd64.deb ...
337s Unpacking libatspi2.0-0t64:amd64 (2.55.90-1) ...
337s Selecting previously unselected package libatk-bridge2.0-0t64:amd64.
337s Preparing to unpack .../037-libatk-bridge2.0-0t64_2.55.90-1_amd64.deb ...
337s Unpacking libatk-bridge2.0-0t64:amd64 (2.55.90-1) ...
337s Selecting previously unselected package fonts-dejavu-mono.
337s Preparing to unpack .../038-fonts-dejavu-mono_2.37-8_all.deb ...
337s Unpacking fonts-dejavu-mono (2.37-8) ...
337s Selecting previously unselected package fonts-dejavu-core.
337s Preparing to unpack .../039-fonts-dejavu-core_2.37-8_all.deb ...
337s Unpacking fonts-dejavu-core (2.37-8) ...
337s Selecting previously unselected package fontconfig-config.
337s Preparing to unpack .../040-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ...
337s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
337s Selecting previously unselected package libfontconfig1:amd64.
337s Preparing to unpack .../041-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ...
337s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
338s Selecting previously unselected package libpixman-1-0:amd64.
338s Preparing to unpack .../042-libpixman-1-0_0.44.0-3_amd64.deb ...
338s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
338s Selecting previously unselected package libxcb-render0:amd64.
338s Preparing to unpack .../043-libxcb-render0_1.17.0-2_amd64.deb ...
338s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
338s Selecting previously unselected package libxcb-shm0:amd64.
338s Preparing to unpack .../044-libxcb-shm0_1.17.0-2_amd64.deb ...
338s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
338s Selecting previously unselected package libxrender1:amd64.
338s Preparing to unpack .../045-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
338s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
338s Selecting previously unselected package libcairo2:amd64.
338s Preparing to unpack .../046-libcairo2_1.18.2-2_amd64.deb ...
338s Unpacking libcairo2:amd64 (1.18.2-2) ...
338s Selecting previously unselected package libcairo-gobject2:amd64.
338s Preparing to unpack .../047-libcairo-gobject2_1.18.2-2_amd64.deb ...
338s Unpacking libcairo-gobject2:amd64 (1.18.2-2) ...
338s Selecting previously unselected package libcolord2:amd64.
338s Preparing to unpack .../048-libcolord2_1.4.7-3_amd64.deb ...
338s Unpacking libcolord2:amd64 (1.4.7-3) ...
338s Selecting previously unselected package libavahi-common-data:amd64.
338s Preparing to unpack .../049-libavahi-common-data_0.8-16ubuntu1_amd64.deb ...
338s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu1) ...
338s Selecting previously unselected package libavahi-common3:amd64.
338s Preparing to unpack .../050-libavahi-common3_0.8-16ubuntu1_amd64.deb ...
338s Unpacking libavahi-common3:amd64 (0.8-16ubuntu1) ...
338s Selecting previously unselected package libavahi-client3:amd64.
338s Preparing to unpack .../051-libavahi-client3_0.8-16ubuntu1_amd64.deb ...
338s Unpacking libavahi-client3:amd64 (0.8-16ubuntu1) ...
338s Selecting previously unselected package libcups2t64:amd64.
338s Preparing to unpack .../052-libcups2t64_2.4.11-0ubuntu2_amd64.deb ...
338s Unpacking libcups2t64:amd64 (2.4.11-0ubuntu2) ...
338s Selecting previously unselected package libepoxy0:amd64.
338s Preparing to unpack .../053-libepoxy0_1.5.10-2_amd64.deb ...
338s Unpacking libepoxy0:amd64 (1.5.10-2) ...
338s Selecting previously unselected package libgraphite2-3:amd64.
338s Preparing to unpack .../054-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
338s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
338s Selecting previously unselected package libharfbuzz0b:amd64.
338s Preparing to unpack .../055-libharfbuzz0b_10.2.0-1_amd64.deb ...
338s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ...
338s Selecting previously unselected package fontconfig.
338s Preparing to unpack .../056-fontconfig_2.15.0-2ubuntu1_amd64.deb ...
338s Unpacking fontconfig (2.15.0-2ubuntu1) ...
338s Selecting previously unselected package libthai-data.
338s Preparing to unpack .../057-libthai-data_0.1.29-2build1_all.deb ...
338s Unpacking libthai-data (0.1.29-2build1) ...
338s Selecting previously unselected package libdatrie1:amd64.
338s Preparing to unpack .../058-libdatrie1_0.2.13-3build1_amd64.deb ...
338s Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
338s Selecting previously unselected package libthai0:amd64.
338s Preparing to unpack .../059-libthai0_0.1.29-2build1_amd64.deb ...
338s Unpacking libthai0:amd64 (0.1.29-2build1) ...
338s Selecting previously unselected package libpango-1.0-0:amd64.
338s Preparing to unpack .../060-libpango-1.0-0_1.56.2-1_amd64.deb ...
338s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ...
338s Selecting previously unselected package libpangoft2-1.0-0:amd64.
338s Preparing to unpack .../061-libpangoft2-1.0-0_1.56.2-1_amd64.deb ...
338s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ...
338s Selecting previously unselected package libpangocairo-1.0-0:amd64.
338s Preparing to unpack .../062-libpangocairo-1.0-0_1.56.2-1_amd64.deb ...
338s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ...
338s Selecting previously unselected package libwayland-client0:amd64.
338s Preparing to unpack .../063-libwayland-client0_1.23.1-3_amd64.deb ...
338s Unpacking libwayland-client0:amd64 (1.23.1-3) ...
338s Selecting previously unselected package libwayland-cursor0:amd64.
338s Preparing to unpack .../064-libwayland-cursor0_1.23.1-3_amd64.deb ...
338s Unpacking libwayland-cursor0:amd64 (1.23.1-3) ...
338s Selecting previously unselected package libwayland-egl1:amd64.
338s Preparing to unpack .../065-libwayland-egl1_1.23.1-3_amd64.deb ...
338s Unpacking libwayland-egl1:amd64 (1.23.1-3) ...
338s Selecting previously unselected package libxcomposite1:amd64.
338s Preparing to unpack .../066-libxcomposite1_1%3a0.4.6-1_amd64.deb ...
338s Unpacking libxcomposite1:amd64 (1:0.4.6-1) ...
338s Selecting previously unselected package libxfixes3:amd64.
338s Preparing to unpack .../067-libxfixes3_1%3a6.0.0-2build1_amd64.deb ...
338s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ...
338s Selecting previously unselected package libxcursor1:amd64.
338s Preparing to unpack .../068-libxcursor1_1%3a1.2.3-1_amd64.deb ...
338s Unpacking libxcursor1:amd64 (1:1.2.3-1) ...
338s Selecting previously unselected package libxdamage1:amd64.
338s Preparing to unpack .../069-libxdamage1_1%3a1.1.6-1build1_amd64.deb ...
338s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ...
338s Selecting previously unselected package libxinerama1:amd64.
338s Preparing to unpack .../070-libxinerama1_2%3a1.1.4-3build1_amd64.deb ...
338s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ...
338s Selecting previously unselected package libxrandr2:amd64.
339s Preparing to unpack .../071-libxrandr2_2%3a1.5.4-1_amd64.deb ...
339s Unpacking libxrandr2:amd64 (2:1.5.4-1) ...
339s Selecting previously unselected package libgtk-3-common.
339s Preparing to unpack .../072-libgtk-3-common_3.24.48-3ubuntu1_all.deb ...
339s Unpacking libgtk-3-common (3.24.48-3ubuntu1) ...
339s Selecting previously unselected package libgtk-3-0t64:amd64.
339s Preparing to unpack .../073-libgtk-3-0t64_3.24.48-3ubuntu1_amd64.deb ...
339s Unpacking libgtk-3-0t64:amd64 (3.24.48-3ubuntu1) ...
339s Selecting previously unselected package libglvnd0:amd64.
339s Preparing to unpack .../074-libglvnd0_1.7.0-1build1_amd64.deb ...
339s Unpacking libglvnd0:amd64 (1.7.0-1build1) ...
339s Selecting previously unselected package libx11-xcb1:amd64.
339s Preparing to unpack .../075-libx11-xcb1_2%3a1.8.10-2_amd64.deb ...
339s Unpacking libx11-xcb1:amd64 (2:1.8.10-2) ...
339s Selecting previously unselected package libxcb-dri3-0:amd64.
339s Preparing to unpack .../076-libxcb-dri3-0_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-dri3-0:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxcb-glx0:amd64.
339s Preparing to unpack .../077-libxcb-glx0_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-glx0:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxcb-present0:amd64.
339s Preparing to unpack .../078-libxcb-present0_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-present0:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxcb-xfixes0:amd64.
339s Preparing to unpack .../079-libxcb-xfixes0_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-xfixes0:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxxf86vm1:amd64.
339s Preparing to unpack .../080-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ...
339s Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ...
339s Selecting previously unselected package libpciaccess0:amd64.
339s Preparing to unpack .../081-libpciaccess0_0.17-3build1_amd64.deb ...
339s Unpacking libpciaccess0:amd64 (0.17-3build1) ...
339s Selecting previously unselected package libdrm-intel1:amd64.
339s Preparing to unpack .../082-libdrm-intel1_2.4.123-1_amd64.deb ...
339s Unpacking libdrm-intel1:amd64 (2.4.123-1) ...
339s Selecting previously unselected package libxcb-randr0:amd64.
339s Preparing to unpack .../083-libxcb-randr0_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-randr0:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxcb-sync1:amd64.
339s Preparing to unpack .../084-libxcb-sync1_1.17.0-2_amd64.deb ...
339s Unpacking libxcb-sync1:amd64 (1.17.0-2) ...
339s Selecting previously unselected package libxshmfence1:amd64.
339s Preparing to unpack .../085-libxshmfence1_1.3-1build5_amd64.deb ...
339s Unpacking libxshmfence1:amd64 (1.3-1build5) ...
339s Selecting previously unselected package mesa-libgallium:amd64.
339s Preparing to unpack .../086-mesa-libgallium_25.0.1-2ubuntu1_amd64.deb ...
339s Unpacking mesa-libgallium:amd64 (25.0.1-2ubuntu1) ...
339s Selecting previously unselected package libwayland-server0:amd64.
339s Preparing to unpack .../087-libwayland-server0_1.23.1-3_amd64.deb ...
339s Unpacking libwayland-server0:amd64 (1.23.1-3) ...
339s Selecting previously unselected package libgbm1:amd64.
339s Preparing to unpack .../088-libgbm1_25.0.1-2ubuntu1_amd64.deb ...
339s Unpacking libgbm1:amd64 (25.0.1-2ubuntu1) ...
339s Selecting previously unselected package libvulkan1:amd64.
339s Preparing to unpack .../089-libvulkan1_1.4.304.0-1_amd64.deb ...
339s Unpacking libvulkan1:amd64 (1.4.304.0-1) ...
339s Selecting previously unselected package libgl1-mesa-dri:amd64.
339s Preparing to unpack .../090-libgl1-mesa-dri_25.0.1-2ubuntu1_amd64.deb ...
340s Unpacking libgl1-mesa-dri:amd64 (25.0.1-2ubuntu1) ...
340s Selecting previously unselected package libglx-mesa0:amd64.
340s Preparing to unpack .../091-libglx-mesa0_25.0.1-2ubuntu1_amd64.deb ...
340s Unpacking libglx-mesa0:amd64 (25.0.1-2ubuntu1) ...
340s Selecting previously unselected package libglx0:amd64.
340s Preparing to unpack .../092-libglx0_1.7.0-1build1_amd64.deb ...
340s Unpacking libglx0:amd64 (1.7.0-1build1) ...
340s Selecting previously unselected package libgl1:amd64.
340s Preparing to unpack .../093-libgl1_1.7.0-1build1_amd64.deb ...
340s Unpacking libgl1:amd64 (1.7.0-1build1) ...
340s Selecting previously unselected package libasound2-data.
340s Preparing to unpack .../094-libasound2-data_1.2.13-1build1_all.deb ...
340s Unpacking libasound2-data (1.2.13-1build1) ...
340s Selecting previously unselected package libasound2t64:amd64.
340s Preparing to unpack .../095-libasound2t64_1.2.13-1build1_amd64.deb ...
340s Unpacking libasound2t64:amd64 (1.2.13-1build1) ...
340s Selecting previously unselected package libgif7:amd64.
340s Preparing to unpack .../096-libgif7_5.2.2-1ubuntu2_amd64.deb ...
340s Unpacking libgif7:amd64 (5.2.2-1ubuntu2) ...
340s Selecting previously unselected package x11-common.
340s Preparing to unpack .../097-x11-common_1%3a7.7+23ubuntu3_all.deb ...
340s Unpacking x11-common (1:7.7+23ubuntu3) ...
340s Selecting previously unselected package libxtst6:amd64.
340s Preparing to unpack .../098-libxtst6_2%3a1.2.5-1_amd64.deb ...
340s Unpacking libxtst6:amd64 (2:1.2.5-1) ...
340s Selecting previously unselected package openjdk-21-jre:amd64.
340s Preparing to unpack .../099-openjdk-21-jre_21.0.6+7-1_amd64.deb ...
340s Unpacking openjdk-21-jre:amd64 (21.0.6+7-1) ...
340s Selecting previously unselected package default-jre.
340s Preparing to unpack .../100-default-jre_2%3a1.21-76_amd64.deb ...
340s Unpacking default-jre (2:1.21-76) ...
340s Selecting previously unselected package fonts-font-awesome.
340s Preparing to unpack .../101-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
340s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
340s Selecting previously unselected package fonts-glyphicons-halflings.
340s Preparing to unpack .../102-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
340s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
340s Selecting previously unselected package fonts-mathjax.
340s Preparing to unpack .../103-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
340s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
340s Selecting previously unselected package hisat2.
340s Preparing to unpack .../104-hisat2_2.2.1-5_amd64.deb ...
340s Unpacking hisat2 (2.2.1-5) ...
340s Selecting previously unselected package jaligner.
340s Preparing to unpack .../105-jaligner_1.0+dfsg-11_all.deb ...
340s Unpacking jaligner (1.0+dfsg-11) ...
340s Selecting previously unselected package javascript-common.
340s Preparing to unpack .../106-javascript-common_12_all.deb ...
340s Unpacking javascript-common (12) ...
340s Selecting previously unselected package libhtscodecs2:amd64.
340s Preparing to unpack .../107-libhtscodecs2_1.6.1-2_amd64.deb ...
340s Unpacking libhtscodecs2:amd64 (1.6.1-2) ...
340s Selecting previously unselected package libhts3t64:amd64.
340s Preparing to unpack .../108-libhts3t64_1.21+ds-1_amd64.deb ...
340s Unpacking libhts3t64:amd64 (1.21+ds-1) ...
340s Selecting previously unselected package libjellyfish-2.0-2:amd64.
340s Preparing to unpack .../109-libjellyfish-2.0-2_2.3.1-4build1_amd64.deb ...
340s Unpacking libjellyfish-2.0-2:amd64 (2.3.1-4build1) ...
341s Selecting previously unselected package jellyfish.
341s Preparing to unpack .../110-jellyfish_2.3.1-4build1_amd64.deb ...
341s Unpacking jellyfish (2.3.1-4build1) ...
341s Selecting previously unselected package libhamcrest-java.
341s Preparing to unpack .../111-libhamcrest-java_2.2-2_all.deb ...
341s Unpacking libhamcrest-java (2.2-2) ...
341s Selecting previously unselected package junit4.
341s Preparing to unpack .../112-junit4_4.13.2-5_all.deb ...
341s Unpacking junit4 (4.13.2-5) ...
341s Selecting previously unselected package kallisto.
341s Preparing to unpack .../113-kallisto_0.48.0+dfsg-4build1_amd64.deb ...
341s Unpacking kallisto (0.48.0+dfsg-4build1) ...
341s Selecting previously unselected package libapache-pom-java.
341s Preparing to unpack .../114-libapache-pom-java_33-2_all.deb ...
341s Unpacking libapache-pom-java (33-2) ...
341s Selecting previously unselected package libasan8:amd64.
341s Preparing to unpack .../115-libasan8_15-20250222-0ubuntu1_amd64.deb ...
341s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ...
341s Selecting previously unselected package libatinject-jsr330-api-java.
341s Preparing to unpack .../116-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ...
341s Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ...
341s Selecting previously unselected package libcommons-parent-java.
341s Preparing to unpack .../117-libcommons-parent-java_56-1_all.deb ...
341s Unpacking libcommons-parent-java (56-1) ...
341s Selecting previously unselected package libcommons-lang3-java.
341s Preparing to unpack .../118-libcommons-lang3-java_3.17.0-1_all.deb ...
341s Unpacking libcommons-lang3-java (3.17.0-1) ...
341s Selecting previously unselected package libfreemarker-java.
341s Preparing to unpack .../119-libfreemarker-java_2.3.32-2_all.deb ...
341s Unpacking libfreemarker-java (2.3.32-2) ...
341s Selecting previously unselected package libgoogle-gson-java.
341s Preparing to unpack .../120-libgoogle-gson-java_2.10.1-1_all.deb ...
341s Unpacking libgoogle-gson-java (2.10.1-1) ...
341s Selecting previously unselected package libjoptsimple-java.
341s Preparing to unpack .../121-libjoptsimple-java_5.0.4-7_all.deb ...
341s Unpacking libjoptsimple-java (5.0.4-7) ...
341s Selecting previously unselected package libcommons-codec-java.
341s Preparing to unpack .../122-libcommons-codec-java_1.17.1-1_all.deb ...
341s Unpacking libcommons-codec-java (1.17.1-1) ...
341s Selecting previously unselected package libcommons-logging-java.
341s Preparing to unpack .../123-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ...
341s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ...
341s Selecting previously unselected package libhttpcore-java.
341s Preparing to unpack .../124-libhttpcore-java_4.4.16-1_all.deb ...
341s Unpacking libhttpcore-java (4.4.16-1) ...
341s Selecting previously unselected package libhttpclient-java.
341s Preparing to unpack .../125-libhttpclient-java_4.5.14-1_all.deb ...
341s Unpacking libhttpclient-java (4.5.14-1) ...
341s Selecting previously unselected package liblightcouch-java.
341s Preparing to unpack .../126-liblightcouch-java_0.2.0-1_all.deb ...
341s Unpacking liblightcouch-java (0.2.0-1) ...
341s Selecting previously unselected package libmongodb-java.
341s Preparing to unpack .../127-libmongodb-java_3.6.3-2_all.deb ...
341s Unpacking libmongodb-java (3.6.3-2) ...
341s Selecting previously unselected package libslf4j-java.
341s Preparing to unpack .../128-libslf4j-java_1.7.32-1_all.deb ...
341s Unpacking libslf4j-java (1.7.32-1) ...
341s Selecting previously unselected package liblog4j2-java.
341s Preparing to unpack .../129-liblog4j2-java_2.19.0-2_all.deb ...
341s Unpacking liblog4j2-java (2.19.0-2) ...
341s Selecting previously unselected package libbarclay-java.
341s Preparing to unpack .../130-libbarclay-java_5.0.0+dfsg-1_all.deb ...
341s Unpacking libbarclay-java (5.0.0+dfsg-1) ...
341s Selecting previously unselected package libgomp1:amd64.
341s Preparing to unpack .../131-libgomp1_15-20250222-0ubuntu1_amd64.deb ...
341s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ...
341s Selecting previously unselected package libitm1:amd64.
341s Preparing to unpack .../132-libitm1_15-20250222-0ubuntu1_amd64.deb ...
341s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package liblsan0:amd64.
342s Preparing to unpack .../133-liblsan0_15-20250222-0ubuntu1_amd64.deb ...
342s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package libtsan2:amd64.
342s Preparing to unpack .../134-libtsan2_15-20250222-0ubuntu1_amd64.deb ...
342s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package libubsan1:amd64.
342s Preparing to unpack .../135-libubsan1_15-20250222-0ubuntu1_amd64.deb ...
342s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package libhwasan0:amd64.
342s Preparing to unpack .../136-libhwasan0_15-20250222-0ubuntu1_amd64.deb ...
342s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package libquadmath0:amd64.
342s Preparing to unpack .../137-libquadmath0_15-20250222-0ubuntu1_amd64.deb ...
342s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ...
342s Selecting previously unselected package libgcc-14-dev:amd64.
342s Preparing to unpack .../138-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ...
342s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ...
342s Selecting previously unselected package libstdc++-14-dev:amd64.
342s Preparing to unpack .../139-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ...
342s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
342s Selecting previously unselected package libboost1.83-dev:amd64.
342s Preparing to unpack .../140-libboost1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ...
342s Unpacking libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ...
345s Selecting previously unselected package libboost-dev:amd64.
345s Preparing to unpack .../141-libboost-dev_1.83.0.2ubuntu1_amd64.deb ...
345s Unpacking libboost-dev:amd64 (1.83.0.2ubuntu1) ...
345s Selecting previously unselected package libboost-iostreams1.83.0:amd64.
345s Preparing to unpack .../142-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_amd64.deb ...
345s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
345s Selecting previously unselected package libclone-perl:amd64.
345s Preparing to unpack .../143-libclone-perl_0.47-1_amd64.deb ...
345s Unpacking libclone-perl:amd64 (0.47-1) ...
345s Selecting previously unselected package libcommons-collections3-java.
345s Preparing to unpack .../144-libcommons-collections3-java_3.2.2-3_all.deb ...
345s Unpacking libcommons-collections3-java (3.2.2-3) ...
345s Selecting previously unselected package libcommons-beanutils-java.
345s Preparing to unpack .../145-libcommons-beanutils-java_1.9.4-2_all.deb ...
345s Unpacking libcommons-beanutils-java (1.9.4-2) ...
345s Selecting previously unselected package libcommons-collections4-java.
345s Preparing to unpack .../146-libcommons-collections4-java_4.4-2_all.deb ...
345s Unpacking libcommons-collections4-java (4.4-2) ...
345s Selecting previously unselected package libcommons-io-java.
345s Preparing to unpack .../147-libcommons-io-java_2.18.0-1_all.deb ...
345s Unpacking libcommons-io-java (2.18.0-1) ...
345s Selecting previously unselected package libcommons-compress-java.
345s Preparing to unpack .../148-libcommons-compress-java_1.27.1-2_all.deb ...
345s Unpacking libcommons-compress-java (1.27.1-2) ...
345s Selecting previously unselected package libcommons-jexl2-java.
345s Preparing to unpack .../149-libcommons-jexl2-java_2.1.1-6_all.deb ...
345s Unpacking libcommons-jexl2-java (2.1.1-6) ...
345s Selecting previously unselected package libcommons-math3-java.
345s Preparing to unpack .../150-libcommons-math3-java_3.6.1-4_all.deb ...
345s Unpacking libcommons-math3-java (3.6.1-4) ...
345s Selecting previously unselected package libencode-locale-perl.
345s Preparing to unpack .../151-libencode-locale-perl_1.05-3_all.deb ...
345s Unpacking libencode-locale-perl (1.05-3) ...
345s Selecting previously unselected package libjsr305-java.
345s Preparing to unpack .../152-libjsr305-java_0.1~+svn49-12_all.deb ...
345s Unpacking libjsr305-java (0.1~+svn49-12) ...
345s Selecting previously unselected package libguava-java.
345s Preparing to unpack .../153-libguava-java_32.0.1-1_all.deb ...
345s Unpacking libguava-java (32.0.1-1) ...
345s Selecting previously unselected package liberror-prone-java.
345s Preparing to unpack .../154-liberror-prone-java_2.18.0-1_all.deb ...
345s Unpacking liberror-prone-java (2.18.0-1) ...
345s Selecting previously unselected package libezmorph-java.
345s Preparing to unpack .../155-libezmorph-java_1.0.6-4_all.deb ...
345s Unpacking libezmorph-java (1.0.6-4) ...
345s Selecting previously unselected package libtimedate-perl.
345s Preparing to unpack .../156-libtimedate-perl_2.3300-2_all.deb ...
345s Unpacking libtimedate-perl (2.3300-2) ...
345s Selecting previously unselected package libhttp-date-perl.
345s Preparing to unpack .../157-libhttp-date-perl_6.06-1_all.deb ...
345s Unpacking libhttp-date-perl (6.06-1) ...
345s Selecting previously unselected package libfile-listing-perl.
345s Preparing to unpack .../158-libfile-listing-perl_6.16-1_all.deb ...
345s Unpacking libfile-listing-perl (6.16-1) ...
345s Selecting previously unselected package libgatk-native-bindings-java.
345s Preparing to unpack .../159-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ...
345s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ...
345s Selecting previously unselected package libgetopt-java.
345s Preparing to unpack .../160-libgetopt-java_1.0.14+dfsg-6_all.deb ...
345s Unpacking libgetopt-java (1.0.14+dfsg-6) ...
345s Selecting previously unselected package libjaxen-java.
345s Preparing to unpack .../161-libjaxen-java_1.1.6-5_all.deb ...
345s Unpacking libjaxen-java (1.1.6-5) ...
346s Selecting previously unselected package libxml-commons-external-java.
346s Preparing to unpack .../162-libxml-commons-external-java_1.4.01-6_all.deb ...
346s Unpacking libxml-commons-external-java (1.4.01-6) ...
346s Selecting previously unselected package libxml-commons-resolver1.1-java.
346s Preparing to unpack .../163-libxml-commons-resolver1.1-java_1.2-11_all.deb ...
346s Unpacking libxml-commons-resolver1.1-java (1.2-11) ...
346s Selecting previously unselected package libxerces2-java.
346s Preparing to unpack .../164-libxerces2-java_2.12.2-1_all.deb ...
346s Unpacking libxerces2-java (2.12.2-1) ...
346s Selecting previously unselected package libxom-java.
346s Preparing to unpack .../165-libxom-java_1.3.9-1_all.deb ...
346s Unpacking libxom-java (1.3.9-1) ...
346s Selecting previously unselected package libjson-java.
346s Preparing to unpack .../166-libjson-java_3.1.0+dfsg-2_all.deb ...
346s Unpacking libjson-java (3.1.0+dfsg-2) ...
346s Selecting previously unselected package libmbedcrypto16:amd64.
346s Preparing to unpack .../167-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ...
346s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ...
346s Selecting previously unselected package libmbedx509-7:amd64.
346s Preparing to unpack .../168-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ...
346s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ...
346s Selecting previously unselected package libmbedtls21:amd64.
346s Preparing to unpack .../169-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ...
346s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ...
346s Selecting previously unselected package ncbi-vdb-data.
346s Preparing to unpack .../170-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ...
346s Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ...
346s Selecting previously unselected package libncbi-vdb3:amd64.
346s Preparing to unpack .../171-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ...
346s Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
346s Selecting previously unselected package libncbi-ngs3:amd64.
346s Preparing to unpack .../172-libncbi-ngs3_3.0.9+dfsg-7.1ubuntu1_amd64.deb ...
346s Unpacking libncbi-ngs3:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
346s Selecting previously unselected package libngs-jni:amd64.
346s Preparing to unpack .../173-libngs-jni_3.0.9+dfsg-7.1ubuntu1_amd64.deb ...
346s Unpacking libngs-jni:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
346s Selecting previously unselected package libngs-java:amd64.
346s Preparing to unpack .../174-libngs-java_3.0.9+dfsg-7.1ubuntu1_amd64.deb ...
346s Unpacking libngs-java:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
346s Selecting previously unselected package librhino-java.
346s Preparing to unpack .../175-librhino-java_1.7.15-1_all.deb ...
346s Unpacking librhino-java (1.7.15-1) ...
346s Selecting previously unselected package libsnappy1v5:amd64.
346s Preparing to unpack .../176-libsnappy1v5_1.2.1-1_amd64.deb ...
346s Unpacking libsnappy1v5:amd64 (1.2.1-1) ...
346s Selecting previously unselected package libsnappy-jni.
346s Preparing to unpack .../177-libsnappy-jni_1.1.10.7-1_amd64.deb ...
346s Unpacking libsnappy-jni (1.1.10.7-1) ...
346s Selecting previously unselected package libsnappy-java.
346s Preparing to unpack .../178-libsnappy-java_1.1.10.7-1_all.deb ...
346s Unpacking libsnappy-java (1.1.10.7-1) ...
346s Selecting previously unselected package libhtsjdk-java.
346s Preparing to unpack .../179-libhtsjdk-java_4.1.3+dfsg-2_all.deb ...
346s Unpacking libhtsjdk-java (4.1.3+dfsg-2) ...
346s Selecting previously unselected package libgkl-java.
346s Preparing to unpack .../180-libgkl-java_0.8.11+dfsg-2build1_all.deb ...
346s Unpacking libgkl-java (0.8.11+dfsg-2build1) ...
346s Selecting previously unselected package libhtml-tagset-perl.
346s Preparing to unpack .../181-libhtml-tagset-perl_3.24-1_all.deb ...
346s Unpacking libhtml-tagset-perl (3.24-1) ...
346s Selecting previously unselected package liburi-perl.
346s Preparing to unpack .../182-liburi-perl_5.30-1_all.deb ...
346s Unpacking liburi-perl (5.30-1) ...
346s Selecting previously unselected package libhtml-parser-perl:amd64.
346s Preparing to unpack .../183-libhtml-parser-perl_3.83-1build1_amd64.deb ...
346s Unpacking libhtml-parser-perl:amd64 (3.83-1build1) ...
346s Selecting previously unselected package libhtml-tree-perl.
346s Preparing to unpack .../184-libhtml-tree-perl_5.07-3_all.deb ...
346s Unpacking libhtml-tree-perl (5.07-3) ...
346s Selecting previously unselected package libio-html-perl.
346s Preparing to unpack .../185-libio-html-perl_1.004-3_all.deb ...
346s Unpacking libio-html-perl (1.004-3) ...
346s Selecting previously unselected package liblwp-mediatypes-perl.
346s Preparing to unpack .../186-liblwp-mediatypes-perl_6.04-2_all.deb ...
346s Unpacking liblwp-mediatypes-perl (6.04-2) ...
346s Selecting previously unselected package libhttp-message-perl.
346s Preparing to unpack .../187-libhttp-message-perl_7.00-2ubuntu1_all.deb ...
346s Unpacking libhttp-message-perl (7.00-2ubuntu1) ...
347s Selecting previously unselected package libhttp-cookies-perl.
347s Preparing to unpack .../188-libhttp-cookies-perl_6.11-1_all.deb ...
347s Unpacking libhttp-cookies-perl (6.11-1) ...
347s Selecting previously unselected package libhttp-negotiate-perl.
347s Preparing to unpack .../189-libhttp-negotiate-perl_6.01-2_all.deb ...
347s Unpacking libhttp-negotiate-perl (6.01-2) ...
347s Selecting previously unselected package libhwloc15:amd64.
347s Preparing to unpack .../190-libhwloc15_2.12.0-1_amd64.deb ...
347s Unpacking libhwloc15:amd64 (2.12.0-1) ...
347s Selecting previously unselected package libice6:amd64.
347s Preparing to unpack .../191-libice6_2%3a1.1.1-1_amd64.deb ...
347s Unpacking libice6:amd64 (2:1.1.1-1) ...
347s Selecting previously unselected package perl-openssl-defaults:amd64.
347s Preparing to unpack .../192-perl-openssl-defaults_7build3_amd64.deb ...
347s Unpacking perl-openssl-defaults:amd64 (7build3) ...
347s Selecting previously unselected package libnet-ssleay-perl:amd64.
347s Preparing to unpack .../193-libnet-ssleay-perl_1.94-3_amd64.deb ...
347s Unpacking libnet-ssleay-perl:amd64 (1.94-3) ...
347s Selecting previously unselected package libio-socket-ssl-perl.
347s Preparing to unpack .../194-libio-socket-ssl-perl_2.089-1_all.deb ...
347s Unpacking libio-socket-ssl-perl (2.089-1) ...
347s Selecting previously unselected package libjs-bootstrap.
347s Preparing to unpack .../195-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
347s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
347s Selecting previously unselected package libjs-popper.js.
347s Preparing to unpack .../196-libjs-popper.js_1.16.1+ds-6_all.deb ...
347s Unpacking libjs-popper.js (1.16.1+ds-6) ...
347s Selecting previously unselected package libjs-bootstrap4.
347s Preparing to unpack .../197-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ...
347s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ...
347s Selecting previously unselected package libjs-d3.
347s Preparing to unpack .../198-libjs-d3_3.5.17-4_all.deb ...
347s Unpacking libjs-d3 (3.5.17-4) ...
347s Selecting previously unselected package libjs-es5-shim.
347s Preparing to unpack .../199-libjs-es5-shim_4.6.7-2_all.deb ...
347s Unpacking libjs-es5-shim (4.6.7-2) ...
347s Selecting previously unselected package libjs-highlight.js.
347s Preparing to unpack .../200-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
347s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
347s Selecting previously unselected package libjs-jquery.
347s Preparing to unpack .../201-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
347s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
347s Selecting previously unselected package libjs-jquery-datatables.
347s Preparing to unpack .../202-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
347s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
347s Selecting previously unselected package libjs-sifter.js.
347s Preparing to unpack .../203-libjs-sifter.js_0.6.0+dfsg-3_all.deb ...
347s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ...
347s Selecting previously unselected package libjs-microplugin.js.
347s Preparing to unpack .../204-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ...
347s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ...
347s Selecting previously unselected package libjs-jquery-selectize.js.
347s Preparing to unpack .../205-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ...
347s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
347s Selecting previously unselected package libjs-jquery-ui.
347s Preparing to unpack .../206-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
347s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
347s Selecting previously unselected package libjs-json.
347s Preparing to unpack .../207-libjs-json_0~20221030+~1.0.8-1_all.deb ...
347s Unpacking libjs-json (0~20221030+~1.0.8-1) ...
347s Selecting previously unselected package libjs-prettify.
347s Preparing to unpack .../208-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ...
347s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ...
348s Selecting previously unselected package libjs-underscore.
348s Preparing to unpack .../209-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
348s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
348s Selecting previously unselected package libjs-sphinxdoc.
348s Preparing to unpack .../210-libjs-sphinxdoc_8.1.3-4_all.deb ...
348s Unpacking libjs-sphinxdoc (8.1.3-4) ...
348s Selecting previously unselected package libjung-free-java.
348s Preparing to unpack .../211-libjung-free-java_2.1.1-3_all.deb ...
348s Unpacking libjung-free-java (2.1.1-3) ...
348s Selecting previously unselected package liblua5.4-0:amd64.
348s Preparing to unpack .../212-liblua5.4-0_5.4.7-1_amd64.deb ...
348s Unpacking liblua5.4-0:amd64 (5.4.7-1) ...
348s Selecting previously unselected package libnet-http-perl.
348s Preparing to unpack .../213-libnet-http-perl_6.23-1_all.deb ...
348s Unpacking libnet-http-perl (6.23-1) ...
348s Selecting previously unselected package libtry-tiny-perl.
348s Preparing to unpack .../214-libtry-tiny-perl_0.32-1_all.deb ...
348s Unpacking libtry-tiny-perl (0.32-1) ...
348s Selecting previously unselected package libwww-robotrules-perl.
348s Preparing to unpack .../215-libwww-robotrules-perl_6.02-1_all.deb ...
348s Unpacking libwww-robotrules-perl (6.02-1) ...
348s Selecting previously unselected package libwww-perl.
348s Preparing to unpack .../216-libwww-perl_6.78-1_all.deb ...
348s Unpacking libwww-perl (6.78-1) ...
348s Selecting previously unselected package liblwp-protocol-https-perl.
348s Preparing to unpack .../217-liblwp-protocol-https-perl_6.14-1_all.deb ...
348s Unpacking liblwp-protocol-https-perl (6.14-1) ...
348s Selecting previously unselected package libpaper2:amd64.
348s Preparing to unpack .../218-libpaper2_2.2.5-0.3_amd64.deb ...
348s Unpacking libpaper2:amd64 (2.2.5-0.3) ...
348s Selecting previously unselected package libpaper-utils.
348s Preparing to unpack .../219-libpaper-utils_2.2.5-0.3_amd64.deb ...
348s Unpacking libpaper-utils (2.2.5-0.3) ...
348s Selecting previously unselected package libpicard-java.
348s Preparing to unpack .../220-libpicard-java_3.3.0+dfsg-2_all.deb ...
348s Unpacking libpicard-java (3.3.0+dfsg-2) ...
348s Selecting previously unselected package libsm6:amd64.
348s Preparing to unpack .../221-libsm6_2%3a1.2.4-1_amd64.deb ...
348s Unpacking libsm6:amd64 (2:1.2.4-1) ...
348s Selecting previously unselected package libstaden-read14t64:amd64.
348s Preparing to unpack .../222-libstaden-read14t64_1.15.0-1.1build2_amd64.deb ...
348s Unpacking libstaden-read14t64:amd64 (1.15.0-1.1build2) ...
348s Selecting previously unselected package libtbbbind-2-5:amd64.
348s Preparing to unpack .../223-libtbbbind-2-5_2022.0.0-2_amd64.deb ...
348s Unpacking libtbbbind-2-5:amd64 (2022.0.0-2) ...
348s Selecting previously unselected package libtbbmalloc2:amd64.
348s Preparing to unpack .../224-libtbbmalloc2_2022.0.0-2_amd64.deb ...
348s Unpacking libtbbmalloc2:amd64 (2022.0.0-2) ...
348s Selecting previously unselected package libtbb12:amd64.
348s Preparing to unpack .../225-libtbb12_2022.0.0-2_amd64.deb ...
348s Unpacking libtbb12:amd64 (2022.0.0-2) ...
348s Selecting previously unselected package libtcl8.6:amd64.
348s Preparing to unpack .../226-libtcl8.6_8.6.16+dfsg-1_amd64.deb ...
348s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ...
348s Selecting previously unselected package libxft2:amd64.
348s Preparing to unpack .../227-libxft2_2.3.6-1build1_amd64.deb ...
348s Unpacking libxft2:amd64 (2.3.6-1build1) ...
348s Selecting previously unselected package libxss1:amd64.
348s Preparing to unpack .../228-libxss1_1%3a1.2.3-1build3_amd64.deb ...
348s Unpacking libxss1:amd64 (1:1.2.3-1build3) ...
348s Selecting previously unselected package libtk8.6:amd64.
348s Preparing to unpack .../229-libtk8.6_8.6.16-1_amd64.deb ...
348s Unpacking libtk8.6:amd64 (8.6.16-1) ...
348s Selecting previously unselected package libxt6t64:amd64.
348s Preparing to unpack .../230-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ...
348s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ...
348s Selecting previously unselected package zip.
348s Preparing to unpack .../231-zip_3.0-14ubuntu2_amd64.deb ...
348s Unpacking zip (3.0-14ubuntu2) ...
348s Selecting previously unselected package unzip.
348s Preparing to unpack .../232-unzip_6.0-28ubuntu6_amd64.deb ...
348s Unpacking unzip (6.0-28ubuntu6) ...
349s Selecting previously unselected package xdg-utils.
349s Preparing to unpack .../233-xdg-utils_1.2.1-2ubuntu1_all.deb ...
349s Unpacking xdg-utils (1.2.1-2ubuntu1) ...
349s Selecting previously unselected package r-base-core.
349s Preparing to unpack .../234-r-base-core_4.4.3-1_amd64.deb ...
349s Unpacking r-base-core (4.4.3-1) ...
349s Selecting previously unselected package r-cran-littler.
349s Preparing to unpack .../235-r-cran-littler_0.3.20-2_amd64.deb ...
349s Unpacking r-cran-littler (0.3.20-2) ...
349s Selecting previously unselected package littler.
349s Preparing to unpack .../236-littler_0.3.20-2_all.deb ...
349s Unpacking littler (0.3.20-2) ...
349s Selecting previously unselected package ncbi-data.
349s Preparing to unpack .../237-ncbi-data_6.1.20170106+dfsg2-5_all.deb ...
349s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ...
349s Selecting previously unselected package ncbi-blast+.
349s Preparing to unpack .../238-ncbi-blast+_2.16.0+ds-6build1_amd64.deb ...
349s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ...
350s Selecting previously unselected package node-bootstrap-sass.
350s Preparing to unpack .../239-node-bootstrap-sass_3.4.3-2_all.deb ...
350s Unpacking node-bootstrap-sass (3.4.3-2) ...
350s Selecting previously unselected package node-html5shiv.
350s Preparing to unpack .../240-node-html5shiv_3.7.3+dfsg-5_all.deb ...
350s Unpacking node-html5shiv (3.7.3+dfsg-5) ...
350s Selecting previously unselected package node-normalize.css.
350s Preparing to unpack .../241-node-normalize.css_8.0.1-5_all.deb ...
350s Unpacking node-normalize.css (8.0.1-5) ...
350s Selecting previously unselected package pandoc-data.
350s Preparing to unpack .../242-pandoc-data_3.1.11.1-3build1_all.deb ...
350s Unpacking pandoc-data (3.1.11.1-3build1) ...
350s Selecting previously unselected package pandoc.
350s Preparing to unpack .../243-pandoc_3.1.11.1+ds-2_amd64.deb ...
350s Unpacking pandoc (3.1.11.1+ds-2) ...
351s Selecting previously unselected package parafly.
351s Preparing to unpack .../244-parafly_0.1.0-5_amd64.deb ...
351s Unpacking parafly (0.1.0-5) ...
351s Selecting previously unselected package python3-hisat2.
351s Preparing to unpack .../245-python3-hisat2_2.2.1-5_all.deb ...
351s Unpacking python3-hisat2 (2.2.1-5) ...
351s Selecting previously unselected package python3-pysam.
351s Preparing to unpack .../246-python3-pysam_0.23.0+ds-1build1_amd64.deb ...
351s Unpacking python3-pysam (0.23.0+ds-1build1) ...
351s Selecting previously unselected package python3-htseq.
351s Preparing to unpack .../247-python3-htseq_2.0.9+dfsg-1build2_amd64.deb ...
351s Unpacking python3-htseq (2.0.9+dfsg-1build2) ...
351s Selecting previously unselected package r-bioc-biocgenerics.
351s Preparing to unpack .../248-r-bioc-biocgenerics_0.52.0-2_all.deb ...
351s Unpacking r-bioc-biocgenerics (0.52.0-2) ...
351s Selecting previously unselected package r-bioc-biobase.
351s Preparing to unpack .../249-r-bioc-biobase_2.66.0-2_amd64.deb ...
351s Unpacking r-bioc-biobase (2.66.0-2) ...
351s Selecting previously unselected package r-bioc-s4vectors.
351s Preparing to unpack .../250-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ...
351s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ...
351s Selecting previously unselected package r-bioc-iranges.
351s Preparing to unpack .../251-r-bioc-iranges_2.40.1-2_amd64.deb ...
351s Unpacking r-bioc-iranges (2.40.1-2) ...
351s Selecting previously unselected package r-cran-dbi.
351s Preparing to unpack .../252-r-cran-dbi_1.2.3-1_all.deb ...
351s Unpacking r-cran-dbi (1.2.3-1) ...
351s Selecting previously unselected package r-cran-bit.
351s Preparing to unpack .../253-r-cran-bit_4.6.0+dfsg-1_amd64.deb ...
351s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
352s Selecting previously unselected package r-cran-bit64.
352s Preparing to unpack .../254-r-cran-bit64_4.6.0-1-1ubuntu2_amd64.deb ...
352s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ...
352s Selecting previously unselected package r-cran-rlang.
352s Preparing to unpack .../255-r-cran-rlang_1.1.5-1_amd64.deb ...
352s Unpacking r-cran-rlang (1.1.5-1) ...
352s Selecting previously unselected package r-cran-cli.
352s Preparing to unpack .../256-r-cran-cli_3.6.4-1_amd64.deb ...
352s Unpacking r-cran-cli (3.6.4-1) ...
352s Selecting previously unselected package r-cran-glue.
352s Preparing to unpack .../257-r-cran-glue_1.8.0-1_amd64.deb ...
352s Unpacking r-cran-glue (1.8.0-1) ...
352s Selecting previously unselected package r-cran-lifecycle.
352s Preparing to unpack .../258-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
352s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
352s Selecting previously unselected package r-cran-vctrs.
352s Preparing to unpack .../259-r-cran-vctrs_0.6.5-1_amd64.deb ...
352s Unpacking r-cran-vctrs (0.6.5-1) ...
352s Selecting previously unselected package r-cran-blob.
352s Preparing to unpack .../260-r-cran-blob_1.2.4-1_all.deb ...
352s Unpacking r-cran-blob (1.2.4-1) ...
352s Selecting previously unselected package r-cran-fastmap.
352s Preparing to unpack .../261-r-cran-fastmap_1.2.0-1_amd64.deb ...
352s Unpacking r-cran-fastmap (1.2.0-1) ...
352s Selecting previously unselected package r-cran-cachem.
352s Preparing to unpack .../262-r-cran-cachem_1.1.0-1_amd64.deb ...
352s Unpacking r-cran-cachem (1.1.0-1) ...
352s Selecting previously unselected package r-cran-memoise.
352s Preparing to unpack .../263-r-cran-memoise_2.0.1-1_all.deb ...
352s Unpacking r-cran-memoise (2.0.1-1) ...
352s Selecting previously unselected package r-cran-pkgconfig.
352s Preparing to unpack .../264-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
352s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
352s Selecting previously unselected package r-cran-plogr.
352s Preparing to unpack .../265-r-cran-plogr_0.2.0-3build1_all.deb ...
352s Unpacking r-cran-plogr (0.2.0-3build1) ...
352s Selecting previously unselected package r-cran-cpp11.
352s Preparing to unpack .../266-r-cran-cpp11_0.5.2-1_all.deb ...
352s Unpacking r-cran-cpp11 (0.5.2-1) ...
352s Selecting previously unselected package r-cran-rsqlite.
352s Preparing to unpack .../267-r-cran-rsqlite_2.3.9-1_amd64.deb ...
352s Unpacking r-cran-rsqlite (2.3.9-1) ...
352s Selecting previously unselected package r-cran-curl.
352s Preparing to unpack .../268-r-cran-curl_6.2.1+dfsg-1ubuntu1_amd64.deb ...
352s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
352s Selecting previously unselected package r-cran-jsonlite.
352s Preparing to unpack .../269-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ...
352s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ...
352s Selecting previously unselected package r-cran-mime.
352s Preparing to unpack .../270-r-cran-mime_0.12-2_amd64.deb ...
352s Unpacking r-cran-mime (0.12-2) ...
352s Selecting previously unselected package r-cran-sys.
352s Preparing to unpack .../271-r-cran-sys_3.4.3-1_amd64.deb ...
352s Unpacking r-cran-sys (3.4.3-1) ...
352s Selecting previously unselected package r-cran-askpass.
352s Preparing to unpack .../272-r-cran-askpass_1.2.1-1_amd64.deb ...
352s Unpacking r-cran-askpass (1.2.1-1) ...
352s Selecting previously unselected package r-cran-openssl.
353s Preparing to unpack .../273-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ...
353s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
353s Selecting previously unselected package r-cran-r6.
353s Preparing to unpack .../274-r-cran-r6_2.6.1-1_all.deb ...
353s Unpacking r-cran-r6 (2.6.1-1) ...
353s Selecting previously unselected package r-cran-httr.
353s Preparing to unpack .../275-r-cran-httr_1.4.7+dfsg-1_all.deb ...
353s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
353s Selecting previously unselected package r-cran-png.
353s Preparing to unpack .../276-r-cran-png_0.1-8-1build2_amd64.deb ...
353s Unpacking r-cran-png (0.1-8-1build2) ...
353s Selecting previously unselected package zlib1g-dev:amd64.
353s Preparing to unpack .../277-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ...
353s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
353s Selecting previously unselected package r-bioc-zlibbioc.
353s Preparing to unpack .../278-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ...
353s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ...
353s Selecting previously unselected package r-bioc-xvector.
353s Preparing to unpack .../279-r-bioc-xvector_0.46.0-2_amd64.deb ...
353s Unpacking r-bioc-xvector (0.46.0-2) ...
353s Selecting previously unselected package r-bioc-ucsc.utils.
353s Preparing to unpack .../280-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ...
353s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ...
353s Selecting previously unselected package r-bioc-genomeinfodbdata.
353s Preparing to unpack .../281-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ...
353s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ...
353s Selecting previously unselected package r-bioc-genomeinfodb.
353s Preparing to unpack .../282-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ...
353s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
353s Selecting previously unselected package r-cran-crayon.
353s Preparing to unpack .../283-r-cran-crayon_1.5.3-1_all.deb ...
353s Unpacking r-cran-crayon (1.5.3-1) ...
353s Selecting previously unselected package r-bioc-biostrings.
353s Preparing to unpack .../284-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ...
353s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ...
353s Selecting previously unselected package r-bioc-keggrest.
353s Preparing to unpack .../285-r-bioc-keggrest_1.46.0+dfsg-2_all.deb ...
353s Unpacking r-bioc-keggrest (1.46.0+dfsg-2) ...
353s Selecting previously unselected package r-bioc-annotationdbi.
353s Preparing to unpack .../286-r-bioc-annotationdbi_1.68.0-2_all.deb ...
353s Unpacking r-bioc-annotationdbi (1.68.0-2) ...
353s Selecting previously unselected package r-cran-xml.
353s Preparing to unpack .../287-r-cran-xml_3.99-0.18-1_amd64.deb ...
353s Unpacking r-cran-xml (3.99-0.18-1) ...
353s Selecting previously unselected package r-cran-xtable.
353s Preparing to unpack .../288-r-cran-xtable_1%3a1.8-4-2_all.deb ...
353s Unpacking r-cran-xtable (1:1.8-4-2) ...
354s Selecting previously unselected package r-bioc-annotate.
354s Preparing to unpack .../289-r-bioc-annotate_1.84.0+dfsg-2_all.deb ...
354s Unpacking r-bioc-annotate (1.84.0+dfsg-2) ...
354s Selecting previously unselected package r-cran-generics.
354s Preparing to unpack .../290-r-cran-generics_0.1.3-1_all.deb ...
354s Unpacking r-cran-generics (0.1.3-1) ...
354s Selecting previously unselected package r-cran-magrittr.
354s Preparing to unpack .../291-r-cran-magrittr_2.0.3-1_amd64.deb ...
354s Unpacking r-cran-magrittr (2.0.3-1) ...
354s Selecting previously unselected package r-cran-utf8.
354s Preparing to unpack .../292-r-cran-utf8_1.2.4-1_amd64.deb ...
354s Unpacking r-cran-utf8 (1.2.4-1) ...
354s Selecting previously unselected package r-cran-pillar.
354s Preparing to unpack .../293-r-cran-pillar_1.10.1+dfsg-1_all.deb ...
354s Unpacking r-cran-pillar (1.10.1+dfsg-1) ...
354s Selecting previously unselected package r-cran-fansi.
354s Preparing to unpack .../294-r-cran-fansi_1.0.5-1_amd64.deb ...
354s Unpacking r-cran-fansi (1.0.5-1) ...
354s Selecting previously unselected package r-cran-tibble.
354s Preparing to unpack .../295-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ...
354s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
354s Selecting previously unselected package r-cran-withr.
354s Preparing to unpack .../296-r-cran-withr_3.0.2+dfsg-1_all.deb ...
354s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
354s Selecting previously unselected package r-cran-tidyselect.
354s Preparing to unpack .../297-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ...
354s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
354s Selecting previously unselected package r-cran-dplyr.
354s Preparing to unpack .../298-r-cran-dplyr_1.1.4-4_amd64.deb ...
354s Unpacking r-cran-dplyr (1.1.4-4) ...
354s Selecting previously unselected package r-cran-purrr.
354s Preparing to unpack .../299-r-cran-purrr_1.0.4-1_amd64.deb ...
354s Unpacking r-cran-purrr (1.0.4-1) ...
354s Selecting previously unselected package r-cran-stringi.
354s Preparing to unpack .../300-r-cran-stringi_1.8.4-1build1_amd64.deb ...
354s Unpacking r-cran-stringi (1.8.4-1build1) ...
354s Selecting previously unselected package r-cran-stringr.
354s Preparing to unpack .../301-r-cran-stringr_1.5.1-1_all.deb ...
354s Unpacking r-cran-stringr (1.5.1-1) ...
354s Selecting previously unselected package r-cran-tidyr.
354s Preparing to unpack .../302-r-cran-tidyr_1.3.1-1_amd64.deb ...
354s Unpacking r-cran-tidyr (1.3.1-1) ...
354s Selecting previously unselected package r-cran-dbplyr.
354s Preparing to unpack .../303-r-cran-dbplyr_2.5.0+dfsg-1_all.deb ...
354s Unpacking r-cran-dbplyr (2.5.0+dfsg-1) ...
354s Selecting previously unselected package r-cran-filelock.
354s Preparing to unpack .../304-r-cran-filelock_1.0.3-1_amd64.deb ...
354s Unpacking r-cran-filelock (1.0.3-1) ...
354s Selecting previously unselected package r-bioc-biocfilecache.
354s Preparing to unpack .../305-r-bioc-biocfilecache_2.14.0+dfsg-2_all.deb ...
354s Unpacking r-bioc-biocfilecache (2.14.0+dfsg-2) ...
354s Selecting previously unselected package r-bioc-biocio.
354s Preparing to unpack .../306-r-bioc-biocio_1.16.0+dfsg-2_all.deb ...
354s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ...
354s Selecting previously unselected package r-cran-formatr.
354s Preparing to unpack .../307-r-cran-formatr_1.14-2_all.deb ...
354s Unpacking r-cran-formatr (1.14-2) ...
354s Selecting previously unselected package r-cran-lambda.r.
355s Preparing to unpack .../308-r-cran-lambda.r_1.2.4-2build1_all.deb ...
355s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
355s Selecting previously unselected package r-cran-futile.options.
355s Preparing to unpack .../309-r-cran-futile.options_1.0.1-3build1_all.deb ...
355s Unpacking r-cran-futile.options (1.0.1-3build1) ...
355s Selecting previously unselected package r-cran-futile.logger.
355s Preparing to unpack .../310-r-cran-futile.logger_1.4.3-4build1_all.deb ...
355s Unpacking r-cran-futile.logger (1.4.3-4build1) ...
355s Selecting previously unselected package r-cran-snow.
355s Preparing to unpack .../311-r-cran-snow_1%3a0.4.4-2_all.deb ...
355s Unpacking r-cran-snow (1:0.4.4-2) ...
355s Selecting previously unselected package r-cran-codetools.
355s Preparing to unpack .../312-r-cran-codetools_0.2-20-1_all.deb ...
355s Unpacking r-cran-codetools (0.2-20-1) ...
355s Selecting previously unselected package r-cran-bh.
355s Preparing to unpack .../313-r-cran-bh_1.84.0-1_all.deb ...
355s Unpacking r-cran-bh (1.84.0-1) ...
355s Selecting previously unselected package r-bioc-biocparallel.
355s Preparing to unpack .../314-r-bioc-biocparallel_1.40.0-2_amd64.deb ...
355s Unpacking r-bioc-biocparallel (1.40.0-2) ...
355s Selecting previously unselected package r-cran-hms.
355s Preparing to unpack .../315-r-cran-hms_1.1.3-1_all.deb ...
355s Unpacking r-cran-hms (1.1.3-1) ...
355s Selecting previously unselected package r-cran-prettyunits.
355s Preparing to unpack .../316-r-cran-prettyunits_1.2.0-1_all.deb ...
355s Unpacking r-cran-prettyunits (1.2.0-1) ...
355s Selecting previously unselected package r-cran-progress.
355s Preparing to unpack .../317-r-cran-progress_1.2.3-1_all.deb ...
355s Unpacking r-cran-progress (1.2.3-1) ...
355s Selecting previously unselected package r-cran-rappdirs.
355s Preparing to unpack .../318-r-cran-rappdirs_0.3.3-1_amd64.deb ...
355s Unpacking r-cran-rappdirs (0.3.3-1) ...
355s Selecting previously unselected package r-cran-httr2.
355s Preparing to unpack .../319-r-cran-httr2_1.1.1-1_all.deb ...
355s Unpacking r-cran-httr2 (1.1.1-1) ...
355s Selecting previously unselected package r-cran-digest.
355s Preparing to unpack .../320-r-cran-digest_0.6.37-1_amd64.deb ...
355s Unpacking r-cran-digest (0.6.37-1) ...
355s Selecting previously unselected package r-cran-xml2.
355s Preparing to unpack .../321-r-cran-xml2_1.3.7-1_amd64.deb ...
355s Unpacking r-cran-xml2 (1.3.7-1) ...
355s Selecting previously unselected package r-bioc-biomart.
355s Preparing to unpack .../322-r-bioc-biomart_2.62.1+dfsg-1_all.deb ...
355s Unpacking r-bioc-biomart (2.62.1+dfsg-1) ...
355s Selecting previously unselected package r-cran-lattice.
355s Preparing to unpack .../323-r-cran-lattice_0.22-6-1_amd64.deb ...
355s Unpacking r-cran-lattice (0.22-6-1) ...
355s Selecting previously unselected package r-cran-matrix.
355s Preparing to unpack .../324-r-cran-matrix_1.7-3-1_amd64.deb ...
355s Unpacking r-cran-matrix (1.7-3-1) ...
355s Selecting previously unselected package r-cran-matrixstats.
355s Preparing to unpack .../325-r-cran-matrixstats_1.5.0-1_amd64.deb ...
355s Unpacking r-cran-matrixstats (1.5.0-1) ...
355s Selecting previously unselected package r-bioc-matrixgenerics.
355s Preparing to unpack .../326-r-bioc-matrixgenerics_1.18.1-1_all.deb ...
355s Unpacking r-bioc-matrixgenerics (1.18.1-1) ...
355s Selecting previously unselected package r-cran-abind.
355s Preparing to unpack .../327-r-cran-abind_1.4-8-1_all.deb ...
355s Unpacking r-cran-abind (1.4-8-1) ...
355s Selecting previously unselected package r-bioc-s4arrays.
355s Preparing to unpack .../328-r-bioc-s4arrays_1.6.0+dfsg-2_amd64.deb ...
355s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ...
355s Selecting previously unselected package r-bioc-sparsearray.
355s Preparing to unpack .../329-r-bioc-sparsearray_1.6.2+dfsg-1_amd64.deb ...
355s Unpacking r-bioc-sparsearray (1.6.2+dfsg-1) ...
356s Selecting previously unselected package r-bioc-delayedarray.
356s Preparing to unpack .../330-r-bioc-delayedarray_0.32.0+dfsg-2_amd64.deb ...
356s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ...
356s Selecting previously unselected package r-bioc-genomicranges.
356s Preparing to unpack .../331-r-bioc-genomicranges_1.58.0+dfsg-2_amd64.deb ...
356s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ...
356s Selecting previously unselected package r-bioc-summarizedexperiment.
356s Preparing to unpack .../332-r-bioc-summarizedexperiment_1.36.0+dfsg-2_all.deb ...
356s Unpacking r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
356s Selecting previously unselected package r-cran-locfit.
356s Preparing to unpack .../333-r-cran-locfit_1.5-9.12-1_amd64.deb ...
356s Unpacking r-cran-locfit (1.5-9.12-1) ...
356s Selecting previously unselected package r-cran-gtable.
356s Preparing to unpack .../334-r-cran-gtable_0.3.6+dfsg-1_all.deb ...
356s Unpacking r-cran-gtable (0.3.6+dfsg-1) ...
356s Selecting previously unselected package r-cran-isoband.
356s Preparing to unpack .../335-r-cran-isoband_0.2.7-1_amd64.deb ...
356s Unpacking r-cran-isoband (0.2.7-1) ...
356s Selecting previously unselected package r-cran-mass.
356s Preparing to unpack .../336-r-cran-mass_7.3-64-1_amd64.deb ...
356s Unpacking r-cran-mass (7.3-64-1) ...
356s Selecting previously unselected package r-cran-nlme.
356s Preparing to unpack .../337-r-cran-nlme_3.1.167-1_amd64.deb ...
356s Unpacking r-cran-nlme (3.1.167-1) ...
356s Selecting previously unselected package r-cran-mgcv.
356s Preparing to unpack .../338-r-cran-mgcv_1.9-1-1_amd64.deb ...
356s Unpacking r-cran-mgcv (1.9-1-1) ...
356s Selecting previously unselected package r-cran-farver.
356s Preparing to unpack .../339-r-cran-farver_2.1.2-1_amd64.deb ...
356s Unpacking r-cran-farver (2.1.2-1) ...
356s Selecting previously unselected package r-cran-labeling.
356s Preparing to unpack .../340-r-cran-labeling_0.4.3-1_all.deb ...
356s Unpacking r-cran-labeling (0.4.3-1) ...
356s Selecting previously unselected package r-cran-colorspace.
356s Preparing to unpack .../341-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ...
356s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ...
356s Selecting previously unselected package r-cran-munsell.
356s Preparing to unpack .../342-r-cran-munsell_0.5.1-1_all.deb ...
356s Unpacking r-cran-munsell (0.5.1-1) ...
356s Selecting previously unselected package r-cran-rcolorbrewer.
356s Preparing to unpack .../343-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
356s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
356s Selecting previously unselected package r-cran-viridislite.
356s Preparing to unpack .../344-r-cran-viridislite_0.4.2-2_all.deb ...
356s Unpacking r-cran-viridislite (0.4.2-2) ...
356s Selecting previously unselected package r-cran-scales.
356s Preparing to unpack .../345-r-cran-scales_1.3.0-1_all.deb ...
356s Unpacking r-cran-scales (1.3.0-1) ...
356s Selecting previously unselected package r-cran-ggplot2.
356s Preparing to unpack .../346-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
356s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
357s Selecting previously unselected package r-cran-pkgkitten.
357s Preparing to unpack .../347-r-cran-pkgkitten_0.2.4-1_all.deb ...
357s Unpacking r-cran-pkgkitten (0.2.4-1) ...
357s Selecting previously unselected package r-cran-rcpp.
357s Preparing to unpack .../348-r-cran-rcpp_1.0.14-1_amd64.deb ...
357s Unpacking r-cran-rcpp (1.0.14-1) ...
357s Selecting previously unselected package r-cran-rcpparmadillo.
357s Preparing to unpack .../349-r-cran-rcpparmadillo_14.2.3-1-1_amd64.deb ...
357s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ...
357s Selecting previously unselected package r-bioc-deseq2.
357s Preparing to unpack .../350-r-bioc-deseq2_1.46.0+dfsg-2_amd64.deb ...
357s Unpacking r-bioc-deseq2 (1.46.0+dfsg-2) ...
357s Selecting previously unselected package r-cran-hwriter.
357s Preparing to unpack .../351-r-cran-hwriter_1.3.2.1-1_all.deb ...
357s Unpacking r-cran-hwriter (1.3.2.1-1) ...
357s Selecting previously unselected package r-cran-bitops.
357s Preparing to unpack .../352-r-cran-bitops_1.0-9-1_amd64.deb ...
357s Unpacking r-cran-bitops (1.0-9-1) ...
357s Selecting previously unselected package r-bioc-rhtslib.
357s Preparing to unpack .../353-r-bioc-rhtslib_3.2.0+dfsg-2_amd64.deb ...
357s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ...
357s Selecting previously unselected package r-bioc-rsamtools.
357s Preparing to unpack .../354-r-bioc-rsamtools_2.22.0+dfsg-2_amd64.deb ...
357s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ...
357s Selecting previously unselected package r-cran-statmod.
357s Preparing to unpack .../355-r-cran-statmod_1.5.0-1_amd64.deb ...
357s Unpacking r-cran-statmod (1.5.0-1) ...
357s Selecting previously unselected package r-bioc-geneplotter.
357s Preparing to unpack .../356-r-bioc-geneplotter_1.84.0+dfsg-2_all.deb ...
357s Unpacking r-bioc-geneplotter (1.84.0+dfsg-2) ...
357s Selecting previously unselected package r-cran-survival.
357s Preparing to unpack .../357-r-cran-survival_3.8-3-1_amd64.deb ...
357s Unpacking r-cran-survival (3.8-3-1) ...
358s Selecting previously unselected package r-bioc-genefilter.
358s Preparing to unpack .../358-r-bioc-genefilter_1.88.0-2_amd64.deb ...
358s Unpacking r-bioc-genefilter (1.88.0-2) ...
358s Selecting previously unselected package r-bioc-dexseq.
358s Preparing to unpack .../359-r-bioc-dexseq_1.52.0+dfsg-2_all.deb ...
358s Unpacking r-bioc-dexseq (1.52.0+dfsg-2) ...
358s Selecting previously unselected package r-bioc-limma.
358s Preparing to unpack .../360-r-bioc-limma_3.62.2+dfsg-1_amd64.deb ...
358s Unpacking r-bioc-limma (3.62.2+dfsg-1) ...
358s Selecting previously unselected package r-bioc-edger.
358s Preparing to unpack .../361-r-bioc-edger_4.4.2+dfsg-1_amd64.deb ...
358s Unpacking r-bioc-edger (4.4.2+dfsg-1) ...
358s Selecting previously unselected package r-bioc-genomicalignments.
358s Preparing to unpack .../362-r-bioc-genomicalignments_1.42.0-2_amd64.deb ...
358s Unpacking r-bioc-genomicalignments (1.42.0-2) ...
358s Selecting previously unselected package r-cran-rcurl.
358s Preparing to unpack .../363-r-cran-rcurl_1.98-1.16+dfsg-1_amd64.deb ...
358s Unpacking r-cran-rcurl (1.98-1.16+dfsg-1) ...
358s Selecting previously unselected package r-cran-rjson.
358s Preparing to unpack .../364-r-cran-rjson_0.2.23-1_amd64.deb ...
358s Unpacking r-cran-rjson (0.2.23-1) ...
358s Selecting previously unselected package r-cran-yaml.
358s Preparing to unpack .../365-r-cran-yaml_2.3.10-1_amd64.deb ...
358s Unpacking r-cran-yaml (2.3.10-1) ...
358s Selecting previously unselected package r-cran-restfulr.
358s Preparing to unpack .../366-r-cran-restfulr_0.0.15-1_amd64.deb ...
358s Unpacking r-cran-restfulr (0.0.15-1) ...
358s Selecting previously unselected package r-bioc-rtracklayer.
358s Preparing to unpack .../367-r-bioc-rtracklayer_1.66.0-2_amd64.deb ...
358s Unpacking r-bioc-rtracklayer (1.66.0-2) ...
358s Selecting previously unselected package r-bioc-genomicfeatures.
358s Preparing to unpack .../368-r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ...
358s Unpacking r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
358s Selecting previously unselected package r-bioc-txdbmaker.
358s Preparing to unpack .../369-r-bioc-txdbmaker_1.2.1+ds-2_all.deb ...
358s Unpacking r-bioc-txdbmaker (1.2.1+ds-2) ...
358s Selecting previously unselected package r-bioc-genelendatabase.
358s Preparing to unpack .../370-r-bioc-genelendatabase_1.42.0-3_all.deb ...
358s Unpacking r-bioc-genelendatabase (1.42.0-3) ...
359s Selecting previously unselected package r-bioc-go.db.
359s Preparing to unpack .../371-r-bioc-go.db_3.20.0-2_all.deb ...
359s Unpacking r-bioc-go.db (3.20.0-2) ...
359s Selecting previously unselected package r-cran-biasedurn.
359s Preparing to unpack .../372-r-cran-biasedurn_2.0.12-1_amd64.deb ...
359s Unpacking r-cran-biasedurn (2.0.12-1) ...
359s Selecting previously unselected package r-bioc-goseq.
359s Preparing to unpack .../373-r-bioc-goseq_1.58.0-2_all.deb ...
359s Unpacking r-bioc-goseq (1.58.0-2) ...
359s Selecting previously unselected package r-cran-plyr.
359s Preparing to unpack .../374-r-cran-plyr_1.8.9-1_amd64.deb ...
359s Unpacking r-cran-plyr (1.8.9-1) ...
359s Selecting previously unselected package r-cran-reshape2.
359s Preparing to unpack .../375-r-cran-reshape2_1.4.4-2build1_amd64.deb ...
359s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
359s Selecting previously unselected package r-bioc-qvalue.
359s Preparing to unpack .../376-r-bioc-qvalue_2.38.0-2_all.deb ...
359s Unpacking r-bioc-qvalue (2.38.0-2) ...
360s Selecting previously unselected package r-cran-findpython.
360s Preparing to unpack .../377-r-cran-findpython_1.0.9-1_all.deb ...
360s Unpacking r-cran-findpython (1.0.9-1) ...
360s Selecting previously unselected package r-cran-argparse.
360s Preparing to unpack .../378-r-cran-argparse_2.2.5+dfsg-1_all.deb ...
360s Unpacking r-cran-argparse (2.2.5+dfsg-1) ...
360s Selecting previously unselected package r-cran-backports.
360s Preparing to unpack .../379-r-cran-backports_1.5.0-2_amd64.deb ...
360s Unpacking r-cran-backports (1.5.0-2) ...
360s Selecting previously unselected package r-cran-base64enc.
360s Preparing to unpack .../380-r-cran-base64enc_0.1-3-3_amd64.deb ...
360s Unpacking r-cran-base64enc (0.1-3-3) ...
360s Selecting previously unselected package r-cran-broom.
360s Preparing to unpack .../381-r-cran-broom_1.0.7+dfsg-1_all.deb ...
360s Unpacking r-cran-broom (1.0.7+dfsg-1) ...
360s Selecting previously unselected package r-cran-htmltools.
360s Preparing to unpack .../382-r-cran-htmltools_0.5.8.1-1_amd64.deb ...
360s Unpacking r-cran-htmltools (0.5.8.1-1) ...
360s Selecting previously unselected package r-cran-jquerylib.
360s Preparing to unpack .../383-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ...
360s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ...
360s Selecting previously unselected package r-cran-fs.
360s Preparing to unpack .../384-r-cran-fs_1.6.5+dfsg-1_amd64.deb ...
360s Unpacking r-cran-fs (1.6.5+dfsg-1) ...
360s Selecting previously unselected package r-cran-sass.
360s Preparing to unpack .../385-r-cran-sass_0.4.9+dfsg-1_amd64.deb ...
360s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
360s Selecting previously unselected package r-cran-bslib.
360s Preparing to unpack .../386-r-cran-bslib_0.8.0+dfsg-1_all.deb ...
360s Unpacking r-cran-bslib (0.8.0+dfsg-1) ...
360s Selecting previously unselected package r-cran-ps.
360s Preparing to unpack .../387-r-cran-ps_1.9.0-1_amd64.deb ...
360s Unpacking r-cran-ps (1.9.0-1) ...
360s Selecting previously unselected package r-cran-processx.
360s Preparing to unpack .../388-r-cran-processx_3.8.6-1_amd64.deb ...
360s Unpacking r-cran-processx (3.8.6-1) ...
360s Selecting previously unselected package r-cran-callr.
360s Preparing to unpack .../389-r-cran-callr_3.7.6-1_all.deb ...
360s Unpacking r-cran-callr (3.7.6-1) ...
360s Selecting previously unselected package r-cran-rematch.
360s Preparing to unpack .../390-r-cran-rematch_2.0.0-1_all.deb ...
360s Unpacking r-cran-rematch (2.0.0-1) ...
360s Selecting previously unselected package r-cran-cellranger.
360s Preparing to unpack .../391-r-cran-cellranger_1.1.0-3_all.deb ...
360s Unpacking r-cran-cellranger (1.1.0-3) ...
360s Selecting previously unselected package r-cran-clipr.
360s Preparing to unpack .../392-r-cran-clipr_0.8.0-1_all.deb ...
360s Unpacking r-cran-clipr (0.8.0-1) ...
360s Selecting previously unselected package r-cran-cluster.
360s Preparing to unpack .../393-r-cran-cluster_2.1.8.1-1_amd64.deb ...
360s Unpacking r-cran-cluster (2.1.8.1-1) ...
360s Selecting previously unselected package r-cran-commonmark.
361s Preparing to unpack .../394-r-cran-commonmark_1.9.2-2_amd64.deb ...
361s Unpacking r-cran-commonmark (1.9.2-2) ...
361s Selecting previously unselected package r-cran-conflicted.
361s Preparing to unpack .../395-r-cran-conflicted_1.2.0-1.1_all.deb ...
361s Unpacking r-cran-conflicted (1.2.0-1.1) ...
361s Selecting previously unselected package r-cran-data.table.
361s Preparing to unpack .../396-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ...
361s Unpacking r-cran-data.table (1.17.0+dfsg-1) ...
361s Selecting previously unselected package r-cran-dtplyr.
361s Preparing to unpack .../397-r-cran-dtplyr_1.3.1-1_all.deb ...
361s Unpacking r-cran-dtplyr (1.3.1-1) ...
361s Selecting previously unselected package r-cran-ellipsis.
361s Preparing to unpack .../398-r-cran-ellipsis_0.3.2-2_amd64.deb ...
361s Unpacking r-cran-ellipsis (0.3.2-2) ...
361s Selecting previously unselected package r-cran-evaluate.
361s Preparing to unpack .../399-r-cran-evaluate_1.0.3-1_all.deb ...
361s Unpacking r-cran-evaluate (1.0.3-1) ...
361s Selecting previously unselected package r-cran-fastcluster.
361s Preparing to unpack .../400-r-cran-fastcluster_1.2.6-2_amd64.deb ...
361s Unpacking r-cran-fastcluster (1.2.6-2) ...
361s Selecting previously unselected package r-cran-fontawesome.
361s Preparing to unpack .../401-r-cran-fontawesome_0.5.3-1_all.deb ...
361s Unpacking r-cran-fontawesome (0.5.3-1) ...
361s Selecting previously unselected package r-cran-forcats.
361s Preparing to unpack .../402-r-cran-forcats_1.0.0-1_all.deb ...
361s Unpacking r-cran-forcats (1.0.0-1) ...
361s Selecting previously unselected package r-cran-gargle.
361s Preparing to unpack .../403-r-cran-gargle_1.5.2-1_all.deb ...
361s Unpacking r-cran-gargle (1.5.2-1) ...
361s Selecting previously unselected package r-cran-ggdendro.
361s Preparing to unpack .../404-r-cran-ggdendro_0.2.0+dfsg-1_all.deb ...
361s Unpacking r-cran-ggdendro (0.2.0+dfsg-1) ...
361s Selecting previously unselected package r-cran-uuid.
361s Preparing to unpack .../405-r-cran-uuid_1.2-1-1_amd64.deb ...
361s Unpacking r-cran-uuid (1.2-1-1) ...
361s Selecting previously unselected package r-cran-googledrive.
361s Preparing to unpack .../406-r-cran-googledrive_2.1.1-3_all.deb ...
361s Unpacking r-cran-googledrive (2.1.1-3) ...
361s Selecting previously unselected package r-cran-ids.
361s Preparing to unpack .../407-r-cran-ids_1.0.1-2_all.deb ...
361s Unpacking r-cran-ids (1.0.1-2) ...
361s Selecting previously unselected package r-cran-rematch2.
361s Preparing to unpack .../408-r-cran-rematch2_2.1.2-2build1_all.deb ...
361s Unpacking r-cran-rematch2 (2.1.2-2build1) ...
361s Selecting previously unselected package r-cran-googlesheets4.
361s Preparing to unpack .../409-r-cran-googlesheets4_1.1.1-1_all.deb ...
361s Unpacking r-cran-googlesheets4 (1.1.1-1) ...
361s Selecting previously unselected package r-cran-gridextra.
361s Preparing to unpack .../410-r-cran-gridextra_2.3-3build1_all.deb ...
361s Unpacking r-cran-gridextra (2.3-3build1) ...
361s Selecting previously unselected package r-cran-goplot.
361s Preparing to unpack .../411-r-cran-goplot_1.0.2-2_all.deb ...
361s Unpacking r-cran-goplot (1.0.2-2) ...
362s Selecting previously unselected package r-cran-tzdb.
362s Preparing to unpack .../412-r-cran-tzdb_0.4.0-2_amd64.deb ...
362s Unpacking r-cran-tzdb (0.4.0-2) ...
362s Selecting previously unselected package r-cran-vroom.
362s Preparing to unpack .../413-r-cran-vroom_1.6.5-1_amd64.deb ...
362s Unpacking r-cran-vroom (1.6.5-1) ...
362s Selecting previously unselected package r-cran-readr.
362s Preparing to unpack .../414-r-cran-readr_2.1.5-1_amd64.deb ...
362s Unpacking r-cran-readr (2.1.5-1) ...
362s Selecting previously unselected package r-cran-haven.
362s Preparing to unpack .../415-r-cran-haven_2.5.4-1_amd64.deb ...
362s Unpacking r-cran-haven (2.5.4-1) ...
362s Selecting previously unselected package r-cran-xfun.
362s Preparing to unpack .../416-r-cran-xfun_0.51+dfsg-1_amd64.deb ...
362s Unpacking r-cran-xfun (0.51+dfsg-1) ...
362s Selecting previously unselected package r-cran-highr.
362s Preparing to unpack .../417-r-cran-highr_0.11+dfsg-1_all.deb ...
362s Unpacking r-cran-highr (0.11+dfsg-1) ...
362s Selecting previously unselected package r-cran-later.
362s Preparing to unpack .../418-r-cran-later_1.4.1+dfsg-1_amd64.deb ...
362s Unpacking r-cran-later (1.4.1+dfsg-1) ...
362s Selecting previously unselected package r-cran-promises.
362s Preparing to unpack .../419-r-cran-promises_1.3.2+dfsg-1_amd64.deb ...
362s Unpacking r-cran-promises (1.3.2+dfsg-1) ...
362s Selecting previously unselected package r-cran-httpuv.
362s Preparing to unpack .../420-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ...
362s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ...
362s Selecting previously unselected package r-cran-kernsmooth.
362s Preparing to unpack .../421-r-cran-kernsmooth_2.23-26-1_amd64.deb ...
362s Unpacking r-cran-kernsmooth (2.23-26-1) ...
362s Selecting previously unselected package libjs-mathjax.
362s Preparing to unpack .../422-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
362s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
363s Selecting previously unselected package r-cran-knitr.
363s Preparing to unpack .../423-r-cran-knitr_1.49+dfsg-1_all.deb ...
363s Unpacking r-cran-knitr (1.49+dfsg-1) ...
363s Selecting previously unselected package r-cran-timechange.
363s Preparing to unpack .../424-r-cran-timechange_0.3.0-1_amd64.deb ...
363s Unpacking r-cran-timechange (0.3.0-1) ...
363s Selecting previously unselected package r-cran-lubridate.
363s Preparing to unpack .../425-r-cran-lubridate_1.9.4+dfsg-1_amd64.deb ...
363s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ...
363s Selecting previously unselected package r-cran-modelr.
363s Preparing to unpack .../426-r-cran-modelr_0.1.11-1_all.deb ...
363s Unpacking r-cran-modelr (0.1.11-1) ...
363s Selecting previously unselected package r-cran-systemfonts.
363s Preparing to unpack .../427-r-cran-systemfonts_1.2.1-1_amd64.deb ...
363s Unpacking r-cran-systemfonts (1.2.1-1) ...
363s Selecting previously unselected package r-cran-textshaping.
363s Preparing to unpack .../428-r-cran-textshaping_0.3.7-2_amd64.deb ...
363s Unpacking r-cran-textshaping (0.3.7-2) ...
363s Selecting previously unselected package r-cran-ragg.
363s Preparing to unpack .../429-r-cran-ragg_1.3.3-1_amd64.deb ...
363s Unpacking r-cran-ragg (1.3.3-1) ...
363s Selecting previously unselected package r-cran-readxl.
363s Preparing to unpack .../430-r-cran-readxl_1.4.4-1_amd64.deb ...
363s Unpacking r-cran-readxl (1.4.4-1) ...
363s Selecting previously unselected package r-cran-tinytex.
363s Preparing to unpack .../431-r-cran-tinytex_0.56-1_all.deb ...
363s Unpacking r-cran-tinytex (0.56-1) ...
363s Selecting previously unselected package libjs-modernizr.
363s Preparing to unpack .../432-libjs-modernizr_3.13.0-0.1_all.deb ...
363s Unpacking libjs-modernizr (3.13.0-0.1) ...
363s Selecting previously unselected package r-cran-sourcetools.
363s Preparing to unpack .../433-r-cran-sourcetools_0.1.7-1-1_amd64.deb ...
363s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
363s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
363s Preparing to unpack .../434-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ...
363s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
363s Selecting previously unselected package r-cran-shiny.
363s Preparing to unpack .../435-r-cran-shiny_1.10.0+dfsg-2_all.deb ...
363s Unpacking r-cran-shiny (1.10.0+dfsg-2) ...
364s Selecting previously unselected package r-cran-rmarkdown.
364s Preparing to unpack .../436-r-cran-rmarkdown_2.29+dfsg-1_all.deb ...
364s Unpacking r-cran-rmarkdown (2.29+dfsg-1) ...
364s Selecting previously unselected package r-cran-rstudioapi.
364s Preparing to unpack .../437-r-cran-rstudioapi_0.17.1-1_all.deb ...
364s Unpacking r-cran-rstudioapi (0.17.1-1) ...
364s Selecting previously unselected package r-cran-reprex.
364s Preparing to unpack .../438-r-cran-reprex_2.1.1-1_all.deb ...
364s Unpacking r-cran-reprex (2.1.1-1) ...
364s Selecting previously unselected package r-cran-selectr.
364s Preparing to unpack .../439-r-cran-selectr_0.4-2-2build1_all.deb ...
364s Unpacking r-cran-selectr (0.4-2-2build1) ...
364s Selecting previously unselected package r-cran-rvest.
364s Preparing to unpack .../440-r-cran-rvest_1.0.4-1_all.deb ...
364s Unpacking r-cran-rvest (1.0.4-1) ...
364s Selecting previously unselected package r-cran-tidyverse.
364s Preparing to unpack .../441-r-cran-tidyverse_2.0.0+dfsg-2_all.deb ...
364s Unpacking r-cran-tidyverse (2.0.0+dfsg-2) ...
364s Selecting previously unselected package bowtie.
364s Preparing to unpack .../442-bowtie_1.3.1-3_amd64.deb ...
364s Unpacking bowtie (1.3.1-3) ...
364s Selecting previously unselected package bowtie2.
364s Preparing to unpack .../443-bowtie2_2.5.4-1_amd64.deb ...
364s Unpacking bowtie2 (2.5.4-1) ...
364s Selecting previously unselected package rsem.
364s Preparing to unpack .../444-rsem_1.3.3+dfsg-3build1_amd64.deb ...
364s Unpacking rsem (1.3.3+dfsg-3build1) ...
364s Selecting previously unselected package salmon.
364s Preparing to unpack .../445-salmon_1.10.2+ds1-1build2_amd64.deb ...
364s Unpacking salmon (1.10.2+ds1-1build2) ...
364s Selecting previously unselected package samtools.
364s Preparing to unpack .../446-samtools_1.21-1_amd64.deb ...
364s Unpacking samtools (1.21-1) ...
364s Selecting previously unselected package subread.
364s Preparing to unpack .../447-subread_2.0.7+dfsg-1_amd64.deb ...
364s Unpacking subread (2.0.7+dfsg-1) ...
365s Selecting previously unselected package libjbzip2-java.
365s Preparing to unpack .../448-libjbzip2-java_0.9.1-8_all.deb ...
365s Unpacking libjbzip2-java (0.9.1-8) ...
365s Selecting previously unselected package trimmomatic.
365s Preparing to unpack .../449-trimmomatic_0.39+dfsg-2_all.deb ...
365s Unpacking trimmomatic (0.39+dfsg-2) ...
365s Selecting previously unselected package trinityrnaseq.
365s Preparing to unpack .../450-trinityrnaseq_2.15.2+dfsg-1_amd64.deb ...
365s Unpacking trinityrnaseq (2.15.2+dfsg-1) ...
365s Selecting previously unselected package trinityrnaseq-examples.
365s Preparing to unpack .../451-trinityrnaseq-examples_2.15.2+dfsg-1_amd64.deb ...
365s Unpacking trinityrnaseq-examples (2.15.2+dfsg-1) ...
367s Setting up libhtscodecs2:amd64 (1.6.1-2) ...
367s Setting up libjs-json (0~20221030+~1.0.8-1) ...
367s Setting up javascript-common (12) ...
367s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
367s Setting up libxcb-dri3-0:amd64 (1.17.0-2) ...
367s Setting up liblcms2-2:amd64 (2.16-2) ...
367s Setting up ncbi-data (6.1.20170106+dfsg2-5) ...
367s Setting up libtbbmalloc2:amd64 (2022.0.0-2) ...
367s Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
367s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
367s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
367s Setting up libwayland-server0:amd64 (1.23.1-3) ...
367s Setting up libx11-xcb1:amd64 (2:1.8.10-2) ...
367s Setting up libpciaccess0:amd64 (0.17-3build1) ...
367s Setting up libslf4j-java (1.7.32-1) ...
367s Setting up libprotobuf32t64:amd64 (3.21.12-10build2) ...
367s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
367s Setting up libxdamage1:amd64 (1:1.1.6-1build1) ...
367s Setting up libxcb-xfixes0:amd64 (1.17.0-2) ...
367s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
367s Setting up libjsr305-java (0.1~+svn49-12) ...
367s Setting up hicolor-icon-theme (0.18-2) ...
367s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
367s Setting up libxi6:amd64 (2:1.8.2-1) ...
367s Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ...
367s Setting up java-common (0.76) ...
367s Setting up bowtie (1.3.1-3) ...
367s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
367s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
367s Setting up libjs-popper.js (1.16.1+ds-6) ...
367s Setting up libxcb-render0:amd64 (1.17.0-2) ...
367s Setting up libclone-perl:amd64 (0.47-1) ...
367s Setting up libgetopt-java (1.0.14+dfsg-6) ...
367s Setting up libjs-sifter.js (0.6.0+dfsg-3) ...
367s Setting up libglvnd0:amd64 (1.7.0-1build1) ...
367s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
367s Setting up libgoogle-gson-java (2.10.1-1) ...
367s Setting up libhtml-tagset-perl (3.24-1) ...
367s Setting up libxcb-glx0:amd64 (1.17.0-2) ...
367s Setting up unzip (6.0-28ubuntu6) ...
367s Setting up libdrm-intel1:amd64 (2.4.123-1) ...
367s Setting up liblwp-mediatypes-perl (6.04-2) ...
367s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-2) ...
367s Setting up x11-common (1:7.7+23ubuntu3) ...
367s Setting up libtry-tiny-perl (0.32-1) ...
367s Setting up node-html5shiv (3.7.3+dfsg-5) ...
367s Setting up libstaden-read14t64:amd64 (1.15.0-1.1build2) ...
367s Setting up libdeflate0:amd64 (1.23-1) ...
367s Setting up perl-openssl-defaults:amd64 (7build3) ...
367s Setting up libboost-thread1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
367s Setting up libencode-locale-perl (1.05-3) ...
367s Setting up libjs-microplugin.js (0.0.3+dfsg-1.1) ...
367s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
367s Setting up libboost-filesystem1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
367s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ...
367s Setting up libjs-modernizr (3.13.0-0.1) ...
367s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
367s Setting up libcolord2:amd64 (1.4.7-3) ...
367s Setting up libxxf86vm1:amd64 (1:1.1.4-1build4) ...
367s Setting up libsnappy1v5:amd64 (1.2.1-1) ...
367s Setting up bowtie2 (2.5.4-1) ...
367s Setting up libjs-es5-shim (4.6.7-2) ...
367s Setting up libxcb-present0:amd64 (1.17.0-2) ...
367s Setting up libdconf1:amd64 (0.40.0-5) ...
367s Setting up libcommons-collections3-java (3.2.2-3) ...
367s Setting up libjellyfish-2.0-2:amd64 (2.3.1-4build1) ...
367s Setting up libasound2-data (1.2.13-1build1) ...
367s Setting up zip (3.0-14ubuntu2) ...
367s Setting up librhino-java (1.7.15-1) ...
367s Setting up libblas3:amd64 (3.12.1-2) ...
367s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
367s Setting up libasound2t64:amd64 (1.2.13-1build1) ...
367s Setting up libjaxen-java (1.1.6-5) ...
367s Setting up libepoxy0:amd64 (1.5.10-2) ...
367s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ...
367s Setting up libxcb-sync1:amd64 (1.17.0-2) ...
367s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.1ubuntu2) ...
367s Setting up libapache-pom-java (33-2) ...
367s Setting up libavahi-common-data:amd64 (0.8-16ubuntu1) ...
367s Setting up libatinject-jsr330-api-java (1.0+ds1-6) ...
367s Setting up libatspi2.0-0t64:amd64 (2.55.90-1) ...
367s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ...
367s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ...
367s Setting up libjs-d3 (3.5.17-4) ...
367s Setting up fonts-dejavu-mono (2.37-8) ...
367s Setting up libhwloc15:amd64 (2.12.0-1) ...
367s Setting up libxml-commons-resolver1.1-java (1.2-11) ...
367s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ...
367s Setting up libio-html-perl (1.004-3) ...
367s Setting up libxrandr2:amd64 (2:1.5.4-1) ...
367s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ...
367s Setting up fonts-dejavu-core (2.37-8) ...
367s Setting up libjbzip2-java (0.9.1-8) ...
367s Setting up libpcsclite1:amd64 (2.3.1-1) ...
367s Setting up libmongodb-java (3.6.3-2) ...
367s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
367s Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6build1) ...
367s Setting up libhamcrest-java (2.2-2) ...
367s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ...
367s Setting up berkeley-express (1.5.3+dfsg-3build5) ...
367s Setting up libvulkan1:amd64 (1.4.304.0-1) ...
367s Setting up libwebp7:amd64 (1.5.0-0.1) ...
367s Setting up libtimedate-perl (2.3300-2) ...
367s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ...
367s Setting up libgif7:amd64 (5.2.2-1ubuntu2) ...
367s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
367s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
367s Setting up hisat2 (2.2.1-5) ...
367s Setting up libfreemarker-java (2.3.32-2) ...
367s Setting up libxshmfence1:amd64 (1.3-1build5) ...
367s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ...
367s Setting up subread (2.0.7+dfsg-1) ...
367s Setting up at-spi2-common (2.55.90-1) ...
367s Setting up libxcb-randr0:amd64 (1.17.0-2) ...
367s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ...
367s Setting up libxml-commons-external-java (1.4.01-6) ...
367s Setting up libhts3t64:amd64 (1.21+ds-1) ...
367s Setting up liblua5.4-0:amd64 (5.4.7-1) ...
367s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
367s Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
367s Setting up libthai-data (0.1.29-2build1) ...
367s Setting up node-bootstrap-sass (3.4.3-2) ...
367s Setting up libcommons-math3-java (3.6.1-4) ...
367s Setting up libjs-prettify (2015.12.04+dfsg-1.1) ...
367s Setting up libwayland-egl1:amd64 (1.23.1-3) ...
367s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
367s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ...
367s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ...
367s Setting up libpaper2:amd64 (2.2.5-0.3) ...
368s Setting up libhttpcore-java (4.4.16-1) ...
368s Setting up pandoc-data (3.1.11.1-3build1) ...
368s Setting up libtsan2:amd64 (15-20250222-0ubuntu1) ...
368s Setting up libjoptsimple-java (5.0.4-7) ...
368s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
368s Setting up ca-certificates-java (20240118) ...
368s No JRE found. Skipping Java certificates setup.
368s Setting up libxerces2-java (2.12.2-1) ...
368s Setting up node-normalize.css (8.0.1-5) ...
368s Setting up kallisto (0.48.0+dfsg-4build1) ...
368s Setting up libsnappy-jni (1.1.10.7-1) ...
368s Setting up libezmorph-java (1.0.6-4) ...
368s Setting up libxcomposite1:amd64 (1:0.4.6-1) ...
368s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
368s Setting up xdg-utils (1.2.1-2ubuntu1) ...
368s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
368s Setting up liburi-perl (5.30-1) ...
368s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ...
368s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
368s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ...
368s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
368s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
368s Setting up libwayland-client0:amd64 (1.23.1-3) ...
368s Setting up libnet-ssleay-perl:amd64 (1.94-3) ...
368s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
368s Setting up libice6:amd64 (2:1.1.1-1) ...
368s Setting up libhttp-date-perl (6.06-1) ...
368s Setting up parafly (0.1.0-5) ...
368s Setting up mesa-libgallium:amd64 (25.0.1-2ubuntu1) ...
368s Setting up liblapack3:amd64 (3.12.1-2) ...
368s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
368s Setting up python3-pysam (0.23.0+ds-1build1) ...
368s Setting up libatk1.0-0t64:amd64 (2.55.90-1) ...
368s Setting up libfile-listing-perl (6.16-1) ...
368s Setting up python3-hisat2 (2.2.1-5) ...
368s Setting up openjdk-21-jre-headless:amd64 (21.0.6+7-1) ...
368s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
368s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
368s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
368s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
368s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
368s Setting up libgbm1:amd64 (25.0.1-2ubuntu1) ...
368s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
368s Setting up libxtst6:amd64 (2:1.2.5-1) ...
368s Setting up libxcursor1:amd64 (1:1.2.3-1) ...
368s Setting up libgl1-mesa-dri:amd64 (25.0.1-2ubuntu1) ...
368s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
368s Setting up libcommons-parent-java (56-1) ...
368s Setting up libavahi-common3:amd64 (0.8-16ubuntu1) ...
368s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ...
368s Setting up libnet-http-perl (6.23-1) ...
368s Setting up dconf-service (0.40.0-5) ...
368s Setting up libpaper-utils (2.2.5-0.3) ...
368s Setting up libxom-java (1.3.9-1) ...
368s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
368s Setting up samtools (1.21-1) ...
368s Setting up libtbbbind-2-5:amd64 (2022.0.0-2) ...
368s Setting up libcommons-jexl2-java (2.1.1-6) ...
368s Setting up libthai0:amd64 (0.1.29-2build1) ...
368s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ...
368s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
368s Setting up pandoc (3.1.11.1+ds-2) ...
368s Setting up jellyfish (2.3.1-4build1) ...
368s Setting up libcommons-collections4-java (4.4-2) ...
368s Setting up python3-numpy (1:2.2.3+ds-5) ...
370s Setting up libjs-sphinxdoc (8.1.3-4) ...
370s Setting up libcommons-lang3-java (3.17.0-1) ...
370s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ...
370s Setting up libwww-robotrules-perl (6.02-1) ...
370s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
370s Setting up libwayland-cursor0:amd64 (1.23.1-3) ...
370s Setting up libhtml-parser-perl:amd64 (3.83-1build1) ...
370s Setting up libcommons-beanutils-java (1.9.4-2) ...
370s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ...
370s Setting up libsnappy-java (1.1.10.7-1) ...
370s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
370s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ...
370s Setting up libcommons-codec-java (1.17.1-1) ...
370s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
370s Setting up libsm6:amd64 (2:1.2.4-1) ...
370s Setting up python3-htseq (2.0.9+dfsg-1build2) ...
370s Setting up libavahi-client3:amd64 (0.8-16ubuntu1) ...
370s Setting up libio-socket-ssl-perl (2.089-1) ...
370s Setting up libhttp-message-perl (7.00-2ubuntu1) ...
370s Setting up libatk-bridge2.0-0t64:amd64 (2.55.90-1) ...
370s Setting up gtk-update-icon-cache (4.17.5+ds-3ubuntu1) ...
370s Setting up libhttp-negotiate-perl (6.01-2) ...
370s Setting up fontconfig (2.15.0-2ubuntu1) ...
372s Regenerating fonts cache... done.
372s Setting up libxft2:amd64 (2.3.6-1build1) ...
372s Setting up libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ...
372s Setting up libglx-mesa0:amd64 (25.0.1-2ubuntu1) ...
372s Setting up libglx0:amd64 (1.7.0-1build1) ...
372s Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ...
372s Setting up libhttp-cookies-perl (6.11-1) ...
372s Setting up libcommons-io-java (2.18.0-1) ...
372s Setting up libhtml-tree-perl (5.07-3) ...
372s Setting up libtk8.6:amd64 (8.6.16-1) ...
372s Setting up libpango-1.0-0:amd64 (1.56.2-1) ...
372s Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
372s Setting up libtbb12:amd64 (2022.0.0-2) ...
372s Setting up libcairo2:amd64 (1.18.2-2) ...
372s Setting up ncbi-blast+ (2.16.0+ds-6build1) ...
372s Setting up salmon (1.10.2+ds1-1build2) ...
372s Setting up libgl1:amd64 (1.7.0-1build1) ...
372s Setting up adwaita-icon-theme (48.0-1) ...
372s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
372s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
372s Setting up libhttpclient-java (4.5.14-1) ...
372s Setting up liblightcouch-java (0.2.0-1) ...
372s Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
372s Setting up libboost-dev:amd64 (1.83.0.2ubuntu1) ...
372s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ...
372s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ...
372s Setting up libgtk-3-common (3.24.48-3ubuntu1) ...
372s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ...
372s Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
372s Setting up libngs-jni:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
372s Setting up libcommons-compress-java (1.27.1-2) ...
372s Setting up liblog4j2-java (2.19.0-2) ...
372s Setting up r-base-core (4.4.3-1) ...
372s Creating config file /etc/R/Renviron with new version
373s Setting up r-cran-crayon (1.5.3-1) ...
373s Setting up r-cran-labeling (0.4.3-1) ...
373s Setting up r-cran-biasedurn (2.0.12-1) ...
373s Setting up r-cran-sourcetools (0.1.7-1-1) ...
373s Setting up r-cran-futile.options (1.0.1-3build1) ...
373s Setting up r-cran-lattice (0.22-6-1) ...
373s Setting up r-cran-ps (1.9.0-1) ...
373s Setting up r-cran-nlme (3.1.167-1) ...
373s Setting up r-cran-farver (2.1.2-1) ...
373s Setting up r-cran-formatr (1.14-2) ...
373s Setting up r-cran-xml (3.99-0.18-1) ...
373s Setting up trinityrnaseq-examples (2.15.2+dfsg-1) ...
373s Setting up r-cran-viridislite (0.4.2-2) ...
373s Setting up r-cran-locfit (1.5-9.12-1) ...
373s Setting up r-cran-cluster (2.1.8.1-1) ...
373s Setting up rsem (1.3.3+dfsg-3build1) ...
373s Setting up r-cran-statmod (1.5.0-1) ...
373s Setting up r-cran-clipr (0.8.0-1) ...
373s Setting up r-cran-commonmark (1.9.2-2) ...
373s Setting up r-cran-rjson (0.2.23-1) ...
373s Setting up libngs-java:amd64 (3.0.9+dfsg-7.1ubuntu1) ...
373s Setting up r-cran-r6 (2.6.1-1) ...
373s Setting up r-cran-pkgkitten (0.2.4-1) ...
373s Setting up r-cran-fastcluster (1.2.6-2) ...
373s Setting up r-cran-magrittr (2.0.3-1) ...
373s Setting up r-cran-rappdirs (0.3.3-1) ...
373s Setting up r-cran-filelock (1.0.3-1) ...
373s Setting up libbarclay-java (5.0.0+dfsg-1) ...
373s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
373s Setting up r-cran-littler (0.3.20-2) ...
373s Setting up r-cran-bh (1.84.0-1) ...
373s Setting up r-cran-fs (1.6.5+dfsg-1) ...
373s Setting up r-cran-rcpp (1.0.14-1) ...
373s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
373s Setting up r-cran-codetools (0.2-20-1) ...
373s Setting up r-cran-rematch (2.0.0-1) ...
373s Setting up r-bioc-biocgenerics (0.52.0-2) ...
373s Setting up r-cran-rlang (1.1.5-1) ...
373s Setting up r-cran-matrixstats (1.5.0-1) ...
373s Setting up r-cran-findpython (1.0.9-1) ...
373s Setting up littler (0.3.20-2) ...
373s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
373s Setting up r-cran-uuid (1.2-1-1) ...
373s Setting up r-cran-xfun (0.51+dfsg-1) ...
373s Setting up r-cran-sys (3.4.3-1) ...
373s Setting up r-cran-plogr (0.2.0-3build1) ...
373s Setting up r-cran-withr (3.0.2+dfsg-1) ...
373s Setting up r-cran-backports (1.5.0-2) ...
373s Setting up r-cran-processx (3.8.6-1) ...
373s Setting up r-cran-mime (0.12-2) ...
373s Setting up r-cran-generics (0.1.3-1) ...
373s Setting up r-cran-base64enc (0.1-3-3) ...
373s Setting up r-cran-abind (1.4-8-1) ...
373s Setting up r-cran-digest (0.6.37-1) ...
373s Setting up r-cran-yaml (2.3.10-1) ...
373s Setting up r-cran-lambda.r (1.2.4-2build1) ...
373s Setting up r-cran-evaluate (1.0.3-1) ...
373s Setting up r-cran-dbi (1.2.3-1) ...
373s Setting up r-cran-highr (0.11+dfsg-1) ...
373s Setting up r-cran-prettyunits (1.2.0-1) ...
373s Setting up r-cran-fansi (1.0.5-1) ...
373s Setting up r-cran-mass (7.3-64-1) ...
373s Setting up r-cran-snow (1:0.4.4-2) ...
373s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
373s Setting up r-cran-glue (1.8.0-1) ...
373s Setting up r-cran-bit (4.6.0+dfsg-1) ...
373s Setting up r-cran-xtable (1:1.8-4-2) ...
373s Setting up r-cran-cli (3.6.4-1) ...
373s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
373s Setting up r-cran-bitops (1.0-9-1) ...
373s Setting up r-cran-bit64 (4.6.0-1-1ubuntu2) ...
373s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
373s Setting up r-cran-askpass (1.2.1-1) ...
373s Setting up r-cran-fastmap (1.2.0-1) ...
373s Setting up r-cran-png (0.1-8-1build2) ...
373s Setting up r-bioc-biobase (2.66.0-2) ...
373s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
373s Setting up r-cran-rstudioapi (0.17.1-1) ...
373s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
373s Setting up r-cran-utf8 (1.2.4-1) ...
373s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
373s Setting up r-cran-stringi (1.8.4-1build1) ...
373s Setting up r-cran-hwriter (1.3.2.1-1) ...
373s Setting up r-cran-cpp11 (0.5.2-1) ...
373s Setting up r-cran-plyr (1.8.9-1) ...
373s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
373s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
373s Setting up r-cran-isoband (0.2.7-1) ...
373s Setting up r-cran-futile.logger (1.4.3-4build1) ...
373s Setting up r-bioc-limma (3.62.2+dfsg-1) ...
373s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
373s Setting up r-cran-later (1.4.1+dfsg-1) ...
373s Setting up r-cran-matrix (1.7-3-1) ...
373s Setting up r-cran-htmltools (0.5.8.1-1) ...
373s Setting up r-cran-tinytex (0.56-1) ...
373s Setting up r-cran-kernsmooth (2.23-26-1) ...
373s Setting up r-cran-knitr (1.49+dfsg-1) ...
373s Setting up r-cran-mgcv (1.9-1-1) ...
373s Setting up r-cran-cachem (1.1.0-1) ...
373s Setting up r-cran-sass (0.4.9+dfsg-1) ...
373s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ...
373s Setting up r-bioc-iranges (2.40.1-2) ...
373s Setting up r-cran-tzdb (0.4.0-2) ...
373s Setting up r-cran-argparse (2.2.5+dfsg-1) ...
373s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
373s Setting up r-cran-restfulr (0.0.15-1) ...
373s Setting up r-cran-vctrs (0.6.5-1) ...
373s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
373s Setting up r-cran-ellipsis (0.3.2-2) ...
373s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
373s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
373s Setting up r-cran-stringr (1.5.1-1) ...
373s Setting up r-bioc-biocparallel (1.40.0-2) ...
373s Setting up r-cran-callr (3.7.6-1) ...
373s Setting up r-cran-selectr (0.4-2-2build1) ...
373s Setting up r-bioc-edger (4.4.2+dfsg-1) ...
373s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
373s Setting up r-cran-xml2 (1.3.7-1) ...
373s Setting up r-cran-munsell (0.5.1-1) ...
373s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
373s Setting up r-cran-fontawesome (0.5.3-1) ...
373s Setting up r-cran-survival (3.8-3-1) ...
373s Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
373s Setting up r-cran-forcats (1.0.0-1) ...
373s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
373s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
373s Setting up r-cran-reshape2 (1.4.4-2build1) ...
373s Setting up r-cran-httr2 (1.1.1-1) ...
373s Setting up r-cran-systemfonts (1.2.1-1) ...
373s Setting up r-cran-ids (1.0.1-2) ...
373s Setting up r-cran-timechange (0.3.0-1) ...
373s Setting up r-cran-httr (1.4.7+dfsg-1) ...
373s Setting up r-cran-gridextra (2.3-3build1) ...
373s Setting up r-cran-hms (1.1.3-1) ...
373s Setting up r-cran-scales (1.3.0-1) ...
373s Setting up r-cran-memoise (2.0.1-1) ...
373s Setting up r-cran-promises (1.3.2+dfsg-1) ...
373s Setting up r-cran-purrr (1.0.4-1) ...
373s Setting up r-cran-blob (1.2.4-1) ...
373s Setting up r-bioc-xvector (0.46.0-2) ...
373s Setting up r-cran-dplyr (1.1.4-4) ...
373s Setting up r-cran-rsqlite (2.3.9-1) ...
373s Setting up r-cran-progress (1.2.3-1) ...
373s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
373s Setting up r-cran-gargle (1.5.2-1) ...
373s Setting up r-cran-vroom (1.6.5-1) ...
373s Setting up r-cran-conflicted (1.2.0-1.1) ...
373s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
373s Setting up r-bioc-sparsearray (1.6.2+dfsg-1) ...
373s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
373s Setting up r-cran-cellranger (1.1.0-3) ...
373s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
373s Setting up r-cran-rematch2 (2.1.2-2build1) ...
373s Setting up r-cran-textshaping (0.3.7-2) ...
373s Setting up r-cran-rvest (1.0.4-1) ...
373s Setting up r-cran-dtplyr (1.3.1-1) ...
373s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
373s Setting up r-cran-bslib (0.8.0+dfsg-1) ...
373s Setting up r-cran-ragg (1.3.3-1) ...
373s Setting up r-cran-readr (2.1.5-1) ...
373s Setting up r-cran-tidyr (1.3.1-1) ...
373s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ...
373s Setting up r-cran-googledrive (2.1.1-3) ...
373s Setting up r-cran-googlesheets4 (1.1.1-1) ...
373s Setting up r-bioc-qvalue (2.38.0-2) ...
373s Setting up r-cran-dbplyr (2.5.0+dfsg-1) ...
373s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
373s Setting up r-cran-readxl (1.4.4-1) ...
373s Setting up r-bioc-biocfilecache (2.14.0+dfsg-2) ...
373s Setting up r-cran-haven (2.5.4-1) ...
373s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
373s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
373s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
373s Setting up r-cran-broom (1.0.7+dfsg-1) ...
373s Setting up r-cran-rmarkdown (2.29+dfsg-1) ...
373s Setting up r-cran-goplot (1.0.2-2) ...
373s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
373s Setting up r-cran-reprex (2.1.1-1) ...
373s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
373s Setting up r-bioc-keggrest (1.46.0+dfsg-2) ...
373s Setting up r-bioc-deseq2 (1.46.0+dfsg-2) ...
373s Setting up r-bioc-annotationdbi (1.68.0-2) ...
373s Setting up r-bioc-go.db (3.20.0-2) ...
373s Setting up r-cran-modelr (0.1.11-1) ...
373s Setting up r-bioc-annotate (1.84.0+dfsg-2) ...
373s Setting up r-bioc-biomart (2.62.1+dfsg-1) ...
373s Setting up r-bioc-genefilter (1.88.0-2) ...
373s Setting up r-bioc-genomicalignments (1.42.0-2) ...
373s Setting up r-bioc-geneplotter (1.84.0+dfsg-2) ...
373s Setting up r-bioc-rtracklayer (1.66.0-2) ...
373s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
373s Setting up r-cran-tidyverse (2.0.0+dfsg-2) ...
373s Setting up r-bioc-dexseq (1.52.0+dfsg-2) ...
373s Setting up r-bioc-txdbmaker (1.2.1+ds-2) ...
373s Setting up r-bioc-genelendatabase (1.42.0-3) ...
373s Setting up r-bioc-goseq (1.58.0-2) ...
373s Setting up liblwp-protocol-https-perl (6.14-1) ...
373s Setting up liberror-prone-java (2.18.0-1) ...
373s Setting up libwww-perl (6.78-1) ...
373s Setting up libguava-java (32.0.1-1) ...
373s Setting up libjung-free-java (2.1.1-3) ...
373s Processing triggers for libglib2.0-0t64:amd64 (2.84.0-1) ...
373s Setting up libgtk-3-0t64:amd64 (3.24.48-3ubuntu1) ...
373s Processing triggers for install-info (7.1.1-1) ...
373s Processing triggers for libc-bin (2.41-1ubuntu2) ...
373s Processing triggers for man-db (2.13.0-1) ...
375s Processing triggers for ca-certificates-java (20240118) ...
375s Adding debian:ACCVRAIZ1.pem
375s Adding debian:AC_RAIZ_FNMT-RCM.pem
375s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
375s Adding debian:ANF_Secure_Server_Root_CA.pem
375s Adding debian:Actalis_Authentication_Root_CA.pem
375s Adding debian:AffirmTrust_Commercial.pem
375s Adding debian:AffirmTrust_Networking.pem
375s Adding debian:AffirmTrust_Premium.pem
375s Adding debian:AffirmTrust_Premium_ECC.pem
375s Adding debian:Amazon_Root_CA_1.pem
375s Adding debian:Amazon_Root_CA_2.pem
375s Adding debian:Amazon_Root_CA_3.pem
375s Adding debian:Amazon_Root_CA_4.pem
375s Adding debian:Atos_TrustedRoot_2011.pem
375s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
375s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
375s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
375s Adding debian:BJCA_Global_Root_CA1.pem
375s Adding debian:BJCA_Global_Root_CA2.pem
375s Adding debian:Baltimore_CyberTrust_Root.pem
375s Adding debian:Buypass_Class_2_Root_CA.pem
375s Adding debian:Buypass_Class_3_Root_CA.pem
375s Adding debian:CA_Disig_Root_R2.pem
375s Adding debian:CFCA_EV_ROOT.pem
375s Adding debian:COMODO_Certification_Authority.pem
375s Adding debian:COMODO_ECC_Certification_Authority.pem
375s Adding debian:COMODO_RSA_Certification_Authority.pem
375s Adding debian:Certainly_Root_E1.pem
375s Adding debian:Certainly_Root_R1.pem
375s Adding debian:Certigna.pem
375s Adding debian:Certigna_Root_CA.pem
375s Adding debian:Certum_EC-384_CA.pem
375s Adding debian:Certum_Trusted_Network_CA.pem
375s Adding debian:Certum_Trusted_Network_CA_2.pem
375s Adding debian:Certum_Trusted_Root_CA.pem
375s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
375s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
375s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
375s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
376s Adding debian:Comodo_AAA_Services_root.pem
376s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
376s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
376s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
376s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
376s Adding debian:DigiCert_Assured_ID_Root_CA.pem
376s Adding debian:DigiCert_Assured_ID_Root_G2.pem
376s Adding debian:DigiCert_Assured_ID_Root_G3.pem
376s Adding debian:DigiCert_Global_Root_CA.pem
376s Adding debian:DigiCert_Global_Root_G2.pem
376s Adding debian:DigiCert_Global_Root_G3.pem
376s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
376s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
376s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
376s Adding debian:DigiCert_Trusted_Root_G4.pem
376s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
376s Adding debian:Entrust_Root_Certification_Authority.pem
376s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
376s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
376s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
376s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
376s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
376s Adding debian:GLOBALTRUST_2020.pem
376s Adding debian:GTS_Root_R1.pem
376s Adding debian:GTS_Root_R2.pem
376s Adding debian:GTS_Root_R3.pem
376s Adding debian:GTS_Root_R4.pem
376s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
376s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
376s Adding debian:GlobalSign_Root_CA.pem
376s Adding debian:GlobalSign_Root_CA_-_R3.pem
376s Adding debian:GlobalSign_Root_CA_-_R6.pem
376s Adding debian:GlobalSign_Root_E46.pem
376s Adding debian:GlobalSign_Root_R46.pem
376s Adding debian:Go_Daddy_Class_2_CA.pem
376s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
376s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
376s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
376s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
376s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
376s Adding debian:HiPKI_Root_CA_-_G1.pem
376s Adding debian:Hongkong_Post_Root_CA_3.pem
376s Adding debian:ISRG_Root_X1.pem
376s Adding debian:ISRG_Root_X2.pem
376s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
376s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
376s Adding debian:Izenpe.com.pem
376s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
376s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
376s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
376s Adding debian:NAVER_Global_Root_Certification_Authority.pem
376s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
376s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
376s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
376s Adding debian:QuoVadis_Root_CA_1_G3.pem
376s Adding debian:QuoVadis_Root_CA_2.pem
376s Adding debian:QuoVadis_Root_CA_2_G3.pem
376s Adding debian:QuoVadis_Root_CA_3.pem
376s Adding debian:QuoVadis_Root_CA_3_G3.pem
376s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
376s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
376s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
376s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
376s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
376s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
376s Adding debian:SZAFIR_ROOT_CA2.pem
376s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
376s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
376s Adding debian:SecureSign_RootCA11.pem
376s Adding debian:SecureSign_Root_CA12.pem
376s Adding debian:SecureSign_Root_CA14.pem
376s Adding debian:SecureSign_Root_CA15.pem
376s Adding debian:SecureTrust_CA.pem
376s Adding debian:Secure_Global_CA.pem
376s Adding debian:Security_Communication_ECC_RootCA1.pem
376s Adding debian:Security_Communication_RootCA2.pem
376s Adding debian:Security_Communication_RootCA3.pem
376s Adding debian:Starfield_Class_2_CA.pem
376s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
376s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
376s Adding debian:SwissSign_Gold_CA_-_G2.pem
376s Adding debian:SwissSign_Silver_CA_-_G2.pem
376s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
376s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
376s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
376s Adding debian:TWCA_CYBER_Root_CA.pem
376s Adding debian:TWCA_Global_Root_CA.pem
376s Adding debian:TWCA_Root_Certification_Authority.pem
376s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
376s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem
376s Adding debian:TeliaSonera_Root_CA_v1.pem
376s Adding debian:Telia_Root_CA_v2.pem
376s Adding debian:TrustAsia_Global_Root_CA_G3.pem
376s Adding debian:TrustAsia_Global_Root_CA_G4.pem
376s Adding debian:Trustwave_Global_Certification_Authority.pem
376s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
376s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
376s Adding debian:TunTrust_Root_CA.pem
376s Adding debian:UCA_Extended_Validation_Root.pem
376s Adding debian:UCA_Global_G2_Root.pem
376s Adding debian:USERTrust_ECC_Certification_Authority.pem
376s Adding debian:USERTrust_RSA_Certification_Authority.pem
376s Adding debian:XRamp_Global_CA_Root.pem
376s Adding debian:certSIGN_ROOT_CA.pem
376s Adding debian:certSIGN_Root_CA_G2.pem
376s Adding debian:e-Szigno_Root_CA_2017.pem
376s Adding debian:ePKI_Root_Certification_Authority.pem
376s Adding debian:emSign_ECC_Root_CA_-_C3.pem
376s Adding debian:emSign_ECC_Root_CA_-_G3.pem
376s Adding debian:emSign_Root_CA_-_C1.pem
376s Adding debian:emSign_Root_CA_-_G1.pem
376s Adding debian:vTrus_ECC_Root_CA.pem
376s Adding debian:vTrus_Root_CA.pem
376s done.
376s Setting up junit4 (4.13.2-5) ...
376s Setting up default-jre-headless (2:1.21-76) ...
376s Setting up jaligner (1.0+dfsg-11) ...
376s Setting up openjdk-21-jre:amd64 (21.0.6+7-1) ...
376s Setting up libjson-java (3.1.0+dfsg-2) ...
376s Setting up libhtsjdk-java (4.1.3+dfsg-2) ...
376s Setting up libgkl-java (0.8.11+dfsg-2build1) ...
376s Setting up default-jre (2:1.21-76) ...
376s Setting up libpicard-java (3.3.0+dfsg-2) ...
376s Setting up trimmomatic (0.39+dfsg-2) ...
376s Setting up trinityrnaseq (2.15.2+dfsg-1) ...
377s autopkgtest [23:37:12]: test run-tests: [-----------------------
378s cd test_Trinity_Assembly && make test_all
378s make[1]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
378s ./runMe.sh
378s #!/bin/bash -ve
378s 
378s #######################################################
378s ##  Run Trinity to Generate Transcriptome Assemblies ##
378s #######################################################
378s 
378s if [ -z ${TRINITY_HOME} ]; then
378s     echo "Must set env var TRINITY_HOME"
378s     exit 1
378s fi
378s 
378s 
378s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
378s               --left reads.left.fq.gz \
378s               --right reads.right.fq.gz \
378s               --SS_lib_type RF \
378s               --CPU 1 \
378s               --no_cleanup
378s 
378s 
378s      ______  ____   ____  ____   ____  ______  __ __
378s     |      ||    \ |    ||    \ |    ||      ||  |  |
378s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
378s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
378s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
378s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
378s       |__|  |__|\_||____||__|__||____|  |__|  |____/
378s 
378s     Trinity-v2.15.2
378s 
378s 
378s 
378s Left read files: $VAR1 = [
378s           'reads.left.fq.gz'
378s         ];
378s Right read files: $VAR1 = [
378s           'reads.right.fq.gz'
378s         ];
378s Saturday, March 15, 2025: 23:37:13	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir
378s Saturday, March 15, 2025: 23:37:13	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis
378s 
378s 
378s ----------------------------------------------------------------------------------
378s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
378s ----------------------------------------------------------------------------------
378s 
378s ---------------------------------------------------------------
378s ------------ In silico Read Normalization ---------------------
378s -- (Removing Excess Reads Beyond 200 Coverage --
378s ---------------------------------------------------------------
378s 
378s # running normalization on reads: $VAR1 = [
378s           [
378s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
378s           ],
378s           [
378s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
378s           ]
378s         ];
378s 
378s 
378s Saturday, March 15, 2025: 23:37:13	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --no_cleanup  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
378s -prepping seqs
378s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
378s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
378s CMD finished (0 seconds)
378s CMD finished (0 seconds)
378s CMD: touch left.fa.ok
378s CMD finished (0 seconds)
378s CMD: touch right.fa.ok
378s CMD finished (0 seconds)
378s  Done converting input files. CMD: cat left.fa right.fa > both.fa
378s CMD finished (0 seconds)
378s CMD: touch both.fa.ok
378s CMD finished (0 seconds)
378s -kmer counting.
378s -------------------------------------------
378s ----------- Jellyfish  --------------------
378s -- (building a k-mer catalog from reads) --
378s -------------------------------------------
378s 
378s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
380s CMD finished (2 seconds)
380s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
380s CMD finished (0 seconds)
380s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
380s CMD finished (0 seconds)
380s CMD: touch jellyfish.K25.min2.kmers.fa.success
380s CMD finished (0 seconds)
380s -generating stats files
380s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
380s -reading Kmer occurrences...
380s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
380s -reading Kmer occurrences...
380s 
380s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
380s 
380s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
380s STATS_GENERATION_TIME: 0 seconds.
380s CMD finished (0 seconds)
381s STATS_GENERATION_TIME: 1 seconds.
381s CMD finished (1 seconds)
381s CMD: touch left.fa.K25.stats.ok
381s CMD finished (0 seconds)
381s CMD: touch right.fa.K25.stats.ok
381s CMD finished (0 seconds)
381s -sorting each stats file by read name.
381s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
381s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
381s CMD finished (0 seconds)
381s CMD finished (0 seconds)
381s CMD: touch left.fa.K25.stats.sort.ok
381s CMD finished (0 seconds)
381s CMD: touch right.fa.K25.stats.sort.ok
381s CMD finished (0 seconds)
381s -defining normalized reads
381s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
381s -opening left.fa.K25.stats.sort
381s -opening right.fa.K25.stats.sort
381s -done opening files.
381s CMD finished (0 seconds)
381s CMD: touch pairs.K25.stats.ok
381s CMD finished (0 seconds)
381s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
381s 30472 / 30575 = 99.66% reads selected during normalization.
381s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
381s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
381s CMD finished (0 seconds)
381s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
381s CMD finished (0 seconds)
381s -search and capture.
382s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
382s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
382s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
382s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
382s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
382s CMD finished (0 seconds)
382s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
382s CMD finished (0 seconds)
382s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
382s CMD finished (0 seconds)
382s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
382s CMD finished (0 seconds)
382s 
382s 
382s Normalization complete. See outputs: 
382s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
382s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
382s Saturday, March 15, 2025: 23:37:17	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok
382s Converting input files. (in parallel)Saturday, March 15, 2025: 23:37:17	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
382s Saturday, March 15, 2025: 23:37:17	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
382s Saturday, March 15, 2025: 23:37:17	CMD: touch left.fa.ok
382s Saturday, March 15, 2025: 23:37:17	CMD: touch right.fa.ok
382s Saturday, March 15, 2025: 23:37:17	CMD: touch left.fa.ok right.fa.ok
382s Saturday, March 15, 2025: 23:37:17	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
382s Saturday, March 15, 2025: 23:37:17	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok
382s -------------------------------------------
382s ----------- Jellyfish  --------------------
382s -- (building a k-mer (25) catalog from reads) --
382s -------------------------------------------
382s 
382s * [Sat Mar 15 23:37:17 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
384s * [Sat Mar 15 23:37:19 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
384s * [Sat Mar 15 23:37:19 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
384s ----------------------------------------------
384s --------------- Inchworm (K=25, asm) ---------------------
384s -- (Linear contig construction from k-mers) --
384s ----------------------------------------------
384s 
384s * [Sat Mar 15 23:37:19 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --keep_tmp_files  --num_threads 1  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp
384s Kmer length set to: 25
384s Min assembly length set to: 25
384s Monitor turned on, set to: 1
384s -retaining tmp files
384s min entropy set to: 1
384s setting number of threads to: 1
384s -setting parallel iworm mode.
384s -reading Kmer occurrences...
385s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
385s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
385s 
385s TIMING KMER_DB_BUILDING 1 s.
385s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
385s Pruned 4252 kmers from catalog.
385s 	Pruning time: 0 seconds = 0 minutes.
385s 
385s TIMING PRUNING 0 s.
385s -populating the kmer seed candidate list.
385s Kcounter hash size: 519541
385s Processed 515289 non-zero abundance kmers in kcounter.
385s -Not sorting list of kmers, given parallel mode in effect.
385s -beginning inchworm contig assembly.
385s Total kcounter hash size: 519541 vs. sorted list size: 515289
385s num threads set to: 1
385s Done opening file. tmp.iworm.fa.pid_6578.thread_0
386s 
386s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
386s 
386s TIMING CONTIG_BUILDING 1 s.
386s 
386s TIMING PROG_RUNTIME 2 s.
386s * [Sat Mar 15 23:37:21 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa
386s Saturday, March 15, 2025: 23:37:21	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished
386s --------------------------------------------------------
386s -------------------- Chrysalis -------------------------
386s -- (Contig Clustering & de Bruijn Graph Construction) --
386s --------------------------------------------------------
386s 
386s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
386s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
386s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
386s * [Sat Mar 15 23:37:21 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100
386s * [Sat Mar 15 23:37:21 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
386s * [Sat Mar 15 23:37:21 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 1 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa  | samtools view -@ 1 -F4 -Sb - | samtools sort -m 1073741824 -@ 1 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
390s * [Sat Mar 15 23:37:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt
390s * [Sat Mar 15 23:37:25 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
391s * [Sat Mar 15 23:37:26 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
391s * [Sat Mar 15 23:37:26 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
391s * [Sat Mar 15 23:37:26 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
391s * [Sat Mar 15 23:37:26 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
392s * [Sat Mar 15 23:37:26 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
396s * [Sat Mar 15 23:37:30 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort
396s Saturday, March 15, 2025: 23:37:31	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0
396s Saturday, March 15, 2025: 23:37:31	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok
396s Saturday, March 15, 2025: 23:37:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --no_cleanup  --no_salmon  > recursive_trinity.cmds
396s Saturday, March 15, 2025: 23:37:31	CMD: touch recursive_trinity.cmds.ok
396s Saturday, March 15, 2025: 23:37:31	CMD: touch recursive_trinity.cmds.ok
396s 
396s 
396s --------------------------------------------------------------------------------
396s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
396s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
396s --------------------------------------------------------------------------------
396s 
396s Saturday, March 15, 2025: 23:37:31	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
396s Number of Commands: 36
489s 
succeeded(1)   2.77778% completed.    
succeeded(2)   5.55556% completed.    
succeeded(3)   8.33333% completed.    
succeeded(4)   11.1111% completed.    
succeeded(5)   13.8889% completed.    
succeeded(6)   16.6667% completed.    
succeeded(7)   19.4444% completed.    
succeeded(8)   22.2222% completed.    
succeeded(9)   25% completed.    
succeeded(10)   27.7778% completed.    
succeeded(11)   30.5556% completed.    
succeeded(12)   33.3333% completed.    
succeeded(13)   36.1111% completed.    
succeeded(14)   38.8889% completed.    
succeeded(15)   41.6667% completed.    
succeeded(16)   44.4444% completed.    
succeeded(17)   47.2222% completed.    
succeeded(18)   50% completed.    
succeeded(19)   52.7778% completed.    
succeeded(20)   55.5556% completed.    
succeeded(21)   58.3333% completed.    
succeeded(22)   61.1111% completed.    
succeeded(23)   63.8889% completed.    
succeeded(24)   66.6667% completed.    
succeeded(25)   69.4444% completed.    
succeeded(26)   72.2222% completed.    
succeeded(27)   75% completed.    
succeeded(28)   77.7778% completed.    
succeeded(29)   80.5556% completed.    
succeeded(30)   83.3333% completed.    
succeeded(31)   86.1111% completed.    
succeeded(32)   88.8889% completed.    
succeeded(33)   91.6667% completed.    
succeeded(34)   94.4444% completed.    
succeeded(35)   97.2222% completed.    
succeeded(36)   100% completed.    
489s 
489s All commands completed successfully. :-)
489s 
489s 
489s 
489s ** Harvesting all assembled transcripts into a single multi-fasta file...
489s 
489s Saturday, March 15, 2025: 23:39:04	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp
489s * [Sat Mar 15 23:39:04 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1
491s * [Sat Mar 15 23:39:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
491s Saturday, March 15, 2025: 23:39:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map
491s 
491s 
491s #############################################################################
491s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
491s #############################################################################
491s 
491s 
491s 
491s ##### Done Running Trinity #####
491s 
491s if [ $* ]; then
491s     # check full-length reconstruction stats:
491s 
491s     ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90
491s 
491s     ./test_FL.sh --query  trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
491s 
491s fi
491s 
491s ./misc_run_tests/__test_runMe_NO_normalization.sh
491s #!/bin/bash -ve
491s 
491s 
491s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
491s     gunzip -c reads.right.fq.gz > reads.right.fq
491s fi
491s 
491s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
491s     gunzip -c reads.left.fq.gz > reads.left.fq
491s fi
491s 
491s 
491s 
491s #######################################################
491s ##  Run Trinity to Generate Transcriptome Assemblies ##
491s #######################################################
491s 
491s CPU=$(nproc || sysctl -n hw.physicalcpu)
491s 
491s ## use jellyfish
491s ${TRINITY_HOME}/Trinity --seqType fq \
491s               --max_memory 2G \
491s               --left reads.left.fq \
491s               --right reads.right.fq \
491s               --SS_lib_type RF \
491s               --CPU ${CPU} \
491s               --no_normalize_reads \
491s               --output __test_trinity_wo_normalization
491s 
491s 
491s      ______  ____   ____  ____   ____  ______  __ __
491s     |      ||    \ |    ||    \ |    ||      ||  |  |
491s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
491s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
491s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
491s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
491s       |__|  |__|\_||____||__|__||____|  |__|  |____/
491s 
491s     Trinity-v2.15.2
491s 
491s 
491s 
491s Left read files: $VAR1 = [
491s           'reads.left.fq'
491s         ];
491s Right read files: $VAR1 = [
491s           'reads.right.fq'
491s         ];
491s Saturday, March 15, 2025: 23:39:06	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization
491s Saturday, March 15, 2025: 23:39:06	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis
491s 
491s 
491s ----------------------------------------------------------------------------------
491s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
491s ----------------------------------------------------------------------------------
491s 
491s Converting input files. (in parallel)Saturday, March 15, 2025: 23:39:06	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
491s Saturday, March 15, 2025: 23:39:06	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa
491s Saturday, March 15, 2025: 23:39:06	CMD: touch left.fa.ok
491s Saturday, March 15, 2025: 23:39:06	CMD: touch right.fa.ok
491s Saturday, March 15, 2025: 23:39:06	CMD: touch left.fa.ok right.fa.ok
491s Saturday, March 15, 2025: 23:39:06	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
491s Saturday, March 15, 2025: 23:39:06	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok
491s -------------------------------------------
491s ----------- Jellyfish  --------------------
491s -- (building a k-mer (25) catalog from reads) --
491s -------------------------------------------
491s 
491s * [Sat Mar 15 23:39:06 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
492s * [Sat Mar 15 23:39:07 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
492s * [Sat Mar 15 23:39:07 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
492s ----------------------------------------------
492s --------------- Inchworm (K=25, asm) ---------------------
492s -- (Linear contig construction from k-mers) --
492s ----------------------------------------------
492s 
492s * [Sat Mar 15 23:39:07 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp
492s Kmer length set to: 25
492s Min assembly length set to: 25
492s Monitor turned on, set to: 1
492s min entropy set to: 1
492s setting number of threads to: 2
492s -setting parallel iworm mode.
492s -reading Kmer occurrences...
492s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
492s  done parsing 520108 Kmers, 520108 added, taking 0 seconds.
492s 
492s TIMING KMER_DB_BUILDING 0 s.
492s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
492s Pruned 4291 kmers from catalog.
492s 	Pruning time: 0 seconds = 0 minutes.
492s 
492s TIMING PRUNING 0 s.
492s -populating the kmer seed candidate list.
492s Kcounter hash size: 520108
492s Processed 515817 non-zero abundance kmers in kcounter.
492s -Not sorting list of kmers, given parallel mode in effect.
492s -beginning inchworm contig assembly.
492s Total kcounter hash size: 520108 vs. sorted list size: 515817
492s num threads set to: 2
492s Done opening file. tmp.iworm.fa.pid_12854.thread_0
492s Done opening file. tmp.iworm.fa.pid_12854.thread_1
493s 
493s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
493s 
493s TIMING CONTIG_BUILDING 1 s.
493s 
493s TIMING PROG_RUNTIME 1 s.
493s * [Sat Mar 15 23:39:08 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa
493s Saturday, March 15, 2025: 23:39:08	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished
493s --------------------------------------------------------
493s -------------------- Chrysalis -------------------------
493s -- (Contig Clustering & de Bruijn Graph Construction) --
493s --------------------------------------------------------
493s 
493s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
493s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
493s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
493s * [Sat Mar 15 23:39:08 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100
493s * [Sat Mar 15 23:39:08 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null
493s * [Sat Mar 15 23:39:08 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 
498s * [Sat Mar 15 23:39:13 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt
499s * [Sat Mar 15 23:39:14 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt
502s * [Sat Mar 15 23:39:17 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted
502s * [Sat Mar 15 23:39:17 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
502s * [Sat Mar 15 23:39:17 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out
502s * [Sat Mar 15 23:39:17 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200
502s * [Sat Mar 15 23:39:17 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
504s * [Sat Mar 15 23:39:19 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort
505s Saturday, March 15, 2025: 23:39:19	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0
505s Saturday, March 15, 2025: 23:39:20	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok
505s Saturday, March 15, 2025: 23:39:20	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
505s Saturday, March 15, 2025: 23:39:20	CMD: touch recursive_trinity.cmds.ok
505s Saturday, March 15, 2025: 23:39:20	CMD: touch recursive_trinity.cmds.ok
505s 
505s 
505s --------------------------------------------------------------------------------
505s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
505s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
505s --------------------------------------------------------------------------------
505s 
505s Saturday, March 15, 2025: 23:39:20	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
505s Number of Commands: 41
569s 
succeeded(1)   2.43902% completed.    
succeeded(2)   4.87805% completed.    
succeeded(3)   7.31707% completed.    
succeeded(4)   9.7561% completed.    
succeeded(5)   12.1951% completed.    
succeeded(6)   14.6341% completed.    
succeeded(7)   17.0732% completed.    
succeeded(8)   19.5122% completed.    
succeeded(9)   21.9512% completed.    
succeeded(10)   24.3902% completed.    
succeeded(11)   26.8293% completed.    
succeeded(12)   29.2683% completed.    
succeeded(13)   31.7073% completed.    
succeeded(14)   34.1463% completed.    
succeeded(15)   36.5854% completed.    
succeeded(16)   39.0244% completed.    
succeeded(17)   41.4634% completed.    
succeeded(18)   43.9024% completed.    
succeeded(19)   46.3415% completed.    
succeeded(20)   48.7805% completed.    
succeeded(21)   51.2195% completed.    
succeeded(22)   53.6585% completed.    
succeeded(23)   56.0976% completed.    
succeeded(24)   58.5366% completed.    
succeeded(25)   60.9756% completed.    
succeeded(26)   63.4146% completed.    
succeeded(27)   65.8537% completed.    
succeeded(28)   68.2927% completed.    
succeeded(29)   70.7317% completed.    
succeeded(30)   73.1707% completed.    
succeeded(31)   75.6098% completed.    
succeeded(32)   78.0488% completed.    
succeeded(33)   80.4878% completed.    
succeeded(34)   82.9268% completed.    
succeeded(35)   85.3659% completed.    
succeeded(36)   87.8049% completed.    
succeeded(37)   90.2439% completed.    
succeeded(38)   92.6829% completed.    
succeeded(39)   95.1219% completed.    
succeeded(40)   97.561% completed.    
succeeded(41)   100% completed.    
569s 
569s All commands completed successfully. :-)
569s 
569s 
569s 
569s ** Harvesting all assembled transcripts into a single multi-fasta file...
569s 
569s Saturday, March 15, 2025: 23:40:24	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp
569s * [Sat Mar 15 23:40:24 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2
570s * [Sat Mar 15 23:40:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
570s Saturday, March 15, 2025: 23:40:25	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map
570s 
570s 
570s #############################################################################
570s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
570s #############################################################################
570s 
570s 
570s ./misc_run_tests/__runMe_with_qual_trimming.sh
570s 
570s 
570s 
570s #!/bin/bash -ve
570s 
570s 
570s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
570s     gunzip -c reads.right.fq.gz > reads.right.fq
570s fi
570s 
570s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
570s     gunzip -c reads.left.fq.gz > reads.left.fq
570s fi
570s 
570s 
570s 
570s #######################################################
570s ##  Run Trinity to Generate Transcriptome Assemblies ##
570s #######################################################
570s 
570s CPU=$(nproc || sysctl -n hw.physicalcpu)
570s 
570s ${TRINITY_HOME}/Trinity \
570s     --seqType fq \
570s     --max_memory 2G \
570s     --left reads.left.fq \
570s     --right reads.right.fq \
570s     --SS_lib_type RF \
570s     --CPU ${CPU} \
570s     --no_normalize_reads \
570s     --trimmomatic \
570s     --output __test_trinity_with_trimmomatic
570s 
570s 
570s      ______  ____   ____  ____   ____  ______  __ __
570s     |      ||    \ |    ||    \ |    ||      ||  |  |
570s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
570s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
570s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
570s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
570s       |__|  |__|\_||____||__|__||____|  |__|  |____/
570s 
570s     Trinity-v2.15.2
570s 
570s 
570s 
570s Left read files: $VAR1 = [
570s           'reads.left.fq'
570s         ];
570s Right read files: $VAR1 = [
570s           'reads.right.fq'
570s         ];
570s Saturday, March 15, 2025: 23:40:25	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic
570s Saturday, March 15, 2025: 23:40:25	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis
570s 
570s 
570s ----------------------------------------------------------------------------------
570s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
570s ----------------------------------------------------------------------------------
570s 
570s ---------------------------------------------------------------
570s ------ Quality Trimming Via Trimmomatic  ---------------------
570s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
570s ---------------------------------------------------------------
570s 
570s 
570s ## Running Trimmomatic on read files: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
570s Saturday, March 15, 2025: 23:40:25	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq  reads.left.fq.P.qtrim reads.left.fq.U.qtrim  reads.right.fq.P.qtrim reads.right.fq.U.qtrim  ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 
570s TrimmomaticPE: Started with arguments:
570s  -threads 2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
570s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
570s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
570s Quality encoding detected as phred33
571s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%)
571s TrimmomaticPE: Completed successfully
571s Saturday, March 15, 2025: 23:40:26	CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq
571s Saturday, March 15, 2025: 23:40:26	CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq
571s Saturday, March 15, 2025: 23:40:26	CMD: touch trimmomatic.ok
571s Saturday, March 15, 2025: 23:40:26	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
571s Converting input files. (in parallel)Saturday, March 15, 2025: 23:40:26	CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
571s Saturday, March 15, 2025: 23:40:26	CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa
571s Saturday, March 15, 2025: 23:40:26	CMD: touch left.fa.ok
571s Saturday, March 15, 2025: 23:40:26	CMD: touch right.fa.ok
571s Saturday, March 15, 2025: 23:40:26	CMD: touch left.fa.ok right.fa.ok
571s Saturday, March 15, 2025: 23:40:26	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
571s Saturday, March 15, 2025: 23:40:26	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok
571s -------------------------------------------
571s ----------- Jellyfish  --------------------
571s -- (building a k-mer (25) catalog from reads) --
571s -------------------------------------------
571s 
571s * [Sat Mar 15 23:40:26 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
572s * [Sat Mar 15 23:40:27 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
572s * [Sat Mar 15 23:40:27 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
572s ----------------------------------------------
572s --------------- Inchworm (K=25, asm) ---------------------
572s -- (Linear contig construction from k-mers) --
572s ----------------------------------------------
572s 
572s * [Sat Mar 15 23:40:27 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp
572s Kmer length set to: 25
572s Min assembly length set to: 25
572s Monitor turned on, set to: 1
572s min entropy set to: 1
572s setting number of threads to: 2
572s -setting parallel iworm mode.
572s -reading Kmer occurrences...
572s 
 [0M] Kmers parsed.     
572s  done parsing 318541 Kmers, 318541 added, taking 0 seconds.
572s 
572s TIMING KMER_DB_BUILDING 0 s.
572s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
573s Pruned 1498 kmers from catalog.
573s 	Pruning time: 1 seconds = 0.0166667 minutes.
573s 
573s TIMING PRUNING 1 s.
573s -populating the kmer seed candidate list.
573s Kcounter hash size: 318541
573s Processed 317043 non-zero abundance kmers in kcounter.
573s -Not sorting list of kmers, given parallel mode in effect.
573s -beginning inchworm contig assembly.
573s Total kcounter hash size: 318541 vs. sorted list size: 317043
573s num threads set to: 2
573s Done opening file. tmp.iworm.fa.pid_20097.thread_0
573s Done opening file. tmp.iworm.fa.pid_20097.thread_1
573s 
573s 	Iworm contig assembly time: 0 seconds = 0 minutes.
573s 
573s TIMING CONTIG_BUILDING 0 s.
573s 
573s TIMING PROG_RUNTIME 1 s.
573s * [Sat Mar 15 23:40:28 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa
573s Saturday, March 15, 2025: 23:40:28	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished
573s --------------------------------------------------------
573s -------------------- Chrysalis -------------------------
573s -- (Contig Clustering & de Bruijn Graph Construction) --
573s --------------------------------------------------------
573s 
573s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
573s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
573s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
573s * [Sat Mar 15 23:40:28 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100
573s * [Sat Mar 15 23:40:28 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null
573s * [Sat Mar 15 23:40:28 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 
577s * [Sat Mar 15 23:40:32 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt
577s * [Sat Mar 15 23:40:32 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt
579s * [Sat Mar 15 23:40:34 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted
579s * [Sat Mar 15 23:40:34 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
579s * [Sat Mar 15 23:40:34 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out
579s * [Sat Mar 15 23:40:34 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200
579s * [Sat Mar 15 23:40:34 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
580s * [Sat Mar 15 23:40:35 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort
580s Saturday, March 15, 2025: 23:40:35	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0
581s Saturday, March 15, 2025: 23:40:35	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok
581s Saturday, March 15, 2025: 23:40:35	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
581s Saturday, March 15, 2025: 23:40:35	CMD: touch recursive_trinity.cmds.ok
581s Saturday, March 15, 2025: 23:40:35	CMD: touch recursive_trinity.cmds.ok
581s 
581s 
581s --------------------------------------------------------------------------------
581s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
581s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
581s --------------------------------------------------------------------------------
581s 
581s Saturday, March 15, 2025: 23:40:36	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
581s Number of Commands: 35
637s 
succeeded(1)   2.85714% completed.    
succeeded(2)   5.71429% completed.    
succeeded(3)   8.57143% completed.    
succeeded(4)   11.4286% completed.    
succeeded(5)   14.2857% completed.    
succeeded(6)   17.1429% completed.    
succeeded(7)   20% completed.    
succeeded(8)   22.8571% completed.    
succeeded(9)   25.7143% completed.    
succeeded(10)   28.5714% completed.    
succeeded(11)   31.4286% completed.    
succeeded(12)   34.2857% completed.    
succeeded(13)   37.1429% completed.    
succeeded(14)   40% completed.    
succeeded(15)   42.8571% completed.    
succeeded(16)   45.7143% completed.    
succeeded(17)   48.5714% completed.    
succeeded(18)   51.4286% completed.    
succeeded(19)   54.2857% completed.    
succeeded(20)   57.1429% completed.    
succeeded(21)   60% completed.    
succeeded(22)   62.8571% completed.    
succeeded(23)   65.7143% completed.    
succeeded(24)   68.5714% completed.    
succeeded(25)   71.4286% completed.    
succeeded(26)   74.2857% completed.    
succeeded(27)   77.1429% completed.    
succeeded(28)   80% completed.    
succeeded(29)   82.8571% completed.    
succeeded(30)   85.7143% completed.    
succeeded(31)   88.5714% completed.    
succeeded(32)   91.4286% completed.    
succeeded(33)   94.2857% completed.    
succeeded(34)   97.1429% completed.    
succeeded(35)   100% completed.    
637s 
637s All commands completed successfully. :-)
637s 
637s 
637s 
637s ** Harvesting all assembled transcripts into a single multi-fasta file...
637s 
637s Saturday, March 15, 2025: 23:41:32	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp
637s * [Sat Mar 15 23:41:32 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2
638s * [Sat Mar 15 23:41:33 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
638s Saturday, March 15, 2025: 23:41:33	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map
638s 
638s 
638s #############################################################################
638s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
638s #############################################################################
638s 
638s 
638s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
638s 
638s ##### Done Running Trinity #####
638s 
638s #!/bin/bash -ve
638s 
638s 
638s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
638s     gunzip -c reads.right.fq.gz > reads.right.fq
638s fi
638s 
638s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
638s     gunzip -c reads.left.fq.gz > reads.left.fq
638s fi
638s 
638s 
638s 
638s #######################################################
638s ##  Run Trinity to Generate Transcriptome Assemblies ##
638s #######################################################
638s 
638s CPU=$(nproc || sysctl -n hw.physicalcpu)
638s 
638s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm
638s 
638s 
638s      ______  ____   ____  ____   ____  ______  __ __
638s     |      ||    \ |    ||    \ |    ||      ||  |  |
638s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
638s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
638s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
638s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
638s       |__|  |__|\_||____||__|__||____|  |__|  |____/
638s 
638s     Trinity-v2.15.2
638s 
638s 
638s 
638s Left read files: $VAR1 = [
638s           'reads.left.fq'
638s         ];
638s Right read files: $VAR1 = [
638s           'reads.right.fq'
638s         ];
638s Saturday, March 15, 2025: 23:41:33	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm
638s Saturday, March 15, 2025: 23:41:33	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis
638s 
638s 
638s ----------------------------------------------------------------------------------
638s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
638s ----------------------------------------------------------------------------------
638s 
638s ---------------------------------------------------------------
638s ------ Quality Trimming Via Trimmomatic  ---------------------
638s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
638s ---------------------------------------------------------------
638s 
638s 
638s ## Running Trimmomatic on read files: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
638s Saturday, March 15, 2025: 23:41:33	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq  reads.left.fq.P.qtrim reads.left.fq.U.qtrim  reads.right.fq.P.qtrim reads.right.fq.U.qtrim  ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 
638s TrimmomaticPE: Started with arguments:
638s  -threads 2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
638s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
638s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
638s Quality encoding detected as phred33
639s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%)
639s TrimmomaticPE: Completed successfully
639s Saturday, March 15, 2025: 23:41:34	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
639s Saturday, March 15, 2025: 23:41:34	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
639s Saturday, March 15, 2025: 23:41:34	CMD: touch trimmomatic.ok
639s Saturday, March 15, 2025: 23:41:34	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
639s ---------------------------------------------------------------
639s ------------ In silico Read Normalization ---------------------
639s -- (Removing Excess Reads Beyond 200 Coverage --
639s ---------------------------------------------------------------
639s 
639s # running normalization on reads: $VAR1 = [
639s           [
639s             'reads.left.fq.PwU.qtrim.fq'
639s           ],
639s           [
639s             'reads.right.fq.PwU.qtrim.fq'
639s           ]
639s         ];
639s 
639s 
639s Saturday, March 15, 2025: 23:41:34	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left reads.left.fq.PwU.qtrim.fq --right reads.right.fq.PwU.qtrim.fq --pairs_together  --PARALLEL_STATS  
639s -prepping seqs
639s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa
639s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa
639s CMD finished (0 seconds)
639s CMD finished (0 seconds)
639s CMD: touch left.fa.ok
639s CMD finished (0 seconds)
639s CMD: touch right.fa.ok
639s CMD finished (0 seconds)
639s  Done converting input files. CMD: cat left.fa right.fa > both.fa
639s CMD finished (0 seconds)
639s CMD: touch both.fa.ok
639s CMD finished (0 seconds)
639s -kmer counting.
639s -------------------------------------------
639s ----------- Jellyfish  --------------------
639s -- (building a k-mer catalog from reads) --
639s -------------------------------------------
639s 
639s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
640s CMD finished (1 seconds)
640s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
640s CMD finished (0 seconds)
640s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
640s CMD finished (0 seconds)
640s CMD: touch jellyfish.K25.min2.kmers.fa.success
640s CMD finished (0 seconds)
640s -generating stats files
640s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
640s -reading Kmer occurrences...
640s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
640s -reading Kmer occurrences...
641s 
641s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
641s 
641s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
641s STATS_GENERATION_TIME: 1 seconds.
641s CMD finished (1 seconds)
641s STATS_GENERATION_TIME: 1 seconds.
641s CMD finished (1 seconds)
641s CMD: touch left.fa.K25.stats.ok
641s CMD finished (0 seconds)
641s CMD: touch right.fa.K25.stats.ok
641s CMD finished (0 seconds)
641s -sorting each stats file by read name.
641s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
641s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
641s CMD finished (0 seconds)
641s CMD finished (0 seconds)
641s CMD: touch left.fa.K25.stats.sort.ok
641s CMD finished (0 seconds)
641s CMD: touch right.fa.K25.stats.sort.ok
641s CMD finished (0 seconds)
641s -defining normalized reads
641s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
641s -opening left.fa.K25.stats.sort
641s -opening right.fa.K25.stats.sort
641s -done opening files.
642s CMD finished (0 seconds)
642s CMD: touch pairs.K25.stats.ok
642s CMD finished (0 seconds)
642s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
642s 27678 / 27726 = 99.83% reads selected during normalization.
642s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
642s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
642s CMD finished (1 seconds)
642s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
642s CMD finished (0 seconds)
642s -search and capture.
642s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq ... done prepping, now search and capture.
642s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq
642s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq ... done prepping, now search and capture.
642s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq
642s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
642s CMD finished (0 seconds)
642s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
642s CMD finished (0 seconds)
642s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
642s CMD finished (0 seconds)
642s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
642s CMD finished (0 seconds)
642s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads
642s 
642s 
642s Normalization complete. See outputs: 
642s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
642s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
642s Saturday, March 15, 2025: 23:41:37	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok
642s Converting input files. (in parallel)Saturday, March 15, 2025: 23:41:37	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
642s Saturday, March 15, 2025: 23:41:37	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
642s Saturday, March 15, 2025: 23:41:37	CMD: touch left.fa.ok
642s Saturday, March 15, 2025: 23:41:37	CMD: touch right.fa.ok
642s Saturday, March 15, 2025: 23:41:37	CMD: touch left.fa.ok right.fa.ok
642s Saturday, March 15, 2025: 23:41:37	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
642s Saturday, March 15, 2025: 23:41:37	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok
642s -------------------------------------------
642s ----------- Jellyfish  --------------------
642s -- (building a k-mer (25) catalog from reads) --
642s -------------------------------------------
642s 
642s * [Sat Mar 15 23:41:37 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
644s * [Sat Mar 15 23:41:39 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
644s * [Sat Mar 15 23:41:39 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
644s ----------------------------------------------
644s --------------- Inchworm (K=25, asm) ---------------------
644s -- (Linear contig construction from k-mers) --
644s ----------------------------------------------
644s 
644s * [Sat Mar 15 23:41:39 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp
644s Kmer length set to: 25
644s Min assembly length set to: 25
644s Monitor turned on, set to: 1
644s min entropy set to: 1
644s setting number of threads to: 2
644s -setting parallel iworm mode.
644s -reading Kmer occurrences...
644s 
 [0M] Kmers parsed.     
644s  done parsing 311705 Kmers, 311705 added, taking 0 seconds.
644s 
644s TIMING KMER_DB_BUILDING 0 s.
644s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
644s Pruned 1486 kmers from catalog.
644s 	Pruning time: 0 seconds = 0 minutes.
644s 
644s TIMING PRUNING 0 s.
644s -populating the kmer seed candidate list.
644s Kcounter hash size: 311705
644s Processed 310219 non-zero abundance kmers in kcounter.
644s -Not sorting list of kmers, given parallel mode in effect.
644s -beginning inchworm contig assembly.
644s Total kcounter hash size: 311705 vs. sorted list size: 310219
644s num threads set to: 2
644s Done opening file. tmp.iworm.fa.pid_26388.thread_0
644s Done opening file. tmp.iworm.fa.pid_26388.thread_1
644s 
644s 	Iworm contig assembly time: 0 seconds = 0 minutes.
644s 
644s TIMING CONTIG_BUILDING 0 s.
644s 
644s TIMING PROG_RUNTIME 0 s.
644s * [Sat Mar 15 23:41:39 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa
644s Saturday, March 15, 2025: 23:41:39	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished
644s --------------------------------------------------------
644s -------------------- Chrysalis -------------------------
644s -- (Contig Clustering & de Bruijn Graph Construction) --
644s --------------------------------------------------------
644s 
644s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
644s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
644s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
644s * [Sat Mar 15 23:41:39 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100
644s * [Sat Mar 15 23:41:39 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null
645s * [Sat Mar 15 23:41:40 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 
648s * [Sat Mar 15 23:41:43 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt
649s * [Sat Mar 15 23:41:43 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt
651s * [Sat Mar 15 23:41:46 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted
651s * [Sat Mar 15 23:41:46 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
651s * [Sat Mar 15 23:41:46 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out
651s * [Sat Mar 15 23:41:46 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200
651s * [Sat Mar 15 23:41:46 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
653s * [Sat Mar 15 23:41:48 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort
653s Saturday, March 15, 2025: 23:41:48	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0
653s Saturday, March 15, 2025: 23:41:48	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok
653s Saturday, March 15, 2025: 23:41:48	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
653s Saturday, March 15, 2025: 23:41:48	CMD: touch recursive_trinity.cmds.ok
653s Saturday, March 15, 2025: 23:41:48	CMD: touch recursive_trinity.cmds.ok
653s 
653s 
653s --------------------------------------------------------------------------------
653s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
653s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
653s --------------------------------------------------------------------------------
653s 
653s Saturday, March 15, 2025: 23:41:48	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
653s Number of Commands: 40
708s 
succeeded(1)   2.5% completed.    
succeeded(2)   5% completed.    
succeeded(3)   7.5% completed.    
succeeded(4)   10% completed.    
succeeded(5)   12.5% completed.    
succeeded(6)   15% completed.    
succeeded(7)   17.5% completed.    
succeeded(8)   20% completed.    
succeeded(9)   22.5% completed.    
succeeded(10)   25% completed.    
succeeded(11)   27.5% completed.    
succeeded(12)   30% completed.    
succeeded(13)   32.5% completed.    
succeeded(14)   35% completed.    
succeeded(15)   37.5% completed.    
succeeded(16)   40% completed.    
succeeded(17)   42.5% completed.    
succeeded(18)   45% completed.    
succeeded(19)   47.5% completed.    
succeeded(20)   50% completed.    
succeeded(21)   52.5% completed.    
succeeded(22)   55% completed.    
succeeded(23)   57.5% completed.    
succeeded(24)   60% completed.    
succeeded(25)   62.5% completed.    
succeeded(26)   65% completed.    
succeeded(27)   67.5% completed.    
succeeded(28)   70% completed.    
succeeded(29)   72.5% completed.    
succeeded(30)   75% completed.    
succeeded(31)   77.5% completed.    
succeeded(32)   80% completed.    
succeeded(33)   82.5% completed.    
succeeded(34)   85% completed.    
succeeded(35)   87.5% completed.    
succeeded(36)   90% completed.    
succeeded(37)   92.5% completed.    
succeeded(38)   95% completed.    
succeeded(39)   97.5% completed.    
succeeded(40)   100% completed.    
708s 
708s All commands completed successfully. :-)
708s 
708s 
708s 
708s ** Harvesting all assembled transcripts into a single multi-fasta file...
708s 
708s Saturday, March 15, 2025: 23:42:43	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp
708s * [Sat Mar 15 23:42:43 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2
709s * [Sat Mar 15 23:42:44 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
709s Saturday, March 15, 2025: 23:42:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map
709s 
709s 
709s #############################################################################
709s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
709s #############################################################################
709s 
709s 
709s 
709s ##### Done Running Trinity #####
709s 
709s exit 0
709s #!/bin/bash -ve
709s 
709s ${TRINITY_HOME}/Trinity --seqType fq --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF  --CPU 1 --jaccard_clip --max_memory 1G --output __test_trinity_w_jaccard --grid_node_max_memory 2G --grid_node_CPU 2
709s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh
709s 
709s 
709s      ______  ____   ____  ____   ____  ______  __ __
709s     |      ||    \ |    ||    \ |    ||      ||  |  |
709s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
709s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
709s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
709s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
709s       |__|  |__|\_||____||__|__||____|  |__|  |____/
709s 
709s     Trinity-v2.15.2
709s 
709s 
709s 
709s Left read files: $VAR1 = [
709s           'reads.left.fq.gz'
709s         ];
709s Right read files: $VAR1 = [
709s           'reads.right.fq.gz'
709s         ];
709s Saturday, March 15, 2025: 23:42:44	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard
709s Saturday, March 15, 2025: 23:42:44	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis
709s 
709s 
709s ----------------------------------------------------------------------------------
709s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
709s ----------------------------------------------------------------------------------
709s 
709s ---------------------------------------------------------------
709s ------------ In silico Read Normalization ---------------------
709s -- (Removing Excess Reads Beyond 200 Coverage --
709s ---------------------------------------------------------------
709s 
709s # running normalization on reads: $VAR1 = [
709s           [
709s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
709s           ],
709s           [
709s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
709s           ]
709s         ];
709s 
709s 
709s Saturday, March 15, 2025: 23:42:44	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
709s -prepping seqs
709s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
709s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
709s CMD finished (0 seconds)
709s CMD finished (0 seconds)
709s CMD: touch left.fa.ok
709s CMD finished (0 seconds)
709s CMD: touch right.fa.ok
709s CMD finished (0 seconds)
709s  Done converting input files. CMD: cat left.fa right.fa > both.fa
709s CMD finished (0 seconds)
709s CMD: touch both.fa.ok
709s CMD finished (0 seconds)
709s -kmer counting.
709s -------------------------------------------
709s ----------- Jellyfish  --------------------
709s -- (building a k-mer catalog from reads) --
709s -------------------------------------------
709s 
709s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
711s CMD finished (2 seconds)
711s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
711s CMD finished (0 seconds)
711s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
711s CMD finished (0 seconds)
711s CMD: touch jellyfish.K25.min2.kmers.fa.success
711s CMD finished (0 seconds)
711s -generating stats files
711s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
711s -reading Kmer occurrences...
711s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
711s -reading Kmer occurrences...
711s 
711s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
711s 
711s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
712s STATS_GENERATION_TIME: 1 seconds.
712s CMD finished (1 seconds)
712s STATS_GENERATION_TIME: 1 seconds.
712s CMD finished (1 seconds)
712s CMD: touch left.fa.K25.stats.ok
712s CMD finished (0 seconds)
712s CMD: touch right.fa.K25.stats.ok
712s CMD finished (0 seconds)
712s -sorting each stats file by read name.
712s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
712s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
712s CMD finished (0 seconds)
712s CMD finished (0 seconds)
712s CMD: touch left.fa.K25.stats.sort.ok
712s CMD finished (0 seconds)
712s CMD: touch right.fa.K25.stats.sort.ok
712s CMD finished (0 seconds)
712s -defining normalized reads
712s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
712s -opening left.fa.K25.stats.sort
712s -opening right.fa.K25.stats.sort
712s -done opening files.
712s CMD finished (0 seconds)
712s CMD: touch pairs.K25.stats.ok
712s CMD finished (0 seconds)
712s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
712s 30472 / 30575 = 99.66% reads selected during normalization.
712s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
712s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
712s CMD finished (0 seconds)
712s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
712s CMD finished (0 seconds)
712s -search and capture.
712s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
712s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
712s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
712s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
713s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
713s CMD finished (0 seconds)
713s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
713s CMD finished (0 seconds)
713s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
713s CMD finished (0 seconds)
713s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
713s CMD finished (0 seconds)
713s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads
713s 
713s 
713s Normalization complete. See outputs: 
713s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
713s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
713s Saturday, March 15, 2025: 23:42:48	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok
713s Converting input files. (in parallel)Saturday, March 15, 2025: 23:42:48	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
713s Saturday, March 15, 2025: 23:42:48	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
713s Saturday, March 15, 2025: 23:42:48	CMD: touch right.fa.ok
713s Saturday, March 15, 2025: 23:42:48	CMD: touch left.fa.ok
713s Saturday, March 15, 2025: 23:42:48	CMD: touch left.fa.ok right.fa.ok
713s Saturday, March 15, 2025: 23:42:48	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
713s Saturday, March 15, 2025: 23:42:48	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok
713s -------------------------------------------
713s ----------- Jellyfish  --------------------
713s -- (building a k-mer (25) catalog from reads) --
713s -------------------------------------------
713s 
713s * [Sat Mar 15 23:42:48 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
715s * [Sat Mar 15 23:42:50 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
715s * [Sat Mar 15 23:42:50 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
715s ----------------------------------------------
715s --------------- Inchworm (K=25, asm) ---------------------
715s -- (Linear contig construction from k-mers) --
715s ----------------------------------------------
715s 
715s * [Sat Mar 15 23:42:50 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 1  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp
715s Kmer length set to: 25
715s Min assembly length set to: 25
715s Monitor turned on, set to: 1
715s min entropy set to: 1
715s setting number of threads to: 1
715s -setting parallel iworm mode.
715s -reading Kmer occurrences...
715s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
715s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
715s 
715s TIMING KMER_DB_BUILDING 0 s.
715s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
715s Pruned 4252 kmers from catalog.
715s 	Pruning time: 0 seconds = 0 minutes.
715s 
715s TIMING PRUNING 0 s.
715s -populating the kmer seed candidate list.
715s Kcounter hash size: 519541
716s Processed 515289 non-zero abundance kmers in kcounter.
716s -Not sorting list of kmers, given parallel mode in effect.
716s -beginning inchworm contig assembly.
716s Total kcounter hash size: 519541 vs. sorted list size: 515289
716s num threads set to: 1
716s Done opening file. tmp.iworm.fa.pid_33513.thread_0
716s 
716s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
716s 
716s TIMING CONTIG_BUILDING 1 s.
716s 
716s TIMING PROG_RUNTIME 1 s.
716s * [Sat Mar 15 23:42:51 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa
716s Saturday, March 15, 2025: 23:42:51	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished
716s --------------------------------------------------------
716s -------------------- Chrysalis -------------------------
716s -- (Contig Clustering & de Bruijn Graph Construction) --
716s --------------------------------------------------------
716s 
716s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
716s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
716s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
716s * [Sat Mar 15 23:42:51 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100
716s * [Sat Mar 15 23:42:51 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null
716s * [Sat Mar 15 23:42:51 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 1 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa  | samtools view -@ 1 -F4 -Sb - | samtools sort -m 536870912 -@ 1 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 
720s * [Sat Mar 15 23:42:55 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt
720s * [Sat Mar 15 23:42:55 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt
721s * [Sat Mar 15 23:42:56 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted
721s * [Sat Mar 15 23:42:56 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
721s * [Sat Mar 15 23:42:56 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out
721s * [Sat Mar 15 23:42:56 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200
721s * [Sat Mar 15 23:42:56 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
724s * [Sat Mar 15 23:42:58 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort
724s Saturday, March 15, 2025: 23:42:59	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0
724s Saturday, March 15, 2025: 23:42:59	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok
724s Saturday, March 15, 2025: 23:42:59	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list --CPU 2 --max_memory 2G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --jaccard_clip  --no_salmon  > recursive_trinity.cmds
724s Saturday, March 15, 2025: 23:42:59	CMD: touch recursive_trinity.cmds.ok
724s Saturday, March 15, 2025: 23:42:59	CMD: touch recursive_trinity.cmds.ok
724s 
724s 
724s --------------------------------------------------------------------------------
724s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
724s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
724s --------------------------------------------------------------------------------
724s 
724s Saturday, March 15, 2025: 23:42:59	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
724s Number of Commands: 36
725s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
725s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
725s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
725s bt2 index files: $VAR1 = [];
725s Note - bowtie-build indices do not yet exist. Indexing genome now.
725s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
725s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
725s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
726s 9900 reads; of these:
726s   9900 (100.00%) were unpaired; of these:
726s     5 (0.05%) aligned 0 times
726s     5821 (58.80%) aligned exactly 1 time
726s     4074 (41.15%) aligned >1 times
726s 99.95% overall alignment rate
726s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
726s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
726s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
726s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
726s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
726s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
726s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
726s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
726s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
726s 
726s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
726s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
727s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
727s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
727s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
727s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
727s -processing jaccard pair sensor
727s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
727s 
[1000 lines read]  scaff:a1;65 lend:476  rend:837     
[2000 lines read]  scaff:a1;65 lend:2420  rend:2904     
[3000 lines read]  scaff:a1;65 lend:3839  rend:4069     
[4000 lines read]  scaff:a1;65 lend:5020  rend:5460     
[5000 lines read]  scaff:a1;65 lend:5930  rend:6005     
[6000 lines read]  scaff:a22;4 lend:1  rend:49     
[7000 lines read]  scaff:a52;2 lend:1  rend:36     
[8000 lines read]  scaff:a65;2 lend:1  rend:36     
[9000 lines read]  scaff:a78;2 lend:2  rend:49     
[10000 lines read]  scaff:a90;2 lend:1  rend:37     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
727s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa.clipped.fa
733s 
succeeded(1)   2.77778% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
733s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
733s bt2 index files: $VAR1 = [];
733s Note - bowtie-build indices do not yet exist. Indexing genome now.
733s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
733s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
733s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
733s 6 reads; of these:
733s   6 (100.00%) were unpaired; of these:
733s     0 (0.00%) aligned 0 times
733s     6 (100.00%) aligned exactly 1 time
733s     0 (0.00%) aligned >1 times
733s 100.00% overall alignment rate
733s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
733s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
733s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
733s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
733s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
733s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
733s 
733s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
733s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
733s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
733s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
733s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
733s -processing jaccard pair sensor
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa.clipped.fa
734s 
succeeded(2)   5.55556% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
734s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
734s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
734s bt2 index files: $VAR1 = [];
734s Note - bowtie-build indices do not yet exist. Indexing genome now.
734s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
735s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
735s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
735s 29 reads; of these:
735s   29 (100.00%) were unpaired; of these:
735s     0 (0.00%) aligned 0 times
735s     29 (100.00%) aligned exactly 1 time
735s     0 (0.00%) aligned >1 times
735s 100.00% overall alignment rate
735s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
735s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
735s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
735s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
735s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
735s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
735s 
735s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
735s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
735s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
735s -processing jaccard pair sensor
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa.clipped.fa
736s 
succeeded(3)   8.33333% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
736s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
736s bt2 index files: $VAR1 = [];
736s Note - bowtie-build indices do not yet exist. Indexing genome now.
736s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
737s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
737s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
737s 33 reads; of these:
737s   33 (100.00%) were unpaired; of these:
737s     0 (0.00%) aligned 0 times
737s     33 (100.00%) aligned exactly 1 time
737s     0 (0.00%) aligned >1 times
737s 100.00% overall alignment rate
737s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
737s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
737s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
737s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
737s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
737s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
737s 
737s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
737s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
737s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
737s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
737s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
737s -processing jaccard pair sensor
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
737s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa.clipped.fa
738s 
succeeded(4)   11.1111% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
738s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
738s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
738s bt2 index files: $VAR1 = [];
738s Note - bowtie-build indices do not yet exist. Indexing genome now.
738s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
739s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
739s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
739s 9 reads; of these:
739s   9 (100.00%) were unpaired; of these:
739s     0 (0.00%) aligned 0 times
739s     9 (100.00%) aligned exactly 1 time
739s     0 (0.00%) aligned >1 times
739s 100.00% overall alignment rate
739s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
739s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
739s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
739s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
739s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
739s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
739s 
739s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
739s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
739s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
739s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
739s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
739s -processing jaccard pair sensor
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa.clipped.fa
740s 
succeeded(5)   13.8889% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
740s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
740s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
740s bt2 index files: $VAR1 = [];
740s Note - bowtie-build indices do not yet exist. Indexing genome now.
740s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
740s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
740s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
740s 8 reads; of these:
740s   8 (100.00%) were unpaired; of these:
740s     0 (0.00%) aligned 0 times
740s     8 (100.00%) aligned exactly 1 time
740s     0 (0.00%) aligned >1 times
740s 100.00% overall alignment rate
740s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
740s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
740s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
740s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
740s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
740s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
741s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
741s 
741s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
741s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
741s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
741s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
741s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
741s -processing jaccard pair sensor
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa.clipped.fa
742s 
succeeded(6)   16.6667% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
742s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
743s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
743s bt2 index files: $VAR1 = [];
743s Note - bowtie-build indices do not yet exist. Indexing genome now.
743s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
743s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
743s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
743s 4987 reads; of these:
743s   4987 (100.00%) were unpaired; of these:
743s     2 (0.04%) aligned 0 times
743s     2643 (53.00%) aligned exactly 1 time
743s     2342 (46.96%) aligned >1 times
743s 99.96% overall alignment rate
743s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
743s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
743s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
744s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
744s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
744s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
744s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
744s 
744s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
744s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
744s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
744s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
744s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
744s -processing jaccard pair sensor
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
744s 
[1000 lines read]  scaff:a1;96 lend:803  rend:1291     
[2000 lines read]  scaff:a1;96 lend:1599  rend:1674     
[3000 lines read]  scaff:a24;3 lend:1  rend:34     
[4000 lines read]  scaff:a39;2 lend:1  rend:49     
[5000 lines read]  scaff:a49;2 lend:1  rend:53     
[6000 lines read]  scaff:a58;2 lend:3  rend:49     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa.clipped.fa
748s 
succeeded(7)   19.4444% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
748s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
748s bt2 index files: $VAR1 = [];
748s Note - bowtie-build indices do not yet exist. Indexing genome now.
748s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
748s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
748s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
748s 15 reads; of these:
748s   15 (100.00%) were unpaired; of these:
748s     0 (0.00%) aligned 0 times
748s     15 (100.00%) aligned exactly 1 time
748s     0 (0.00%) aligned >1 times
748s 100.00% overall alignment rate
748s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
748s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
748s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
748s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
748s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
748s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
748s 
748s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
748s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
749s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
749s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
749s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
749s -processing jaccard pair sensor
749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa.clipped.fa
750s 
succeeded(8)   22.2222% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
750s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
750s bt2 index files: $VAR1 = [];
750s Note - bowtie-build indices do not yet exist. Indexing genome now.
750s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
750s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
750s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
750s 17 reads; of these:
750s   17 (100.00%) were unpaired; of these:
750s     0 (0.00%) aligned 0 times
750s     17 (100.00%) aligned exactly 1 time
750s     0 (0.00%) aligned >1 times
750s 100.00% overall alignment rate
750s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
750s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
750s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
750s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
750s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
751s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
751s 
751s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
751s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
751s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
751s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
751s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
751s -processing jaccard pair sensor
751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa.clipped.fa
752s 
succeeded(9)   25% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
753s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
753s bt2 index files: $VAR1 = [];
753s Note - bowtie-build indices do not yet exist. Indexing genome now.
753s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
753s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
753s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
753s 7052 reads; of these:
753s   7052 (100.00%) were unpaired; of these:
753s     4 (0.06%) aligned 0 times
753s     5120 (72.60%) aligned exactly 1 time
753s     1928 (27.34%) aligned >1 times
753s 99.94% overall alignment rate
753s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
753s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
754s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
754s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
754s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
754s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
754s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
754s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
754s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
754s 
754s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
754s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
754s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
754s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
754s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
754s -processing jaccard pair sensor
754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
755s 
[1000 lines read]  scaff:a1;37 lend:3075  rend:3272     
[2000 lines read]  scaff:a1;37 lend:5784  rend:6268     
[3000 lines read]  scaff:a1;37 lend:7480  rend:7705     
[4000 lines read]  scaff:a24;2 lend:1  rend:48     
[5000 lines read]  scaff:a55;2 lend:1  rend:44     
[6000 lines read]  scaff:a83;2 lend:1  rend:48     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
755s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa.clipped.fa
764s 
succeeded(10)   27.7778% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
764s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
764s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
764s bt2 index files: $VAR1 = [];
764s Note - bowtie-build indices do not yet exist. Indexing genome now.
764s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
765s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
765s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
765s 7 reads; of these:
765s   7 (100.00%) were unpaired; of these:
765s     3 (42.86%) aligned 0 times
765s     4 (57.14%) aligned exactly 1 time
765s     0 (0.00%) aligned >1 times
765s 57.14% overall alignment rate
765s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
765s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
765s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
765s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
765s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
765s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
765s 
765s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
765s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
765s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
765s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
765s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
765s -processing jaccard pair sensor
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa.clipped.fa
766s 
succeeded(11)   30.5556% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
766s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
766s bt2 index files: $VAR1 = [];
766s Note - bowtie-build indices do not yet exist. Indexing genome now.
766s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
766s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
766s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
767s 28 reads; of these:
767s   28 (100.00%) were unpaired; of these:
767s     0 (0.00%) aligned 0 times
767s     28 (100.00%) aligned exactly 1 time
767s     0 (0.00%) aligned >1 times
767s 100.00% overall alignment rate
767s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
767s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
767s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
767s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
767s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
767s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
767s 
767s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
767s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
767s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
767s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
767s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
767s -processing jaccard pair sensor
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa.clipped.fa
768s 
succeeded(12)   33.3333% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
768s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
768s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
768s bt2 index files: $VAR1 = [];
768s Note - bowtie-build indices do not yet exist. Indexing genome now.
768s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
769s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
769s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
769s 24 reads; of these:
769s   24 (100.00%) were unpaired; of these:
769s     0 (0.00%) aligned 0 times
769s     24 (100.00%) aligned exactly 1 time
769s     0 (0.00%) aligned >1 times
769s 100.00% overall alignment rate
769s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
769s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
769s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
769s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
769s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
769s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
769s 
769s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
769s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
769s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
769s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
769s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
769s -processing jaccard pair sensor
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa.clipped.fa
771s 
succeeded(13)   36.1111% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
771s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
771s bt2 index files: $VAR1 = [];
771s Note - bowtie-build indices do not yet exist. Indexing genome now.
771s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
771s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
771s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
772s 5130 reads; of these:
772s   5130 (100.00%) were unpaired; of these:
772s     6 (0.12%) aligned 0 times
772s     4306 (83.94%) aligned exactly 1 time
772s     818 (15.95%) aligned >1 times
772s 99.88% overall alignment rate
772s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
772s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
772s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
772s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
772s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
772s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
772s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
772s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
772s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
772s 
772s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
772s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
772s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
772s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
772s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
772s -processing jaccard pair sensor
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
772s 
[1000 lines read]  scaff:a25;2 lend:1  rend:45     
[2000 lines read]  scaff:a3;25 lend:514  rend:589     
[3000 lines read]  scaff:a3;25 lend:4028  rend:4299     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa.clipped.fa
777s 
succeeded(14)   38.8889% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
777s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
777s bt2 index files: $VAR1 = [];
777s Note - bowtie-build indices do not yet exist. Indexing genome now.
777s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
777s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
777s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
777s 3374 reads; of these:
777s   3374 (100.00%) were unpaired; of these:
777s     1 (0.03%) aligned 0 times
777s     2870 (85.06%) aligned exactly 1 time
777s     503 (14.91%) aligned >1 times
777s 99.97% overall alignment rate
777s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
777s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
777s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
777s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
777s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
778s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
778s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
778s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
778s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
778s 
778s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
778s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
778s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
778s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
778s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
778s -processing jaccard pair sensor
778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
778s 
[1000 lines read]  scaff:a1;29 lend:1682  rend:1757     
[2000 lines read]  scaff:a1;29 lend:4783  rend:5150     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa.clipped.fa
781s 
succeeded(15)   41.6667% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
781s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
781s bt2 index files: $VAR1 = [];
781s Note - bowtie-build indices do not yet exist. Indexing genome now.
781s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
781s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
781s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
781s 6 reads; of these:
781s   6 (100.00%) were unpaired; of these:
781s     0 (0.00%) aligned 0 times
781s     6 (100.00%) aligned exactly 1 time
781s     0 (0.00%) aligned >1 times
781s 100.00% overall alignment rate
781s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
781s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
781s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
781s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
781s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
781s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
781s 
781s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
781s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
781s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
781s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
781s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
781s -processing jaccard pair sensor
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa.clipped.fa
783s 
succeeded(16)   44.4444% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
783s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
783s bt2 index files: $VAR1 = [];
783s Note - bowtie-build indices do not yet exist. Indexing genome now.
783s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
783s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
783s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
783s 8 reads; of these:
783s   8 (100.00%) were unpaired; of these:
783s     0 (0.00%) aligned 0 times
783s     8 (100.00%) aligned exactly 1 time
783s     0 (0.00%) aligned >1 times
783s 100.00% overall alignment rate
783s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
783s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
783s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
783s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
783s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
783s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
783s 
783s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
783s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
783s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
783s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
783s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
783s -processing jaccard pair sensor
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa.clipped.fa
784s 
succeeded(17)   47.2222% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
784s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
784s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
784s bt2 index files: $VAR1 = [];
784s Note - bowtie-build indices do not yet exist. Indexing genome now.
784s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
785s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
785s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
785s 14 reads; of these:
785s   14 (100.00%) were unpaired; of these:
785s     0 (0.00%) aligned 0 times
785s     14 (100.00%) aligned exactly 1 time
785s     0 (0.00%) aligned >1 times
785s 100.00% overall alignment rate
785s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
785s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
785s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
785s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
785s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
785s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
785s 
785s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
785s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
785s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
785s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
785s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
785s -processing jaccard pair sensor
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa.clipped.fa
786s 
succeeded(18)   50% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
786s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
786s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
786s bt2 index files: $VAR1 = [];
786s Note - bowtie-build indices do not yet exist. Indexing genome now.
786s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
787s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
787s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
787s 15 reads; of these:
787s   15 (100.00%) were unpaired; of these:
787s     0 (0.00%) aligned 0 times
787s     15 (100.00%) aligned exactly 1 time
787s     0 (0.00%) aligned >1 times
787s 100.00% overall alignment rate
787s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
787s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
787s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
787s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
787s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
787s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
787s 
787s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
787s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
787s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
787s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
787s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
787s -processing jaccard pair sensor
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa.clipped.fa
789s 
succeeded(19)   52.7778% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
789s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
789s bt2 index files: $VAR1 = [];
789s Note - bowtie-build indices do not yet exist. Indexing genome now.
789s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
789s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
789s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
789s 2351 reads; of these:
789s   2351 (100.00%) were unpaired; of these:
789s     1 (0.04%) aligned 0 times
789s     1736 (73.84%) aligned exactly 1 time
789s     614 (26.12%) aligned >1 times
789s 99.96% overall alignment rate
789s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
789s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
789s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
789s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
789s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
790s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
790s 
790s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
790s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
790s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
790s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
790s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
790s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
790s -processing jaccard pair sensor
790s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
790s 
[1000 lines read]  scaff:a1;39 lend:1891  rend:2041     
[2000 lines read]  scaff:a42;2 lend:1  rend:49     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
790s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa.clipped.fa
794s 
succeeded(20)   55.5556% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
794s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
794s bt2 index files: $VAR1 = [];
794s Note - bowtie-build indices do not yet exist. Indexing genome now.
794s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
794s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
794s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
794s 1875 reads; of these:
794s   1875 (100.00%) were unpaired; of these:
794s     2 (0.11%) aligned 0 times
794s     1543 (82.29%) aligned exactly 1 time
794s     330 (17.60%) aligned >1 times
794s 99.89% overall alignment rate
794s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
794s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
794s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
794s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
794s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
794s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
794s 
794s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
794s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
794s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
794s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
794s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
794s -processing jaccard pair sensor
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
794s 
[1000 lines read]  scaff:a21;2 lend:1  rend:49     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa.clipped.fa
797s 
succeeded(21)   58.3333% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
797s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
797s bt2 index files: $VAR1 = [];
797s Note - bowtie-build indices do not yet exist. Indexing genome now.
797s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
798s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
798s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
798s 40 reads; of these:
798s   40 (100.00%) were unpaired; of these:
798s     0 (0.00%) aligned 0 times
798s     36 (90.00%) aligned exactly 1 time
798s     4 (10.00%) aligned >1 times
798s 100.00% overall alignment rate
798s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
798s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
798s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
798s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
798s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
798s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
798s 
798s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
798s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
798s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
798s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
798s -processing jaccard pair sensor
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa.clipped.fa
800s 
succeeded(22)   61.1111% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
800s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
800s bt2 index files: $VAR1 = [];
800s Note - bowtie-build indices do not yet exist. Indexing genome now.
800s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
800s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
800s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
800s 28 reads; of these:
800s   28 (100.00%) were unpaired; of these:
800s     0 (0.00%) aligned 0 times
800s     28 (100.00%) aligned exactly 1 time
800s     0 (0.00%) aligned >1 times
800s 100.00% overall alignment rate
800s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
800s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
800s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
800s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
800s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
800s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
800s 
800s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
800s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
800s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
800s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
800s -processing jaccard pair sensor
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa.clipped.fa
802s 
succeeded(23)   63.8889% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
802s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
802s bt2 index files: $VAR1 = [];
802s Note - bowtie-build indices do not yet exist. Indexing genome now.
802s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
802s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
802s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
802s 29 reads; of these:
802s   29 (100.00%) were unpaired; of these:
802s     0 (0.00%) aligned 0 times
802s     23 (79.31%) aligned exactly 1 time
802s     6 (20.69%) aligned >1 times
802s 100.00% overall alignment rate
802s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
802s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
802s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
802s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
802s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
802s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
802s 
802s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
802s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
802s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
802s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
802s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
802s -processing jaccard pair sensor
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa.clipped.fa
804s 
succeeded(24)   66.6667% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
804s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
804s bt2 index files: $VAR1 = [];
804s Note - bowtie-build indices do not yet exist. Indexing genome now.
804s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
804s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
804s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
804s 8 reads; of these:
804s   8 (100.00%) were unpaired; of these:
804s     0 (0.00%) aligned 0 times
804s     8 (100.00%) aligned exactly 1 time
804s     0 (0.00%) aligned >1 times
804s 100.00% overall alignment rate
804s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
804s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
804s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
804s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
804s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
804s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
804s 
804s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
804s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
804s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
804s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
804s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
804s -processing jaccard pair sensor
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa.clipped.fa
806s 
succeeded(25)   69.4444% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
806s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
806s bt2 index files: $VAR1 = [];
806s Note - bowtie-build indices do not yet exist. Indexing genome now.
806s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
806s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
806s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
806s 81 reads; of these:
806s   81 (100.00%) were unpaired; of these:
806s     0 (0.00%) aligned 0 times
806s     78 (96.30%) aligned exactly 1 time
806s     3 (3.70%) aligned >1 times
806s 100.00% overall alignment rate
806s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
806s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
806s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
806s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
806s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
806s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
806s 
806s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
806s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
806s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
806s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
806s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
806s -processing jaccard pair sensor
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa.clipped.fa
808s 
succeeded(26)   72.2222% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
808s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
808s bt2 index files: $VAR1 = [];
808s Note - bowtie-build indices do not yet exist. Indexing genome now.
808s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
808s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
808s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
808s 13 reads; of these:
808s   13 (100.00%) were unpaired; of these:
808s     0 (0.00%) aligned 0 times
808s     13 (100.00%) aligned exactly 1 time
808s     0 (0.00%) aligned >1 times
808s 100.00% overall alignment rate
808s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
808s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
808s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
808s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
808s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
809s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
809s 
809s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
809s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
809s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
809s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
809s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
809s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
809s -processing jaccard pair sensor
809s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
809s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
809s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa.clipped.fa
810s 
succeeded(27)   75% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
810s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
810s bt2 index files: $VAR1 = [];
810s Note - bowtie-build indices do not yet exist. Indexing genome now.
810s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
810s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
810s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
811s 1556 reads; of these:
811s   1556 (100.00%) were unpaired; of these:
811s     1 (0.06%) aligned 0 times
811s     1328 (85.35%) aligned exactly 1 time
811s     227 (14.59%) aligned >1 times
811s 99.94% overall alignment rate
811s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
811s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
811s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
811s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
811s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
811s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
811s 
811s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
811s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
811s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
811s -processing jaccard pair sensor
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
811s 
[1000 lines read]  scaff:a4;5 lend:109  rend:184     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa.clipped.fa
813s 
succeeded(28)   77.7778% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
813s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
813s bt2 index files: $VAR1 = [];
813s Note - bowtie-build indices do not yet exist. Indexing genome now.
813s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
814s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
814s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
814s 20 reads; of these:
814s   20 (100.00%) were unpaired; of these:
814s     0 (0.00%) aligned 0 times
814s     20 (100.00%) aligned exactly 1 time
814s     0 (0.00%) aligned >1 times
814s 100.00% overall alignment rate
814s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
814s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
814s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
814s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
814s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
814s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
814s 
814s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
814s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
814s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
814s -processing jaccard pair sensor
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa.clipped.fa
816s 
succeeded(29)   80.5556% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
816s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
816s bt2 index files: $VAR1 = [];
816s Note - bowtie-build indices do not yet exist. Indexing genome now.
816s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
816s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
816s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
817s 8656 reads; of these:
817s   8656 (100.00%) were unpaired; of these:
817s     6 (0.07%) aligned 0 times
817s     5677 (65.58%) aligned exactly 1 time
817s     2973 (34.35%) aligned >1 times
817s 99.93% overall alignment rate
817s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
817s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
818s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
818s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
818s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
818s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
818s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
818s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
818s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
818s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
818s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
818s 
818s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
818s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
818s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
818s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
818s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
818s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
818s -processing jaccard pair sensor
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
819s 
[1000 lines read]  scaff:a1;61 lend:632  rend:881     
[2000 lines read]  scaff:a1;61 lend:2374  rend:2686     
[3000 lines read]  scaff:a1;61 lend:3935  rend:4312     
[4000 lines read]  scaff:a1;61 lend:5397  rend:5666     
[5000 lines read]  scaff:a1;61 lend:6299  rend:6522     
[6000 lines read]  scaff:a38;2 lend:1  rend:38     
[7000 lines read]  scaff:a53;2 lend:1  rend:33     
[8000 lines read]  scaff:a70;2 lend:1  rend:40     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa.clipped.fa
823s 
succeeded(30)   83.3333% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
824s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
824s bt2 index files: $VAR1 = [];
824s Note - bowtie-build indices do not yet exist. Indexing genome now.
824s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
824s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
824s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
824s 9 reads; of these:
824s   9 (100.00%) were unpaired; of these:
824s     0 (0.00%) aligned 0 times
824s     9 (100.00%) aligned exactly 1 time
824s     0 (0.00%) aligned >1 times
824s 100.00% overall alignment rate
824s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
824s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
824s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
824s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
824s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
824s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
824s 
824s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
824s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
824s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
824s -processing jaccard pair sensor
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa.clipped.fa
826s 
succeeded(31)   86.1111% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
826s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
826s bt2 index files: $VAR1 = [];
826s Note - bowtie-build indices do not yet exist. Indexing genome now.
826s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
826s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
826s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
826s 20 reads; of these:
826s   20 (100.00%) were unpaired; of these:
826s     0 (0.00%) aligned 0 times
826s     20 (100.00%) aligned exactly 1 time
826s     0 (0.00%) aligned >1 times
826s 100.00% overall alignment rate
826s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
826s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
826s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
826s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
826s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
826s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
826s 
826s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
826s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
826s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
826s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
826s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
826s -processing jaccard pair sensor
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa.clipped.fa
828s 
succeeded(32)   88.8889% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
828s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
828s bt2 index files: $VAR1 = [];
828s Note - bowtie-build indices do not yet exist. Indexing genome now.
828s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
828s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
828s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
828s 11 reads; of these:
828s   11 (100.00%) were unpaired; of these:
828s     0 (0.00%) aligned 0 times
828s     11 (100.00%) aligned exactly 1 time
828s     0 (0.00%) aligned >1 times
828s 100.00% overall alignment rate
828s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
828s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
828s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
828s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
828s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
828s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
828s 
828s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
828s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
828s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
828s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
828s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
828s -processing jaccard pair sensor
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa.clipped.fa
829s 
succeeded(33)   91.6667% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
829s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
829s bt2 index files: $VAR1 = [];
829s Note - bowtie-build indices do not yet exist. Indexing genome now.
829s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
830s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
830s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
830s 9 reads; of these:
830s   9 (100.00%) were unpaired; of these:
830s     0 (0.00%) aligned 0 times
830s     9 (100.00%) aligned exactly 1 time
830s     0 (0.00%) aligned >1 times
830s 100.00% overall alignment rate
830s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
830s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
830s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
830s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
830s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
830s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
830s 
830s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
830s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
830s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
830s -processing jaccard pair sensor
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa.clipped.fa
832s 
succeeded(34)   94.4444% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
832s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
832s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
832s bt2 index files: $VAR1 = [];
832s Note - bowtie-build indices do not yet exist. Indexing genome now.
832s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
833s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
833s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
834s 11272 reads; of these:
834s   11272 (100.00%) were unpaired; of these:
834s     2 (0.02%) aligned 0 times
834s     1241 (11.01%) aligned exactly 1 time
834s     10029 (88.97%) aligned >1 times
834s 99.98% overall alignment rate
834s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
836s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
836s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
836s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
836s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
836s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
836s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
836s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
836s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
836s 
837s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
837s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
837s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
837s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
837s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
837s -processing jaccard pair sensor
838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
839s 
[1000 lines read]  scaff:a107;3 lend:1  rend:45     
[2000 lines read]  scaff:a113;2 lend:1  rend:42     
[3000 lines read]  scaff:a118;2 lend:14  rend:59     
[4000 lines read]  scaff:a123;3 lend:1  rend:35     
[5000 lines read]  scaff:a131;2 lend:1  rend:44     
[6000 lines read]  scaff:a137;2 lend:1  rend:49     
[7000 lines read]  scaff:a144;2 lend:45  rend:84     
[8000 lines read]  scaff:a153;2 lend:7  rend:49     
[9000 lines read]  scaff:a162;2 lend:1  rend:46     
[10000 lines read]  scaff:a170;2 lend:3  rend:78     
[11000 lines read]  scaff:a175;2 lend:1  rend:49     
[12000 lines read]  scaff:a181;2 lend:26  rend:57     
[13000 lines read]  scaff:a187;2 lend:1  rend:41     
[14000 lines read]  scaff:a192;2 lend:8  rend:51     
[15000 lines read]  scaff:a198;2 lend:1  rend:49     
[16000 lines read]  scaff:a1;139 lend:291  rend:478     
[17000 lines read]  scaff:a1;139 lend:907  rend:1219     
[18000 lines read]  scaff:a1;139 lend:1602  rend:1915     
[19000 lines read]  scaff:a1;139 lend:2262  rend:2337     
[20000 lines read]  scaff:a1;139 lend:2817  rend:2946     
[21000 lines read]  scaff:a1;139 lend:3282  rend:3521     
[22000 lines read]  scaff:a205;2 lend:1  rend:40     
[23000 lines read]  scaff:a210;2 lend:1  rend:35     
[24000 lines read]  scaff:a221;2 lend:1  rend:49     
[25000 lines read]  scaff:a226;2 lend:3  rend:38     
[26000 lines read]  scaff:a235;2 lend:19  rend:60     
[27000 lines read]  scaff:a250;2 lend:1  rend:49     
[28000 lines read]  scaff:a258;2 lend:1  rend:35     
[29000 lines read]  scaff:a27;2 lend:77  rend:126     
[30000 lines read]  scaff:a36;4 lend:1  rend:47     
[31000 lines read]  scaff:a42;2 lend:1  rend:55     
[32000 lines read]  scaff:a51;2 lend:16  rend:91     
[33000 lines read]  scaff:a58;3 lend:1  rend:47     
[34000 lines read]  scaff:a62;2 lend:13  rend:43     
[35000 lines read]  scaff:a6;2 lend:4  rend:43     
[36000 lines read]  scaff:a76;2 lend:15  rend:57     
[37000 lines read]  scaff:a81;2 lend:20  rend:63     
[38000 lines read]  scaff:a8;5 lend:4  rend:52     
[39000 lines read]  scaff:a95;2 lend:1  rend:45     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa.clipped.fa
844s 
succeeded(35)   97.2222% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
844s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
844s bt2 index files: $VAR1 = [];
844s Note - bowtie-build indices do not yet exist. Indexing genome now.
844s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
844s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
844s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
844s 18 reads; of these:
844s   18 (100.00%) were unpaired; of these:
844s     0 (0.00%) aligned 0 times
844s     18 (100.00%) aligned exactly 1 time
844s     0 (0.00%) aligned >1 times
844s 100.00% overall alignment rate
844s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
844s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
844s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
844s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
844s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
844s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
844s 
844s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
844s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
844s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
844s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
844s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
844s -processing jaccard pair sensor
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
844s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa.clipped.fa
845s 
succeeded(36)   100% completed.    
845s 
845s All commands completed successfully. :-)
845s 
845s 
845s 
845s ** Harvesting all assembled transcripts into a single multi-fasta file...
845s 
845s Saturday, March 15, 2025: 23:45:00	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp
845s * [Sat Mar 15 23:45:00 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1
846s * [Sat Mar 15 23:45:01 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
847s Saturday, March 15, 2025: 23:45:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map
847s 
847s 
847s #############################################################################
847s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
847s #############################################################################
847s 
847s 
847s 
847s 
847s exit 0
847s #!/bin/bash -ve
847s 
847s 
847s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
847s     gunzip -c reads.right.fq.gz > reads.right.fq
847s fi
847s 
847s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
847s     gunzip -c reads.left.fq.gz > reads.left.fq
847s fi
847s 
847s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
847s     gunzip -c reads2.right.fq.gz > reads2.right.fq
847s fi
847s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
847s 
847s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
847s     gunzip -c reads2.left.fq.gz > reads2.left.fq
847s fi
847s 
847s 
847s #######################################################
847s ##  Run Trinity to Generate Transcriptome Assemblies ##
847s #######################################################
847s 
847s CPU=$(nproc || sysctl -n hw.physicalcpu)
847s 
847s ${TRINITY_HOME}/Trinity --seqType fq \
847s               --max_memory 2G \
847s               --left reads.left.fq,reads2.left.fq \
847s               --right reads.right.fq,reads2.right.fq \
847s               --SS_lib_type RF \
847s               --CPU ${CPU} \
847s               --trimmomatic \
847s               --normalize_reads \
847s               --normalize_by_read_set \
847s               --output trinity_trim_and_norm_outdir
847s 
847s 
847s      ______  ____   ____  ____   ____  ______  __ __
847s     |      ||    \ |    ||    \ |    ||      ||  |  |
847s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
847s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
847s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
847s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
847s       |__|  |__|\_||____||__|__||____|  |__|  |____/
847s 
847s     Trinity-v2.15.2
847s 
847s 
847s 
847s Left read files: $VAR1 = [
847s           'reads.left.fq',
847s           'reads2.left.fq'
847s         ];
847s Right read files: $VAR1 = [
847s           'reads.right.fq',
847s           'reads2.right.fq'
847s         ];
847s Saturday, March 15, 2025: 23:45:02	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir
847s Saturday, March 15, 2025: 23:45:02	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis
847s 
847s 
847s ----------------------------------------------------------------------------------
847s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
847s ----------------------------------------------------------------------------------
847s 
847s ---------------------------------------------------------------
847s ------ Quality Trimming Via Trimmomatic  ---------------------
847s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
847s ---------------------------------------------------------------
847s 
847s 
847s ## Running Trimmomatic on read files: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
847s Saturday, March 15, 2025: 23:45:02	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq  reads.left.fq.P.qtrim reads.left.fq.U.qtrim  reads.right.fq.P.qtrim reads.right.fq.U.qtrim  ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 
847s TrimmomaticPE: Started with arguments:
847s  -threads 2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
847s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
847s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
847s Quality encoding detected as phred33
847s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%)
847s TrimmomaticPE: Completed successfully
848s Saturday, March 15, 2025: 23:45:02	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
848s Saturday, March 15, 2025: 23:45:02	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
848s Saturday, March 15, 2025: 23:45:02	CMD: touch trimmomatic.ok
848s Saturday, March 15, 2025: 23:45:02	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
848s 
848s ## Running Trimmomatic on read files: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq
848s Saturday, March 15, 2025: 23:45:02	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq  reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim  reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim  ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 
848s TrimmomaticPE: Started with arguments:
848s  -threads 2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
848s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
848s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
848s Quality encoding detected as phred33
848s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%)
848s TrimmomaticPE: Completed successfully
848s Saturday, March 15, 2025: 23:45:03	CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq
848s Saturday, March 15, 2025: 23:45:03	CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq
848s Saturday, March 15, 2025: 23:45:03	CMD: touch trimmomatic.ok
848s Saturday, March 15, 2025: 23:45:03	CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim &
848s ---------------------------------------------------------------
848s ------------ In silico Read Normalization ---------------------
848s -- (Removing Excess Reads Beyond 200 Coverage --
848s ---------------------------------------------------------------
848s 
848s 
848s ## Running in silico normalization, processing each read set separately
848s # running normalization on reads: $VAR1 = [
848s           [
848s             'reads.left.fq.PwU.qtrim.fq'
848s           ],
848s           [
848s             'reads.right.fq.PwU.qtrim.fq'
848s           ]
848s         ];
848s 
848s 
848s Saturday, March 15, 2025: 23:45:03	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1 --max_CV 10000  --SS_lib_type RF  --left reads.left.fq.PwU.qtrim.fq --right reads.right.fq.PwU.qtrim.fq --pairs_together  --PARALLEL_STATS  
849s -prepping seqs
849s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa
849s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa
849s CMD finished (0 seconds)
849s CMD finished (0 seconds)
849s CMD: touch left.fa.ok
849s CMD finished (0 seconds)
849s CMD: touch right.fa.ok
849s CMD finished (0 seconds)
849s  Done converting input files. CMD: cat left.fa right.fa > both.fa
849s CMD finished (0 seconds)
849s CMD: touch both.fa.ok
849s CMD finished (0 seconds)
849s -kmer counting.
849s -------------------------------------------
849s ----------- Jellyfish  --------------------
849s -- (building a k-mer catalog from reads) --
849s -------------------------------------------
849s 
849s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
850s CMD finished (1 seconds)
850s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
850s CMD finished (0 seconds)
850s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
850s CMD finished (0 seconds)
850s CMD: touch jellyfish.K25.min2.kmers.fa.success
850s CMD finished (0 seconds)
850s -generating stats files
850s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
850s -reading Kmer occurrences...
850s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
850s -reading Kmer occurrences...
850s 
850s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
850s 
850s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
851s STATS_GENERATION_TIME: 1 seconds.
851s CMD finished (1 seconds)
851s STATS_GENERATION_TIME: 1 seconds.
851s CMD finished (1 seconds)
851s CMD: touch left.fa.K25.stats.ok
851s CMD finished (0 seconds)
851s CMD: touch right.fa.K25.stats.ok
851s CMD finished (0 seconds)
851s -sorting each stats file by read name.
851s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
851s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
851s CMD finished (0 seconds)
851s CMD finished (0 seconds)
851s CMD: touch left.fa.K25.stats.sort.ok
851s CMD finished (0 seconds)
851s CMD: touch right.fa.K25.stats.sort.ok
851s CMD finished (0 seconds)
851s -defining normalized reads
851s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
851s -opening left.fa.K25.stats.sort
851s -opening right.fa.K25.stats.sort
851s -done opening files.
851s CMD finished (0 seconds)
851s CMD: touch pairs.K25.stats.ok
851s CMD finished (0 seconds)
851s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
851s 27678 / 27726 = 99.83% reads selected during normalization.
851s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
851s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
851s CMD finished (0 seconds)
851s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
851s CMD finished (0 seconds)
851s -search and capture.
852s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq ... done prepping, now search and capture.
852s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq
852s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq ... done prepping, now search and capture.
852s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq
852s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
852s CMD finished (0 seconds)
852s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
852s CMD finished (0 seconds)
852s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
852s CMD finished (0 seconds)
852s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
852s CMD finished (0 seconds)
852s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads
852s 
852s 
852s Normalization complete. See outputs: 
852s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
852s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
852s Saturday, March 15, 2025: 23:45:07	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok
852s # running normalization on reads: $VAR1 = [
852s           [
852s             'reads2.left.fq.PwU.qtrim.fq'
852s           ],
852s           [
852s             'reads2.right.fq.PwU.qtrim.fq'
852s           ]
852s         ];
852s 
852s 
852s Saturday, March 15, 2025: 23:45:07	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2 --max_CV 10000  --SS_lib_type RF  --left reads2.left.fq.PwU.qtrim.fq --right reads2.right.fq.PwU.qtrim.fq --pairs_together  --PARALLEL_STATS  
852s -prepping seqs
852s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa
852s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa
852s CMD finished (0 seconds)
852s CMD finished (0 seconds)
852s CMD: touch left.fa.ok
852s CMD finished (0 seconds)
852s CMD: touch right.fa.ok
852s CMD finished (0 seconds)
852s  Done converting input files. CMD: cat left.fa right.fa > both.fa
852s CMD finished (0 seconds)
852s CMD: touch both.fa.ok
852s CMD finished (0 seconds)
852s -kmer counting.
852s -------------------------------------------
852s ----------- Jellyfish  --------------------
852s -- (building a k-mer catalog from reads) --
852s -------------------------------------------
852s 
852s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
853s CMD finished (1 seconds)
853s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
853s CMD finished (0 seconds)
853s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
853s CMD finished (0 seconds)
853s CMD: touch jellyfish.K25.min2.kmers.fa.success
853s CMD finished (0 seconds)
853s -generating stats files
853s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
853s -reading Kmer occurrences...
853s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
853s -reading Kmer occurrences...
853s 
853s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
853s 
853s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
854s STATS_GENERATION_TIME: 1 seconds.
854s CMD finished (1 seconds)
854s STATS_GENERATION_TIME: 1 seconds.
854s CMD finished (1 seconds)
854s CMD: touch left.fa.K25.stats.ok
854s CMD finished (0 seconds)
854s CMD: touch right.fa.K25.stats.ok
854s CMD finished (0 seconds)
854s -sorting each stats file by read name.
854s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
854s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
854s CMD finished (0 seconds)
854s CMD finished (0 seconds)
854s CMD: touch left.fa.K25.stats.sort.ok
854s CMD finished (0 seconds)
854s CMD: touch right.fa.K25.stats.sort.ok
854s CMD finished (0 seconds)
854s -defining normalized reads
854s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
854s -opening left.fa.K25.stats.sort
854s -opening right.fa.K25.stats.sort
854s -done opening files.
854s CMD finished (0 seconds)
854s CMD: touch pairs.K25.stats.ok
854s CMD finished (0 seconds)
854s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
854s 27678 / 27726 = 99.83% reads selected during normalization.
854s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
854s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
854s CMD finished (0 seconds)
854s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
854s CMD finished (0 seconds)
854s -search and capture.
855s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq ... done prepping, now search and capture.
855s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq
855s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq ... done prepping, now search and capture.
855s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq
855s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
855s CMD finished (0 seconds)
855s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
855s CMD finished (0 seconds)
855s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
855s CMD finished (0 seconds)
855s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
855s CMD finished (0 seconds)
855s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads
855s 
855s 
855s Normalization complete. See outputs: 
855s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
855s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
855s Saturday, March 15, 2025: 23:45:10	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok
855s # running normalization on reads: $VAR1 = [
855s           [
855s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq',
855s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq'
855s           ],
855s           [
855s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq',
855s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq'
855s           ]
855s         ];
855s 
855s 
855s Saturday, March 15, 2025: 23:45:10	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq --pairs_together  --PARALLEL_STATS  
855s -prepping seqs
855s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa
855s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa
855s CMD finished (0 seconds)
855s CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa
855s CMD finished (0 seconds)
855s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa
855s CMD finished (0 seconds)
855s CMD finished (0 seconds)
855s CMD: touch left.fa.ok
855s CMD finished (0 seconds)
855s CMD: touch right.fa.ok
855s CMD finished (0 seconds)
855s  Done converting input files. CMD: cat left.fa right.fa > both.fa
855s CMD finished (0 seconds)
855s CMD: touch both.fa.ok
855s CMD finished (0 seconds)
855s -kmer counting.
855s -------------------------------------------
855s ----------- Jellyfish  --------------------
855s -- (building a k-mer catalog from reads) --
855s -------------------------------------------
855s 
855s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
856s CMD finished (1 seconds)
856s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
856s CMD finished (0 seconds)
856s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
856s CMD finished (0 seconds)
856s CMD: touch jellyfish.K25.min2.kmers.fa.success
856s CMD finished (0 seconds)
856s -generating stats files
856s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
856s -reading Kmer occurrences...
856s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
856s -reading Kmer occurrences...
857s 
857s  done parsing 311705 Kmers, 310319 added, taking 1 seconds.
857s 
857s  done parsing 311705 Kmers, 310319 added, taking 1 seconds.
858s STATS_GENERATION_TIME: 1 seconds.
858s CMD finished (2 seconds)
858s STATS_GENERATION_TIME: 1 seconds.
858s CMD finished (2 seconds)
858s CMD: touch left.fa.K25.stats.ok
858s CMD finished (0 seconds)
858s CMD: touch right.fa.K25.stats.ok
858s CMD finished (0 seconds)
858s -sorting each stats file by read name.
858s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
858s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
858s CMD finished (0 seconds)
858s CMD finished (0 seconds)
858s CMD: touch left.fa.K25.stats.sort.ok
858s CMD finished (0 seconds)
858s CMD: touch right.fa.K25.stats.sort.ok
858s CMD finished (0 seconds)
858s -defining normalized reads
858s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
858s -opening left.fa.K25.stats.sort
858s -opening right.fa.K25.stats.sort
858s -done opening files.
859s CMD finished (1 seconds)
859s CMD: touch pairs.K25.stats.ok
859s CMD finished (0 seconds)
859s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
859s 51602 / 55356 = 93.22% reads selected during normalization.
859s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles.
859s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1
859s CMD finished (0 seconds)
859s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
859s CMD finished (0 seconds)
859s -search and capture.
860s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq ... done prepping, now search and capture.
860s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq
860s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq
860s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq ... done prepping, now search and capture.
860s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq
860s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq
860s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
860s CMD finished (0 seconds)
860s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
860s CMD finished (0 seconds)
860s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
860s CMD finished (0 seconds)
860s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
860s CMD finished (0 seconds)
860s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads
860s 
860s 
860s Normalization complete. See outputs: 
860s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
860s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
860s Saturday, March 15, 2025: 23:45:15	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok
860s Converting input files. (in parallel)Saturday, March 15, 2025: 23:45:15	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
860s Saturday, March 15, 2025: 23:45:15	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
860s Saturday, March 15, 2025: 23:45:15	CMD: touch left.fa.ok
860s Saturday, March 15, 2025: 23:45:15	CMD: touch right.fa.ok
860s Saturday, March 15, 2025: 23:45:15	CMD: touch left.fa.ok right.fa.ok
860s Saturday, March 15, 2025: 23:45:15	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
860s Saturday, March 15, 2025: 23:45:15	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok
860s -------------------------------------------
860s ----------- Jellyfish  --------------------
860s -- (building a k-mer (25) catalog from reads) --
860s -------------------------------------------
860s 
860s * [Sat Mar 15 23:45:15 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
861s * [Sat Mar 15 23:45:16 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
862s * [Sat Mar 15 23:45:17 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
862s ----------------------------------------------
862s --------------- Inchworm (K=25, asm) ---------------------
862s -- (Linear contig construction from k-mers) --
862s ----------------------------------------------
862s 
862s * [Sat Mar 15 23:45:17 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp
862s Kmer length set to: 25
862s Min assembly length set to: 25
862s Monitor turned on, set to: 1
862s min entropy set to: 1
862s setting number of threads to: 2
862s -setting parallel iworm mode.
862s -reading Kmer occurrences...
862s 
 [0M] Kmers parsed.     
862s  done parsing 309493 Kmers, 309493 added, taking 0 seconds.
862s 
862s TIMING KMER_DB_BUILDING 0 s.
862s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
862s Pruned 1482 kmers from catalog.
862s 	Pruning time: 0 seconds = 0 minutes.
862s 
862s TIMING PRUNING 0 s.
862s -populating the kmer seed candidate list.
862s Kcounter hash size: 309493
862s Processed 308011 non-zero abundance kmers in kcounter.
862s -Not sorting list of kmers, given parallel mode in effect.
862s -beginning inchworm contig assembly.
862s Total kcounter hash size: 309493 vs. sorted list size: 308011
862s num threads set to: 2
862s Done opening file. tmp.iworm.fa.pid_42964.thread_0
862s Done opening file. tmp.iworm.fa.pid_42964.thread_1
862s 
862s 	Iworm contig assembly time: 0 seconds = 0 minutes.
862s 
862s TIMING CONTIG_BUILDING 0 s.
862s 
862s TIMING PROG_RUNTIME 0 s.
862s * [Sat Mar 15 23:45:17 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa
862s Saturday, March 15, 2025: 23:45:17	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished
862s --------------------------------------------------------
862s -------------------- Chrysalis -------------------------
862s -- (Contig Clustering & de Bruijn Graph Construction) --
862s --------------------------------------------------------
862s 
862s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
862s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
862s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
862s * [Sat Mar 15 23:45:17 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100
863s * [Sat Mar 15 23:45:18 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null
863s * [Sat Mar 15 23:45:18 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 
869s * [Sat Mar 15 23:45:24 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt
870s * [Sat Mar 15 23:45:25 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt
871s * [Sat Mar 15 23:45:26 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
871s * [Sat Mar 15 23:45:26 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
871s * [Sat Mar 15 23:45:26 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out
871s * [Sat Mar 15 23:45:26 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200
871s * [Sat Mar 15 23:45:26 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
874s * [Sat Mar 15 23:45:28 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort
874s Saturday, March 15, 2025: 23:45:29	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0
874s Saturday, March 15, 2025: 23:45:29	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok
874s Saturday, March 15, 2025: 23:45:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
874s Saturday, March 15, 2025: 23:45:29	CMD: touch recursive_trinity.cmds.ok
874s Saturday, March 15, 2025: 23:45:29	CMD: touch recursive_trinity.cmds.ok
874s 
874s 
874s --------------------------------------------------------------------------------
874s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
874s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
874s --------------------------------------------------------------------------------
874s 
874s Saturday, March 15, 2025: 23:45:29	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
874s Number of Commands: 51
962s 
succeeded(1)   1.96078% completed.    
succeeded(2)   3.92157% completed.    
succeeded(3)   5.88235% completed.    
succeeded(4)   7.84314% completed.    
succeeded(5)   9.80392% completed.    
succeeded(6)   11.7647% completed.    
succeeded(7)   13.7255% completed.    
succeeded(8)   15.6863% completed.    
succeeded(9)   17.6471% completed.    
succeeded(10)   19.6078% completed.    
succeeded(11)   21.5686% completed.    
succeeded(12)   23.5294% completed.    
succeeded(13)   25.4902% completed.    
succeeded(14)   27.451% completed.    
succeeded(15)   29.4118% completed.    
succeeded(16)   31.3726% completed.    
succeeded(17)   33.3333% completed.    
succeeded(18)   35.2941% completed.    
succeeded(19)   37.2549% completed.    
succeeded(20)   39.2157% completed.    
succeeded(21)   41.1765% completed.    
succeeded(22)   43.1373% completed.    
succeeded(23)   45.098% completed.    
succeeded(24)   47.0588% completed.    
succeeded(25)   49.0196% completed.    
succeeded(26)   50.9804% completed.    
succeeded(27)   52.9412% completed.    
succeeded(28)   54.902% completed.    
succeeded(29)   56.8627% completed.    
succeeded(30)   58.8235% completed.    
succeeded(31)   60.7843% completed.    
succeeded(32)   62.7451% completed.    
succeeded(33)   64.7059% completed.    
succeeded(34)   66.6667% completed.    
succeeded(35)   68.6275% completed.    
succeeded(36)   70.5882% completed.    
succeeded(37)   72.549% completed.    
succeeded(38)   74.5098% completed.    
succeeded(39)   76.4706% completed.    
succeeded(40)   78.4314% completed.    
succeeded(41)   80.3922% completed.    
succeeded(42)   82.3529% completed.    
succeeded(43)   84.3137% completed.    
succeeded(44)   86.2745% completed.    
succeeded(45)   88.2353% completed.    
succeeded(46)   90.1961% completed.    
succeeded(47)   92.1569% completed.    
succeeded(48)   94.1176% completed.    
succeeded(49)   96.0784% completed.    
succeeded(50)   98.0392% completed.    
succeeded(51)   100% completed.    
962s 
962s All commands completed successfully. :-)
962s 
962s 
962s 
962s ** Harvesting all assembled transcripts into a single multi-fasta file...
962s 
962s Saturday, March 15, 2025: 23:46:57	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp
962s * [Sat Mar 15 23:46:57 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2
963s * [Sat Mar 15 23:46:58 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
963s Saturday, March 15, 2025: 23:46:58	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map
963s 
963s 
963s #############################################################################
963s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
963s #############################################################################
963s 
963s 
963s ./misc_run_tests/__runMe_include_long_reads.sh
963s 
963s 
963s 
963s exit 0
963s #!/bin/bash -ve
963s 
963s #######################################################
963s ##  Run Trinity to Generate Transcriptome Assemblies ##
963s #######################################################
963s 
963s CPU=$(nproc || sysctl -n hw.physicalcpu)
963s 
963s ${TRINITY_HOME}/Trinity --seqType fq \
963s               --max_memory 2G \
963s               --left reads.left.fq.gz \
963s               --right reads.right.fq.gz \
963s               --SS_lib_type RF \
963s               --CPU ${CPU} \
963s               --no_cleanup \
963s               --long_reads longReads.fa \
963s               --output test_trinity_long_reads
963s 
963s 
963s      ______  ____   ____  ____   ____  ______  __ __
963s     |      ||    \ |    ||    \ |    ||      ||  |  |
963s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
963s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
963s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
963s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
963s       |__|  |__|\_||____||__|__||____|  |__|  |____/
963s 
963s     Trinity-v2.15.2
963s 
963s 
963s 
963s Left read files: $VAR1 = [
963s           'reads.left.fq.gz'
963s         ];
963s Right read files: $VAR1 = [
963s           'reads.right.fq.gz'
963s         ];
963s Saturday, March 15, 2025: 23:46:58	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads
963s Saturday, March 15, 2025: 23:46:58	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis
963s 
963s 
963s ----------------------------------------------------------------------------------
963s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
963s ----------------------------------------------------------------------------------
963s 
963s ---------------------------------------------------------------
963s ------------ In silico Read Normalization ---------------------
963s -- (Removing Excess Reads Beyond 200 Coverage --
963s ---------------------------------------------------------------
963s 
963s # running normalization on reads: $VAR1 = [
963s           [
963s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
963s           ],
963s           [
963s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
963s           ]
963s         ];
963s 
963s 
963s Saturday, March 15, 2025: 23:46:58	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --no_cleanup  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
963s -prepping seqs
963s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
963s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
963s CMD finished (0 seconds)
963s CMD finished (0 seconds)
963s CMD: touch left.fa.ok
963s CMD finished (0 seconds)
963s CMD: touch right.fa.ok
963s CMD finished (0 seconds)
963s  Done converting input files. CMD: cat left.fa right.fa > both.fa
963s CMD finished (0 seconds)
963s CMD: touch both.fa.ok
963s CMD finished (0 seconds)
963s -kmer counting.
963s -------------------------------------------
963s ----------- Jellyfish  --------------------
963s -- (building a k-mer catalog from reads) --
963s -------------------------------------------
963s 
963s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
964s CMD finished (1 seconds)
964s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
964s CMD finished (0 seconds)
964s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
964s CMD finished (0 seconds)
964s CMD: touch jellyfish.K25.min2.kmers.fa.success
964s CMD finished (0 seconds)
964s -generating stats files
964s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
964s -reading Kmer occurrences...
964s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
964s -reading Kmer occurrences...
964s 
964s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
964s 
964s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
965s STATS_GENERATION_TIME: 1 seconds.
965s CMD finished (1 seconds)
965s STATS_GENERATION_TIME: 1 seconds.
965s CMD finished (1 seconds)
965s CMD: touch left.fa.K25.stats.ok
965s CMD finished (0 seconds)
965s CMD: touch right.fa.K25.stats.ok
965s CMD finished (0 seconds)
965s -sorting each stats file by read name.
965s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
965s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
965s CMD finished (0 seconds)
965s CMD finished (0 seconds)
965s CMD: touch left.fa.K25.stats.sort.ok
965s CMD finished (0 seconds)
965s CMD: touch right.fa.K25.stats.sort.ok
965s CMD finished (0 seconds)
965s -defining normalized reads
965s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
965s -opening left.fa.K25.stats.sort
965s -opening right.fa.K25.stats.sort
965s -done opening files.
965s CMD finished (0 seconds)
965s CMD: touch pairs.K25.stats.ok
965s CMD finished (0 seconds)
965s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
966s 30472 / 30575 = 99.66% reads selected during normalization.
966s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
966s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
966s CMD finished (1 seconds)
966s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
966s CMD finished (0 seconds)
966s -search and capture.
966s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
966s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
966s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
966s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
966s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
966s CMD finished (0 seconds)
966s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
966s CMD finished (0 seconds)
966s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
966s CMD finished (0 seconds)
966s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
966s CMD finished (0 seconds)
966s 
966s 
966s Normalization complete. See outputs: 
966s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
966s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
966s Saturday, March 15, 2025: 23:47:01	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok
966s Converting input files. (in parallel)Saturday, March 15, 2025: 23:47:01	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
966s Saturday, March 15, 2025: 23:47:01	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
966s Saturday, March 15, 2025: 23:47:01	CMD: touch right.fa.ok
966s Saturday, March 15, 2025: 23:47:01	CMD: touch left.fa.ok
966s Saturday, March 15, 2025: 23:47:01	CMD: touch left.fa.ok right.fa.ok
966s Saturday, March 15, 2025: 23:47:01	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
966s Saturday, March 15, 2025: 23:47:01	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok
966s Saturday, March 15, 2025: 23:47:01	CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
966s Saturday, March 15, 2025: 23:47:01	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
966s Saturday, March 15, 2025: 23:47:01	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok
966s -------------------------------------------
966s ----------- Jellyfish  --------------------
966s -- (building a k-mer (25) catalog from reads) --
966s -------------------------------------------
966s 
966s * [Sat Mar 15 23:47:01 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
967s * [Sat Mar 15 23:47:02 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
967s * [Sat Mar 15 23:47:02 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
968s ----------------------------------------------
968s --------------- Inchworm (K=25, asm) ---------------------
968s -- (Linear contig construction from k-mers) --
968s ----------------------------------------------
968s 
968s * [Sat Mar 15 23:47:02 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --keep_tmp_files  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp
968s Kmer length set to: 25
968s Min assembly length set to: 25
968s Monitor turned on, set to: 1
968s -retaining tmp files
968s min entropy set to: 1
968s setting number of threads to: 2
968s -setting parallel iworm mode.
968s -reading Kmer occurrences...
968s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
968s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
968s 
968s TIMING KMER_DB_BUILDING 0 s.
968s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
968s Pruned 4252 kmers from catalog.
968s 	Pruning time: 0 seconds = 0 minutes.
968s 
968s TIMING PRUNING 0 s.
968s -populating the kmer seed candidate list.
968s Kcounter hash size: 519541
968s Processed 515289 non-zero abundance kmers in kcounter.
968s -Not sorting list of kmers, given parallel mode in effect.
968s -beginning inchworm contig assembly.
968s Total kcounter hash size: 519541 vs. sorted list size: 515289
968s num threads set to: 2
968s Done opening file. tmp.iworm.fa.pid_51924.thread_0
968s Done opening file. tmp.iworm.fa.pid_51924.thread_1
969s 
969s 	Iworm contig assembly time: 0 seconds = 0 minutes.
969s 
969s TIMING CONTIG_BUILDING 0 s.
969s 
969s TIMING PROG_RUNTIME 0 s.
969s * [Sat Mar 15 23:47:04 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa
969s Saturday, March 15, 2025: 23:47:04	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished
969s --------------------------------------------------------
969s -------------------- Chrysalis -------------------------
969s -- (Contig Clustering & de Bruijn Graph Construction) --
969s --------------------------------------------------------
969s 
969s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
969s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
969s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
969s * [Sat Mar 15 23:47:04 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100
969s * [Sat Mar 15 23:47:04 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null
969s * [Sat Mar 15 23:47:04 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 
973s * [Sat Mar 15 23:47:08 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt
974s * [Sat Mar 15 23:47:09 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt
978s * [Sat Mar 15 23:47:13 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted
978s * [Sat Mar 15 23:47:13 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
978s * [Sat Mar 15 23:47:13 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out
978s * [Sat Mar 15 23:47:13 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200
978s * [Sat Mar 15 23:47:13 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
979s * [Sat Mar 15 23:47:14 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort
980s Saturday, March 15, 2025: 23:47:15	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0
980s Saturday, March 15, 2025: 23:47:15	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok
980s Saturday, March 15, 2025: 23:47:15	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --no_cleanup  --long_reads_mode  --no_salmon  > recursive_trinity.cmds
980s Saturday, March 15, 2025: 23:47:15	CMD: touch recursive_trinity.cmds.ok
980s Saturday, March 15, 2025: 23:47:15	CMD: touch recursive_trinity.cmds.ok
980s 
980s 
980s --------------------------------------------------------------------------------
980s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
980s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
980s --------------------------------------------------------------------------------
980s 
980s Saturday, March 15, 2025: 23:47:15	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
980s Number of Commands: 41
1039s 
succeeded(1)   2.43902% completed.    
succeeded(2)   4.87805% completed.    
succeeded(3)   7.31707% completed.    
succeeded(4)   9.7561% completed.    
succeeded(5)   12.1951% completed.    
succeeded(6)   14.6341% completed.    
succeeded(7)   17.0732% completed.    
succeeded(8)   19.5122% completed.    
succeeded(9)   21.9512% completed.    
succeeded(10)   24.3902% completed.    
succeeded(11)   26.8293% completed.    
succeeded(12)   29.2683% completed.    
succeeded(13)   31.7073% completed.    
succeeded(14)   34.1463% completed.    
succeeded(15)   36.5854% completed.    
succeeded(16)   39.0244% completed.    
succeeded(17)   41.4634% completed.    
succeeded(18)   43.9024% completed.    
succeeded(19)   46.3415% completed.    
succeeded(20)   48.7805% completed.    
succeeded(21)   51.2195% completed.    
succeeded(22)   53.6585% completed.    
succeeded(23)   56.0976% completed.    
succeeded(24)   58.5366% completed.    
succeeded(25)   60.9756% completed.    
succeeded(26)   63.4146% completed.    
succeeded(27)   65.8537% completed.    
succeeded(28)   68.2927% completed.    
succeeded(29)   70.7317% completed.    
succeeded(30)   73.1707% completed.    
succeeded(31)   75.6098% completed.    
succeeded(32)   78.0488% completed.    
succeeded(33)   80.4878% completed.    
succeeded(34)   82.9268% completed.    
succeeded(35)   85.3659% completed.    
succeeded(36)   87.8049% completed.    
succeeded(37)   90.2439% completed.    
succeeded(38)   92.6829% completed.    
succeeded(39)   95.1219% completed.    
succeeded(40)   97.561% completed.    
succeeded(41)   100% completed.    
1039s 
1039s All commands completed successfully. :-)
1039s 
1039s 
1039s 
1039s ** Harvesting all assembled transcripts into a single multi-fasta file...
1039s 
1039s Saturday, March 15, 2025: 23:48:14	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp
1039s * [Sat Mar 15 23:48:14 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2
1040s * [Sat Mar 15 23:48:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1040s Saturday, March 15, 2025: 23:48:15	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map
1040s 
1040s 
1040s #############################################################################
1040s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1040s #############################################################################
1040s 
1040s 
1040s 
1040s 
1040s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta"  -exec cat {} \; | grep LR
1040s >c0_g1_i3 len=2433 path=[1:0-610 589:611-1077 2766:1078-1168 1078:1169-1610 1520:1611-1690 1600:1691-1863 1773:1864-2097 2007:2098-2098 2008:2099-2432] [-1, 1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1040s >c0_g1_i5 len=2364 path=[1:0-610 589:611-1077 1056:1078-1099 1078:1100-1541 1520:1542-1621 1600:1622-1794 1773:1795-2028 2007:2029-2029 2008:2030-2363] [-1, 1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1040s >c0_g3_i2 len=3966 path=[5835:0-165 147:166-1345 5978:1346-1417 1348:1418-1418 7191:1419-1442 1373:1443-1489 1420:1490-1490 1421:1491-1650 1581:1651-2963 2894:2964-3730 6074:3731-3965] [-1, 5835, 147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074, -2] long_read_mappings: {PairPath [_paths=[[147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074], []]]=[LR$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]}
1040s >c0_g3_i6 len=7669 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 8735:7624-7668] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 8735, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
1040s >c0_g3_i8 len=8757 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 7602:7624-7968 7947:7969-7969 7948:7970-7982 7961:7983-7983 7962:7984-8252 8231:8253-8747 8726:8748-8756] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 7602, 7947, 7948, 7961, 7962, 8231, 8726, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
1040s >c0_g1_i1 len=6205 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 7380:6204-6204] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 7380, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1040s >c0_g1_i2 len=6219 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 7351:6174-6177 7355:6178-6178 7445:6179-6218] [-1, 1, 1784, 1801, 5576, 5717, 5718, 7351, 7355, 7445, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1040s >c0_g1_i5 len=7194 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 6182:6204-6219 6198:6220-6729 6708:6730-6733 6712:6734-6735 6714:6736-7193] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 6182, 6198, 6708, 6712, 6714, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1040s >c0_g2_i8 len=2514 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 2227:2249-2513] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 2227, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1040s >c0_g2_i16 len=2273 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 6207:2249-2272] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 6207, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1040s >c0_g1_i2 len=3739 path=[1:0-286 265:287-289 268:290-399 3806:400-459 396:460-3738] [-1, 1, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1040s >c0_g1_i3 len=3590 path=[3675:0-117 3770:118-137 265:138-140 268:141-250 3806:251-310 396:311-3589] [-1, 3675, 3770, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1040s >c0_g2_i1 len=2118 path=[2641:0-65 2684:66-412 3031:413-413 8119:414-436 3114:437-2097 8302:2098-2117] [-1, 2641, 2684, 3031, 8119, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1040s >c0_g2_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1040s >c0_g2_i3 len=5435 path=[2641:0-65 2684:66-412 3031:413-413 8119:414-436 3114:437-2097 4775:2098-3844 6522:3845-3860 6538:3861-4938 7616:4939-4939 7617:4940-4976 7616:4977-4977 7654:4978-5434] [-1, 2641, 2684, 3031, 8119, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1040s >c0_g2_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1040s >c0_g1_i2 len=1946 path=[1:0-219 198:220-220 199:221-304 283:305-325 304:326-1945] [-1, 1, 198, 199, 283, 304, -2] long_read_mappings: {PairPath [_paths=[[1, 198, 199, 283, 304], []]]=[LR$|mm9chr9-NM_026942;mm9chr9-69106_Stoml1_stomatin-like_1_mm9chr9:58101074-58109646(+)]}
1040s >c0_g1_i1 len=3823 path=[1:0-2158 2137:2159-2410 2389:2411-3822] [-1, 1, 2137, 2389, -2] long_read_mappings: {PairPath [_paths=[[1, 2137, 2389], []]]=[LR$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]}
1040s >c0_g1_i2 len=4179 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 5684:4165-4178] [-1, 1, 1730, 1752, 2672, 5684, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
1040s >c0_g1_i5 len=5399 path
1040s 
1040s exit 0
1040s =[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 4143:4165-5398] [-1, 1, 1730, 1752, 2672, 4143, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
1040s ./misc_run_tests/__run_PE_samples_file.sh
1040s #!/bin/bash -ve
1040s 
1040s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1040s               --seqType fq \
1040s               --max_memory 1G \
1040s               --output trinity_test_samples_PE
1040s 
1040s 
1040s      ______  ____   ____  ____   ____  ______  __ __
1040s     |      ||    \ |    ||    \ |    ||      ||  |  |
1040s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1040s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1040s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1040s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1040s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1040s 
1040s     Trinity-v2.15.2
1040s 
1040s 
1040s 
1040s Left read files: $VAR1 = [
1040s           'reads.left.fq.gz',
1040s           'reads2.left.fq.gz'
1040s         ];
1040s Right read files: $VAR1 = [
1040s           'reads.right.fq.gz',
1040s           'reads2.right.fq.gz'
1040s         ];
1040s Saturday, March 15, 2025: 23:48:15	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE
1040s Saturday, March 15, 2025: 23:48:15	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis
1040s 
1040s 
1040s ----------------------------------------------------------------------------------
1040s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1040s ----------------------------------------------------------------------------------
1040s 
1040s ---------------------------------------------------------------
1040s ------------ In silico Read Normalization ---------------------
1040s -- (Removing Excess Reads Beyond 200 Coverage --
1040s ---------------------------------------------------------------
1040s 
1040s # running normalization on reads: $VAR1 = [
1040s           [
1040s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1040s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1040s           ],
1040s           [
1040s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1040s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1040s           ]
1040s         ];
1040s 
1040s 
1040s Saturday, March 15, 2025: 23:48:15	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1040s -prepping seqs
1040s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1040s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1040s CMD finished (0 seconds)
1040s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1040s CMD finished (0 seconds)
1040s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1040s CMD finished (0 seconds)
1040s CMD finished (0 seconds)
1040s CMD: touch left.fa.ok
1040s CMD finished (0 seconds)
1040s CMD: touch right.fa.ok
1040s CMD finished (0 seconds)
1040s  Done converting input files. CMD: cat left.fa right.fa > both.fa
1040s CMD finished (0 seconds)
1040s CMD: touch both.fa.ok
1040s CMD finished (0 seconds)
1040s -kmer counting.
1040s -------------------------------------------
1040s ----------- Jellyfish  --------------------
1040s -- (building a k-mer catalog from reads) --
1040s -------------------------------------------
1040s 
1040s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1042s CMD finished (2 seconds)
1042s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1042s CMD finished (0 seconds)
1042s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1042s CMD finished (0 seconds)
1042s CMD: touch jellyfish.K25.min2.kmers.fa.success
1042s CMD finished (0 seconds)
1042s -generating stats files
1042s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1042s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1042s -reading Kmer occurrences...
1042s -reading Kmer occurrences...
1042s 
1042s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
1043s 
1043s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1044s STATS_GENERATION_TIME: 2 seconds.
1044s CMD finished (2 seconds)
1044s STATS_GENERATION_TIME: 1 seconds.
1044s CMD finished (2 seconds)
1044s CMD: touch left.fa.K25.stats.ok
1044s CMD finished (0 seconds)
1044s CMD: touch right.fa.K25.stats.ok
1044s CMD finished (0 seconds)
1044s -sorting each stats file by read name.
1044s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
1044s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
1044s CMD finished (0 seconds)
1044s CMD finished (0 seconds)
1044s CMD: touch left.fa.K25.stats.sort.ok
1044s CMD finished (0 seconds)
1044s CMD: touch right.fa.K25.stats.sort.ok
1044s CMD finished (0 seconds)
1044s -defining normalized reads
1044s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
1044s -opening left.fa.K25.stats.sort
1044s -opening right.fa.K25.stats.sort
1044s -done opening files.
1045s CMD finished (1 seconds)
1045s CMD: touch pairs.K25.stats.ok
1045s CMD finished (0 seconds)
1045s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
1046s 56508 / 61150 = 92.41% reads selected during normalization.
1046s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1046s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1046s CMD finished (1 seconds)
1046s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1046s CMD finished (0 seconds)
1046s -search and capture.
1046s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1046s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1046s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1046s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1046s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1046s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1047s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1047s CMD finished (0 seconds)
1047s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1047s CMD finished (0 seconds)
1047s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
1047s CMD finished (0 seconds)
1047s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
1047s CMD finished (0 seconds)
1047s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads
1047s 
1047s 
1047s Normalization complete. See outputs: 
1047s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
1047s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
1047s Saturday, March 15, 2025: 23:48:22	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok
1047s Converting input files. (in parallel)Saturday, March 15, 2025: 23:48:22	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
1047s Saturday, March 15, 2025: 23:48:22	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1047s Saturday, March 15, 2025: 23:48:22	CMD: touch left.fa.ok
1047s Saturday, March 15, 2025: 23:48:22	CMD: touch right.fa.ok
1047s Saturday, March 15, 2025: 23:48:22	CMD: touch left.fa.ok right.fa.ok
1047s Saturday, March 15, 2025: 23:48:22	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1047s Saturday, March 15, 2025: 23:48:22	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok
1047s -------------------------------------------
1047s ----------- Jellyfish  --------------------
1047s -- (building a k-mer (25) catalog from reads) --
1047s -------------------------------------------
1047s 
1047s * [Sat Mar 15 23:48:22 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1048s * [Sat Mar 15 23:48:23 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1048s * [Sat Mar 15 23:48:23 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1048s ----------------------------------------------
1048s --------------- Inchworm (K=25, asm) ---------------------
1048s -- (Linear contig construction from k-mers) --
1048s ----------------------------------------------
1048s 
1048s * [Sat Mar 15 23:48:23 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp
1048s Kmer length set to: 25
1048s Min assembly length set to: 25
1048s Monitor turned on, set to: 1
1048s double stranded mode set
1048s min entropy set to: 1
1048s setting number of threads to: 2
1048s -setting parallel iworm mode.
1048s -reading Kmer occurrences...
1049s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1049s  done parsing 515206 Kmers, 515206 added, taking 1 seconds.
1049s 
1049s TIMING KMER_DB_BUILDING 1 s.
1049s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1049s Pruned 4139 kmers from catalog.
1049s 	Pruning time: 0 seconds = 0 minutes.
1049s 
1049s TIMING PRUNING 0 s.
1049s -populating the kmer seed candidate list.
1049s Kcounter hash size: 515206
1049s Processed 511067 non-zero abundance kmers in kcounter.
1049s -Not sorting list of kmers, given parallel mode in effect.
1049s -beginning inchworm contig assembly.
1049s Total kcounter hash size: 515206 vs. sorted list size: 511067
1049s num threads set to: 2
1049s Done opening file. tmp.iworm.fa.pid_59414.thread_0
1049s Done opening file. tmp.iworm.fa.pid_59414.thread_1
1050s 
1050s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1050s 
1050s TIMING CONTIG_BUILDING 1 s.
1050s 
1050s TIMING PROG_RUNTIME 2 s.
1050s * [Sat Mar 15 23:48:25 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa
1050s Saturday, March 15, 2025: 23:48:25	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished
1050s --------------------------------------------------------
1050s -------------------- Chrysalis -------------------------
1050s -- (Contig Clustering & de Bruijn Graph Construction) --
1050s --------------------------------------------------------
1050s 
1050s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1050s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1050s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1050s * [Sat Mar 15 23:48:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100
1050s * [Sat Mar 15 23:48:25 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1051s * [Sat Mar 15 23:48:26 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 268435456 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 
1060s * [Sat Mar 15 23:48:35 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt
1061s * [Sat Mar 15 23:48:36 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt
1067s * [Sat Mar 15 23:48:42 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1067s * [Sat Mar 15 23:48:42 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1067s * [Sat Mar 15 23:48:42 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out
1067s * [Sat Mar 15 23:48:42 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200
1067s * [Sat Mar 15 23:48:42 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1073s * [Sat Mar 15 23:48:48 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort
1073s Saturday, March 15, 2025: 23:48:48	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0
1073s Saturday, March 15, 2025: 23:48:48	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok
1073s Saturday, March 15, 2025: 23:48:48	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
1073s Saturday, March 15, 2025: 23:48:48	CMD: touch recursive_trinity.cmds.ok
1073s Saturday, March 15, 2025: 23:48:48	CMD: touch recursive_trinity.cmds.ok
1073s 
1073s 
1073s --------------------------------------------------------------------------------
1073s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1073s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1073s --------------------------------------------------------------------------------
1073s 
1073s Saturday, March 15, 2025: 23:48:48	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1073s Number of Commands: 62
1178s 
succeeded(1)   1.6129% completed.    
succeeded(2)   3.22581% completed.    
succeeded(3)   4.83871% completed.    
succeeded(4)   6.45161% completed.    
succeeded(5)   8.06452% completed.    
succeeded(6)   9.67742% completed.    
succeeded(7)   11.2903% completed.    
succeeded(8)   12.9032% completed.    
succeeded(9)   14.5161% completed.    
succeeded(10)   16.129% completed.    
succeeded(11)   17.7419% completed.    
succeeded(12)   19.3548% completed.    
succeeded(13)   20.9677% completed.    
succeeded(14)   22.5806% completed.    
succeeded(15)   24.1935% completed.    
succeeded(16)   25.8064% completed.    
succeeded(17)   27.4194% completed.    
succeeded(18)   29.0323% completed.    
succeeded(19)   30.6452% completed.    
succeeded(20)   32.2581% completed.    
succeeded(21)   33.871% completed.    
succeeded(22)   35.4839% completed.    
succeeded(23)   37.0968% completed.    
succeeded(24)   38.7097% completed.    
succeeded(25)   40.3226% completed.    
succeeded(26)   41.9355% completed.    
succeeded(27)   43.5484% completed.    
succeeded(28)   45.1613% completed.    
succeeded(29)   46.7742% completed.    
succeeded(30)   48.3871% completed.    
succeeded(31)   50% completed.    
succeeded(32)   51.6129% completed.    
succeeded(33)   53.2258% completed.    
succeeded(34)   54.8387% completed.    
succeeded(35)   56.4516% completed.    
succeeded(36)   58.0645% completed.    
succeeded(37)   59.6774% completed.    
succeeded(38)   61.2903% completed.    
succeeded(39)   62.9032% completed.    
succeeded(40)   64.5161% completed.    
succeeded(41)   66.129% completed.    
succeeded(42)   67.7419% completed.    
succeeded(43)   69.3548% completed.    
succeeded(44)   70.9677% completed.    
succeeded(45)   72.5807% completed.    
succeeded(46)   74.1936% completed.    
succeeded(47)   75.8064% completed.    
succeeded(48)   77.4193% completed.    
succeeded(49)   79.0323% completed.    
succeeded(50)   80.6452% completed.    
succeeded(51)   82.2581% completed.    
succeeded(52)   83.871% completed.    
succeeded(53)   85.4839% completed.    
succeeded(54)   87.0968% completed.    
succeeded(55)   88.7097% completed.    
succeeded(56)   90.3226% completed.    
succeeded(57)   91.9355% completed.    
succeeded(58)   93.5484% completed.    
succeeded(59)   95.1613% completed.    
succeeded(60)   96.7742% completed.    
succeeded(61)   98.3871% completed.    
succeeded(62)   100% completed.    
1178s 
1178s All commands completed successfully. :-)
1178s 
1178s 
1178s 
1178s ** Harvesting all assembled transcripts into a single multi-fasta file...
1178s 
1178s Saturday, March 15, 2025: 23:50:33	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp
1178s * [Sat Mar 15 23:50:33 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2
1180s * [Sat Mar 15 23:50:35 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1180s Saturday, March 15, 2025: 23:50:35	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map
1180s 
1180s 
1180s #############################################################################
1180s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1180s #############################################################################
1180s 
1180s 
1180s 
1180s exit 0
1180s ./misc_run_tests/__run_SE_samples_file.sh
1180s #!/bin/bash -ve
1180s 
1180s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \
1180s               --seqType fq \
1180s               --max_memory 1G \
1180s               --output trinity_test_samples_SE
1180s 
1180s 
1180s      ______  ____   ____  ____   ____  ______  __ __
1180s     |      ||    \ |    ||    \ |    ||      ||  |  |
1180s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1180s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1180s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1180s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1180s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1180s 
1180s     Trinity-v2.15.2
1180s 
1180s 
1180s 
1180s Single read files: $VAR1 = [
1180s           'reads.left.fq.gz',
1180s           'reads2.left.fq.gz'
1180s         ];
1180s Saturday, March 15, 2025: 23:50:35	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE
1180s Saturday, March 15, 2025: 23:50:35	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis
1180s 
1180s 
1180s ----------------------------------------------------------------------------------
1180s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1180s ----------------------------------------------------------------------------------
1180s 
1180s ---------------------------------------------------------------
1180s ------------ In silico Read Normalization ---------------------
1180s -- (Removing Excess Reads Beyond 200 Coverage --
1180s ---------------------------------------------------------------
1180s 
1180s # running normalization on reads: $VAR1 = [
1180s           [
1180s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1180s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1180s           ]
1180s         ];
1180s 
1180s 
1180s Saturday, March 15, 2025: 23:50:35	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000  --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1180s -prepping seqs
1180s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa
1180s CMD finished (0 seconds)
1180s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa
1180s CMD finished (0 seconds)
1180s CMD: touch single.fa.ok
1180s CMD finished (0 seconds)
1180s -kmer counting.
1180s -------------------------------------------
1180s ----------- Jellyfish  --------------------
1180s -- (building a k-mer catalog from reads) --
1180s -------------------------------------------
1180s 
1180s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
1181s CMD finished (1 seconds)
1181s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1181s CMD finished (0 seconds)
1181s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1181s CMD finished (0 seconds)
1181s CMD: touch jellyfish.K25.min2.kmers.fa.success
1181s CMD finished (0 seconds)
1181s -generating stats files
1181s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
1181s -reading Kmer occurrences...
1181s 
1181s  done parsing 288470 Kmers, 288470 added, taking 0 seconds.
1182s STATS_GENERATION_TIME: 1 seconds.
1182s CMD finished (1 seconds)
1182s CMD: touch single.fa.K25.stats.ok
1182s CMD finished (0 seconds)
1182s -sorting each stats file by read name.
1182s CMD: head -n1 single.fa.K25.stats > single.fa.K25.stats.sort && tail -n +2 single.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> single.fa.K25.stats.sort
1182s CMD finished (0 seconds)
1182s CMD: touch single.fa.K25.stats.sort.ok
1182s CMD finished (0 seconds)
1182s -defining normalized reads
1182s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file single.fa.K25.stats.sort  --max_cov 200  --min_cov 1  --max_CV 10000 > single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs
1182s 59311 / 61150 = 96.99% reads selected during normalization.
1182s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1182s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1182s CMD finished (0 seconds)
1182s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok
1182s CMD finished (0 seconds)
1182s -search and capture.
1182s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1182s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1183s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1183s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1183s CMD finished (0 seconds)
1183s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq single.norm.fq
1183s CMD finished (0 seconds)
1183s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads
1183s 
1183s 
1183s Normalization complete. See outputs: 
1183s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
1183s Saturday, March 15, 2025: 23:50:38	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok
1183s Saturday, March 15, 2025: 23:50:38	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/single.norm.fq | seqtk-trinity seq -A -R 1 - >> single.fa
1183s Saturday, March 15, 2025: 23:50:38	CMD: touch single.fa.ok
1183s Saturday, March 15, 2025: 23:50:38	CMD: touch single.fa.ok
1183s -------------------------------------------
1183s ----------- Jellyfish  --------------------
1183s -- (building a k-mer (25) catalog from reads) --
1183s -------------------------------------------
1183s 
1183s * [Sat Mar 15 23:50:38 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1184s * [Sat Mar 15 23:50:39 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1185s * [Sat Mar 15 23:50:40 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1185s ----------------------------------------------
1185s --------------- Inchworm (K=25, asm) ---------------------
1185s -- (Linear contig construction from k-mers) --
1185s ----------------------------------------------
1185s 
1185s * [Sat Mar 15 23:50:40 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp
1185s Kmer length set to: 25
1185s Min assembly length set to: 25
1185s Monitor turned on, set to: 1
1185s double stranded mode set
1185s min entropy set to: 1
1185s setting number of threads to: 2
1185s -setting parallel iworm mode.
1185s -reading Kmer occurrences...
1185s 
 [0M] Kmers parsed.     
1185s  done parsing 287930 Kmers, 287930 added, taking 0 seconds.
1185s 
1185s TIMING KMER_DB_BUILDING 0 s.
1185s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1185s Pruned 2078 kmers from catalog.
1185s 	Pruning time: 0 seconds = 0 minutes.
1185s 
1185s TIMING PRUNING 0 s.
1185s -populating the kmer seed candidate list.
1185s Kcounter hash size: 287930
1185s Processed 285852 non-zero abundance kmers in kcounter.
1185s -Not sorting list of kmers, given parallel mode in effect.
1185s -beginning inchworm contig assembly.
1185s Total kcounter hash size: 287930 vs. sorted list size: 285852
1185s num threads set to: 2
1185s Done opening file. tmp.iworm.fa.pid_69765.thread_0
1185s Done opening file. tmp.iworm.fa.pid_69765.thread_1
1185s 
1185s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1185s 
1185s TIMING CONTIG_BUILDING 0 s.
1185s 
1185s TIMING PROG_RUNTIME 0 s.
1185s * [Sat Mar 15 23:50:40 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa
1185s Saturday, March 15, 2025: 23:50:40	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished
1185s --------------------------------------------------------
1185s -------------------- Chrysalis -------------------------
1185s -- (Contig Clustering & de Bruijn Graph Construction) --
1185s --------------------------------------------------------
1185s 
1185s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1185s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1185s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1185s * [Sat Mar 15 23:50:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100
1186s * [Sat Mar 15 23:50:41 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt
1188s * [Sat Mar 15 23:50:43 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1188s * [Sat Mar 15 23:50:43 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1188s * [Sat Mar 15 23:50:43 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out
1188s * [Sat Mar 15 23:50:43 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200
1188s * [Sat Mar 15 23:50:43 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1191s * [Sat Mar 15 23:50:46 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort
1191s Saturday, March 15, 2025: 23:50:46	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0
1192s Saturday, March 15, 2025: 23:50:47	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok
1192s Saturday, March 15, 2025: 23:50:47	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list --CPU 1 --max_memory 1G  --seqType fa --trinity_complete --full_cleanup  --no_salmon  > recursive_trinity.cmds
1192s Saturday, March 15, 2025: 23:50:47	CMD: touch recursive_trinity.cmds.ok
1192s Saturday, March 15, 2025: 23:50:47	CMD: touch recursive_trinity.cmds.ok
1192s 
1192s 
1192s --------------------------------------------------------------------------------
1192s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1192s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1192s --------------------------------------------------------------------------------
1192s 
1192s Saturday, March 15, 2025: 23:50:47	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1192s Number of Commands: 45
1257s 
succeeded(1)   2.22222% completed.    
succeeded(2)   4.44444% completed.    
succeeded(3)   6.66667% completed.    
succeeded(4)   8.88889% completed.    
succeeded(5)   11.1111% completed.    
succeeded(6)   13.3333% completed.    
succeeded(7)   15.5556% completed.    
succeeded(8)   17.7778% completed.    
succeeded(9)   20% completed.    
succeeded(10)   22.2222% completed.    
succeeded(11)   24.4444% completed.    
succeeded(12)   26.6667% completed.    
succeeded(13)   28.8889% completed.    
succeeded(14)   31.1111% completed.    
succeeded(15)   33.3333% completed.    
succeeded(16)   35.5556% completed.    
succeeded(17)   37.7778% completed.    
succeeded(18)   40% completed.    
succeeded(19)   42.2222% completed.    
succeeded(20)   44.4444% completed.    
succeeded(21)   46.6667% completed.    
succeeded(22)   48.8889% completed.    
succeeded(23)   51.1111% completed.    
succeeded(24)   53.3333% completed.    
succeeded(25)   55.5556% completed.    
succeeded(26)   57.7778% completed.    
succeeded(27)   60% completed.    
succeeded(28)   62.2222% completed.    
succeeded(29)   64.4444% completed.    
succeeded(30)   66.6667% completed.    
succeeded(31)   68.8889% completed.    
succeeded(32)   71.1111% completed.    
succeeded(33)   73.3333% completed.    
succeeded(34)   75.5556% completed.    
succeeded(35)   77.7778% completed.    
succeeded(36)   80% completed.    
succeeded(37)   82.2222% completed.    
succeeded(38)   84.4444% completed.    
succeeded(39)   86.6667% completed.    
succeeded(40)   88.8889% completed.    
succeeded(41)   91.1111% completed.    
succeeded(42)   93.3333% completed.    
succeeded(43)   95.5556% completed.    
succeeded(44)   97.7778% completed.    
succeeded(45)   100% completed.    
1257s 
1257s All commands completed successfully. :-)
1257s 
1257s 
1257s 
1257s ** Harvesting all assembled transcripts into a single multi-fasta file...
1257s 
1257s Saturday, March 15, 2025: 23:51:52	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp
1257s * [Sat Mar 15 23:51:52 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2
1258s * [Sat Mar 15 23:51:53 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1258s Saturday, March 15, 2025: 23:51:53	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map
1258s 
1258s 
1258s #############################################################################
1258s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1258s #############################################################################
1258s 
1258s 
1258s ./misc_run_tests/__runMe_use_workdir.sh
1258s 
1258s 
1258s exit 0
1258s #!/bin/bash -ve
1258s 
1258s 
1258s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
1258s     gunzip -c reads.right.fq.gz > reads.right.fq
1258s fi
1258s 
1258s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
1258s     gunzip -c reads.left.fq.gz > reads.left.fq
1258s fi
1258s 
1258s 
1258s 
1258s #######################################################
1258s ##  Run Trinity to Generate Transcriptome Assemblies ##
1258s #######################################################
1258s 
1258s CPU=$(nproc || sysctl -n hw.physicalcpu)
1258s 
1258s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
1258s               --left reads.left.fq \
1258s               --right reads.right.fq \
1258s               --SS_lib_type RF \
1258s               --CPU ${CPU}\
1258s               --output trinity_with_workdir \
1258s               --workdir  /tmp/trinity.workdir.$$ --full_cleanup
1258s 
1258s 
1258s      ______  ____   ____  ____   ____  ______  __ __
1258s     |      ||    \ |    ||    \ |    ||      ||  |  |
1258s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1258s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1258s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1258s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1258s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1258s 
1258s     Trinity-v2.15.2
1258s 
1258s 
1258s 
1258s Left read files: $VAR1 = [
1258s           'reads.left.fq'
1258s         ];
1258s Right read files: $VAR1 = [
1258s           'reads.right.fq'
1258s         ];
1258s Saturday, March 15, 2025: 23:51:53	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir
1258s Saturday, March 15, 2025: 23:51:53	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis
1258s 
1258s 
1258s ----------------------------------------------------------------------------------
1258s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1258s ----------------------------------------------------------------------------------
1258s 
1258s ---------------------------------------------------------------
1258s ------------ In silico Read Normalization ---------------------
1258s -- (Removing Excess Reads Beyond 200 Coverage --
1258s ---------------------------------------------------------------
1258s 
1258s # running normalization on reads: $VAR1 = [
1258s           [
1258s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq'
1258s           ],
1258s           [
1258s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq'
1258s           ]
1258s         ];
1258s 
1258s 
1258s Saturday, March 15, 2025: 23:51:53	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together  --PARALLEL_STATS  
1258s -prepping seqs
1258s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa
1258s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa
1258s CMD finished (0 seconds)
1258s CMD finished (0 seconds)
1258s CMD: touch left.fa.ok
1258s CMD finished (0 seconds)
1258s CMD: touch right.fa.ok
1258s CMD finished (0 seconds)
1258s  Done converting input files. CMD: cat left.fa right.fa > both.fa
1258s CMD finished (0 seconds)
1258s CMD: touch both.fa.ok
1258s CMD finished (0 seconds)
1258s -kmer counting.
1258s -------------------------------------------
1258s ----------- Jellyfish  --------------------
1258s -- (building a k-mer catalog from reads) --
1258s -------------------------------------------
1258s 
1258s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1259s CMD finished (1 seconds)
1259s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1259s CMD finished (0 seconds)
1259s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1260s CMD finished (1 seconds)
1260s CMD: touch jellyfish.K25.min2.kmers.fa.success
1260s CMD finished (0 seconds)
1260s -generating stats files
1260s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1260s -reading Kmer occurrences...
1260s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1260s -reading Kmer occurrences...
1260s 
1260s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1260s 
1260s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1260s STATS_GENERATION_TIME: 0 seconds.
1260s CMD finished (0 seconds)
1260s STATS_GENERATION_TIME: 0 seconds.
1260s CMD finished (0 seconds)
1260s CMD: touch left.fa.K25.stats.ok
1260s CMD finished (0 seconds)
1260s CMD: touch right.fa.K25.stats.ok
1260s CMD finished (0 seconds)
1260s -sorting each stats file by read name.
1260s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
1260s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
1260s CMD finished (0 seconds)
1260s CMD finished (0 seconds)
1260s CMD: touch left.fa.K25.stats.sort.ok
1260s CMD finished (0 seconds)
1260s CMD: touch right.fa.K25.stats.sort.ok
1260s CMD finished (0 seconds)
1260s -defining normalized reads
1260s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
1260s -opening left.fa.K25.stats.sort
1260s -opening right.fa.K25.stats.sort
1260s -done opening files.
1261s CMD finished (1 seconds)
1261s CMD: touch pairs.K25.stats.ok
1261s CMD finished (0 seconds)
1261s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
1261s 30472 / 30575 = 99.66% reads selected during normalization.
1261s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1261s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1261s CMD finished (0 seconds)
1261s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1261s CMD finished (0 seconds)
1261s -search and capture.
1262s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture.
1262s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq
1262s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture.
1262s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
1262s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1262s CMD finished (0 seconds)
1262s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1262s CMD finished (0 seconds)
1262s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
1262s CMD finished (0 seconds)
1262s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
1262s CMD finished (0 seconds)
1262s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads
1262s 
1262s 
1262s Normalization complete. See outputs: 
1262s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1262s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1262s Saturday, March 15, 2025: 23:51:57	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok
1262s Converting input files. (in parallel)Saturday, March 15, 2025: 23:51:57	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
1262s Saturday, March 15, 2025: 23:51:57	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1262s Saturday, March 15, 2025: 23:51:57	CMD: touch left.fa.ok
1262s Saturday, March 15, 2025: 23:51:57	CMD: touch right.fa.ok
1262s Saturday, March 15, 2025: 23:51:57	CMD: touch left.fa.ok right.fa.ok
1262s Saturday, March 15, 2025: 23:51:57	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1262s Saturday, March 15, 2025: 23:51:57	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok
1262s -------------------------------------------
1262s ----------- Jellyfish  --------------------
1262s -- (building a k-mer (25) catalog from reads) --
1262s -------------------------------------------
1262s 
1262s * [Sat Mar 15 23:51:57 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1263s * [Sat Mar 15 23:51:58 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1263s * [Sat Mar 15 23:51:58 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1263s ----------------------------------------------
1263s --------------- Inchworm (K=25, asm) ---------------------
1263s -- (Linear contig construction from k-mers) --
1263s ----------------------------------------------
1263s 
1263s * [Sat Mar 15 23:51:58 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp
1263s Kmer length set to: 25
1263s Min assembly length set to: 25
1263s Monitor turned on, set to: 1
1263s min entropy set to: 1
1263s setting number of threads to: 2
1263s -setting parallel iworm mode.
1263s -reading Kmer occurrences...
1264s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1264s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
1264s 
1264s TIMING KMER_DB_BUILDING 1 s.
1264s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1264s Pruned 4252 kmers from catalog.
1264s 	Pruning time: 0 seconds = 0 minutes.
1264s 
1264s TIMING PRUNING 0 s.
1264s -populating the kmer seed candidate list.
1264s Kcounter hash size: 519541
1264s Processed 515289 non-zero abundance kmers in kcounter.
1264s -Not sorting list of kmers, given parallel mode in effect.
1264s -beginning inchworm contig assembly.
1264s Total kcounter hash size: 519541 vs. sorted list size: 515289
1264s num threads set to: 2
1264s Done opening file. tmp.iworm.fa.pid_76667.thread_0
1264s Done opening file. tmp.iworm.fa.pid_76667.thread_1
1264s 
1264s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1264s 
1264s TIMING CONTIG_BUILDING 0 s.
1264s 
1264s TIMING PROG_RUNTIME 1 s.
1264s * [Sat Mar 15 23:51:59 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa
1264s Saturday, March 15, 2025: 23:51:59	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished
1264s --------------------------------------------------------
1264s -------------------- Chrysalis -------------------------
1264s -- (Contig Clustering & de Bruijn Graph Construction) --
1264s --------------------------------------------------------
1264s 
1264s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1264s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1264s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1264s * [Sat Mar 15 23:51:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100
1264s * [Sat Mar 15 23:51:59 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null
1265s * [Sat Mar 15 23:52:00 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 
1268s * [Sat Mar 15 23:52:03 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt
1268s * [Sat Mar 15 23:52:03 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -strand  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt
1270s * [Sat Mar 15 23:52:05 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
1270s * [Sat Mar 15 23:52:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1270s * [Sat Mar 15 23:52:05 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out
1270s * [Sat Mar 15 23:52:05 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200
1270s * [Sat Mar 15 23:52:05 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
1272s * [Sat Mar 15 23:52:07 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort
1272s Saturday, March 15, 2025: 23:52:07	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0
1272s Saturday, March 15, 2025: 23:52:07	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok
1272s Saturday, March 15, 2025: 23:52:07	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --workdir  /tmp/trinity.workdir.76528  --no_salmon  > recursive_trinity.cmds
1272s Saturday, March 15, 2025: 23:52:07	CMD: touch recursive_trinity.cmds.ok
1272s Saturday, March 15, 2025: 23:52:07	CMD: touch recursive_trinity.cmds.ok
1272s 
1272s 
1272s --------------------------------------------------------------------------------
1272s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1272s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1272s --------------------------------------------------------------------------------
1272s 
1272s Saturday, March 15, 2025: 23:52:07	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1272s Number of Commands: 40
1339s 
succeeded(1)   2.5% completed.    
succeeded(2)   5% completed.    
succeeded(3)   7.5% completed.    
succeeded(4)   10% completed.    
succeeded(5)   12.5% completed.    
succeeded(6)   15% completed.    
succeeded(7)   17.5% completed.    
succeeded(8)   20% completed.    
succeeded(9)   22.5% completed.    
succeeded(10)   25% completed.    
succeeded(11)   27.5% completed.    
succeeded(12)   30% completed.    
succeeded(13)   32.5% completed.    
succeeded(14)   35% completed.    
succeeded(15)   37.5% completed.    
succeeded(16)   40% completed.    
succeeded(17)   42.5% completed.    
succeeded(18)   45% completed.    
succeeded(19)   47.5% completed.    
succeeded(20)   50% completed.    
succeeded(21)   52.5% completed.    
succeeded(22)   55% completed.    
succeeded(23)   57.5% completed.    
succeeded(24)   60% completed.    
succeeded(25)   62.5% completed.    
succeeded(26)   65% completed.    
succeeded(27)   67.5% completed.    
succeeded(28)   70% completed.    
succeeded(29)   72.5% completed.    
succeeded(30)   75% completed.    
succeeded(31)   77.5% completed.    
succeeded(32)   80% completed.    
succeeded(33)   82.5% completed.    
succeeded(34)   85% completed.    
succeeded(35)   87.5% completed.    
succeeded(36)   90% completed.    
succeeded(37)   92.5% completed.    
succeeded(38)   95% completed.    
succeeded(39)   97.5% completed.    
succeeded(40)   100% completed.    
1339s 
1339s All commands completed successfully. :-)
1339s 
1339s 
1339s 
1339s ** Harvesting all assembled transcripts into a single multi-fasta file...
1339s 
1339s Saturday, March 15, 2025: 23:53:14	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp
1339s * [Sat Mar 15 23:53:14 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2
1340s * [Sat Mar 15 23:53:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1340s 
1340s 
1340s #############################################################################
1340s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1340s #############################################################################
1340s 
1340s 
1340s Saturday, March 15, 2025: 23:53:15	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map
1340s 
1340s ./misc_run_tests/__runMe_piecemeal.sh
1340s 
1340s exit 0
1340s #!/bin/bash -ve
1340s 
1340s #######################################################
1340s ##  Run Trinity to Generate Transcriptome Assemblies ##
1340s #######################################################
1340s 
1340s CPU=$(nproc || sysctl -n hw.physicalcpu)
1340s 
1340s # stop before inchworm (just in silico norm)
1340s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal --no_run_inchworm
1340s 
1340s 
1340s      ______  ____   ____  ____   ____  ______  __ __
1340s     |      ||    \ |    ||    \ |    ||      ||  |  |
1340s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1340s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1340s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1340s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1340s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1340s 
1340s     Trinity-v2.15.2
1340s 
1340s 
1340s 
1340s Left read files: $VAR1 = [
1340s           'reads.left.fq.gz'
1340s         ];
1340s Right read files: $VAR1 = [
1340s           'reads.right.fq.gz'
1340s         ];
1340s Saturday, March 15, 2025: 23:53:15	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal
1340s Saturday, March 15, 2025: 23:53:15	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis
1340s 
1340s 
1340s ----------------------------------------------------------------------------------
1340s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1340s ----------------------------------------------------------------------------------
1340s 
1340s ---------------------------------------------------------------
1340s ------------ In silico Read Normalization ---------------------
1340s -- (Removing Excess Reads Beyond 200 Coverage --
1340s ---------------------------------------------------------------
1340s 
1340s # running normalization on reads: $VAR1 = [
1340s           [
1340s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1340s           ],
1340s           [
1340s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1340s           ]
1340s         ];
1340s 
1340s 
1340s Saturday, March 15, 2025: 23:53:15	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
1340s -prepping seqs
1340s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1340s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1340s CMD finished (0 seconds)
1340s CMD finished (0 seconds)
1340s CMD: touch left.fa.ok
1340s CMD finished (0 seconds)
1340s CMD: touch right.fa.ok
1340s CMD finished (0 seconds)
1340s  Done converting input files. CMD: cat left.fa right.fa > both.fa
1340s CMD finished (0 seconds)
1340s CMD: touch both.fa.ok
1340s CMD finished (0 seconds)
1340s -kmer counting.
1340s -------------------------------------------
1340s ----------- Jellyfish  --------------------
1340s -- (building a k-mer catalog from reads) --
1340s -------------------------------------------
1340s 
1340s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1342s CMD finished (2 seconds)
1342s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1342s CMD finished (0 seconds)
1342s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1342s CMD finished (0 seconds)
1342s CMD: touch jellyfish.K25.min2.kmers.fa.success
1342s CMD finished (0 seconds)
1342s -generating stats files
1342s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1342s -reading Kmer occurrences...
1342s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1342s -reading Kmer occurrences...
1342s 
1342s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1342s 
1342s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1342s STATS_GENERATION_TIME: 0 seconds.
1342s CMD finished (0 seconds)
1342s STATS_GENERATION_TIME: 0 seconds.
1342s CMD finished (0 seconds)
1342s CMD: touch left.fa.K25.stats.ok
1342s CMD finished (0 seconds)
1342s CMD: touch right.fa.K25.stats.ok
1342s CMD finished (0 seconds)
1342s -sorting each stats file by read name.
1342s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
1342s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
1342s CMD finished (0 seconds)
1342s CMD finished (0 seconds)
1342s CMD: touch left.fa.K25.stats.sort.ok
1342s CMD finished (0 seconds)
1342s CMD: touch right.fa.K25.stats.sort.ok
1342s CMD finished (0 seconds)
1342s -defining normalized reads
1342s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
1342s -opening left.fa.K25.stats.sort
1342s -opening right.fa.K25.stats.sort
1342s -done opening files.
1343s CMD finished (1 seconds)
1343s CMD: touch pairs.K25.stats.ok
1343s CMD finished (0 seconds)
1343s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
1343s 30472 / 30575 = 99.66% reads selected during normalization.
1343s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1343s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1343s CMD finished (0 seconds)
1343s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1343s CMD finished (0 seconds)
1343s -search and capture.
1343s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
1343s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1343s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
1343s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1344s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1344s CMD finished (0 seconds)
1344s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1344s CMD finished (0 seconds)
1344s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
1344s CMD finished (0 seconds)
1344s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
1344s CMD finished (0 seconds)
1344s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads
1344s 
1344s 
1344s Normalization complete. See outputs: 
1344s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1344s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1344s Saturday, March 15, 2025: 23:53:19	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok
1344s Converting input files. (in parallel)Saturday, March 15, 2025: 23:53:19	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
1344s Saturday, March 15, 2025: 23:53:19	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1344s Saturday, March 15, 2025: 23:53:19	CMD: touch right.fa.ok
1344s Saturday, March 15, 2025: 23:53:19	CMD: touch left.fa.ok
1344s Saturday, March 15, 2025: 23:53:19	CMD: touch left.fa.ok right.fa.ok
1344s Saturday, March 15, 2025: 23:53:19	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1344s Saturday, March 15, 2025: 23:53:19	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok
1344s WARNING:  --no_run_inchworm parameter in effect.  Stopping here prior to running inchworm.
1344s 
1344s # stop before chrysalis
1344s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal --no_run_chrysalis
1344s 
1344s 
1344s      ______  ____   ____  ____   ____  ______  __ __
1344s     |      ||    \ |    ||    \ |    ||      ||  |  |
1344s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1344s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1344s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1344s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1344s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1344s 
1344s     Trinity-v2.15.2
1344s 
1344s 
1344s 
1344s Left read files: $VAR1 = [
1344s           'reads.left.fq.gz'
1344s         ];
1344s Right read files: $VAR1 = [
1344s           'reads.right.fq.gz'
1344s         ];
1344s 
1344s 
1344s ----------------------------------------------------------------------------------
1344s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1344s ----------------------------------------------------------------------------------
1344s 
1344s ---------------------------------------------------------------
1344s ------------ In silico Read Normalization ---------------------
1344s -- (Removing Excess Reads Beyond 200 Coverage --
1344s ---------------------------------------------------------------
1344s 
1344s # running normalization on reads: $VAR1 = [
1344s           [
1344s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1344s           ],
1344s           [
1344s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1344s           ]
1344s         ];
1344s 
1344s 
1344s -------------------------------------------
1344s ----------- Jellyfish  --------------------
1344s -- (building a k-mer (25) catalog from reads) --
1344s -------------------------------------------
1344s 
1344s * [Sat Mar 15 23:53:19 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1345s * [Sat Mar 15 23:53:20 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1346s * [Sat Mar 15 23:53:21 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1346s ----------------------------------------------
1346s --------------- Inchworm (K=25, asm) ---------------------
1346s -- (Linear contig construction from k-mers) --
1346s ----------------------------------------------
1346s 
1346s * [Sat Mar 15 23:53:21 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp
1346s Kmer length set to: 25
1346s Min assembly length set to: 25
1346s Monitor turned on, set to: 1
1346s double stranded mode set
1346s min entropy set to: 1
1346s setting number of threads to: 2
1346s -setting parallel iworm mode.
1346s -reading Kmer occurrences...
1346s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1346s  done parsing 517949 Kmers, 517949 added, taking 0 seconds.
1346s 
1346s TIMING KMER_DB_BUILDING 0 s.
1346s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1346s Pruned 4114 kmers from catalog.
1346s 	Pruning time: 0 seconds = 0 minutes.
1346s 
1346s TIMING PRUNING 0 s.
1346s -populating the kmer seed candidate list.
1346s Kcounter hash size: 517949
1346s Processed 513835 non-zero abundance kmers in kcounter.
1346s -Not sorting list of kmers, given parallel mode in effect.
1346s -beginning inchworm contig assembly.
1346s Total kcounter hash size: 517949 vs. sorted list size: 513835
1346s num threads set to: 2
1346s Done opening file. tmp.iworm.fa.pid_83954.thread_0
1346s Done opening file. tmp.iworm.fa.pid_83954.thread_1
1347s 
1347s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1347s 
1347s TIMING CONTIG_BUILDING 1 s.
1347s 
1347s TIMING PROG_RUNTIME 1 s.
1347s * [Sat Mar 15 23:53:22 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa
1347s Saturday, March 15, 2025: 23:53:22	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished
1347s 
1347s 
1347s 
1347s #########################################################################
1347s Inchworm is complete.  --no_run_chrysalis was specified, so stopping here.
1347s #########################################################################
1347s 
1347s 
1347s 
1347s # stop before phase 2
1347s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal --no_distributed_trinity_exec
1347s 
1347s 
1347s      ______  ____   ____  ____   ____  ______  __ __
1347s     |      ||    \ |    ||    \ |    ||      ||  |  |
1347s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1347s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1347s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1347s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1347s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1347s 
1347s     Trinity-v2.15.2
1347s 
1347s 
1347s 
1347s Left read files: $VAR1 = [
1347s           'reads.left.fq.gz'
1347s         ];
1347s Right read files: $VAR1 = [
1347s           'reads.right.fq.gz'
1347s         ];
1347s 
1347s 
1347s ----------------------------------------------------------------------------------
1347s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1347s ----------------------------------------------------------------------------------
1347s 
1347s ---------------------------------------------------------------
1347s ------------ In silico Read Normalization ---------------------
1347s -- (Removing Excess Reads Beyond 200 Coverage --
1347s ---------------------------------------------------------------
1347s 
1347s # running normalization on reads: $VAR1 = [
1347s           [
1347s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1347s           ],
1347s           [
1347s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1347s           ]
1347s         ];
1347s 
1347s 
1347s --------------------------------------------------------
1347s -------------------- Chrysalis -------------------------
1347s -- (Contig Clustering & de Bruijn Graph Construction) --
1347s --------------------------------------------------------
1347s 
1347s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1347s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1347s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1347s 
1347s 
1347s #######################################################################
1347s Inchworm file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1347s Skipping Inchworm Step, Using Previous Inchworm Assembly
1347s #######################################################################
1347s 
1347s * [Sat Mar 15 23:53:22 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100
1347s * [Sat Mar 15 23:53:22 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1347s * [Sat Mar 15 23:53:22 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 
1350s * [Sat Mar 15 23:53:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt
1351s * [Sat Mar 15 23:53:26 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt
1353s * [Sat Mar 15 23:53:28 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted
1353s * [Sat Mar 15 23:53:28 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1353s * [Sat Mar 15 23:53:28 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out
1353s * [Sat Mar 15 23:53:28 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200
1353s * [Sat Mar 15 23:53:28 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1356s * [Sat Mar 15 23:53:31 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort
1356s Saturday, March 15, 2025: 23:53:31	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0
1356s Saturday, March 15, 2025: 23:53:31	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok
1356s Saturday, March 15, 2025: 23:53:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --no_distributed_trinity_exec  --no_salmon  > recursive_trinity.cmds
1356s Saturday, March 15, 2025: 23:53:31	CMD: touch recursive_trinity.cmds.ok
1356s 
1356s # finish it up
1356s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal 
1356s Saturday, March 15, 2025: 23:53:31	CMD: touch recursive_trinity.cmds.ok
1356s 
1356s 
1356s ###################################################################
1356s ##  Stopping here due to --no_distributed_trinity_exec in effect ##
1356s ###################################################################
1356s 
1356s 
1356s 
1356s      ______  ____   ____  ____   ____  ______  __ __
1356s     |      ||    \ |    ||    \ |    ||      ||  |  |
1356s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1356s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1356s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1356s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1356s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1356s 
1356s     Trinity-v2.15.2
1356s 
1356s 
1356s 
1356s Left read files: $VAR1 = [
1356s           'reads.left.fq.gz'
1356s         ];
1356s Right read files: $VAR1 = [
1356s           'reads.right.fq.gz'
1356s         ];
1356s 
1356s 
1356s ----------------------------------------------------------------------------------
1356s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1356s ----------------------------------------------------------------------------------
1356s 
1356s ---------------------------------------------------------------
1356s ------------ In silico Read Normalization ---------------------
1356s -- (Removing Excess Reads Beyond 200 Coverage --
1356s ---------------------------------------------------------------
1356s 
1356s # running normalization on reads: $VAR1 = [
1356s           [
1356s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1356s           ],
1356s           [
1356s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1356s           ]
1356s         ];
1356s 
1356s 
1356s --------------------------------------------------------
1356s -------------------- Chrysalis -------------------------
1356s -- (Contig Clustering & de Bruijn Graph Construction) --
1356s --------------------------------------------------------
1356s 
1356s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1356s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1356s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1356s 
1356s 
1356s #######################################################################
1356s Inchworm file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1356s Skipping Inchworm Step, Using Previous Inchworm Assembly
1356s #######################################################################
1356s 
1356s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists.
1356s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists.
1356s -- Skipping CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists.
1356s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists.
1356s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists.
1356s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists.
1356s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists.
1356s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists.
1356s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists.
1356s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 , checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists.
1356s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists.
1356s 
1356s 
1356s --------------------------------------------------------------------------------
1356s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1356s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1356s --------------------------------------------------------------------------------
1356s 
1356s Saturday, March 15, 2025: 23:53:31	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1356s Number of Commands: 38
1422s 
succeeded(1)   2.63158% completed.    
succeeded(2)   5.26316% completed.    
succeeded(3)   7.89474% completed.    
succeeded(4)   10.5263% completed.    
succeeded(5)   13.1579% completed.    
succeeded(6)   15.7895% completed.    
succeeded(7)   18.4211% completed.    
succeeded(8)   21.0526% completed.    
succeeded(9)   23.6842% completed.    
succeeded(10)   26.3158% completed.    
succeeded(11)   28.9474% completed.    
succeeded(12)   31.5789% completed.    
succeeded(13)   34.2105% completed.    
succeeded(14)   36.8421% completed.    
succeeded(15)   39.4737% completed.    
succeeded(16)   42.1053% completed.    
succeeded(17)   44.7368% completed.    
succeeded(18)   47.3684% completed.    
succeeded(19)   50% completed.    
succeeded(20)   52.6316% completed.    
succeeded(21)   55.2632% completed.    
succeeded(22)   57.8947% completed.    
succeeded(23)   60.5263% completed.    
succeeded(24)   63.1579% completed.    
succeeded(25)   65.7895% completed.    
succeeded(26)   68.4211% completed.    
succeeded(27)   71.0526% completed.    
succeeded(28)   73.6842% completed.    
succeeded(29)   76.3158% completed.    
succeeded(30)   78.9474% completed.    
succeeded(31)   81.5789% completed.    
succeeded(32)   84.2105% completed.    
succeeded(33)   86.8421% completed.    
succeeded(34)   89.4737% completed.    
succeeded(35)   92.1053% completed.    
succeeded(36)   94.7368% completed.    
succeeded(37)   97.3684% completed.    
succeeded(38)   100% completed.    
1422s 
1422s All commands completed successfully. :-)
1422s 
1422s 
1422s 
1422s ** Harvesting all assembled transcripts into a single multi-fasta file...
1422s 
1422s Saturday, March 15, 2025: 23:54:37	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp
1422s * [Sat Mar 15 23:54:37 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2
1423s * [Sat Mar 15 23:54:38 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1423s Saturday, March 15, 2025: 23:54:38	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map
1423s 
1423s 
1423s #############################################################################
1423s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1423s #############################################################################
1423s 
1423s 
1423s 
1423s 
1423s 
1423s 
1423s ##### Done Running Trinity #####
1423s 
1423s exit 0
1423s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh
1423s #!/bin/bash -ve
1423s 
1423s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1423s               --seqType fq \
1423s               --max_memory 1G \
1423s               --min_kmer_cov 3 \
1423s               --output trinity_test_samples_PE_min_kmer_cov_3
1423s 
1423s 
1423s      ______  ____   ____  ____   ____  ______  __ __
1423s     |      ||    \ |    ||    \ |    ||      ||  |  |
1423s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1423s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1423s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1423s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1423s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1423s 
1423s     Trinity-v2.15.2
1423s 
1423s 
1423s 
1423s Left read files: $VAR1 = [
1423s           'reads.left.fq.gz',
1423s           'reads2.left.fq.gz'
1423s         ];
1423s Right read files: $VAR1 = [
1423s           'reads.right.fq.gz',
1423s           'reads2.right.fq.gz'
1423s         ];
1423s Saturday, March 15, 2025: 23:54:38	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3
1423s Saturday, March 15, 2025: 23:54:38	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis
1423s 
1423s 
1423s ----------------------------------------------------------------------------------
1423s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1423s ----------------------------------------------------------------------------------
1423s 
1423s ---------------------------------------------------------------
1423s ------------ In silico Read Normalization ---------------------
1423s -- (Removing Excess Reads Beyond 200 Coverage --
1423s ---------------------------------------------------------------
1423s 
1423s # running normalization on reads: $VAR1 = [
1423s           [
1423s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1423s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1423s           ],
1423s           [
1423s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1423s             '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1423s           ]
1423s         ];
1423s 
1423s 
1423s Saturday, March 15, 2025: 23:54:38	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1423s -prepping seqs
1423s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1423s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1424s CMD finished (1 seconds)
1424s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1424s CMD finished (1 seconds)
1424s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1424s CMD finished (0 seconds)
1424s CMD finished (0 seconds)
1424s CMD: touch left.fa.ok
1424s CMD finished (0 seconds)
1424s CMD: touch right.fa.ok
1424s CMD finished (0 seconds)
1424s  Done converting input files. CMD: cat left.fa right.fa > both.fa
1424s CMD finished (0 seconds)
1424s CMD: touch both.fa.ok
1424s CMD finished (0 seconds)
1424s -kmer counting.
1424s -------------------------------------------
1424s ----------- Jellyfish  --------------------
1424s -- (building a k-mer catalog from reads) --
1424s -------------------------------------------
1424s 
1424s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1425s CMD finished (1 seconds)
1425s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1425s CMD finished (0 seconds)
1425s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1425s CMD finished (0 seconds)
1425s CMD: touch jellyfish.K25.min2.kmers.fa.success
1425s CMD finished (0 seconds)
1425s -generating stats files
1425s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1425s -reading Kmer occurrences...
1425s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1425s -reading Kmer occurrences...
1426s 
1426s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1426s 
1426s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1427s STATS_GENERATION_TIME: 1 seconds.
1427s CMD finished (2 seconds)
1427s STATS_GENERATION_TIME: 1 seconds.
1427s CMD finished (2 seconds)
1427s CMD: touch left.fa.K25.stats.ok
1427s CMD finished (0 seconds)
1427s CMD: touch right.fa.K25.stats.ok
1427s CMD finished (0 seconds)
1427s -sorting each stats file by read name.
1427s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort
1427s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort
1427s CMD finished (0 seconds)
1427s CMD finished (0 seconds)
1427s CMD: touch left.fa.K25.stats.sort.ok
1427s CMD finished (0 seconds)
1427s CMD: touch right.fa.K25.stats.sort.ok
1427s CMD finished (0 seconds)
1427s -defining normalized reads
1427s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
1427s -opening left.fa.K25.stats.sort
1427s -opening right.fa.K25.stats.sort
1427s -done opening files.
1428s CMD finished (1 seconds)
1428s CMD: touch pairs.K25.stats.ok
1428s CMD finished (0 seconds)
1428s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 3 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
1428s 53574 / 61150 = 87.61% reads selected during normalization.
1428s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1428s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3
1428s CMD finished (0 seconds)
1428s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1428s CMD finished (0 seconds)
1428s -search and capture.
1428s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1428s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1428s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1428s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1429s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1429s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1430s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq.ok
1430s CMD finished (0 seconds)
1430s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq.ok
1430s CMD finished (0 seconds)
1430s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq left.norm.fq
1430s CMD finished (0 seconds)
1430s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq right.norm.fq
1430s CMD finished (0 seconds)
1430s -removing tmp dir /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads
1430s 
1430s 
1430s Normalization complete. See outputs: 
1430s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq
1430s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq
1430s Saturday, March 15, 2025: 23:54:45	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok
1430s Converting input files. (in parallel)Saturday, March 15, 2025: 23:54:45	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
1430s Saturday, March 15, 2025: 23:54:45	CMD: cat /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1430s Saturday, March 15, 2025: 23:54:45	CMD: touch left.fa.ok
1430s Saturday, March 15, 2025: 23:54:45	CMD: touch right.fa.ok
1430s Saturday, March 15, 2025: 23:54:45	CMD: touch left.fa.ok right.fa.ok
1430s Saturday, March 15, 2025: 23:54:45	CMD: cat left.fa right.fa > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1430s Saturday, March 15, 2025: 23:54:45	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok
1430s -------------------------------------------
1430s ----------- Jellyfish  --------------------
1430s -- (building a k-mer (25) catalog from reads) --
1430s -------------------------------------------
1430s 
1430s * [Sat Mar 15 23:54:45 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1431s * [Sat Mar 15 23:54:46 2025] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1431s * [Sat Mar 15 23:54:46 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1431s ----------------------------------------------
1431s --------------- Inchworm (K=25, asm) ---------------------
1431s -- (Linear contig construction from k-mers) --
1431s ----------------------------------------------
1431s 
1431s * [Sat Mar 15 23:54:46 2025] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp
1431s Kmer length set to: 25
1431s Min assembly length set to: 25
1431s Monitor turned on, set to: 1
1431s double stranded mode set
1431s min entropy set to: 1
1431s setting number of threads to: 2
1431s -setting parallel iworm mode.
1431s -reading Kmer occurrences...
1431s 
1431s  done parsing 96295 Kmers, 96295 added, taking 0 seconds.
1431s 
1431s TIMING KMER_DB_BUILDING 0 s.
1431s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1431s Pruned 474 kmers from catalog.
1431s 	Pruning time: 0 seconds = 0 minutes.
1431s 
1431s TIMING PRUNING 0 s.
1431s -populating the kmer seed candidate list.
1431s Kcounter hash size: 96295
1431s Processed 95821 non-zero abundance kmers in kcounter.
1431s -Not sorting list of kmers, given parallel mode in effect.
1431s -beginning inchworm contig assembly.
1431s Total kcounter hash size: 96295 vs. sorted list size: 95821
1431s num threads set to: 2
1431s Done opening file. tmp.iworm.fa.pid_90832.thread_0
1431s Done opening file. tmp.iworm.fa.pid_90832.thread_1
1431s 
1431s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1431s 
1431s TIMING CONTIG_BUILDING 0 s.
1431s 
1431s TIMING PROG_RUNTIME 0 s.
1432s * [Sat Mar 15 23:54:46 2025] Running CMD: mv /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa
1432s Saturday, March 15, 2025: 23:54:46	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished
1432s --------------------------------------------------------
1432s -------------------- Chrysalis -------------------------
1432s -- (Contig Clustering & de Bruijn Graph Construction) --
1432s --------------------------------------------------------
1432s 
1432s inchworm_target: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1432s bowtie_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1432s chrysalis_reads_fa: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1432s * [Sat Mar 15 23:54:46 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100
1432s * [Sat Mar 15 23:54:47 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1432s * [Sat Mar 15 23:54:47 2025] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa  | samtools view -@ 2 -F4 -Sb - | samtools sort -m 268435456 -@ 2 -no /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 
1441s * [Sat Mar 15 23:54:56 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt
1442s * [Sat Mar 15 23:54:57 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48  -scaffolding /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt
1445s * [Sat Mar 15 23:55:00 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted
1445s * [Sat Mar 15 23:55:00 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1445s * [Sat Mar 15 23:55:00 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out
1445s * [Sat Mar 15 23:55:00 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200
1445s * [Sat Mar 15 23:55:00 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1451s * [Sat Mar 15 23:55:06 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort
1451s Saturday, March 15, 2025: 23:55:06	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0
1452s Saturday, March 15, 2025: 23:55:07	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok
1452s Saturday, March 15, 2025: 23:55:07	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  --min_kmer_cov  3  --no_salmon  > recursive_trinity.cmds
1452s Saturday, March 15, 2025: 23:55:07	CMD: touch recursive_trinity.cmds.ok
1452s Saturday, March 15, 2025: 23:55:07	CMD: touch recursive_trinity.cmds.ok
1452s 
1452s 
1452s --------------------------------------------------------------------------------
1452s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1452s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1452s --------------------------------------------------------------------------------
1452s 
1452s Saturday, March 15, 2025: 23:55:07	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1452s Number of Commands: 17
1510s 
succeeded(1)   5.88235% completed.    
succeeded(2)   11.7647% completed.    
succeeded(3)   17.6471% completed.    
succeeded(4)   23.5294% completed.    
succeeded(5)   29.4118% completed.    
succeeded(6)   35.2941% completed.    
succeeded(7)   41.1765% completed.    
succeeded(8)   47.0588% completed.    
succeeded(9)   52.9412% completed.    
succeeded(10)   58.8235% completed.    
succeeded(11)   64.7059% completed.    
succeeded(12)   70.5882% completed.    
succeeded(13)   76.4706% completed.    
succeeded(14)   82.3529% completed.    
succeeded(15)   88.2353% completed.    
succeeded(16)   94.1176% completed.    
succeeded(17)   100% completed.    
1510s 
1510s All commands completed successfully. :-)
1510s 
1510s 
1510s 
1510s ** Harvesting all assembled transcripts into a single multi-fasta file...
1510s 
1510s Saturday, March 15, 2025: 23:56:05	CMD: find /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/ -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp
1510s * [Sat Mar 15 23:56:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2
1511s * [Sat Mar 15 23:56:06 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1511s Saturday, March 15, 2025: 23:56:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta.gene_trans_map
1511s 
1511s 
1511s #############################################################################
1511s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1511s #############################################################################
1511s 
1511s 
1511s 
1511s 
1511s exit 0
1511s touch test_all
1511s make[1]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
1511s Running example in test_GenomeGuidedTrinity...
1511s make[1]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
1511s ./run_genome-guided_Trinity_use_existing_bam.sh
1511s #!/bin/bash -ve
1511s 
1511s if [ -e top100k.Left.fq.gz ] && ! [ -e top100k.Left.fq ]
1511s then
1511s 	gunzip -c top100k.Left.fq.gz > top100k.Left.fq
1511s fi
1511s 
1511s if [ -e top100k.Right.fq.gz ] && ! [ -e top100k.Right.fq ]
1511s then
1511s 	gunzip -c top100k.Right.fq.gz > top100k.Right.fq
1511s fi
1511s 
1511s 
1511s 
1511s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ]
1511s then
1511s 	gunzip -c top100k.genome.gz > top100k.genome
1511s fi
1511s 
1511s 
1511s 
1511s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G  --output test_GG_use_bam_trinity_outdir
1511s 
1511s 
1511s      ______  ____   ____  ____   ____  ______  __ __
1511s     |      ||    \ |    ||    \ |    ||      ||  |  |
1511s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1511s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1511s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1511s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1511s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1511s 
1511s     Trinity-v2.15.2
1511s 
1511s 
1511s 
1511s Saturday, March 15, 2025: 23:56:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1512s -appears to be a coordinate sorted bam file. ok.
1512s Saturday, March 15, 2025: 23:56:07	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir
1512s 
1512s 
1512s ----------------------------------------------------------------------------------
1512s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1512s ----------------------------------------------------------------------------------
1512s 
1512s -found paired-end aligned read. Running in paired-end mode.
1512s Saturday, March 15, 2025: 23:56:07	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1512s Saturday, March 15, 2025: 23:56:07	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok
1512s Saturday, March 15, 2025: 23:56:07	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam -I 1000 --sort_buffer 2G --CPU 2 
1512s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 2G --sam SP2.chr.bam.norm_200.bam --min_insert_size 1 --max_insert_size 1000 
1512s -extracting read coordinates from SP2.chr.bam.norm_200.bam into SP2.chr.bam.norm_200.bam.read_coords
1512s 
1513s CMD: touch SP2.chr.bam.norm_200.bam.read_coords.ok
1513s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.read_coords > SP2.chr.bam.norm_200.bam.read_coords.sort_by_readname
1513s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.read_coords.sort_by_readname
1513s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.frag_coords > SP2.chr.bam.norm_200.bam.frag_coords.coord_sorted
1513s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.frag_coords > SP2.chr.bam.norm_200.bam.frag_coverage.wig
1514s 
[1000 lines read]  scaff:7000000090838467 lend:6192  rend:6455     
[2000 lines read]  scaff:7000000090838467 lend:7884  rend:8105     
[3000 lines read]  scaff:7000000090838467 lend:8425  rend:8630     
[4000 lines read]  scaff:7000000090838467 lend:15701  rend:15766     
[5000 lines read]  scaff:7000000090838467 lend:28756  rend:28823     
[6000 lines read]  scaff:7000000090838467 lend:29930  rend:29996     
[7000 lines read]  scaff:7000000090838467 lend:41235  rend:41435     
[8000 lines read]  scaff:7000000090838467 lend:48174  rend:48296     
[9000 lines read]  scaff:7000000090838467 lend:53158  rend:53531     
[10000 lines read]  scaff:7000000090838467 lend:56567  rend:56797     
[11000 lines read]  scaff:7000000090838467 lend:57552  rend:57733     
[12000 lines read]  scaff:7000000090838467 lend:59947  rend:60266     
[13000 lines read]  scaff:7000000090838467 lend:60447  rend:60807     
[14000 lines read]  scaff:7000000090838467 lend:64892  rend:65152     
[15000 lines read]  scaff:7000000090838467 lend:65475  rend:65843     
[16000 lines read]  scaff:7000000090838467 lend:65983  rend:66211     
[17000 lines read]  scaff:7000000090838467 lend:66810  rend:67149     
[18000 lines read]  scaff:7000000090838467 lend:67928  rend:68077     
[19000 lines read]  scaff:7000000090838467 lend:68811  rend:69080     
[20000 lines read]  scaff:7000000090838467 lend:74885  rend:75229     
[21000 lines read]  scaff:7000000090838467 lend:83034  rend:83388     
[22000 lines read]  scaff:7000000090838467 lend:83791  rend:83830     
[23000 lines read]  scaff:7000000090838467 lend:84357  rend:84586     
[24000 lines read]  scaff:7000000090838467 lend:93383  rend:93626     CMD: touch SP2.chr.bam.norm_200.bam.frag_coverage.wig.ok
1514s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.frag_coverage.wig 1 + > SP2.chr.bam.norm_200.bam.minC1.gff
1514s CMD: touch SP2.chr.bam.norm_200.bam.minC1.gff.ok
1514s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.minC1.gff  --coord_sorted_SAM SP2.chr.bam.norm_200.bam --parts_per_directory 100 --min_reads_per_partition 10 
1514s // parsing paritions.
1514s 
[71]  -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/2163_3611.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/4913_5681.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/11319_11903.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/12073_12996.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/15124_16713.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17151_17239.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17291_17395.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17403_17460.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17486_18615.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/18669_19255.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/25542_25904.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/27107_27961.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/29764_32484.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads
1514s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1515s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads
1515s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok
1515s ##
1515s Done
1515s ##
1515s 
1515s Saturday, March 15, 2025: 23:56:10	CMD: touch partitions.ok
1515s Saturday, March 15, 2025: 23:56:10	CMD: find Dir_* -name '*reads' > read_files.list
1515s Saturday, March 15, 2025: 23:56:10	CMD: touch read_files.list.ok
1515s Saturday, March 15, 2025: 23:56:10	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  > trinity_GG.cmds
1515s Saturday, March 15, 2025: 23:56:10	CMD: touch trinity_GG.cmds.ok
1515s Saturday, March 15, 2025: 23:56:10	CMD: touch trinity_GG.cmds.ok
1515s 
1515s 
1515s --------------------------------------------------------------------------------
1515s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1515s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1515s --------------------------------------------------------------------------------
1515s 
1515s Saturday, March 15, 2025: 23:56:10	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1515s Number of Commands: 37
1571s 
succeeded(1)   2.7027% completed.    
succeeded(2)   5.40541% completed.    
succeeded(3)   8.10811% completed.    
succeeded(4)   10.8108% completed.    
succeeded(5)   13.5135% completed.    
succeeded(6)   16.2162% completed.    
succeeded(7)   18.9189% completed.    
succeeded(8)   21.6216% completed.    
succeeded(9)   24.3243% completed.    
succeeded(10)   27.027% completed.    
succeeded(11)   29.7297% completed.    
succeeded(12)   32.4324% completed.    
succeeded(13)   35.1351% completed.    
succeeded(14)   37.8378% completed.    
succeeded(15)   40.5405% completed.    
succeeded(16)   43.2432% completed.    
succeeded(17)   45.9459% completed.    
succeeded(18)   48.6487% completed.    
succeeded(19)   51.3513% completed.    
succeeded(20)   54.0541% completed.    
succeeded(21)   56.7568% completed.    
succeeded(22)   59.4595% completed.    
succeeded(23)   62.1622% completed.    
succeeded(24)   64.8649% completed.    
succeeded(25)   67.5676% completed.    
succeeded(26)   70.2703% completed.    
succeeded(27)   72.973% completed.    
succeeded(28)   75.6757% completed.    
succeeded(29)   78.3784% completed.    
succeeded(30)   81.0811% completed.    
succeeded(31)   83.7838% completed.    
succeeded(32)   86.4865% completed.    
succeeded(33)   89.1892% completed.    
succeeded(34)   91.8919% completed.    
succeeded(35)   94.5946% completed.    
succeeded(36)   97.2973% completed.    
succeeded(37)   100% completed.    
1571s 
1571s All commands completed successfully. :-)
1571s 
1571s Saturday, March 15, 2025: 23:57:06	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp
1571s Saturday, March 15, 2025: 23:57:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
1571s 
1571s 
1571s Finished. See /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
1571s 
1571s 
1571s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta")
1571s if [ $asmsize -le 50000 ]; then
1571s     echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete"
1571s     exit 1
1571s else
1571s     echo "ok"
1571s     exit 0
1571s fi
1571s ok
1571s ./run_Schizo_TrinityGG_jaccard_clip.sh
1571s #!/bin/bash -ve
1571s 
1571s $TRINITY_HOME/Trinity --genome_guided_bam SP2.chr.bam --max_memory 1G --CPU 2 --genome_guided_max_intron 1000 --jaccard_clip --SS_lib_type RF --output test_Schizo_trinityGG_jaccard_RF_outdir
1571s 
1571s 
1571s      ______  ____   ____  ____   ____  ______  __ __
1571s     |      ||    \ |    ||    \ |    ||      ||  |  |
1571s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1571s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1571s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1571s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1571s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1571s 
1571s     Trinity-v2.15.2
1571s 
1571s 
1571s 
1571s Saturday, March 15, 2025: 23:57:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1571s -appears to be a coordinate sorted bam file. ok.
1571s Saturday, March 15, 2025: 23:57:06	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir
1571s 
1571s 
1571s ----------------------------------------------------------------------------------
1571s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1571s ----------------------------------------------------------------------------------
1571s 
1571s -found paired-end aligned read. Running in paired-end mode.
1571s Saturday, March 15, 2025: 23:57:06	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1572s Saturday, March 15, 2025: 23:57:07	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok
1572s Saturday, March 15, 2025: 23:57:07	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam -I 1000 --sort_buffer 1G --CPU 2  --SS_lib_type RF 
1572s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 1G --sam SP2.chr.bam.norm_200.bam.+.sam --min_insert_size 1 --max_insert_size 1000 
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 1G --sam SP2.chr.bam.norm_200.bam.-.sam --min_insert_size 1 --max_insert_size 1000 
1573s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords
1573s 
1573s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords
1573s 
1573s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok
1573s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.-.sam.read_coords > SP2.chr.bam.norm_200.bam.-.sam.read_coords.sort_by_readname
1573s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok
1573s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.+.sam.read_coords > SP2.chr.bam.norm_200.bam.+.sam.read_coords.sort_by_readname
1573s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.-.sam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.-.sam.read_coords.sort_by_readname
1573s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.+.sam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.+.sam.read_coords.sort_by_readname
1573s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.-.sam.frag_coords > SP2.chr.bam.norm_200.bam.-.sam.frag_coords.coord_sorted
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.-.sam.frag_coords > SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig
1573s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.+.sam.frag_coords > SP2.chr.bam.norm_200.bam.+.sam.frag_coords.coord_sorted
1573s 
[1000 lines read]  scaff:7000000090838467 lend:6194  rend:6433     
[2000 lines read]  scaff:7000000090838467 lend:46308  rend:46696     CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.+.sam.frag_coords > SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig
1574s 
[3000 lines read]  scaff:7000000090838467 lend:59573  rend:59951     
[1000 lines read]  scaff:7000000090838467 lend:8022  rend:8237     
[4000 lines read]  scaff:7000000090838467 lend:60068  rend:60313     
[2000 lines read]  scaff:7000000090838467 lend:8568  rend:8635     
[3000 lines read]  scaff:7000000090838467 lend:21591  rend:21888     
[4000 lines read]  scaff:7000000090838467 lend:29215  rend:29340     
[5000 lines read]  scaff:7000000090838467 lend:60602  rend:60807     
[5000 lines read]  scaff:7000000090838467 lend:30519  rend:30759     
[6000 lines read]  scaff:7000000090838467 lend:65099  rend:65468     
[6000 lines read]  scaff:7000000090838467 lend:52660  rend:52989     
[7000 lines read]  scaff:7000000090838467 lend:65621  rend:65957     
[7000 lines read]  scaff:7000000090838467 lend:56475  rend:56834     
[8000 lines read]  scaff:7000000090838467 lend:57224  rend:57489     
[8000 lines read]  scaff:7000000090838467 lend:66173  rend:66538     
[9000 lines read]  scaff:7000000090838467 lend:67627  rend:67818     
[9000 lines read]  scaff:7000000090838467 lend:88962  rend:89278     
[10000 lines read]  scaff:7000000090838467 lend:68505  rend:68690     
[11000 lines read]  scaff:7000000090838467 lend:69245  rend:69544     
[12000 lines read]  scaff:7000000090838467 lend:82862  rend:83065     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok
1574s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig 1 - > SP2.chr.bam.norm_200.bam.-.sam.minC1.gff
1574s 
[13000 lines read]  scaff:7000000090838467 lend:83622  rend:83842     
[14000 lines read]  scaff:7000000090838467 lend:84137  rend:84436     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok
1574s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig 1 + > SP2.chr.bam.norm_200.bam.+.sam.minC1.gff
1574s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1574s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.-.sam.minC1.gff  --coord_sorted_SAM SP2.chr.bam.norm_200.bam.-.sam --parts_per_directory 100 --min_reads_per_partition 10  --SS_lib_type RF 
1574s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1574s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.+.sam.minC1.gff  --coord_sorted_SAM SP2.chr.bam.norm_200.bam.+.sam --parts_per_directory 100 --min_reads_per_partition 10  --SS_lib_type RF 
1574s // parsing paritions.
1574s 
[73]  -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1574s // parsing paritions.
1574s 
[57]  -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads
1574s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads
1574s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads
1574s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1574s ##
1574s Done
1574s ##
1574s 
1574s Saturday, March 15, 2025: 23:57:09	CMD: touch partitions.ok
1574s Saturday, March 15, 2025: 23:57:09	CMD: find Dir_* -name '*reads' > read_files.list
1574s Saturday, March 15, 2025: 23:57:09	CMD: touch read_files.list.ok
1574s Saturday, March 15, 2025: 23:57:09	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --jaccard_clip  > trinity_GG.cmds
1574s Saturday, March 15, 2025: 23:57:09	CMD: touch trinity_GG.cmds.ok
1574s Saturday, March 15, 2025: 23:57:09	CMD: touch trinity_GG.cmds.ok
1574s 
1574s 
1574s --------------------------------------------------------------------------------
1574s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1574s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1574s --------------------------------------------------------------------------------
1574s 
1574s Saturday, March 15, 2025: 23:57:09	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1574s Number of Commands: 53
1575s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1575s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1575s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s bt2 index files: $VAR1 = [];
1575s Note - bowtie-build indices do not yet exist. Indexing genome now.
1575s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s bt2 index files: $VAR1 = [];
1575s Note - bowtie-build indices do not yet exist. Indexing genome now.
1575s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1575s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1575s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1575s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1575s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1575s 70 reads; of these:
1575s   70 (100.00%) were unpaired; of these:
1575s     10 (14.29%) aligned 0 times
1575s     59 (84.29%) aligned exactly 1 time
1575s     1 (1.43%) aligned >1 times
1575s 85.71% overall alignment rate
1575s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1575s 309 reads; of these:
1575s   309 (100.00%) were unpaired; of these:
1575s     3 (0.97%) aligned 0 times
1575s     201 (65.05%) aligned exactly 1 time
1575s     105 (33.98%) aligned >1 times
1575s 99.03% overall alignment rate
1575s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1575s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1575s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1575s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1575s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1575s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1575s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1575s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1575s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1575s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1575s 
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1575s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1575s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1575s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1575s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1575s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1575s 
1575s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1575s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1575s -processing jaccard pair sensor
1575s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1575s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1575s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1575s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa.clipped.fa
1575s -processing jaccard pair sensor
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa.clipped.fa
1578s 
succeeded(1)   1.88679% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1578s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1578s bt2 index files: $VAR1 = [];
1578s Note - bowtie-build indices do not yet exist. Indexing genome now.
1578s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1578s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1578s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1578s 213 reads; of these:
1578s   213 (100.00%) were unpaired; of these:
1578s     1 (0.47%) aligned 0 times
1578s     121 (56.81%) aligned exactly 1 time
1578s     91 (42.72%) aligned >1 times
1578s 99.53% overall alignment rate
1578s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1578s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1578s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1578s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1578s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1578s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1578s 
1578s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1578s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1578s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1578s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1578s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1578s -processing jaccard pair sensor
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa.clipped.fa
1579s 
succeeded(2)   3.77358% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1579s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1579s bt2 index files: $VAR1 = [];
1579s Note - bowtie-build indices do not yet exist. Indexing genome now.
1579s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1579s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1579s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1579s 52 reads; of these:
1579s   52 (100.00%) were unpaired; of these:
1579s     5 (9.62%) aligned 0 times
1579s     47 (90.38%) aligned exactly 1 time
1579s     0 (0.00%) aligned >1 times
1579s 90.38% overall alignment rate
1579s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1579s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1579s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1579s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1579s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1580s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1580s 
1580s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1580s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1580s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1580s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1580s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1580s -processing jaccard pair sensor
1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa.clipped.fa
1582s 
succeeded(3)   5.66038% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1582s 
succeeded(4)   7.54717% completed.    CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s bt2 index files: $VAR1 = [];
1582s Note - bowtie-build indices do not yet exist. Indexing genome now.
1582s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1582s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s bt2 index files: $VAR1 = [];
1582s Note - bowtie-build indices do not yet exist. Indexing genome now.
1582s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1582s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1582s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1582s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1582s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1583s 20 reads; of these:
1583s   20 (100.00%) were unpaired; of these:
1583s     4 (20.00%) aligned 0 times
1583s     16 (80.00%) aligned exactly 1 time
1583s     0 (0.00%) aligned >1 times
1583s 80.00% overall alignment rate
1583s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1583s 5953 reads; of these:
1583s   5953 (100.00%) were unpaired; of these:
1583s     11 (0.18%) aligned 0 times
1583s     3807 (63.95%) aligned exactly 1 time
1583s     2135 (35.86%) aligned >1 times
1583s 99.82% overall alignment rate
1583s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1583s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1583s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1583s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1583s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1583s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1583s 
1583s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1583s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1583s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1583s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1583s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1583s -processing jaccard pair sensor
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1583s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa.clipped.fa
1583s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1583s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1583s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1583s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1583s 
1583s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1583s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1583s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1583s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1583s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1583s -processing jaccard pair sensor
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1584s 
[1000 lines read]  scaff:a1;90 lend:143  rend:454     
[2000 lines read]  scaff:a1;90 lend:1115  rend:1442     
[3000 lines read]  scaff:a1;90 lend:1905  rend:2258     
[4000 lines read]  scaff:a21;2 lend:5  rend:43     
[5000 lines read]  scaff:a39;2 lend:10  rend:46     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1584s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa.clipped.fa
1585s 
succeeded(5)   9.43396% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1585s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1585s bt2 index files: $VAR1 = [];
1585s Note - bowtie-build indices do not yet exist. Indexing genome now.
1585s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1585s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1585s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1585s 42 reads; of these:
1585s   42 (100.00%) were unpaired; of these:
1585s     18 (42.86%) aligned 0 times
1585s     24 (57.14%) aligned exactly 1 time
1585s     0 (0.00%) aligned >1 times
1585s 57.14% overall alignment rate
1585s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1585s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1585s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1585s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1585s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1585s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1585s 
1585s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1585s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1585s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1585s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1585s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1585s -processing jaccard pair sensor
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa.clipped.fa
1587s 
succeeded(6)   11.3208% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1587s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1587s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1587s bt2 index files: $VAR1 = [];
1587s Note - bowtie-build indices do not yet exist. Indexing genome now.
1587s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1587s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1587s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1587s 371 reads; of these:
1587s   371 (100.00%) were unpaired; of these:
1587s     2 (0.54%) aligned 0 times
1587s     296 (79.78%) aligned exactly 1 time
1587s     73 (19.68%) aligned >1 times
1587s 99.46% overall alignment rate
1587s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1587s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1587s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1587s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1587s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1587s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1587s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1587s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1588s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1588s 
1588s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1588s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1588s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1588s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1588s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1588s -processing jaccard pair sensor
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa.clipped.fa
1588s 
succeeded(7)   13.2075% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1588s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1588s bt2 index files: $VAR1 = [];
1588s Note - bowtie-build indices do not yet exist. Indexing genome now.
1588s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1589s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1589s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1589s 18 reads; of these:
1589s   18 (100.00%) were unpaired; of these:
1589s     5 (27.78%) aligned 0 times
1589s     13 (72.22%) aligned exactly 1 time
1589s     0 (0.00%) aligned >1 times
1589s 72.22% overall alignment rate
1589s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1589s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1589s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1589s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1589s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1589s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1589s 
1589s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1589s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1589s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1589s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1589s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1589s -processing jaccard pair sensor
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa.clipped.fa
1590s 
succeeded(8)   15.0943% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1590s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s bt2 index files: $VAR1 = [];
1590s Note - bowtie-build indices do not yet exist. Indexing genome now.
1590s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s 
succeeded(9)   16.9811% completed.    CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1590s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1590s 24 reads; of these:
1590s   24 (100.00%) were unpaired; of these:
1590s     3 (12.50%) aligned 0 times
1590s     21 (87.50%) aligned exactly 1 time
1590s     0 (0.00%) aligned >1 times
1590s 87.50% overall alignment rate
1590s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1590s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1590s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1590s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1590s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1590s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1590s 
1590s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1590s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1590s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1590s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1590s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1590s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1590s -processing jaccard pair sensor
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1590s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s bt2 index files: $VAR1 = [];
1590s Note - bowtie-build indices do not yet exist. Indexing genome now.
1590s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa.clipped.fa
1591s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1591s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1591s 1717 reads; of these:
1591s   1717 (100.00%) were unpaired; of these:
1591s     1 (0.06%) aligned 0 times
1591s     1511 (88.00%) aligned exactly 1 time
1591s     205 (11.94%) aligned >1 times
1591s 99.94% overall alignment rate
1591s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1591s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1591s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1591s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1591s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1591s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1591s 
1591s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1591s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1591s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1591s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1591s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1591s -processing jaccard pair sensor
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1591s 
[1000 lines read]  scaff:a2;50 lend:1  rend:68     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa.clipped.fa
1592s 
succeeded(10)   18.8679% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1592s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1592s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1592s bt2 index files: $VAR1 = [];
1592s Note - bowtie-build indices do not yet exist. Indexing genome now.
1592s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1592s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1592s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1592s 293 reads; of these:
1592s   293 (100.00%) were unpaired; of these:
1593s     0 (0.00%) aligned 0 times
1593s     293 (100.00%) aligned exactly 1 time
1593s     0 (0.00%) aligned >1 times
1593s 100.00% overall alignment rate
1593s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1593s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1593s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1593s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1593s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1593s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1593s 
1593s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1593s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1593s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1593s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1593s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1593s -processing jaccard pair sensor
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa.clipped.fa
1595s 
succeeded(11)   20.7547% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1595s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1595s bt2 index files: $VAR1 = [];
1595s Note - bowtie-build indices do not yet exist. Indexing genome now.
1595s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1595s 
succeeded(12)   22.6415% completed.    CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1595s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1595s 30 reads; of these:
1595s   30 (100.00%) were unpaired; of these:
1595s     0 (0.00%) aligned 0 times
1595s     18 (60.00%) aligned exactly 1 time
1595s     12 (40.00%) aligned >1 times
1595s 100.00% overall alignment rate
1595s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1595s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1595s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1595s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1595s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1595s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1595s 
1595s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1595s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1595s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1595s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1595s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1595s -processing jaccard pair sensor
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa.clipped.fa
1595s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1595s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1595s bt2 index files: $VAR1 = [];
1595s Note - bowtie-build indices do not yet exist. Indexing genome now.
1595s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1596s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1596s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1596s 3962 reads; of these:
1596s   3962 (100.00%) were unpaired; of these:
1596s     2 (0.05%) aligned 0 times
1596s     2253 (56.87%) aligned exactly 1 time
1596s     1707 (43.08%) aligned >1 times
1596s 99.95% overall alignment rate
1596s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1596s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1596s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1596s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1596s 
succeeded(13)   24.5283% completed.    CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1596s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1596s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
1596s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1596s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1596s 
1597s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1597s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1597s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1597s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1597s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1597s -processing jaccard pair sensor
1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1597s 
[1000 lines read]  scaff:a21;2 lend:1  rend:35     
[2000 lines read]  scaff:a38;2 lend:1  rend:49     
[3000 lines read]  scaff:a3;145 lend:155  rend:222     
[4000 lines read]  scaff:a4;148 lend:1  rend:68     
[5000 lines read]  scaff:a5;138 lend:67  rend:134     
[6000 lines read]  scaff:a8;8 lend:26  rend:93     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa.clipped.fa
1597s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1597s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1597s bt2 index files: $VAR1 = [];
1597s Note - bowtie-build indices do not yet exist. Indexing genome now.
1597s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1598s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1598s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1598s 7038 reads; of these:
1598s   7038 (100.00%) were unpaired; of these:
1598s     25 (0.36%) aligned 0 times
1598s     2368 (33.65%) aligned exactly 1 time
1598s     4645 (66.00%) aligned >1 times
1598s 99.64% overall alignment rate
1599s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1599s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1599s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1599s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1599s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1599s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1599s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1599s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
1599s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1599s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1599s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1599s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1599s 
1600s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1600s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1600s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1600s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1600s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1600s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1600s -processing jaccard pair sensor
1601s 
succeeded(14)   26.4151% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1601s 
[1000 lines read]  scaff:a16;2 lend:11  rend:42     CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1601s 
[2000 lines read]  scaff:a1;131 lend:621  rend:903     CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1601s bt2 index files: $VAR1 = [];
1601s Note - bowtie-build indices do not yet exist. Indexing genome now.
1601s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1601s 
[3000 lines read]  scaff:a1;131 lend:1136  rend:1543     
[4000 lines read]  scaff:a1;131 lend:1699  rend:1900     
[5000 lines read]  scaff:a25;2 lend:31  rend:73     
[6000 lines read]  scaff:a30;2 lend:1  rend:37     
[7000 lines read]  scaff:a3;9 lend:1  rend:43     
[8000 lines read]  scaff:a53;2 lend:1  rend:49     
[9000 lines read]  scaff:a5;2 lend:16  rend:60     
[10000 lines read]  scaff:a69;2 lend:1  rend:43     
[11000 lines read]  scaff:a79;2 lend:1  rend:50     
[12000 lines read]  scaff:a9;3 lend:1  rend:36     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa.clipped.fa
1601s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1601s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1601s 10 reads; of these:
1601s   10 (100.00%) were unpaired; of these:
1601s     5 (50.00%) aligned 0 times
1601s     5 (50.00%) aligned exactly 1 time
1601s     0 (0.00%) aligned >1 times
1601s 50.00% overall alignment rate
1601s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1601s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1601s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1601s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1601s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1601s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1601s 
1601s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1601s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1601s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1601s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1601s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1601s -processing jaccard pair sensor
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa.clipped.fa
1603s 
succeeded(15)   28.3019% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1603s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1603s bt2 index files: $VAR1 = [];
1603s Note - bowtie-build indices do not yet exist. Indexing genome now.
1603s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1603s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1603s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1603s 85 reads; of these:
1603s   85 (100.00%) were unpaired; of these:
1603s     3 (3.53%) aligned 0 times
1603s     82 (96.47%) aligned exactly 1 time
1603s     0 (0.00%) aligned >1 times
1603s 96.47% overall alignment rate
1603s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1603s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1603s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1603s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1603s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1603s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1603s 
1603s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1603s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1603s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1603s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1603s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1603s -processing jaccard pair sensor
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa.clipped.fa
1606s 
succeeded(16)   30.1887% completed.    
succeeded(17)   32.0755% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1606s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1606s bt2 index files: $VAR1 = [];
1606s Note - bowtie-build indices do not yet exist. Indexing genome now.
1606s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1606s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1606s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1606s bt2 index files: $VAR1 = [];
1606s Note - bowtie-build indices do not yet exist. Indexing genome now.
1606s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1607s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1607s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1607s 34 reads; of these:
1607s   34 (100.00%) were unpaired; of these:
1607s     1 (2.94%) aligned 0 times
1607s     33 (97.06%) aligned exactly 1 time
1607s     0 (0.00%) aligned >1 times
1607s 97.06% overall alignment rate
1607s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1607s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1607s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1607s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1607s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1607s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1607s 
1607s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1607s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1607s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1607s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1607s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1607s -processing jaccard pair sensor
1607s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1607s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa.clipped.fa
1607s 818 reads; of these:
1607s   818 (100.00%) were unpaired; of these:
1607s     1 (0.12%) aligned 0 times
1607s     758 (92.67%) aligned exactly 1 time
1607s     59 (7.21%) aligned >1 times
1607s 99.88% overall alignment rate
1607s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1607s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1607s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1607s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1607s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1607s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1607s 
1607s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1607s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1607s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1607s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1607s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1607s -processing jaccard pair sensor
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa.clipped.fa
1608s 
succeeded(18)   33.9623% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1608s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1608s bt2 index files: $VAR1 = [];
1608s Note - bowtie-build indices do not yet exist. Indexing genome now.
1608s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1609s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1609s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1609s 85 reads; of these:
1609s   85 (100.00%) were unpaired; of these:
1609s     6 (7.06%) aligned 0 times
1609s     79 (92.94%) aligned exactly 1 time
1609s     0 (0.00%) aligned >1 times
1609s 92.94% overall alignment rate
1609s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1609s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1609s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1609s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1609s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1609s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1609s 
1609s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1609s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1609s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1609s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1609s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1609s -processing jaccard pair sensor
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa.clipped.fa
1610s 
succeeded(19)   35.8491% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1610s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1610s bt2 index files: $VAR1 = [];
1610s Note - bowtie-build indices do not yet exist. Indexing genome now.
1610s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1611s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1611s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1611s 538 reads; of these:
1611s   538 (100.00%) were unpaired; of these:
1611s     2 (0.37%) aligned 0 times
1611s     530 (98.51%) aligned exactly 1 time
1611s     6 (1.12%) aligned >1 times
1611s 99.63% overall alignment rate
1611s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1611s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1611s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1611s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1611s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1611s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1611s 
1611s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1611s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1611s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1611s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1611s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1611s -processing jaccard pair sensor
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa.clipped.fa
1612s 
succeeded(20)   37.7359% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1612s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1612s bt2 index files: $VAR1 = [];
1612s Note - bowtie-build indices do not yet exist. Indexing genome now.
1612s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1612s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1612s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1612s 76 reads; of these:
1612s   76 (100.00%) were unpaired; of these:
1612s     0 (0.00%) aligned 0 times
1612s     76 (100.00%) aligned exactly 1 time
1612s     0 (0.00%) aligned >1 times
1612s 100.00% overall alignment rate
1612s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1612s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1612s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1612s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1612s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1612s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1612s 
1612s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1612s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1612s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1612s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1612s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1612s -processing jaccard pair sensor
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa.clipped.fa
1614s 
succeeded(21)   39.6226% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1614s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1614s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1614s bt2 index files: $VAR1 = [];
1614s Note - bowtie-build indices do not yet exist. Indexing genome now.
1614s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1615s 
succeeded(22)   41.5094% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1615s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1615s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1615s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1615s bt2 index files: $VAR1 = [];
1615s Note - bowtie-build indices do not yet exist. Indexing genome now.
1615s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1615s 26 reads; of these:
1615s   26 (100.00%) were unpaired; of these:
1615s     6 (23.08%) aligned 0 times
1615s     20 (76.92%) aligned exactly 1 time
1615s     0 (0.00%) aligned >1 times
1615s 76.92% overall alignment rate
1615s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1615s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1615s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1615s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1615s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1615s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1615s 
1615s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1615s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1615s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1615s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1615s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1615s -processing jaccard pair sensor
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa.clipped.fa
1615s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1615s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1615s 18 reads; of these:
1615s   18 (100.00%) were unpaired; of these:
1615s     1 (5.56%) aligned 0 times
1615s     17 (94.44%) aligned exactly 1 time
1615s     0 (0.00%) aligned >1 times
1615s 94.44% overall alignment rate
1615s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1615s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1615s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1615s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1615s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1615s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1615s 
1615s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1615s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1615s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1615s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1615s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1615s -processing jaccard pair sensor
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa.clipped.fa
1617s 
succeeded(23)   43.3962% completed.    
succeeded(24)   45.283% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1617s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s bt2 index files: $VAR1 = [];
1617s Note - bowtie-build indices do not yet exist. Indexing genome now.
1617s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1617s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s bt2 index files: $VAR1 = [];
1617s Note - bowtie-build indices do not yet exist. Indexing genome now.
1617s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1617s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1617s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1617s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1617s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1617s 16 reads; of these:
1617s   16 (100.00%) were unpaired; of these:
1617s     0 (0.00%) aligned 0 times
1617s     14 (87.50%) aligned exactly 1 time
1617s     2 (12.50%) aligned >1 times
1617s 100.00% overall alignment rate
1617s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1617s 98 reads; of these:
1617s   98 (100.00%) were unpaired; of these:
1617s     0 (0.00%) aligned 0 times
1617s     98 (100.00%) aligned exactly 1 time
1617s     0 (0.00%) aligned >1 times
1617s 100.00% overall alignment rate
1617s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1617s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1617s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1617s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1617s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1617s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1617s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1617s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1617s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1617s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1617s 
1617s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1617s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1617s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1617s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1617s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1617s 
1617s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1617s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1617s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1617s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1617s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1617s -processing jaccard pair sensor
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1618s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1618s -processing jaccard pair sensor
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa.clipped.fa
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa.clipped.fa
1618s 
succeeded(25)   47.1698% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1618s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1618s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1618s bt2 index files: $VAR1 = [];
1618s Note - bowtie-build indices do not yet exist. Indexing genome now.
1618s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1619s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1619s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1619s 145 reads; of these:
1619s   145 (100.00%) were unpaired; of these:
1619s     1 (0.69%) aligned 0 times
1619s     144 (99.31%) aligned exactly 1 time
1619s     0 (0.00%) aligned >1 times
1619s 99.31% overall alignment rate
1619s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1619s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1619s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1619s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1619s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1619s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1619s 
1619s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1619s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1619s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1619s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1619s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1619s -processing jaccard pair sensor
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa.clipped.fa
1620s 
succeeded(26)   49.0566% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1620s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1620s bt2 index files: $VAR1 = [];
1620s Note - bowtie-build indices do not yet exist. Indexing genome now.
1620s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1620s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1620s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1620s 454 reads; of these:
1620s   454 (100.00%) were unpaired; of these:
1620s     1 (0.22%) aligned 0 times
1620s     368 (81.06%) aligned exactly 1 time
1620s     85 (18.72%) aligned >1 times
1620s 99.78% overall alignment rate
1620s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1620s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1620s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1620s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1620s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1620s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1620s 
1620s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1620s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1620s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1620s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1620s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1620s -processing jaccard pair sensor
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa.clipped.fa
1621s 
succeeded(27)   50.9434% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1621s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1622s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1622s bt2 index files: $VAR1 = [];
1622s Note - bowtie-build indices do not yet exist. Indexing genome now.
1622s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1622s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1622s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1622s 10 reads; of these:
1622s   10 (100.00%) were unpaired; of these:
1622s     3 (30.00%) aligned 0 times
1622s     7 (70.00%) aligned exactly 1 time
1622s     0 (0.00%) aligned >1 times
1622s 70.00% overall alignment rate
1622s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1622s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1622s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1622s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1622s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1622s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1622s 
1622s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1622s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1622s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1622s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1622s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1622s -processing jaccard pair sensor
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1622s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa.clipped.fa
1623s 
succeeded(28)   52.8302% completed.    
succeeded(29)   54.717% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1623s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s bt2 index files: $VAR1 = [];
1623s Note - bowtie-build indices do not yet exist. Indexing genome now.
1623s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1623s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s bt2 index files: $VAR1 = [];
1623s Note - bowtie-build indices do not yet exist. Indexing genome now.
1623s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1623s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1623s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1623s 46 reads; of these:
1623s   46 (100.00%) were unpaired; of these:
1623s     0 (0.00%) aligned 0 times
1623s     44 (95.65%) aligned exactly 1 time
1623s     2 (4.35%) aligned >1 times
1623s 100.00% overall alignment rate
1623s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1623s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1623s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1623s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1623s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1623s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1623s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1623s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1623s 
1623s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1623s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1623s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1623s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1624s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1624s -processing jaccard pair sensor
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1624s 1733 reads; of these:
1624s   1733 (100.00%) were unpaired; of these:
1624s     0 (0.00%) aligned 0 times
1624s     794 (45.82%) aligned exactly 1 time
1624s     939 (54.18%) aligned >1 times
1624s 100.00% overall alignment rate
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1624s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa.clipped.fa
1624s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1624s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1624s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1624s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1624s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1624s 
1624s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1624s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1624s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1624s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1624s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1624s -processing jaccard pair sensor
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1624s 
[1000 lines read]  scaff:a22;2 lend:1  rend:49     
[2000 lines read]  scaff:a3;97 lend:65  rend:131     
[3000 lines read]  scaff:a9;12 lend:1  rend:38     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa.clipped.fa
1626s 
succeeded(30)   56.6038% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1626s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1626s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1626s bt2 index files: $VAR1 = [];
1626s Note - bowtie-build indices do not yet exist. Indexing genome now.
1626s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1626s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1626s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1626s 277 reads; of these:
1626s   277 (100.00%) were unpaired; of these:
1626s     0 (0.00%) aligned 0 times
1626s     277 (100.00%) aligned exactly 1 time
1626s     0 (0.00%) aligned >1 times
1626s 100.00% overall alignment rate
1626s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1626s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1626s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1626s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1626s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1626s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1626s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1627s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1627s 
1627s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1627s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1627s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1627s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1627s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1627s -processing jaccard pair sensor
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa.clipped.fa
1627s 
succeeded(31)   58.4906% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1627s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1627s bt2 index files: $VAR1 = [];
1627s Note - bowtie-build indices do not yet exist. Indexing genome now.
1627s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1628s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1628s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1628s 5664 reads; of these:
1628s   5664 (100.00%) were unpaired; of these:
1628s     8 (0.14%) aligned 0 times
1628s     3217 (56.80%) aligned exactly 1 time
1628s     2439 (43.06%) aligned >1 times
1628s 99.86% overall alignment rate
1628s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1628s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1629s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1629s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1629s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1629s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1629s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1629s 
1629s 
succeeded(32)   60.3774% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1629s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1629s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1629s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1629s bt2 index files: $VAR1 = [];
1629s Note - bowtie-build indices do not yet exist. Indexing genome now.
1629s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1629s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1629s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1629s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1629s -processing jaccard pair sensor
1629s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1629s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1629s 30 reads; of these:
1629s   30 (100.00%) were unpaired; of these:
1629s     9 (30.00%) aligned 0 times
1629s     21 (70.00%) aligned exactly 1 time
1629s     0 (0.00%) aligned >1 times
1629s 70.00% overall alignment rate
1629s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1630s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1630s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1630s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1630s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1630s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1630s 
1630s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1630s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1630s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1630s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1630s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1630s -processing jaccard pair sensor
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa.clipped.fa
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1630s 
[1000 lines read]  scaff:a1;95 lend:117  rend:350     
[2000 lines read]  scaff:a1;95 lend:928  rend:1277     
[3000 lines read]  scaff:a1;95 lend:1591  rend:1658     
[4000 lines read]  scaff:a26;2 lend:1  rend:43     
[5000 lines read]  scaff:a2;68 lend:175  rend:389     
[6000 lines read]  scaff:a39;2 lend:1  rend:42     
[7000 lines read]  scaff:a6;42 lend:15  rend:68     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa.clipped.fa
1631s 
succeeded(33)   62.2641% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1631s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1631s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1631s bt2 index files: $VAR1 = [];
1631s Note - bowtie-build indices do not yet exist. Indexing genome now.
1631s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1631s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1631s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1631s 997 reads; of these:
1631s   997 (100.00%) were unpaired; of these:
1631s     3 (0.30%) aligned 0 times
1631s     568 (56.97%) aligned exactly 1 time
1631s     426 (42.73%) aligned >1 times
1631s 99.70% overall alignment rate
1631s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1631s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1631s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1631s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1631s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1631s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1631s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1631s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1631s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1631s 
1632s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1632s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1632s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1632s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1632s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1632s -processing jaccard pair sensor
1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1632s 
[1000 lines read]  scaff:a6;10 lend:1  rend:64     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa.clipped.fa
1636s 
succeeded(34)   64.1509% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1636s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s bt2 index files: $VAR1 = [];
1636s Note - bowtie-build indices do not yet exist. Indexing genome now.
1636s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s 
succeeded(35)   66.0377% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1636s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1636s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1636s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s bt2 index files: $VAR1 = [];
1636s Note - bowtie-build indices do not yet exist. Indexing genome now.
1636s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1636s 907 reads; of these:
1636s   907 (100.00%) were unpaired; of these:
1636s     2 (0.22%) aligned 0 times
1636s     839 (92.50%) aligned exactly 1 time
1636s     66 (7.28%) aligned >1 times
1636s 99.78% overall alignment rate
1636s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1636s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1636s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1636s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1636s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1636s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1636s 
1636s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1636s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1636s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1636s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1636s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1636s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1636s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1636s -processing jaccard pair sensor
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1636s 77 reads; of these:
1636s   77 (100.00%) were unpaired; of these:
1636s     2 (2.60%) aligned 0 times
1636s     75 (97.40%) aligned exactly 1 time
1636s     0 (0.00%) aligned >1 times
1636s 97.40% overall alignment rate
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1636s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa.clipped.fa
1636s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1636s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1636s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1636s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1637s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1637s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1637s 
1637s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1637s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1637s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1637s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1637s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1637s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1637s -processing jaccard pair sensor
1637s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1637s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1637s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa.clipped.fa
1639s 
succeeded(36)   67.9245% completed.    
succeeded(37)   69.8113% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1639s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s bt2 index files: $VAR1 = [];
1639s Note - bowtie-build indices do not yet exist. Indexing genome now.
1639s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1639s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s bt2 index files: $VAR1 = [];
1639s Note - bowtie-build indices do not yet exist. Indexing genome now.
1639s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1639s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1639s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1639s 10 reads; of these:
1639s   10 (100.00%) were unpaired; of these:
1639s     2 (20.00%) aligned 0 times
1639s     8 (80.00%) aligned exactly 1 time
1639s     0 (0.00%) aligned >1 times
1639s 80.00% overall alignment rate
1639s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1639s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1639s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1639s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1639s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1639s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1639s 
1639s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1639s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1639s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1639s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1639s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1639s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1639s -processing jaccard pair sensor
1639s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa.clipped.fa
1640s 1811 reads; of these:
1640s   1811 (100.00%) were unpaired; of these:
1640s     6 (0.33%) aligned 0 times
1640s     1189 (65.65%) aligned exactly 1 time
1640s     616 (34.01%) aligned >1 times
1640s 99.67% overall alignment rate
1640s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1640s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1640s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1640s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1640s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1640s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1640s 
1640s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1640s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1640s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1640s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1640s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1640s -processing jaccard pair sensor
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1640s 
[1000 lines read]  scaff:a1;56 lend:769  rend:1089     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa.clipped.fa
1641s 
succeeded(38)   71.6981% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1641s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1641s bt2 index files: $VAR1 = [];
1641s Note - bowtie-build indices do not yet exist. Indexing genome now.
1641s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1641s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1641s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1641s 27 reads; of these:
1641s   27 (100.00%) were unpaired; of these:
1641s     6 (22.22%) aligned 0 times
1641s     21 (77.78%) aligned exactly 1 time
1641s     0 (0.00%) aligned >1 times
1641s 77.78% overall alignment rate
1641s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1641s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1641s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1641s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1641s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1641s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1641s 
1641s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1641s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1641s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1641s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1641s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1641s -processing jaccard pair sensor
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa.clipped.fa
1643s 
succeeded(39)   73.5849% completed.    
succeeded(40)   75.4717% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1643s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s bt2 index files: $VAR1 = [];
1643s Note - bowtie-build indices do not yet exist. Indexing genome now.
1643s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1643s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1643s 20 reads; of these:
1643s   20 (100.00%) were unpaired; of these:
1643s     12 (60.00%) aligned 0 times
1643s     8 (40.00%) aligned exactly 1 time
1643s     0 (0.00%) aligned >1 times
1643s 40.00% overall alignment rate
1643s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1643s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1643s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1643s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1643s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1643s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1643s bt2 index files: $VAR1 = [];
1643s Note - bowtie-build indices do not yet exist. Indexing genome now.
1643s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1643s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1643s 
1643s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1643s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1643s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1643s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1643s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1643s -processing jaccard pair sensor
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa.clipped.fa
1643s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1643s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1644s 2557 reads; of these:
1644s   2557 (100.00%) were unpaired; of these:
1644s     11 (0.43%) aligned 0 times
1644s     1332 (52.09%) aligned exactly 1 time
1644s     1214 (47.48%) aligned >1 times
1644s 99.57% overall alignment rate
1644s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1644s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1644s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1644s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1644s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1644s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1644s 
1644s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1644s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1644s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1644s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1644s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1644s -processing jaccard pair sensor
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1644s 
[1000 lines read]  scaff:a1;81 lend:250  rend:502     
[2000 lines read]  scaff:a22;2 lend:4  rend:34     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa.clipped.fa
1645s 
succeeded(41)   77.3585% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1645s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1645s bt2 index files: $VAR1 = [];
1645s Note - bowtie-build indices do not yet exist. Indexing genome now.
1645s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1645s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1645s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1645s 115 reads; of these:
1645s   115 (100.00%) were unpaired; of these:
1645s     6 (5.22%) aligned 0 times
1645s     109 (94.78%) aligned exactly 1 time
1645s     0 (0.00%) aligned >1 times
1645s 94.78% overall alignment rate
1645s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1645s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1645s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1645s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1645s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1645s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1645s 
1645s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1645s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1645s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1645s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1645s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1645s -processing jaccard pair sensor
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa.clipped.fa
1647s 
succeeded(42)   79.2453% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1647s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1647s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1647s bt2 index files: $VAR1 = [];
1647s Note - bowtie-build indices do not yet exist. Indexing genome now.
1647s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1647s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1647s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1647s 26 reads; of these:
1647s   26 (100.00%) were unpaired; of these:
1647s     17 (65.38%) aligned 0 times
1647s     9 (34.62%) aligned exactly 1 time
1647s     0 (0.00%) aligned >1 times
1647s 34.62% overall alignment rate
1647s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1647s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1647s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1647s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1647s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1648s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1648s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1648s 
1648s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1648s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1648s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1648s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1648s 
succeeded(43)   81.1321% completed.    CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1648s -processing jaccard pair sensor
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa.clipped.fa
1648s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1648s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1648s bt2 index files: $VAR1 = [];
1648s Note - bowtie-build indices do not yet exist. Indexing genome now.
1648s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1648s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1648s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1648s 953 reads; of these:
1648s   953 (100.00%) were unpaired; of these:
1648s     4 (0.42%) aligned 0 times
1648s     555 (58.24%) aligned exactly 1 time
1648s     394 (41.34%) aligned >1 times
1648s 99.58% overall alignment rate
1648s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1648s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1648s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1648s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1648s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1648s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1648s 
1648s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1648s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1648s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1648s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1648s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1648s -processing jaccard pair sensor
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1649s 
[1000 lines read]  scaff:a7;10 lend:1  rend:54     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1649s 
succeeded(44)   83.0189% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa.clipped.fa
1649s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1649s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1649s bt2 index files: $VAR1 = [];
1649s Note - bowtie-build indices do not yet exist. Indexing genome now.
1649s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1649s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1649s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1649s 24 reads; of these:
1649s   24 (100.00%) were unpaired; of these:
1649s     1 (4.17%) aligned 0 times
1649s     23 (95.83%) aligned exactly 1 time
1649s     0 (0.00%) aligned >1 times
1649s 95.83% overall alignment rate
1649s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1649s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1649s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1649s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1649s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1649s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1649s 
1649s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1649s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1649s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1649s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1649s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1649s -processing jaccard pair sensor
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa.clipped.fa
1652s 
succeeded(45)   84.9057% completed.    
succeeded(46)   86.7924% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1652s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s bt2 index files: $VAR1 = [];
1652s Note - bowtie-build indices do not yet exist. Indexing genome now.
1652s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1652s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1652s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s bt2 index files: $VAR1 = [];
1652s Note - bowtie-build indices do not yet exist. Indexing genome now.
1652s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1652s 51 reads; of these:
1652s   51 (100.00%) were unpaired; of these:
1652s     4 (7.84%) aligned 0 times
1652s     47 (92.16%) aligned exactly 1 time
1652s     0 (0.00%) aligned >1 times
1652s 92.16% overall alignment rate
1652s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1652s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1652s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1652s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1652s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1652s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1652s 
1652s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1652s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1652s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1652s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1652s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1652s -processing jaccard pair sensor
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1652s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa.clipped.fa
1652s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1652s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1653s 2128 reads; of these:
1653s   2128 (100.00%) were unpaired; of these:
1653s     6 (0.28%) aligned 0 times
1653s     1722 (80.92%) aligned exactly 1 time
1653s     400 (18.80%) aligned >1 times
1653s 99.72% overall alignment rate
1653s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1653s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1653s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1653s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1653s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1653s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1653s 
1653s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1653s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1653s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1653s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1653s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1653s -processing jaccard pair sensor
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1653s 
[1000 lines read]  scaff:a1;40 lend:1330  rend:1645     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa.clipped.fa
1654s 
succeeded(47)   88.6792% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1654s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1654s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1654s bt2 index files: $VAR1 = [];
1654s Note - bowtie-build indices do not yet exist. Indexing genome now.
1654s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1655s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1655s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1655s 54 reads; of these:
1655s   54 (100.00%) were unpaired; of these:
1655s     9 (16.67%) aligned 0 times
1655s     45 (83.33%) aligned exactly 1 time
1655s     0 (0.00%) aligned >1 times
1655s 83.33% overall alignment rate
1655s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1655s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1655s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1655s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1655s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1655s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1655s 
1655s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1655s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1655s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1655s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1655s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1655s -processing jaccard pair sensor
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa.clipped.fa
1657s 
succeeded(48)   90.566% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1657s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s bt2 index files: $VAR1 = [];
1657s Note - bowtie-build indices do not yet exist. Indexing genome now.
1657s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s 
succeeded(49)   92.4528% completed.    CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1657s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1657s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1657s 10 reads; of these:
1657s   10 (100.00%) were unpaired; of these:
1657s     7 (70.00%) aligned 0 times
1657s     3 (30.00%) aligned exactly 1 time
1657s     0 (0.00%) aligned >1 times
1657s 30.00% overall alignment rate
1657s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1657s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s bt2 index files: $VAR1 = [];
1657s Note - bowtie-build indices do not yet exist. Indexing genome now.
1657s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1657s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1657s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1657s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1657s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1657s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1657s 
1657s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1657s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1657s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1657s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1657s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1657s -processing jaccard pair sensor
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa.clipped.fa
1657s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1657s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1658s 26 reads; of these:
1658s   26 (100.00%) were unpaired; of these:
1658s     0 (0.00%) aligned 0 times
1658s     26 (100.00%) aligned exactly 1 time
1658s     0 (0.00%) aligned >1 times
1658s 100.00% overall alignment rate
1658s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1658s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1658s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1658s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1658s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1658s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1658s 
1658s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1658s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1658s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1658s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1658s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1658s -processing jaccard pair sensor
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa.clipped.fa
1659s 
succeeded(50)   94.3396% completed.    CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1659s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1659s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1659s bt2 index files: $VAR1 = [];
1659s Note - bowtie-build indices do not yet exist. Indexing genome now.
1659s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1659s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1659s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1660s 
succeeded(51)   96.2264% completed.    4380 reads; of these:
1660s   4380 (100.00%) were unpaired; of these:
1660s     10 (0.23%) aligned 0 times
1660s     2462 (56.21%) aligned exactly 1 time
1660s     1908 (43.56%) aligned >1 times
1660s 99.77% overall alignment rate
1660s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1660s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads --CPU 1 --target /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
1660s CMD: samtools faidx /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1660s bt2 index files: $VAR1 = [];
1660s Note - bowtie-build indices do not yet exist. Indexing genome now.
1660s CMD: bowtie2-build -q /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa
1660s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1660s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1660s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1660s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
1660s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1660s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
1660s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1660s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1660s 
1660s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
1660s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
1660s 16 reads; of these:
1660s   16 (100.00%) were unpaired; of these:
1660s     10 (62.50%) aligned 0 times
1660s     6 (37.50%) aligned exactly 1 time
1660s     0 (0.00%) aligned >1 times
1660s 37.50% overall alignment rate
1660s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
1660s CMD: samtools view -bt /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1660s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1660s CMD: samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
1660s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1660s -cleaning up and removing intermediate file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
1660s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
1660s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1660s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1660s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1660s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1660s 
1660s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1660s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1660s -processing jaccard pair sensor
1660s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
1660s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
1660s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1660s -processing jaccard pair sensor
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1660s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa.clipped.fa
1661s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
1661s 
[1000 lines read]  scaff:a1;135 lend:78  rend:364     
[2000 lines read]  scaff:a1;135 lend:614  rend:934     
[3000 lines read]  scaff:a20;2 lend:7  rend:49     
[4000 lines read]  scaff:a34;2 lend:1  rend:36     
[5000 lines read]  scaff:a5;2 lend:1  rend:43     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1661s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa  bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa.clipped.fa
1664s 
succeeded(52)   98.1132% completed.    
succeeded(53)   100% completed.    
1664s 
1664s All commands completed successfully. :-)
1664s 
1664s Saturday, March 15, 2025: 23:58:39	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp
1664s Saturday, March 15, 2025: 23:58:39	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map
1664s 
1664s 
1664s Finished. See /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts
1664s 
1664s 
1664s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta"
1664s asmsize=$(wc -c <"${outfile}")
1664s if [ $asmsize -le 50000 ]; then
1664s     echo "Error, ${outfile} potentially incomplete"
1664s     exit 1
1664s else
1664s     echo "ok"
1664s     exit 0
1664s fi
1664s #!/bin/bash -ve
1664s 
1664s 
1664s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam transAligns.cSorted.bam --max_memory 2G  --output test_GG_use_small_multiscaff_bam_trinity_outdir
1664s ok
1664s ./run_small_GG_mutliScaff_test.sh
1664s 
1664s 
1664s      ______  ____   ____  ____   ____  ______  __ __
1664s     |      ||    \ |    ||    \ |    ||      ||  |  |
1664s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1664s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1664s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1664s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1664s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1664s 
1664s     Trinity-v2.15.2
1664s 
1664s 
1664s 
1664s Saturday, March 15, 2025: 23:58:39	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam
1664s -appears to be a coordinate sorted bam file. ok.
1664s Saturday, March 15, 2025: 23:58:39	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir
1664s 
1664s 
1664s ----------------------------------------------------------------------------------
1664s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1664s ----------------------------------------------------------------------------------
1664s 
1664s -found paired-end aligned read. Running in paired-end mode.
1664s Saturday, March 15, 2025: 23:58:39	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam
1666s Done with chr TRINITY_DN0_c0_g1_i1.
1666s Done with chr TRINITY_DN10_c0_g1_i1.
1666s Done with chr TRINITY_DN12_c0_g1_i1.
1666s Done with chr TRINITY_DN12_c0_g1_i2.
1666s Done with chr TRINITY_DN14_c0_g1_i1.
1666s Done with chr TRINITY_DN14_c0_g2_i1.
1666s Done with chr TRINITY_DN15_c0_g1_i1.
1666s Done with chr TRINITY_DN16_c0_g1_i1.
1666s Done with chr TRINITY_DN16_c0_g2_i1.
1666s Done with chr TRINITY_DN18_c0_g1_i1.
1666s Done with chr TRINITY_DN18_c0_g1_i2.
1666s Done with chr TRINITY_DN19_c0_g1_i1.
1666s Done with chr TRINITY_DN20_c0_g1_i1.
1666s Done with chr TRINITY_DN20_c0_g2_i1.
1666s Done with chr TRINITY_DN20_c0_g1_i2.
1666s Done with chr TRINITY_DN20_c0_g1_i3.
1666s Done with chr TRINITY_DN20_c0_g1_i4.
1666s Done with chr TRINITY_DN20_c0_g1_i5.
1666s Done with chr TRINITY_DN20_c0_g1_i6.
1666s Done with chr TRINITY_DN20_c0_g1_i7.
1666s Done with chr TRINITY_DN21_c0_g1_i1.
1666s Done with chr TRINITY_DN21_c0_g1_i2.
1666s Done with chr TRINITY_DN22_c0_g1_i1.
1666s Done with chr TRINITY_DN22_c0_g2_i1.
1666s Done with chr TRINITY_DN22_c0_g3_i1.
1666s Done with chr TRINITY_DN22_c0_g4_i1.
1666s Done with chr TRINITY_DN22_c0_g3_i2.
1666s Done with chr TRINITY_DN22_c0_g3_i3.
1666s Done with chr TRINITY_DN22_c0_g3_i4.
1666s Done with chr TRINITY_DN22_c0_g5_i1.
1666s Done with chr TRINITY_DN22_c0_g6_i1.
1666s Done with chr TRINITY_DN22_c0_g3_i5.
1666s Done with chr TRINITY_DN22_c0_g7_i1.
1666s Done with chr TRINITY_DN23_c0_g1_i1.
1666s Done with chr TRINITY_DN23_c0_g2_i1.
1666s Done with chr TRINITY_DN23_c0_g1_i2.
1666s Done with chr TRINITY_DN23_c0_g3_i1.
1666s Done with chr TRINITY_DN23_c0_g4_i1.
1666s Done with chr TRINITY_DN23_c0_g5_i1.
1666s Done with chr TRINITY_DN23_c0_g1_i3.
1666s Done with chr TRINITY_DN23_c0_g1_i4.
1666s Done with chr TRINITY_DN24_c0_g1_i1.
1666s Done with chr TRINITY_DN24_c0_g2_i1.
1666s Done with chr TRINITY_DN24_c0_g3_i1.
1666s Done with chr TRINITY_DN24_c0_g3_i2.
1666s Done with chr TRINITY_DN25_c1_g1_i1.
1666s Done with chr TRINITY_DN25_c1_g1_i2.
1666s Done with chr TRINITY_DN25_c1_g1_i3.
1666s Done with chr TRINITY_DN25_c1_g1_i4.
1666s Done with chr TRINITY_DN25_c1_g1_i5.
1666s Done with chr TRINITY_DN26_c0_g1_i1.
1666s Done with chr TRINITY_DN26_c0_g1_i2.
1666s Done with chr TRINITY_DN26_c1_g1_i1.
1666s Done with chr TRINITY_DN26_c1_g1_i2.
1666s Done with chr TRINITY_DN26_c1_g1_i3.
1666s Done with chr TRINITY_DN26_c1_g1_i4.
1666s Done with chr TRINITY_DN26_c1_g1_i5.
1666s Done with chr TRINITY_DN26_c1_g1_i6.
1666s Done with chr TRINITY_DN26_c1_g2_i1.
1666s Done with chr TRINITY_DN26_c1_g1_i7.
1666s Done with chr TRINITY_DN26_c1_g3_i1.
1666s Done with chr TRINITY_DN26_c1_g1_i8.
1666s Done with chr TRINITY_DN26_c1_g1_i9.
1666s Done with chr TRINITY_DN26_c1_g1_i10.
1666s Done with chr TRINITY_DN26_c1_g1_i11.
1666s Done with chr TRINITY_DN26_c1_g3_i2.
1666s Done with chr TRINITY_DN26_c1_g1_i12.
1666s Done with chr TRINITY_DN26_c1_g4_i1.
1666s Done with chr TRINITY_DN26_c1_g1_i13.
1666s Done with chr TRINITY_DN26_c1_g1_i14.
1666s Done with chr TRINITY_DN26_c1_g1_i15.
1666s Done with chr TRINITY_DN26_c1_g1_i16.
1666s Done with chr TRINITY_DN26_c1_g1_i17.
1666s Done with chr TRINITY_DN26_c1_g1_i18.
1666s Done with chr TRINITY_DN26_c1_g3_i3.
1666s Done with chr TRINITY_DN26_c1_g1_i19.
1666s Done with chr TRINITY_DN26_c1_g3_i4.
1666s Done with chr TRINITY_DN26_c1_g5_i1.
1666s Done with chr TRINITY_DN26_c1_g1_i20.
1666s Done with chr TRINITY_DN26_c1_g1_i21.
1666s Done with chr TRINITY_DN26_c1_g3_i5.
1666s Done with chr TRINITY_DN26_c2_g1_i1.
1666s Done with chr TRINITY_DN26_c2_g1_i2.
1666s Done with chr TRINITY_DN26_c2_g2_i1.
1666s Done with chr TRINITY_DN26_c2_g3_i1.
1666s Done with chr TRINITY_DN26_c2_g1_i3.
1666s Done with chr TRINITY_DN26_c2_g1_i4.
1666s Done with chr TRINITY_DN26_c2_g1_i5.
1666s Done with chr TRINITY_DN27_c0_g1_i1.
1666s Done with chr TRINITY_DN4_c0_g1_i1.
1666s Done with chr TRINITY_DN5_c0_g1_i1.
1666s Saturday, March 15, 2025: 23:58:41	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok
1666s Saturday, March 15, 2025: 23:58:41	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam -I 1000 --sort_buffer 2G --CPU 2 
1666s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 2G --sam transAligns.cSorted.bam.norm_200.bam --min_insert_size 1 --max_insert_size 1000 
1666s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords
1666s 
1672s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok
1672s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k2,2 -k4,4n transAligns.cSorted.bam.norm_200.bam.read_coords > transAligns.cSorted.bam.norm_200.bam.read_coords.sort_by_readname
1672s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.read_coords.sort_by_readname
1673s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k3,3n transAligns.cSorted.bam.norm_200.bam.frag_coords > transAligns.cSorted.bam.norm_200.bam.frag_coords.coord_sorted
1673s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl transAligns.cSorted.bam.norm_200.bam.frag_coords > transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig
1676s 
[1000 lines read]  scaff:TRINITY_DN20_c0_g1_i3 lend:239  rend:679     
[2000 lines read]  scaff:TRINITY_DN20_c0_g1_i4 lend:1507  rend:1760     
[3000 lines read]  scaff:TRINITY_DN20_c0_g1_i6 lend:1153  rend:1530     
[4000 lines read]  scaff:TRINITY_DN20_c0_g1_i7 lend:2556  rend:2779     
[5000 lines read]  scaff:TRINITY_DN21_c0_g1_i2 lend:2348  rend:2568     
[6000 lines read]  scaff:TRINITY_DN22_c0_g3_i1 lend:829  rend:1294     
[7000 lines read]  scaff:TRINITY_DN22_c0_g3_i1 lend:1692  rend:2029     
[8000 lines read]  scaff:TRINITY_DN22_c0_g3_i3 lend:157  rend:523     
[9000 lines read]  scaff:TRINITY_DN22_c0_g3_i3 lend:1182  rend:1523     
[10000 lines read]  scaff:TRINITY_DN22_c0_g3_i3 lend:1902  rend:2126     
[11000 lines read]  scaff:TRINITY_DN22_c0_g3_i4 lend:1028  rend:1456     
[12000 lines read]  scaff:TRINITY_DN22_c0_g3_i4 lend:1758  rend:1956     
[13000 lines read]  scaff:TRINITY_DN22_c0_g3_i5 lend:948  rend:1211     
[14000 lines read]  scaff:TRINITY_DN22_c0_g3_i5 lend:1737  rend:1980     
[15000 lines read]  scaff:TRINITY_DN23_c0_g1_i2 lend:706  rend:1098     
[16000 lines read]  scaff:TRINITY_DN23_c0_g1_i3 lend:463  rend:897     
[17000 lines read]  scaff:TRINITY_DN24_c0_g1_i1 lend:21  rend:96     
[18000 lines read]  scaff:TRINITY_DN24_c0_g3_i1 lend:2084  rend:2302     
[19000 lines read]  scaff:TRINITY_DN24_c0_g3_i1 lend:3550  rend:3977     
[20000 lines read]  scaff:TRINITY_DN24_c0_g3_i1 lend:4820  rend:5143     
[21000 lines read]  scaff:TRINITY_DN24_c0_g3_i1 lend:5830  rend:6117     
[22000 lines read]  scaff:TRINITY_DN24_c0_g3_i1 lend:6807  rend:7101     
[23000 lines read]  scaff:TRINITY_DN25_c1_g1_i1 lend:348  rend:648     
[24000 lines read]  scaff:TRINITY_DN25_c1_g1_i2 lend:106  rend:469     
[25000 lines read]  scaff:TRINITY_DN25_c1_g1_i2 lend:699  rend:940     
[26000 lines read]  scaff:TRINITY_DN25_c1_g1_i2 lend:1478  rend:1730     
[27000 lines read]  scaff:TRINITY_DN25_c1_g1_i2 lend:2198  rend:2415     
[28000 lines read]  scaff:TRINITY_DN25_c1_g1_i2 lend:2932  rend:3417     
[29000 lines read]  scaff:TRINITY_DN25_c1_g1_i3 lend:172  rend:350     
[30000 lines read]  scaff:TRINITY_DN25_c1_g1_i3 lend:860  rend:1098     
[31000 lines read]  scaff:TRINITY_DN25_c1_g1_i3 lend:1632  rend:2117     
[32000 lines read]  scaff:TRINITY_DN25_c1_g1_i3 lend:2355  rend:2639     
[33000 lines read]  scaff:TRINITY_DN25_c1_g1_i3 lend:3089  rend:3401     
[34000 lines read]  scaff:TRINITY_DN25_c1_g1_i4 lend:179  rend:396     
[35000 lines read]  scaff:TRINITY_DN25_c1_g1_i4 lend:883  rend:1108     
[36000 lines read]  scaff:TRINITY_DN25_c1_g1_i4 lend:1649  rend:2110     
[37000 lines read]  scaff:TRINITY_DN25_c1_g1_i4 lend:2375  rend:2701     
[38000 lines read]  scaff:TRINITY_DN25_c1_g1_i4 lend:3111  rend:3471     
[39000 lines read]  scaff:TRINITY_DN26_c0_g1_i1 lend:1083  rend:1530     
[40000 lines read]  scaff:TRINITY_DN26_c0_g1_i1 lend:3886  rend:4099     
[41000 lines read]  scaff:TRINITY_DN26_c0_g1_i2 lend:2009  rend:2185     
[42000 lines read]  scaff:TRINITY_DN26_c0_g1_i2 lend:5292  rend:5468     
[43000 lines read]  scaff:TRINITY_DN26_c1_g1_i1 lend:3670  rend:3941     
[44000 lines read]  scaff:TRINITY_DN26_c1_g1_i1 lend:6356  rend:6724     
[45000 lines read]  scaff:TRINITY_DN26_c1_g1_i10 lend:917  rend:1161     
[46000 lines read]  scaff:TRINITY_DN26_c1_g1_i10 lend:4502  rend:4753     
[47000 lines read]  scaff:TRINITY_DN26_c1_g1_i10 lend:7064  rend:7139     
[48000 lines read]  scaff:TRINITY_DN26_c1_g1_i11 lend:1958  rend:2158     
[49000 lines read]  scaff:TRINITY_DN26_c1_g1_i11 lend:5030  rend:5273     
[50000 lines read]  scaff:TRINITY_DN26_c1_g1_i12 lend:2479  rend:2741     
[51000 lines read]  scaff:TRINITY_DN26_c1_g1_i12 lend:5516  rend:5882     
[52000 lines read]  scaff:TRINITY_DN26_c1_g1_i12 lend:7708  rend:8081     
[53000 lines read]  scaff:TRINITY_DN26_c1_g1_i13 lend:3311  rend:3522     
[54000 lines read]  scaff:TRINITY_DN26_c1_g1_i13 lend:6051  rend:6401     
[55000 lines read]  scaff:TRINITY_DN26_c1_g1_i14 lend:491  rend:724     
[56000 lines read]  scaff:TRINITY_DN26_c1_g1_i14 lend:4077  rend:4301     
[57000 lines read]  scaff:TRINITY_DN26_c1_g1_i14 lend:6738  rend:6933     
[58000 lines read]  scaff:TRINITY_DN26_c1_g1_i15 lend:1550  rend:2012     
[59000 lines read]  scaff:TRINITY_DN26_c1_g1_i15 lend:4771  rend:4846     
[60000 lines read]  scaff:TRINITY_DN26_c1_g1_i15 lend:7318  rend:7576     
[61000 lines read]  scaff:TRINITY_DN26_c1_g1_i16 lend:2570  rend:2757     
[62000 lines read]  scaff:TRINITY_DN26_c1_g1_i16 lend:5596  rend:5899     
[63000 lines read]  scaff:TRINITY_DN26_c1_g1_i16 lend:7788  rend:8031     
[64000 lines read]  scaff:TRINITY_DN26_c1_g1_i17 lend:3454  rend:3833     
[65000 lines read]  scaff:TRINITY_DN26_c1_g1_i17 lend:6209  rend:6523     
[66000 lines read]  scaff:TRINITY_DN26_c1_g1_i18 lend:639  rend:1145     
[67000 lines read]  scaff:TRINITY_DN26_c1_g1_i18 lend:4280  rend:4782     
[68000 lines read]  scaff:TRINITY_DN26_c1_g1_i18 lend:6870  rend:7061     
[69000 lines read]  scaff:TRINITY_DN26_c1_g1_i19 lend:1781  rend:2159     
[70000 lines read]  scaff:TRINITY_DN26_c1_g1_i19 lend:4977  rend:5000     
[71000 lines read]  scaff:TRINITY_DN26_c1_g1_i2 lend:1904  rend:2258     
[72000 lines read]  scaff:TRINITY_DN26_c1_g1_i2 lend:5014  rend:5341     
[73000 lines read]  scaff:TRINITY_DN26_c1_g1_i2 lend:7475  rend:7729     
[74000 lines read]  scaff:TRINITY_DN26_c1_g1_i20 lend:2908  rend:3109     
[75000 lines read]  scaff:TRINITY_DN26_c1_g1_i20 lend:5787  rend:6209     
[76000 lines read]  scaff:TRINITY_DN26_c1_g1_i20 lend:7967  rend:8042     
[77000 lines read]  scaff:TRINITY_DN26_c1_g1_i21 lend:3555  rend:3822     
[78000 lines read]  scaff:TRINITY_DN26_c1_g1_i3 lend:415  rend:702     
[79000 lines read]  scaff:TRINITY_DN26_c1_g1_i3 lend:4010  rend:4297     
[80000 lines read]  scaff:TRINITY_DN26_c1_g1_i3 lend:6763  rend:7122     
[81000 lines read]  scaff:TRINITY_DN26_c1_g1_i4 lend:1553  rend:1772     
[82000 lines read]  scaff:TRINITY_DN26_c1_g1_i4 lend:4772  rend:4847     
[83000 lines read]  scaff:TRINITY_DN26_c1_g1_i4 lend:7340  rend:7721     
[84000 lines read]  scaff:TRINITY_DN26_c1_g1_i5 lend:2538  rend:2988     
[85000 lines read]  scaff:TRINITY_DN26_c1_g1_i5 lend:5541  rend:5960     
[86000 lines read]  scaff:TRINITY_DN26_c1_g1_i5 lend:7740  rend:8038     
[87000 lines read]  scaff:TRINITY_DN26_c1_g1_i6 lend:3490  rend:3730     
[88000 lines read]  scaff:TRINITY_DN26_c1_g1_i6 lend:6205  rend:6497     
[89000 lines read]  scaff:TRINITY_DN26_c1_g1_i7 lend:631  rend:918     
[90000 lines read]  scaff:TRINITY_DN26_c1_g1_i7 lend:4279  rend:4599     
[91000 lines read]  scaff:TRINITY_DN26_c1_g1_i7 lend:6844  rend:7088     
[92000 lines read]  scaff:TRINITY_DN26_c1_g1_i8 lend:1731  rend:1973     
[93000 lines read]  scaff:TRINITY_DN26_c1_g1_i8 lend:4917  rend:4940     
[94000 lines read]  scaff:TRINITY_DN26_c1_g1_i8 lend:7416  rend:7628     
[95000 lines read]  scaff:TRINITY_DN26_c1_g1_i9 lend:2864  rend:3179     
[96000 lines read]  scaff:TRINITY_DN26_c1_g1_i9 lend:5771  rend:6205     
[97000 lines read]  scaff:TRINITY_DN26_c1_g1_i9 lend:7872  rend:8074     
[98000 lines read]  scaff:TRINITY_DN26_c1_g3_i1 lend:1725  rend:2172     
[99000 lines read]  scaff:TRINITY_DN26_c1_g3_i1 lend:3369  rend:3556     
[100000 lines read]  scaff:TRINITY_DN26_c1_g3_i1 lend:4963  rend:5166     
[101000 lines read]  scaff:TRINITY_DN26_c1_g3_i2 lend:730  rend:1055     
[102000 lines read]  scaff:TRINITY_DN26_c1_g3_i2 lend:2492  rend:2771     
[103000 lines read]  scaff:TRINITY_DN26_c1_g3_i2 lend:4155  rend:4362     
[104000 lines read]  scaff:TRINITY_DN26_c1_g3_i2 lend:5546  rend:5852     
[105000 lines read]  scaff:TRINITY_DN26_c1_g3_i3 lend:1418  rend:1631     
[106000 lines read]  scaff:TRINITY_DN26_c1_g3_i4 lend:312  rend:579     
[107000 lines read]  scaff:TRINITY_DN26_c1_g3_i4 lend:2113  rend:2396     
[108000 lines read]  scaff:TRINITY_DN26_c1_g3_i4 lend:3741  rend:3970     
[109000 lines read]  scaff:TRINITY_DN26_c1_g3_i4 lend:5312  rend:5790     
[110000 lines read]  scaff:TRINITY_DN26_c1_g3_i5 lend:959  rend:1186     
[111000 lines read]  scaff:TRINITY_DN26_c1_g3_i5 lend:2690  rend:3027     
[112000 lines read]  scaff:TRINITY_DN26_c2_g1_i1 lend:2009  rend:2303     
[113000 lines read]  scaff:TRINITY_DN26_c2_g1_i1 lend:5214  rend:5424     
[114000 lines read]  scaff:TRINITY_DN26_c2_g1_i1 lend:7232  rend:7518     
[115000 lines read]  scaff:TRINITY_DN26_c2_g1_i1 lend:8563  rend:8806     
[116000 lines read]  scaff:TRINITY_DN26_c2_g1_i3 lend:3594  rend:3804     
[117000 lines read]  scaff:TRINITY_DN26_c2_g1_i3 lend:6104  rend:6308     
[118000 lines read]  scaff:TRINITY_DN26_c2_g1_i3 lend:7756  rend:8174     
[119000 lines read]  scaff:TRINITY_DN26_c2_g1_i4 lend:1469  rend:1695     
[120000 lines read]  scaff:TRINITY_DN26_c2_g1_i4 lend:4612  rend:4930     
[121000 lines read]  scaff:TRINITY_DN26_c2_g1_i5 lend:319  rend:619     
[122000 lines read]  scaff:TRINITY_DN26_c2_g1_i5 lend:4182  rend:4550     
[123000 lines read]  scaff:TRINITY_DN26_c2_g1_i5 lend:6476  rend:6807     
[124000 lines read]  scaff:TRINITY_DN26_c2_g1_i5 lend:8272  rend:8467     CMD: touch transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig.ok
1676s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig 1 + > transAligns.cSorted.bam.norm_200.bam.minC1.gff
1677s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
1677s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff transAligns.cSorted.bam.norm_200.bam.minC1.gff  --coord_sorted_SAM transAligns.cSorted.bam.norm_200.bam --parts_per_directory 100 --min_reads_per_partition 10 
1677s // parsing paritions.
1677s 
[92]  -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads
1677s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads
1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads
1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads
1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads
1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads
1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads
1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads
1683s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
1683s ##
1683s Done
1683s ##
1683s 
1683s Saturday, March 15, 2025: 23:58:58	CMD: touch partitions.ok
1683s Saturday, March 15, 2025: 23:58:58	CMD: find Dir_* -name '*reads' > read_files.list
1683s Saturday, March 15, 2025: 23:58:58	CMD: touch read_files.list.ok
1683s Saturday, March 15, 2025: 23:58:58	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --full_cleanup  > trinity_GG.cmds
1683s Saturday, March 15, 2025: 23:58:58	CMD: touch trinity_GG.cmds.ok
1683s Saturday, March 15, 2025: 23:58:58	CMD: touch trinity_GG.cmds.ok
1683s 
1683s 
1683s --------------------------------------------------------------------------------
1683s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1683s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1683s --------------------------------------------------------------------------------
1683s 
1683s Saturday, March 15, 2025: 23:58:58	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1683s Number of Commands: 85
1926s 
succeeded(1)   1.17647% completed.    
succeeded(2)   2.35294% completed.    
succeeded(3)   3.52941% completed.    
succeeded(4)   4.70588% completed.    
succeeded(5)   5.88235% completed.    
succeeded(6)   7.05882% completed.    
succeeded(7)   8.23529% completed.    
succeeded(8)   9.41177% completed.    
succeeded(9)   10.5882% completed.    
succeeded(10)   11.7647% completed.    
succeeded(11)   12.9412% completed.    
succeeded(12)   14.1176% completed.    
succeeded(13)   15.2941% completed.    
succeeded(14)   16.4706% completed.    
succeeded(15)   17.6471% completed.    
succeeded(16)   18.8235% completed.    
succeeded(17)   20% completed.    
succeeded(18)   21.1765% completed.    
succeeded(19)   22.3529% completed.    
succeeded(20)   23.5294% completed.    
succeeded(21)   24.7059% completed.    
succeeded(22)   25.8824% completed.    
succeeded(23)   27.0588% completed.    
succeeded(24)   28.2353% completed.    
succeeded(25)   29.4118% completed.    
succeeded(26)   30.5882% completed.    
succeeded(27)   31.7647% completed.    
succeeded(28)   32.9412% completed.    
succeeded(29)   34.1176% completed.    
succeeded(30)   35.2941% completed.    
succeeded(31)   36.4706% completed.    
succeeded(32)   37.6471% completed.    
succeeded(33)   38.8235% completed.    
succeeded(34)   40% completed.    
succeeded(35)   41.1765% completed.    
succeeded(36)   42.3529% completed.    
succeeded(37)   43.5294% completed.    
succeeded(38)   44.7059% completed.    
succeeded(39)   45.8824% completed.    
succeeded(40)   47.0588% completed.    
succeeded(41)   48.2353% completed.    
succeeded(42)   49.4118% completed.    
succeeded(43)   50.5882% completed.    
succeeded(44)   51.7647% completed.    
succeeded(45)   52.9412% completed.    
succeeded(46)   54.1176% completed.    
succeeded(47)   55.2941% completed.    
succeeded(48)   56.4706% completed.    
succeeded(49)   57.6471% completed.    
succeeded(50)   58.8235% completed.    
succeeded(51)   60% completed.    
succeeded(52)   61.1765% completed.    
succeeded(53)   62.3529% completed.    
succeeded(54)   63.5294% completed.    
succeeded(55)   64.7059% completed.    
succeeded(56)   65.8824% completed.    
succeeded(57)   67.0588% completed.    
succeeded(58)   68.2353% completed.    
succeeded(59)   69.4118% completed.    
succeeded(60)   70.5882% completed.    
succeeded(61)   71.7647% completed.    
succeeded(62)   72.9412% completed.    
succeeded(63)   74.1176% completed.    
succeeded(64)   75.2941% completed.    
succeeded(65)   76.4706% completed.    
succeeded(66)   77.6471% completed.    
succeeded(67)   78.8235% completed.    
succeeded(68)   80% completed.    
succeeded(69)   81.1765% completed.    
succeeded(70)   82.3529% completed.    
succeeded(71)   83.5294% completed.    
succeeded(72)   84.7059% completed.    
succeeded(73)   85.8824% completed.    
succeeded(74)   87.0588% completed.    
succeeded(75)   88.2353% completed.    
succeeded(76)   89.4118% completed.    
succeeded(77)   90.5882% completed.    
succeeded(78)   91.7647% completed.    
succeeded(79)   92.9412% completed.    
succeeded(80)   94.1176% completed.    
succeeded(81)   95.2941% completed.    
succeeded(82)   96.4706% completed.    
succeeded(83)   97.6471% completed.    
succeeded(84)   98.8235% completed.    
succeeded(85)   100% completed.    
1926s 
1926s All commands completed successfully. :-)
1926s 
1926s Sunday, March 16, 2025: 00:03:01	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp
1926s Sunday, March 16, 2025: 00:03:01	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
1926s 
1926s 
1926s Finished. See /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
1926s 
1926s 
1926s 
1926s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta"
1926s asmsize=$(wc -c <"${outfile}")
1926s if [ $asmsize -le 650000 ]; then
1926s     echo "Error, ${outfile} potentially incomplete"
1926s     exit 1
1926s else
1926s     echo "ok"
1926s     exit 0
1926s fi
1926s #!/bin/bash -ve
1926s 
1926s 
1926s $TRINITY_HOME/Trinity --genome_guided_max_intron 100000 --genome_guided_bam chr17.illumina.bam --long_reads_bam chr17.pbio.bam --max_memory 2G  --output test_chr17_LR_GG_trinity_outdir --CPU 5 --no_cleanup
1926s ok
1926s ./run_chr17_GG_wLongreads.sh
1926s 
1926s 
1926s      ______  ____   ____  ____   ____  ______  __ __
1926s     |      ||    \ |    ||    \ |    ||      ||  |  |
1926s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1926s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1926s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1926s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1926s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1926s 
1926s     Trinity-v2.15.2
1926s 
1926s 
1926s 
1926s Sunday, March 16, 2025: 00:03:01	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam
1926s -appears to be a coordinate sorted bam file. ok.
1926s Sunday, March 16, 2025: 00:03:01	CMD: mkdir -p /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir
1926s 
1926s 
1926s ----------------------------------------------------------------------------------
1926s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1926s ----------------------------------------------------------------------------------
1926s 
1926s -found paired-end aligned read. Running in paired-end mode.
1926s Sunday, March 16, 2025: 00:03:01	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam
1928s Done with chr chr1.
1928s Sunday, March 16, 2025: 00:03:03	CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok
1928s * [Sun Mar 16 00:03:03 2025] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam  O=/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam  RGID=PBLR  RGLB=lib2  RGPL=pacbio  RGPU=unit2  RGSM=pacbio VALIDATION_STRINGENCY=LENIENT
1929s INFO	2025-03-16 00:03:04	AddOrReplaceReadGroups	
1929s 
1929s ********** NOTE: Picard's command line syntax is changing.
1929s **********
1929s ********** For more information, please see:
1929s ********** 
1929s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
1929s **********
1929s ********** The command line looks like this in the new syntax:
1929s **********
1929s **********    AddOrReplaceReadGroups -I /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam -RGID PBLR -RGLB lib2 -RGPL pacbio -RGPU unit2 -RGSM pacbio -VALIDATION_STRINGENCY LENIENT
1929s **********
1929s 
1929s 
1929s 00:03:04.364 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1929s 00:03:04.367 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
1929s 00:03:04.368 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1929s 00:03:04.369 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1929s 00:03:04.370 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
1929s 00:03:04.370 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1929s [Sun Mar 16 00:03:04 UTC 2025] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam RGID=PBLR RGLB=lib2 RGPL=pacbio RGPU=unit2 RGSM=pacbio VALIDATION_STRINGENCY=LENIENT    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
1929s [Sun Mar 16 00:03:04 UTC 2025] Executing as ubuntu@autopkgtest on Linux 6.14.0-10-generic amd64; OpenJDK 64-Bit Server VM 21.0.6+7-Ubuntu-1; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.3.0
1929s 00:03:04.387 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
1929s 00:03:04.392 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
1929s INFO	2025-03-16 00:03:04	AddOrReplaceReadGroups	Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio
1929s 
1929s 00:03:04.431 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
1929s [Sun Mar 16 00:03:04 UTC 2025] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes.
1929s Runtime.totalMemory()=67108864
1929s * [Sun Mar 16 00:03:04 2025] Running CMD: samtools merge /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam
1930s Sunday, March 16, 2025: 00:03:05	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam -I 100000 --sort_buffer 2G --CPU 5 
1930s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 5 --sort_buffer 2G --sam merged_wRGLR.bam --min_insert_size 1 --max_insert_size 100000 
1930s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords
1930s 
1932s CMD: touch merged_wRGLR.bam.read_coords.ok
1932s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k2,2 -k4,4n merged_wRGLR.bam.read_coords > merged_wRGLR.bam.read_coords.sort_by_readname
1932s CMD: cp /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname
1932s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted
1933s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig
1949s 
[1000 lines read]  scaff:chr17 lend:441683  rend:441971     
[2000 lines read]  scaff:chr17 lend:745759  rend:746264     
[3000 lines read]  scaff:chr17 lend:770696  rend:770752     
[4000 lines read]  scaff:chr17 lend:1344888  rend:1345193     
[5000 lines read]  scaff:chr17 lend:1420877  rend:1421141     
[6000 lines read]  scaff:chr17 lend:1464472  rend:1465037     
[7000 lines read]  scaff:chr17 lend:1519178  rend:1519476     
[8000 lines read]  scaff:chr17 lend:1646492  rend:1647958     
[9000 lines read]  scaff:chr17 lend:1653900  rend:1658553     
[10000 lines read]  scaff:chr17 lend:1660471  rend:1660818     
[11000 lines read]  scaff:chr17 lend:1675653  rend:1676697     
[12000 lines read]  scaff:chr17 lend:1681518  rend:1681972     
[13000 lines read]  scaff:chr17 lend:1776582  rend:1777325     
[14000 lines read]  scaff:chr17 lend:1879302  rend:1891925     
[15000 lines read]  scaff:chr17 lend:2042921  rend:2043283     
[16000 lines read]  scaff:chr17 lend:2322233  rend:2322871     
[17000 lines read]  scaff:chr17 lend:2325416  rend:2331108     
[18000 lines read]  scaff:chr17 lend:2377747  rend:2379616     
[19000 lines read]  scaff:chr17 lend:2486702  rend:2487026     
[20000 lines read]  scaff:chr17 lend:2682083  rend:2682640     
[21000 lines read]  scaff:chr17 lend:2689842  rend:2690324     
[22000 lines read]  scaff:chr17 lend:2698334  rend:2701265     
[23000 lines read]  scaff:chr17 lend:3663158  rend:3664210     
[24000 lines read]  scaff:chr17 lend:3811005  rend:3811630     
[25000 lines read]  scaff:chr17 lend:3894240  rend:3894816     
[26000 lines read]  scaff:chr17 lend:3926179  rend:3926793     
[27000 lines read]  scaff:chr17 lend:4009633  rend:4016371     
[28000 lines read]  scaff:chr17 lend:4165239  rend:4165812     
[29000 lines read]  scaff:chr17 lend:4260001  rend:4263956     
[30000 lines read]  scaff:chr17 lend:4289368  rend:4366449     
[31000 lines read]  scaff:chr17 lend:4552617  rend:4555359     
[32000 lines read]  scaff:chr17 lend:4717232  rend:4720296     
[33000 lines read]  scaff:chr17 lend:4892199  rend:4893532     
[34000 lines read]  scaff:chr17 lend:4940095  rend:4940710     
[35000 lines read]  scaff:chr17 lend:4946801  rend:4948447     
[36000 lines read]  scaff:chr17 lend:4982444  rend:4986216     CMD: touch merged_wRGLR.bam.frag_coverage.wig.ok
1949s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff
1955s CMD: touch merged_wRGLR.bam.minC1.gff.ok
1955s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff merged_wRGLR.bam.minC1.gff  --coord_sorted_SAM merged_wRGLR.bam --parts_per_directory 100 --min_reads_per_partition 10 
1955s // parsing paritions.
1955s 
[100]  
[116]  -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/732418_752287.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/752375_752769.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/753167_754706.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/758974_782331.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/782362_792510.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/793543_794109.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/795176_795754.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/799707_800316.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/800915_803792.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/981902_982655.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/997125_1091796.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1146722_1146846.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1148302_1149226.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1151011_1152011.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1153293_1153810.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1226770_1227467.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1257967_1400270.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1414443_1415081.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1420724_2022954.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2030147_2043980.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2044654_2045225.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2047917_2048512.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2049091_2049553.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2051694_2052378.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2053479_2053635.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054237_2054372.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054544_2056751.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2056812_2057391.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2058177_2058912.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2059847_2303836.trinity.reads
1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2303955_2336468.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3706252_3917856.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3923874_3964467.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3964821_3965192.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4001444_4001952.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4003050_4003706.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4004424_4555389.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4660854_4661151.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4667839_4668289.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4671192_4704136.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4704234_4705420.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4710502_4721496.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4731419_4733592.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4734646_4739376.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4787354_4789638.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4796155_4798495.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4805950_4806545.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4807192_4823373.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4833366_4897982.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4904417_4904897.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4927248_4928577.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4928729_4928949.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4929025_4934979.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935086_4935300.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935439_4945214.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4945652_4997520.trinity.reads
1956s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4997681_5001302.trinity.reads
1956s CMD: touch Dir_merged_wRGLR.bam.minC1.gff.ok
1956s ##
1956s Done
1956s ##
1956s 
1956s Sunday, March 16, 2025: 00:03:31	CMD: touch partitions.ok
1956s Sunday, March 16, 2025: 00:03:31	CMD: find Dir_* -name '*reads' > read_files.list
1956s Sunday, March 16, 2025: 00:03:31	CMD: touch read_files.list.ok
1956s Sunday, March 16, 2025: 00:03:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G  --run_as_paired  --seqType fa --trinity_complete --no_cleanup  --long_reads_mode  > trinity_GG.cmds
1956s Sunday, March 16, 2025: 00:03:31	CMD: touch trinity_GG.cmds.ok
1956s Sunday, March 16, 2025: 00:03:31	CMD: touch trinity_GG.cmds.ok
1956s 
1956s 
1956s --------------------------------------------------------------------------------
1956s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1956s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1956s --------------------------------------------------------------------------------
1956s 
1956s Sunday, March 16, 2025: 00:03:31	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 
1956s Number of Commands: 44
2826s 
succeeded(1)   2.27273% completed.    
succeeded(2)   4.54545% completed.    
succeeded(3)   6.81818% completed.    
succeeded(4)   9.09091% completed.    
succeeded(5)   11.3636% completed.    
succeeded(6)   13.6364% completed.    
succeeded(7)   15.9091% completed.    
succeeded(8)   18.1818% completed.    
succeeded(9)   20.4545% completed.    
succeeded(10)   22.7273% completed.    
succeeded(11)   25% completed.    
succeeded(12)   27.2727% completed.    
succeeded(13)   29.5455% completed.    
succeeded(14)   31.8182% completed.    
succeeded(15)   34.0909% completed.    
succeeded(16)   36.3636% completed.    
succeeded(17)   38.6364% completed.    
succeeded(18)   40.9091% completed.    
succeeded(19)   43.1818% completed.    
succeeded(20)   45.4545% completed.    
succeeded(21)   47.7273% completed.    
succeeded(22)   50% completed.    
succeeded(23)   52.2727% completed.    
succeeded(24)   54.5455% completed.    
succeeded(25)   56.8182% completed.    
succeeded(26)   59.0909% completed.    
succeeded(27)   61.3636% completed.    
succeeded(28)   63.6364% completed.    
succeeded(29)   65.9091% completed.    
succeeded(30)   68.1818% completed.    
succeeded(31)   70.4545% completed.    
succeeded(32)   72.7273% completed.    
succeeded(33)   75% completed.    
succeeded(34)   77.2727% completed.    
succeeded(35)   79.5455% completed.    
succeeded(36)   81.8182% completed.    
succeeded(37)   84.0909% completed.    
succeeded(38)   86.3636% completed.    
succeeded(39)   88.6364% completed.    
succeeded(40)   90.9091% completed.    
succeeded(41)   93.1818% completed.    
succeeded(42)   95.4545% completed.    
succeeded(43)   97.7273% completed.    
succeeded(44)   100% completed.    
2826s 
2826s All commands completed successfully. :-)
2826s 
2826s Sunday, March 16, 2025: 00:18:01	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.tmp
2826s Sunday, March 16, 2025: 00:18:01	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.gene_trans_map
2827s 
2827s 
2827s Finished. See /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
2827s 
2827s 
2827s find test_chr17_LR_GG_trinity_outdir/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep '>' | grep 'LR\$' > test_chr17_LR_GG_trinity_outdir.LR
2828s 
2828s if [[ $(wc -l <test_chr17_LR_GG_trinity_outdir.LR) -le 200 ]]; then
2828s     echo "Error, fewer than expected pbio read-integrated assembled transcripts"
2828s     exit 1
2828s fi
2828s 
2828s 
2828s exit 0
2828s touch test
2828s make[1]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
2828s Running example in test_InSilicoReadNormalization...
2828s make[1]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
2828s ./test_PE_normalization.sh
2828s #!/bin/bash -ve
2828s 
2828s CPU=$(nproc || sysctl -n hw.physicalcpu)
2828s 
2828s # just for testing purposes, use --max_cov 30 or higher for real applications.
2828s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --left ../test_DATA/reads.left.fq.gz --right ../test_DATA/reads.right.fq.gz --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_norm_dir --min_cov 2
2828s -prepping seqs
2828s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
2828s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
2828s CMD finished (0 seconds)
2828s CMD finished (0 seconds)
2828s CMD: touch left.fa.ok
2828s CMD finished (0 seconds)
2828s CMD: touch right.fa.ok
2828s CMD finished (0 seconds)
2828s  Done converting input files. CMD: cat left.fa right.fa > both.fa
2828s CMD finished (0 seconds)
2828s CMD: touch both.fa.ok
2828s CMD finished (0 seconds)
2828s -kmer counting.
2828s -------------------------------------------
2828s ----------- Jellyfish  --------------------
2828s -- (building a k-mer catalog from reads) --
2828s -------------------------------------------
2828s 
2828s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
2829s CMD finished (1 seconds)
2829s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2829s CMD finished (0 seconds)
2829s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2829s CMD finished (0 seconds)
2829s CMD: touch jellyfish.K25.min2.kmers.fa.success
2829s CMD finished (0 seconds)
2829s -generating stats files
2829s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
2829s -reading Kmer occurrences...
2829s 
2829s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
2829s STATS_GENERATION_TIME: 0 seconds.
2829s CMD finished (0 seconds)
2829s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
2829s -reading Kmer occurrences...
2829s 
2829s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
2830s STATS_GENERATION_TIME: 1 seconds.
2830s CMD finished (1 seconds)
2830s CMD: touch left.fa.K25.stats.ok
2830s CMD finished (0 seconds)
2830s CMD: touch right.fa.K25.stats.ok
2830s CMD finished (0 seconds)
2830s -sorting each stats file by read name.
2830s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> left.fa.K25.stats.sort
2830s CMD finished (0 seconds)
2830s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> right.fa.K25.stats.sort
2830s CMD finished (0 seconds)
2830s CMD: touch left.fa.K25.stats.sort.ok
2830s CMD finished (0 seconds)
2830s CMD: touch right.fa.K25.stats.sort.ok
2830s CMD finished (0 seconds)
2830s -defining normalized reads
2830s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
2830s -opening left.fa.K25.stats.sort
2830s -opening right.fa.K25.stats.sort
2830s -done opening files.
2830s CMD finished (0 seconds)
2830s CMD: touch pairs.K25.stats.ok
2830s CMD finished (0 seconds)
2830s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 5  --min_cov 2 --max_CV 10000 > pairs.K25.stats.C5.maxCV10000.accs
2831s 3826 / 30575 = 12.51% reads selected during normalization.
2831s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2831s 1797 / 30575 = 5.88% reads discarded as below minimum coverage threshold=2
2831s CMD finished (1 seconds)
2831s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
2831s CMD finished (0 seconds)
2831s -search and capture.
2831s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz ... done prepping, now search and capture.
2831s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
2831s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz ... done prepping, now search and capture.
2831s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
2831s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
2831s CMD finished (0 seconds)
2831s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
2831s CMD finished (0 seconds)
2831s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq left.norm.fq
2831s CMD finished (0 seconds)
2831s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq right.norm.fq
2831s CMD finished (0 seconds)
2831s 
2831s 
2831s Normalization complete. See outputs: 
2831s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
2831s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
2831s 
2831s 
2831s 
2831s ./test_SE_normalization.sh
2831s #!/bin/bash -ve
2831s 
2831s if [ ! -e reads.single.fq ]; then
2831s     gunzip -c ../test_DATA/reads.left.fq.gz > reads.single.fq
2831s fi
2831s 
2831s 
2831s # just for testing purposes, use --max_cov 30 or higher for real applications.
2831s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --single reads.single.fq --seqType fq --max_cov 5 --no_cleanup --tmp_dir_name single_tmp_norm_reads
2831s -prepping seqs
2831s CMD: seqtk-trinity seq -A -R 1  /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq >> single.fa
2831s CMD finished (0 seconds)
2831s CMD: touch single.fa.ok
2831s CMD finished (0 seconds)
2831s -kmer counting.
2831s -------------------------------------------
2831s ----------- Jellyfish  --------------------
2831s -- (building a k-mer catalog from reads) --
2831s -------------------------------------------
2831s 
2831s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
2833s CMD finished (2 seconds)
2833s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2833s CMD finished (0 seconds)
2833s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2833s CMD finished (0 seconds)
2833s CMD: touch jellyfish.K25.min2.kmers.fa.success
2833s CMD finished (0 seconds)
2833s -generating stats files
2833s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
2833s -reading Kmer occurrences...
2833s 
2833s  done parsing 70076 Kmers, 70076 added, taking 0 seconds.
2833s STATS_GENERATION_TIME: 0 seconds.
2833s CMD finished (0 seconds)
2833s CMD: touch single.fa.K25.stats.ok
2833s CMD finished (0 seconds)
2833s -sorting each stats file by read name.
2833s CMD: head -n1 single.fa.K25.stats > single.fa.K25.stats.sort && tail -n +2 single.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> single.fa.K25.stats.sort
2833s CMD finished (0 seconds)
2833s CMD: touch single.fa.K25.stats.sort.ok
2833s CMD finished (0 seconds)
2833s -defining normalized reads
2833s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file single.fa.K25.stats.sort  --max_cov 5  --min_cov 0  --max_CV 10000 > single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs
2833s 9127 / 30575 = 29.85% reads selected during normalization.
2833s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2833s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=0
2833s CMD finished (0 seconds)
2833s CMD: touch single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs.ok
2833s CMD finished (0 seconds)
2833s -search and capture.
2834s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq ... done prepping, now search and capture.
2834s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq
2834s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq.ok
2834s CMD finished (0 seconds)
2834s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq single.norm.fq
2834s CMD finished (0 seconds)
2834s 
2834s 
2834s Normalization complete. See outputs: 
2834s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq
2834s 
2834s 
2834s 
2834s #!/bin/bash -ve
2834s ./test_PE_normalization.mult_read_sets.sh
2834s 
2834s CPU=$(nproc || sysctl -n hw.physicalcpu)
2834s 
2834s # just for testing purposes, use --max_cov 30 or higher for real applications.
2834s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \
2834s      --left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \
2834s      --right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \
2834s      --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \
2834s      --output test_multi_read_sets_norm_outdir
2834s -prepping seqs
2834s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
2834s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
2834s CMD finished (0 seconds)
2834s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz) >> left.fa
2834s CMD finished (0 seconds)
2834s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz) >> right.fa
2834s CMD finished (0 seconds)
2834s CMD finished (0 seconds)
2834s CMD: touch left.fa.ok
2834s CMD finished (0 seconds)
2834s CMD: touch right.fa.ok
2834s CMD finished (0 seconds)
2834s  Done converting input files. CMD: cat left.fa right.fa > both.fa
2834s CMD finished (0 seconds)
2834s CMD: touch both.fa.ok
2834s CMD finished (0 seconds)
2834s -kmer counting.
2834s -------------------------------------------
2834s ----------- Jellyfish  --------------------
2834s -- (building a k-mer catalog from reads) --
2834s -------------------------------------------
2834s 
2834s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
2835s CMD finished (1 seconds)
2835s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2835s CMD finished (0 seconds)
2835s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2835s CMD finished (0 seconds)
2835s CMD: touch jellyfish.K25.min2.kmers.fa.success
2835s CMD finished (0 seconds)
2835s -generating stats files
2835s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
2835s -reading Kmer occurrences...
2836s 
2836s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
2837s STATS_GENERATION_TIME: 1 seconds.
2837s CMD finished (2 seconds)
2837s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
2837s -reading Kmer occurrences...
2837s 
2837s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
2838s STATS_GENERATION_TIME: 1 seconds.
2838s CMD finished (1 seconds)
2838s CMD: touch left.fa.K25.stats.ok
2838s CMD finished (0 seconds)
2838s CMD: touch right.fa.K25.stats.ok
2838s CMD finished (0 seconds)
2838s -sorting each stats file by read name.
2838s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> left.fa.K25.stats.sort
2838s CMD finished (0 seconds)
2838s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> right.fa.K25.stats.sort
2838s CMD finished (0 seconds)
2838s CMD: touch left.fa.K25.stats.sort.ok
2838s CMD finished (0 seconds)
2838s CMD: touch right.fa.K25.stats.sort.ok
2838s CMD finished (0 seconds)
2838s -defining normalized reads
2838s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
2838s -opening left.fa.K25.stats.sort
2838s -opening right.fa.K25.stats.sort
2838s -done opening files.
2839s CMD finished (1 seconds)
2839s CMD: touch pairs.K25.stats.ok
2839s CMD finished (0 seconds)
2839s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 5  --min_cov 0 --max_CV 10000 > pairs.K25.stats.C5.maxCV10000.accs
2840s 7970 / 61150 = 13.03% reads selected during normalization.
2840s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2840s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=0
2840s CMD finished (1 seconds)
2840s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
2840s CMD finished (0 seconds)
2840s -search and capture.
2840s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz ... done prepping, now search and capture.
2840s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
2840s -preparing to extract selected reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz ... done prepping, now search and capture.
2840s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
2840s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz
2840s -capturing normalized reads from: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz
2841s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq.ok
2841s CMD finished (0 seconds)
2841s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq.ok
2841s CMD finished (0 seconds)
2841s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq left.norm.fq
2841s CMD finished (0 seconds)
2841s CMD: ln -sf /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq right.norm.fq
2841s CMD finished (0 seconds)
2841s 
2841s 
2841s Normalization complete. See outputs: 
2841s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq
2841s 	/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq
2841s 
2841s touch test
2841s make[1]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
2841s Running example in test_DE_analysis...
2841s make[1]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
2841s Running example in Candida_example...
2841s make[2]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
2841s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
2841s $VAR1 = {
2841s           'wt_ph8' => [
2841s                         'wt_ph8_1',
2841s                         'wt_ph8_2',
2841s                         'wt_ph8_3'
2841s                       ],
2841s           'wt_37' => [
2841s                        'wt_37_1',
2841s                        'wt_37_2',
2841s                        'wt_37_3'
2841s                      ],
2841s           'wt_GSNO' => [
2841s                          'wt_GSNO_1',
2841s                          'wt_GSNO_2',
2841s                          'wt_GSNO_3'
2841s                        ]
2841s         };
2841s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.EdgeR.Rscript
2841s 
2841s 
2841s Got 9 samples, and got: 10 data fields.
2841s Header: wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
2841s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2841s 
2841s $VAR1 = {
2841s           'wt_GSNO_3' => 4,
2841s           'wt_GSNO_2' => 6,
2841s           'wt_37_2' => 1,
2841s           'wt_GSNO_1' => 5,
2841s           'wt_ph8_2' => 9,
2841s           'wt_ph8_3' => 7,
2841s           'wt_37_3' => 2,
2841s           'wt_37_1' => 3,
2841s           'wt_ph8_1' => 8
2841s         };
2841s Contrasts to perform are: $VAR1 = [
2841s           [
2841s             'wt_37',
2841s             'wt_GSNO'
2841s           ],
2841s           [
2841s             'wt_37',
2841s             'wt_ph8'
2841s           ],
2841s           [
2841s             'wt_GSNO',
2841s             'wt_ph8'
2841s           ]
2841s         ];
2841s Loading required package: edgeR
2841s Loading required package: limma
2841s Using classic mode.
2843s null device 
2843s           1 
2843s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.EdgeR.Rscript
2843s Loading required package: edgeR
2843s Loading required package: limma
2844s Using classic mode.
2845s null device 
2845s           1 
2845s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.EdgeR.Rscript
2845s Loading required package: edgeR
2845s Loading required package: limma
2846s Using classic mode.
2848s null device 
2848s           1 
2848s cd edgeR_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2848s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
2848s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2848s 
2848s 
2848s ** Found 2060 features as differentially expressed.
2848s 
2848s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  -s ../samples.txt
2848s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2848s Loading required package: BiocGenerics
2848s 
2848s Attaching package: ‘BiocGenerics’
2848s 
2848s The following objects are masked from ‘package:stats’:
2848s 
2848s     IQR, mad, sd, var, xtabs
2848s 
2848s The following objects are masked from ‘package:base’:
2848s 
2848s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2848s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2848s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2848s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2848s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2848s     table, tapply, union, unique, unsplit, which.max, which.min
2848s 
2848s Welcome to Bioconductor
2848s 
2848s     Vignettes contain introductory material; view with
2848s     'browseVignettes()'. To cite Bioconductor, see
2848s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2848s 
2849s 
2849s Attaching package: ‘fastcluster’
2849s 
2849s [1] "Reading matrix file."
2849s The following object is masked from ‘package:stats’:
2849s 
2849s     hclust
2849s 
2850s for plotting:: min.raw: -0.642808465476069 max.raw: 1
2850s null device 
2850s           1 
2851s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2851s null device 
2851s           1 
2852s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
2852s sampleA_mean:  5395.606 1816.62 1412.697 637.4673 1681.385 1262.588 20787.35 1013.064 502.9777 665.289 620.238 1371.045 470.179 1407.266 3549.085 1046.9 6030.232 296.1627 982.539 1833.283 4954.434 499.8527 1120.621 2191.464 1037.645 838.8547 581.2863 484.398 522.8673 559.8297 887.2083 1326.5 4776.171 810.3883 533.844 854.0897 2460.887 335.7477 781.6647 198.9307 2059.192 333.5833 11423.35 1066.12 1319.258 400.0377 545.5957 5637.134 562.1487 480.5827 409.7437 1532.142 4182.673 335.4993 134.168 5797.692 244.753 323.5933 647.4437 301.1237 1445.705 350.1547 1707.219 1512.754 198.8237 4784.861 231.4073 567.2883 298.6353 629 350.3023 15024.4 604.7417 564.1773 923.62 249.8873 494.789 104.2153 363.4713 338.9207 122.4237 508.1423 150.8137 114.485 207.4947 252.8977 2602.336 114.123 148.374 941.4197 180.1727 162.433 322.1607 219.039 933.0403 2616.495 1272.664 310.3963 388.648 1088.069 393.785 2442.782 178.6107 425.4187 241.211 323.2733 762.2617 1265.232 203.246 530.7697 4913.275 872.2057 2891.881 335.637 490.2657 2465.916 89.249 209.749 419.6373 772.306 456.1583 335.2157 182.1447 2635.243 1939.628 373.2207 85.82433 731.256 876.645 1291.39 3468.578 1718.763 4534.064 218.991 127.1483 1326.869 914.4587 1753.538 211.844 583.6803 201.4867 339.0793 693.0703 124.028 4713.887 579.459 177.4467 744.858 2207.998 122.234 167.1063 481.5627 134.0677 599.1197 742.0153 1315.006 1640.267 1229.376 579.619 435.0017 719.3537 584.709 119.932 221.959 310.3323 272.6143 183.172 300.3533 172.982 482.3557 122.591 2446.14 574.8767 161.9753 99.45067 243.326 197.342 340.5557 455.3783 156.8307 262.1497 323.746 154.4447 71.71033 991.437 303.8613 2002.536 352.3153 97.82467 446.9747 1214.03 156.591 111.007 505.6607 510.4197 210.486 711.3287 313.843 189.715 1099.802 318.1197 912.636 354.781 1606.153 407.805 330.6623 123.246 1547.728 136.2463 243.9703 192.5983 432.0453 169.0567 256.9907 62.65367 676.234 783.8573 62.56033 168.189 356.3497 196.6567 152.1197 176.9843 2688.784 112.757 334.935 160.8853 387.8127 369.791 234.695 1125.723 146.7767 690.4453 252.697 210.2437 199.325 75.336 87.49733 83.07667 328.3217 216.15 60.22767 67.469 250.2393 563.9263 1815.027 294.269 594.819 356.783 69.89367 26.93367 110.791 109.0817 83.207 407.6713 342.712 78.31633 617.054 122.177 220.177 324.5383 207.939 239.7997 97.23167 86.386 57.64267 240.267 160.1673 421.348 571.859 721.5107 94.07567 104.0613 322.742 320.023 118.5347 133.1057 334.361 76.27033 86.67367 52.74467 371.817 354.898 144.7257 299.966 42.552 81.80933 93.672 228.911 135.433 115.132 134.6873 207.397 1557.898 91.61633 99.03533 112.5293 6660.051 306.508 110.5993 79.282 280.7067 55.68233 363.302 79.07433 307.9013 33.26767 105.6967 80.98433 78.67633 85.95367 58.232 76.09067 59.60267 32.351 64.34933 114.563 108.859 31.38733 94.133 93.57967 94.69467 3561.451 155.7297 67.206 84.25 64.515 112.884 172.4453 2952.358 37.59833 84.972 38.966 361.8817 31.766 84.98533 80.43867 603.3643 551.5827 66.88467 77.01533 526.9727 98.302 87.15633 91.79433 35.384 158.1847 204.481 73.085 398.1303 46.65767 44.71033 100.0123 422.5397 41.339 39.99867 47.17133 73.806 442.0453 38.21567 62.81 89.883 31.01767 74.26433 56.34967 164.921 69.21367 280.1693 21.82767 64.40333 30.17067 69.72667 112.7063 703.739 47.40267 405.356 51.06833 1172.149 37.93767 144.1087 84.101 67.623 38.01367 176.214 340.941 34.95267 58.726 103.086 279.711 32.60533 32 306.441 20.93567 44.67767 40.988 31.13533 52.91967 74.20533 53.25667 56.22233 197.0237 32.07433 71.85 39.204 246.2103 15.402 49.19267 38.41333 9.429667 30.96067 47.775 78.667 131.435 36.76933 66.12467 43.95233 37.304 40.022 23.42167 16.46033 69.92267 38.414 171.2653 95.708 69.90667 84.52867 54.81767 56.78633 85.27667 65.34533 5495.505 50.27133 27.49133 51.916 163.5027 52.662 168.4167 28.112 31.93633 33.50367 24.04867 115.2073 52.49167 71.55767 89.08767 8.473333 34.237 14.64167 29.75167 38.44933 35.23567 16.59667 42.42 10.73367 36.44033 15.47467 23.565 20.16567 41.489 158.4163 209.263 88.74833 23.62733 26.74467 43.001 56.72833 24.90267 40.90567 40.95667 19.56433 14.972 16.558 14.82667 66.32833 23.34767 22.18367 23.36033 36.86033 16.92233 27.81033 20.61433 68.59733 18.50767 35.217 46.006 10.08733 16.066 22.395 23.236 32.359 33.16667 59.42267 27.801 31.332 59.42133 36.55567 23.66867 9.629333 23.232 12.32167 21.92233 49.753 21.21933 67.70667 28.092 28.812 16.79467 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2852s 18.73767 39.53833 45.49933 17.69467 176.112 15.77833 29.40667 19.11367 15.04667 25.49633 21.19933 13.554 22.47933 73.985 13.172 26.41767 23.48733 9.539333 30.22433 11.36333 23.85333 21.16733 13.02633 17.51267 24.04533 21.95267 5.914333 18.054 28.304 
2852s sampleB_mean:  4.127667 3.202333 4.412333 2.778333 10.849 9.133333 336.3973 18.23967 9.088 12.67333 12.49967 28.87167 10.76867 33.63533 84.42267 27.41467 173.6673 8.580333 33.35533 63.97333 175.7007 18.18567 43.62667 98.61433 47.461 39.777 27.60133 24.33867 28.62567 32.483 55.41567 98.97567 543.417 63.963 47.52733 11.05733 73.97767 21.376 4.512667 5.223667 313.6673 36.39433 534.2237 183.983 117.2063 24.273 72.053 68.49367 52.09567 39.797 42.68733 225.2773 658.8357 2.287 13.52433 900.1817 5.388667 38.47567 49.48767 55.75367 139.4193 36.41067 218.998 281.149 22.41533 299.0663 7.825667 23.51433 26.58267 94.08633 19.23033 661.7387 95.47967 68.27467 79.21633 36.231 58.90833 14.398 12.30667 50.10333 3.616 79.409 10.44 2.967333 28.87667 15.51133 514.415 2.461333 9.605 232.083 27.94467 11.277 6.660667 9.034667 143.4493 629.0693 217.05 29.69867 85.85133 145.798 68.88567 563.4113 32.70533 72.874 22.455 25.39133 43.57767 250.9827 32.93 110.7323 1003.238 116.6427 125.8543 74.29867 44.471 7.979667 1.321667 15.964 50.429 68.979 80.21667 43.422 18.134 623.5437 297.3653 53.687 10.49667 170.8453 94.216 194.2893 457.8803 296.743 3.101333 48.99067 14.087 191.8153 213.755 375.202 29.54433 85.73633 23.402 70.59233 150.937 15.837 338.805 102.7107 21.00533 132.8633 412.998 10.49233 33.283 105.7627 23.18133 130.483 62.58133 131.764 280.8763 124.0153 113.0753 66.97833 119.1803 122.476 22.87333 45.02367 21.807 38.81867 26.18 29.063 6.052333 70.27367 8.546333 582.8023 56.695 35.82667 10.675 43.417 29.96067 72.46567 92.838 2.732333 40.96933 38.353 37.50533 10.603 223.4383 49.50333 429.5973 56.458 10.31967 88.46167 230.2087 30.82233 11.71333 118.5987 126.7297 32.109 118.5947 74.91 31.15267 170.561 73.76233 115.6623 80.928 6.318 58.22233 43.27 29.317 377.1183 14.554 60.89033 26.01033 70.388 14.82467 62.40367 4.263 116.0857 170.3357 11.399 28.625 58.833 42.91667 26.68733 39.035 462.724 12.85033 64.78933 14.26033 89.28567 70.13033 45.62033 261.706 32.132 154.972 52.69567 28.455 20.14333 6.437333 6.740333 18.13133 43.231 45.433 12.03667 8.652333 48.89067 120.0037 402.3693 55.04367 131.159 68.36967 8.867667 0 26.685 19.12733 20.623 96.276 71.40267 14.54933 115.9157 19.68333 16.50567 55.915 51.52233 41.856 22.98467 15.947 13.374 44.52567 36.07133 75.955 87.39733 80.658 12.35967 16.69133 73.756 71.137 28.90033 24.22767 72.094 15.62833 17.759 4.583667 78.80367 7.045667 29.59733 72.38467 10.51167 10.94967 16.16267 40.359 15.437 26.14833 31.58467 47.833 260.6453 15.559 19.23 15.32067 938.454 71.361 16.40267 17.413 65.26833 7.72 64.46467 12.544 65.235 6.353667 15.246 15.42567 7.913667 20.73367 8.792667 14.33167 14.42733 7.566333 15.44967 26.33733 21.776 6.926 19.81633 18.108 18.174 499.6263 27.02667 12.19033 14.04867 0.6243333 14.411 32.75133 424.5863 3.122 14.10833 9.231 69.556 5.709667 18.931 19.83467 118.617 19.63133 7.66 14.676 73.07533 12.226 14.08133 19.28233 2.032 28.212 40.363 12.023 84.71567 10.23033 7.395 16.38067 1.723667 9.647 6.174667 10.679 11.486 40.53433 6.723333 12.327 21.74733 2.410333 17.83733 6.977333 28.223 10.57833 20.15033 0.8883333 9.925 7.087667 13.91533 22.84267 138.602 8.274 22.77967 7.516667 228.7547 2.177 21.41267 5.474333 15.98533 9.294667 17.25667 67.14133 5.981333 2.115333 23.04733 58.535 5.685 7.807333 72.50367 2.503 9.524 4.98 5.992 9.865667 13.76033 8.352 9.195667 37.02633 4.789 15.521 8.836 14.50533 0.4626667 8.369 2.327667 0 5.838 11.013 17.55633 21.67067 3.465 15.28167 10.124 4.895 4.636667 5.664333 3.596 8.412333 8.525667 21.40333 23.05433 11.173 4.385333 13.31333 5.468 15.31167 13.338 10.288 10.828 6.127333 10.462 23.191 8.300333 29.664 1.195 5.784 7.374 1.734333 9.423667 9.638667 13.186 9.302667 0.093 8.232 3.51 5.607667 9.153 5.763333 0.668 6.257667 0 1.998667 3.68 1.755667 3.966667 5.190667 23.73867 18.65833 10.806 2.341667 1.905667 10.293 6.641667 5.709333 5.354333 4.074333 2.98 2.939 3.201 3.158 5.685333 0 3.513333 1.651333 4.132667 1.497 3.141333 4.44 5.035 2.188333 4.641667 3.210667 0.5686667 1.586 3.095667 3.540333 7.557333 7.033 10.216 0 0 13.56433 6.03 5.790333 2.409667 0.1823333 2.956333 2.302 7.787667 1.153 13.44 5.750667 3.694 0 0.983 6.688 10.00833 2.606 8.689333 0 5.14 0 1.536333 2.441 4.922 2.830667 4.562 15.67833 0.6903333 4.982333 3.702333 0 0 1.582333 3.677333 2.279 1.234 1.876667 0 3.117 1.506333 0 6.093667 
2852s num discordant:  0 
2852s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2852s sampleA_mean:  0.838 2.696667 3.078667 2.398333 20.01233 2.713333 16.51667 4.654333 7.951667 15.838 279.6767 5.762333 98.85333 13.98533 68.104 691.0767 20.97667 72.55133 103.6867 96.61333 558.1363 526.2243 17.37067 539.652 81.319 226.9223 641.1777 478.7223 96.77733 251.019 45.76333 300.087 38.978 1406.461 536.193 620.406 35.44767 11.583 4.080333 5.017333 9.434667 213.4847 21.39933 7.282667 33.62067 850.6397 93.42833 15.04567 57.26933 7.212667 733.6827 876.482 967.4877 1005.984 1005.984 113.178 114.5207 40.61467 37.255 98.448 655.8127 915.841 903.1557 18.754 37.25567 866.6187 57.579 128.1763 39.57833 3.139 7.601333 4.244 2.177333 31.501 509.7623 954.153 70.24967 103.9153 62.50533 10.53633 224.904 555.952 37.21967 409.1913 27.52967 861.8193 27.29 1117.319 76.41333 2.280333 884.0843 29.18933 18.30633 33.57133 1220.149 551.9577 1784.069 28.45833 2.592667 3.516 18.88733 16.528 7.412333 5.682 20.36667 18.96267 950.0057 260.666 10.30533 94.089 25.55733 4.745 121.0697 15.73033 2042.114 504.111 642.0663 22.627 360.2233 44.93767 14.91467 29.55 27.48633 56.797 6.496333 17.221 35.29633 443.633 1690.757 39.67767 6.546 75.48133 67.08167 866.9083 86.883 6.167 5.016 3.586667 1385.135 4.361 1545.514 7.963667 1.292667 1.460333 141.697 3.595333 237.8803 1.919333 5.627 17.48067 6.515667 77.21567 20.37167 9.896333 65.027 94.847 223.9227 100.1173 35.529 71.78533 617.7277 1681.069 6.455667 3.451 22.92133 43.09833 425.357 27.23133 50.14667 16.54033 697.2287 5.802333 11.52 64.19 27.59267 129.326 6.300667 16.27833 22.74167 393.3037 23.04333 188.4693 2466.545 31.92667 503.5693 1094.775 5.474667 560.8327 43.50567 47.34533 66.65833 37.942 1593.583 15.54567 660.21 63.58333 23.33733 1313.1 7.685 15.08833 42.57533 15.92433 14.33333 9.969333 1584.902 40.12067 51.407 30.828 2590.581 1834.914 9.613667 603.456 42.16667 898.047 0.8066667 337.399 18.233 20.135 5.557333 2.433333 12.30833 6.745333 18.592 7.059 3.979 670.486 7.980667 134.6073 91.49933 118.9327 40.25467 1.574667 7.909333 28.839 4.531333 74.00233 2.900667 23.09367 34.16433 443.3597 4.281667 17.96533 110.725 40.23433 46.75733 123.0927 14.71933 1.991 6.527333 48.27367 302.136 8.791 73.27533 9.824333 50.11167 6.812333 73.59667 2.154 61.43567 759.571 225.547 11.312 47.651 27.61367 22.68433 15.46533 824.9103 9.274 6.250667 13.78833 7.252667 1666.136 25.71133 1796.241 15.18033 0.1093333 18.317 12.40267 6.929 4.766333 46.23067 18.67133 44.97967 49.835 93.21667 474.4033 22.375 354.6413 46.17067 33.815 43.83633 1846.256 7.083333 36.11867 10.12033 5.733 19.73 24.63167 2166.993 23.127 759.148 29.26167 8.807333 28.26467 25.208 2.068 27.77367 17.59867 109.3627 0.713 1.851 497.7577 34.33067 25.73033 15.25233 251.833 3.200667 11.93267 48.562 2.811 20.71867 66.73133 35.802 7.48 13.58 9.767333 7.869333 21.67167 17.53667 7.107 11.286 8.292 30.97967 6.248333 3.762 325.5413 8.395 59.43533 43.001 33.21467 8.866333 8.631333 112.283 13.64567 18.33267 25.40433 87.024 2.682667 8.002 14.93733 46.73367 49.788 22.31833 25.089 6.686 5775.202 483.664 11.98267 5.558333 5.931333 321.257 275.3867 9.773333 12.79833 3.293333 4.59 20.81133 5.895 6.863 37.152 5.603 756.3963 17.85933 16.116 16.64833 15.94867 31.12967 25.32233 2.163667 16.899 26.40167 48.976 15.01 21.32033 30.75333 7.782667 7.700667 9.616 5.615667 27.14367 7.766333 1001.993 15.57933 21.74467 16.66533 6.204 4.341667 2.723 27.53867 2.800667 5.364667 4.926 7.226333 0.9146667 12.36433 8.077 27.83967 21.06767 8.316667 16.73 2.534667 16.303 11.40267 12.443 10.471 25.646 11.22367 20.261 12.753 1.695333 1.688667 7.884667 18.23433 5.415 22.93933 14.83533 14.18933 1.160333 14.558 74.79833 266.444 13.22967 275.0887 12.76533 4064.721 2.243333 6.091333 7.310333 5.740333 12.44167 1.288 9.105333 11.22367 16.40367 95.166 24.758 10.85033 8.028 7.039 13.71433 2.194 1.577 9.510333 3.424 1956.885 12.90733 11.59067 20.74967 22.17067 7.844 0 13.917 11.227 5.421333 6.524 2.818 8.791667 3.109667 13.106 12.394 5.630333 20.36133 2.411 0.248 6.559667 6.380333 7.672667 7.621667 1.302333 9.378667 9.436667 8.497 11.91033 63.63933 8.578333 4.676 9.471667 1.363333 34.157 3.857 26.291 17.75767 7.711667 3.294667 12.388 6.778333 10.72933 13.50467 13.65367 6.567 6.625333 16.556 12.14267 5.416333 6.067667 3.09 8.293333 5.332667 6.861667 7.431333 6.829333 0.409 6.066 6.512667 17.19233 2.758667 11.758 9.694667 11.36067 11.94067 0 7.325667 0.01 10.12333 4.963667 23.38367 11.994 3.165 3.468 5.177333 9.299667 7.585333 12.01933 9.557333 3.493 2.976667 3.268333 0 1.407667 6.521 4.482333 1.911333 3.736333 7.337333 19.73733 3.301333 10.216 0 11.46067 5.422333 26.67367 39.729 3.489667 3.822 0 5.633333 8.411333 2.467333 1.547 4.053 0.4346667 11.24533 15.47733 1.897333 10.201 3.680333 4.765 8.445667 0.7683333 4.638 15.75333 9.507333 1.384 3.27 8.805333 2.745 6.326 17.23067 4.293333 6.395 4.695333 1.184333 5.581333 3.051 2.219333 0.6643333 1.870667 4.127333 2.550333 2.517333 1.252 6.813333 6.606667 0.3906667 2.14 2.605 4.484 2.330333 4.196667 8.839 3.021333 1.153667 1.56 5.001333 2.578333 2.448333 1.169 9.374333 7.634333 2.692333 5.019333 12.573 4.009 4.196 0.9123333 3.043 2.011 3.090333 8.218333 3.162667 1.351667 0.724 4.126 4.223333 9.984333 1.122 1.344 2.242667 21.42967 1.469333 2.678 4.744333 8.963667 8.504333 7.756333 3.484667 3.986667 35.57467 1.637333 4.41 2.573667 4.724667 8.025 1.836 3.393667 11.52467 1.089 3.328 5.509667 3.398 35.02267 2.804667 1.980333 1.696667 2.523667 0 2.844 10.61867 3.570667 2.056667 0 3.682667 0 3.077333 2.577667 2.877333 8.773 8.003 19.30967 1.863 1.994667 0 4.313333 3.945667 1.102667 1.978 1.784333 3.675333 1.800333 3.851333 0 2.192 4.52 4.102333 3.773 2.335333 4.572333 0 4.021333 0.989 12.372 5.391333 10.20033 0 1.697667 2.944667 0 0.768 9.440333 1.092333 1.981333 2.347333 0 0 0.3666667 0.5473333 9.496333 4.55 1.414333 4.251333 0.8833333 3.630667 4.372 0.7693333 2.396667 6.084 2.943333 2.881333 0 2.291 14.29267 2.337333 0 1.477667 2.404667 0 2.190333 3.280333 0 3.352 0 0.9593333 1.992 3.248333 0.4253333 7.155333 3.064667 2.304333 
2852s sampleB_mean:  381.073 324.8553 363.4697 136.0917 1076.978 135.6287 721.2523 193.995 322.6313 501.0717 7779.492 155.6753 2550.414 340.8923 1492.051 9939.373 303.273 1007.03 1438.471 1331.648 7520.41 6944.853 217.5877 6464.644 973.0083 2510.784 7181.47 5346.478 971.4367 2449.757 440.9727 2827.345 347.4017 10849.9 3982.392 11165.49 722.7793 188.059 204.688 183.432 227.1767 1506.715 341.9023 304.1167 318.3057 6705.697 1192.947 147.2877 644.756 98.27667 5036.385 6887.084 5874.642 8614.152 8614.152 1781.496 876.8277 510.9113 568.9407 819.1427 4540.328 6156.043 5974.238 176.1237 636.1717 5515.698 512.042 850.5097 381.4813 293.4293 204.598 88.77667 132.997 297.5633 3398.294 7405.14 493.2167 803.7297 820.1 224.959 1237.565 3104.744 337.5617 2649.173 374.99 4809.412 347.1993 7596.105 395.6523 91.93733 5589.41 568.3683 728.6047 286.7303 8313.711 3325.992 8625.824 464.25 199.5333 615.4837 234.8707 210.5073 327.728 190.3363 237.9167 165.5147 8726.054 4978.607 254.0923 592.331 229.8227 177.6103 1183.775 126.265 12136.75 3101.543 4181.758 257.8713 4624.974 330.2803 307.597 178.331 318.668 498.566 96.888 209.5997 265.4807 2806.072 11956.17 437.8937 124.821 369.4417 497.3057 5311.835 880.4753 59.968 133.1137 107.6607 10695.83 565.0517 9160.812 189.81 65.022 66.28233 624.4283 92.04867 1147.187 79.23 148.3807 361.7567 240.9067 617.5097 169.5693 130.7987 744.834 501.203 1388.008 464.656 277.6277 437.7077 3477.406 10005.84 163.2497 85.369 177.0987 365.9053 3135.76 396.4167 223.6213 159.9217 5150.462 87.30767 139.8577 303.588 248.7967 784.5 58.786 201.1477 151.089 2813.865 227.959 1232.959 12803.12 205.964 2069.238 7921.826 129.359 4052.112 242.2357 309.0137 365.304 198.0453 7646.521 196.2657 3606.195 366.6233 146.225 8077.68 53.11833 102.4913 221.5063 171.415 198.031 76.629 9231.562 244.213 346.0203 221.3943 14596.83 11807.78 141.1233 3043.903 228.616 7137.863 94.084 1727.754 134.7863 171.2443 41.92667 176.1103 186.3673 115.6383 160.6447 118.4783 343.3797 3497.592 79.78767 794.7277 383.3883 954.507 243.0527 374.3023 132.86 204.0893 102.4957 434.0653 56.084 332.1927 383.105 2899.79 160.461 153.6373 473.468 259.974 306.1523 566.3103 93.961 88.20067 138.7943 297.5293 1314.765 92.801 376.801 165.6487 208.997 175.727 324.095 38.50333 261.1813 5955.872 1374.415 166.719 219.043 146.7367 145.871 88.84733 5402.498 109.0163 578.1793 112.8707 55.56067 7998.991 217.828 7391.381 106.9733 58.52433 92.66933 110.12 65.82467 82.77467 199.25 84.19433 506.512 317.4007 434.0367 1924.887 162.353 2636.168 241.8647 264.5573 279.8187 10466.26 51.48067 210.276 104.7473 79.15267 108.0163 102.9103 12057.81 125.9207 4659.391 120.016 44.52667 130.4647 434.5497 54.28 219.1713 102.8277 502.0593 60.909 59.07767 2478.864 189.876 109.1297 138.9953 1538.062 67.97633 92.14267 404.8233 42.94067 94.855 288.2643 221.9553 53.67933 205.7273 63.51467 49.84633 91.36867 88.724 72.27033 139.4217 71.07333 155.6507 65.14433 136.3853 1485.8 91.96267 451.6893 251.6407 147.5143 101.2043 98.42267 446.5917 142.4997 125.6427 150.83 391.7213 64.48933 72.04033 114.7247 244.312 217.945 188.654 313.5353 92.354 31019.62 2983.166 54.17467 78.15767 98.59367 1573.052 1190.783 94.036 71.95633 57.289 57.92467 138.8203 72.229 48.662 329.0943 284.8557 3680.324 89.19033 359.4497 112.4907 117.3687 160.033 147.9097 323.135 80.658 143.6177 272.869 75.13167 177.7223 205.2823 67.32633 55.31033 92.10033 71.83833 111.3283 92.91767 6554.638 83.32767 97.74133 92.673 68.93667 58.84033 64.96333 123.7103 66.58633 33.64933 86.666 63.519 61.049 61.75633 52.40167 126.6667 114.413 62.202 70.82967 31.92033 558.288 86.82867 55.42833 51.40267 189.338 54.697 97.67333 98.25867 26.105 27.42533 69.31567 185.3687 36.84367 143.2053 63.39167 106.367 29.412 84.09433 654.0063 1437.071 92.58367 1768.526 65.265 23095.85 25.16133 30.305 61.927 49.55567 59.70833 23.09333 44.59133 47.69867 91.34767 629.935 108.9977 60.39433 37.13833 59.309 80.30267 38.35733 21.31667 40.01867 36.129 12433.72 74.47967 56.87433 97.91867 101.2333 44.65167 41.25767 75.314 100.9357 40.88467 29.19933 81.03933 67.40867 52.62167 70.48667 63.275 28.11233 89.473 20.836 18.746 65.641 57.89033 36.83567 39.14833 63.43233 51.208 50.94033 37.861 59.017 269.8203 51.20733 45.43467 53.35367 33.71767 180.145 46.01667 105.9517 72.092 37.373 17.67167 82.208 38.239 43.553 70.23367 58.72433 40.58467 36.76167 104.9537 118.5717 31.81733 48.09067 32.39167 95.03067 24.105 74.76 42.02167 63.80367 40.14133 44.57067 134.3513 71.77333 37.18267 83.02567 44.80233 60.34067 49.809 17.20333 49.184 16.39933 52.59533 24.998 275.1827 77.42067 16.98933 22.795 42.55233 39.439 57.38933 58.53467 43.199 22.759 23.031 134.6853 9.080667 17.978 31.64467 50.66867 19.87967 50.351 80.83067 89.41967 28.618 49.53233 8.385 147.841 28.99667 170.258 170.7703 79.93733 19.01033 101.7453 79.05433 56.735 82.00433 27.15533 24.42933 9.165333 59.187 64.17467 17.666 45.68133 28.08767 46.573 72.57967 12.81233 39.557 63.14133 38.56967 45.292 21.26833 40.58733 25.20967 25.818 69.73067 21.37133 35.30367 130.2143 47.25833 31.359 19.069 16.69733 12.13567 125.1613 31.40267 17.60767 26.59233 16.692 34.963 33.96667 17.79667 33.96833 16.98933 38.06967 16.53733 18.67167 43.21967 51.753 58.21167 22.82667 38.21633 28.28967 37.33167 55.27767 50.767 62.14133 21.58933 42.533 122.654 21.925 37.97 17.76433 15.914 70.339 13.31667 69.305 13.12667 8.173667 23.8 18.98967 52.68633 48.78233 10.06533 10.878 19.56367 133.2117 11.03933 23.558 23.01233 63.401 37.642 37.89133 37.25433 49.67067 200.7123 14.71567 49.08533 22.41933 24.04433 43.66433 26.17633 23.021 76.51933 8.213333 20.035 24.348 14.291 139.358 27.69933 12.07167 34.59267 23.64233 116.5107 13.166 45.16833 15.776 11.24133 29.38867 22.33433 11.09467 30.44067 20.69233 12.62967 51.325 34.98133 92.552 45.16467 11.69767 44.84 23.05967 26.364 27.504 35.719 14.12933 57.80667 17.39633 26.279 35.64 14.443 29.65133 23.06333 18.868 18.31433 21.97667 12.82333 23.808 22.85333 63.05533 29.06367 64.09967 23.75833 9.625667 16.55933 7.635333 17.268 48.198 15.14 14.02 9.959 5.506667 33.81667 2.727 14.585 43.573 31.779 17.85033 27.65767 11.04933 28.30367 28.58167 10.03867 16.253 27.41967 17.96567 14.46867 1.073 9.625667 59.659 14.20067 10.958 27.819 11.44933 18.55767 21.40767 13.08833 8.730667 35.49 11.718 16.94833 29.841 14.722 7.215 40.67867 28.26067 16.25467 
2852s num discordant:  0 
2852s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
2852s sampleA_mean:  5395.606 781.6647 1816.62 5495.505 734.0483 1412.697 1120.621 502.9777 1262.588 310.3963 1751.765 620.238 665.289 1833.283 2602.336 6030.232 1291.39 887.2083 3549.085 494.789 637.4673 1371.045 1013.064 499.8527 1681.385 1046.9 1445.705 647.4437 521.84 470.179 2191.464 5797.692 371.296 4954.434 1326.5 4191.816 982.539 944.0123 1407.266 4913.275 12222.46 335.7477 2635.243 1265.232 559.8297 20787.35 1512.754 15024.4 1593.001 854.0897 2002.536 1272.664 154.4447 116.9527 567.2883 326.0873 4784.861 198.9307 258.5643 3468.578 244.753 234.695 1348.496 564.1773 933.0403 296.1627 178.6107 810.3883 999.5363 1939.628 562.1487 36600.33 405.9907 1532.142 335.2157 194.6923 1233.492 335.4993 335.637 388.648 581.2863 405.4877 4713.887 393.785 104.2153 1933.215 5645.434 1088.069 1718.763 594.819 1707.219 521.2813 1031.742 1656.826 209.749 1037.645 1091.041 499.693 435.0017 300.2583 387.8127 252.8977 298.6353 2446.14 272.6143 923.62 925.3123 425.4187 210.2437 363.4713 533.844 1640.267 344.3147 150.8137 590.469 103.573 3088.486 460.3903 1179.723 114.123 146.7767 122.4237 176.112 1753.538 2891.881 2237.79 4534.064 876.645 322.1607 772.306 244.4597 825.5967 337.406 159.0503 122.591 233.2683 531.0443 337.767 762.2617 168.438 133.8673 581.914 838.8547 122.177 872.2057 604.7417 1707.261 2017.126 617.5563 610.589 1547.728 89.249 100.0037 114.485 664.8137 568.889 508.1423 1434.927 1030.087 378.0157 5637.134 356.3497 482.3557 480.5827 156.8307 1756.628 147.324 109.0817 1198.79 349.218 89.41233 156.591 432.0453 563.9263 310.3323 199.325 3561.451 99.45067 85.82433 219.039 97.82467 323.746 164.5937 201.4867 241.211 350.3023 182.1447 210.486 368.628 176.9843 128.0267 407.6713 207.397 120.7347 94.07567 189.715 991.437 1125.723 71.71033 125.2723 719.3537 164.083 437.1223 240.267 116.1613 62.56033 324.5383 770.6237 389.129 198.061 81.80933 328.3217 1315.006 603.3643 183.172 207.939 177.4467 63.90033 78.31633 78.67633 52.74467 721.5107 132.971 104.0613 105.1747 160.8853 354.7773 316.5037 26.93367 60.22767 127.1483 91.99833 206.046 169.0567 300.3533 161.1783 66.11467 84.98533 407.805 294.269 168.189 2465.916 1229.376 94.133 98.94267 519.577 212.7377 250.2393 172.982 124.4867 291.7607 129.574 132.1053 236.6537 1099.802 59.607 87.49733 280.7067 471.4763 115.35 181.09 421.348 173.3993 93.672 562.891 278.785 1557.898 60.025 76.27033 1606.153 154.7137 55.68233 98.85333 93.57967 363.302 354.898 90.65667 136.4807 62.65367 86.272 40.38733 171.9977 105.6967 73.156 51.06833 204.4367 305.3177 113.344 80.98433 214.102 304.6523 2036.308 38.966 280.1693 53.23867 46.29267 1505.046 77.01533 44.27933 66.88467 54.279 971.5327 66.544 62.81 87.15633 425.4893 95.84833 64.515 135.433 56.42633 35.384 38.21567 97.46133 407.7717 32.07433 47.17133 69.30367 233.2737 194.3693 751.6327 74.26433 471.7457 6075.931 144.1087 16.066 47.40267 171.2653 56.34967 86.26767 69.90667 33.614 93.98167 26.77667 630.4887 27.49133 38.41333 40.022 158.4977 44.67767 187.0867 50.39 71.55767 101.362 32.60533 31.01767 71.85 58.726 51.916 115.2073 84.101 40.76933 37.746 37.93767 30.31033 131.435 141.5087 35.92467 50.27133 56.78633 114.1953 42.259 49.19267 82.45067 42.52667 47.12267 56.986 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2852s 58.77867 51.68567 34.524 41.489 7.951667 38.467 496.4993 51.49667 163.5027 42.42 209.263 70.90433 27.86967 52.054 422.5397 33.66067 34.55067 51.36633 45.27567 26.74467 48.80533 32.359 56.72833 142.1963 19.379 10.913 43.001 19.36133 32.87767 42.69267 52.49167 269.428 45.48233 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2852s 66.32833 69.761 59.42267 45.49933 26.72567 84.52867 20.61433 24.04867 28.092 59.42133 73.985 31.80833 36.76933 36.44033 40.90567 20.94233 38.71367 27.07933 132.0313 28.112 36.69767 27.81033 31.895 13.58767 86.196 20.89067 13.46233 14.06933 27.92067 23.675 27.10933 23.51567 43.59833 22.01133 19.87867 23.62733 32.296 23.94367 30.83533 36.86033 45.54267 24.69267 27.52167 16.59667 20.281 191.9503 68.59733 22.18367 14.442 26.41767 27.188 11.48267 29.40667 20.15333 26.73867 27.801 22.07333 9.022333 25.49633 18.73767 37.072 20.84167 23.66867 20.21567 44.083 13.02633 26.52667 13.554 23.232 40.67567 18.52533 14.434 41.65 20.87967 13.54667 18.24067 12.43333 28.812 15.60267 30.77433 15.976 35.217 16.92233 15.92 17.69467 17.132 25.093 8.334333 28.27267 22.21567 67.70667 46.006 35.653 25.03867 19.03867 8.423667 38.67233 66.471 25.646 20.36367 27.70233 30.20433 24.57 15.579 21.81067 12.36533 24.97367 26.937 14.50367 19.224 12.97133 51.373 10.894 20.40767 11.617 18.127 15.803 26.99167 56.10667 20.359 36.983 23.34767 13.338 9.058333 8.6 23.038 19.135 24.79867 
2852s sampleB_mean:  4.892333 0.8923333 3.02 10.731 1.413333 4.947333 4.916 2.201 5.897667 1.439333 11.541 5.31 5.982333 18.24467 28.83167 71.58533 15.897 11.73133 54.76233 7.353333 9.523667 20.785 20.73967 10.32667 34.85667 21.734 39.02467 18.007 15.272 14.071 67.15133 190.2367 11.974 175.0553 46.38933 162.736 38.35033 40.62 61.93367 231.01 644.6073 17.87533 149.0183 70.315 38.834 1576.856 120.2997 126.2827 84.69133 10.01733 60.698 122.321 6.593 6.833333 5.055333 34.29367 176.7203 5.075 20.43633 143.0547 4.303333 6.119333 62.01667 44.774 82.944 21.86767 17.35367 97.40133 52.632 191.4833 41.809 312.258 33.76633 216.263 18.10167 11.08667 131.954 2.999 31.756 51.789 69.84367 68.43533 184.242 46.20633 10.803 91.85267 1058.536 85.388 167.6013 21.75133 199.414 34.63 146.7283 70.838 6.52 154.1127 78.63867 5.957333 18.98533 8.328333 32.09667 13.45833 29.81633 327.4777 14.93967 94.25133 167.5307 62.69867 3.039667 18.10667 99.03833 172.0003 48.44967 13.40767 19.323 1.620333 8.807333 86.94433 120.642 5.291 9.162667 7.044667 10.14033 290.869 107.587 176.0093 1.982 96.643 17.25433 52.029 33.99767 138.9923 44.574 29.81667 5.435 22.66633 59.39767 57.83967 60.149 24.10267 18.47767 81.38067 157.5777 3.384 151.9077 135.326 274.274 263.582 35.93933 119.8197 296.326 5.086333 7.705667 12.202 138.5447 98.93967 111.2203 147.5103 236.2837 60.40333 585.796 45.153 78.18267 81.65333 3.080667 288.293 29.03533 9.454333 112.516 81.69867 11.83333 25.95767 62.152 71.425 36.04767 11.36967 52.72333 11.37767 16.697 31.115 10.11133 40.80033 15.18533 37.04267 52.859 68.39567 31.26267 33.16933 77.462 33.04933 15.958 77.499 22.379 4.436 4.922 31.045 228.12 239.1367 14.63133 22.86333 131.7207 29.20433 64.78833 46.24133 26.55867 9.876 44.73367 76.85 52.96867 43.10367 6.152333 46.83533 252.1407 32.20767 41.53733 42.20867 41.19767 12.78767 11.56533 2.519 3.457 64.61967 21.17867 14.93967 20.32033 19.13967 81.672 66.14267 0.388 12.457 28.43733 21.33367 27.23467 24.19267 55.72533 33.53433 3.929667 11.13 80.735 60.023 37.84833 192.615 252.5313 13.001 15.63733 68.06833 22.53 50.52767 27.607 21.97267 49.06433 25.094 28.67333 53.45667 262.4237 9.053333 16.72967 57.499 103.8797 24.55133 29.328 77.08667 41.26233 16.52467 92.249 38.40433 221.51 12.56167 17.05033 129.8027 36.59667 8.892333 16.70467 15.72 72.445 10.47367 15.84233 23.92933 14.59467 4.478333 7.813 26.382 19.338 3.546 3.424 41.21667 58.95767 26.43 16.686 49.04333 72.39567 456.8783 6.782 10.048 9.581333 6.808667 300.8857 15.967 2.343667 10.61567 9.956333 161.046 15.178 11.71167 10.136 38.81867 20.181 3.776 30.64367 6.818 2.932 7.134 19.69133 79.67267 2.596 10.08733 12.49533 47.94933 41.753 131.0337 14.317 63.54133 603.3247 22.72933 0 9.795333 6.163 9.696333 13.70767 4.551667 5.698 11.88467 6.056667 144.8737 3.111 0.77 2.558333 24.952 9.568 44.787 8.024 6.153 8.861667 6.225333 6.028 15.87967 3.721 9.442 0.8253333 9.684333 5.855333 7.286 5.482333 5.053 23.79767 5.704667 5.451 9.387667 5.819667 25.736 6.709 9.898 12.136 8.245667 10.034 3.947333 13.348 11.101 6.474667 1.601 0 2.289 96.05 3.487 30.05333 5.672667 9.86 15.06367 5.932 9.460667 25.345 1.628667 4.229333 10.76167 10.75867 0 4.762667 1.994333 2.356667 34.28533 2.445 0 6.886 2.312667 6.930333 6.758333 12.28333 60.65633 4.818333 2.695333 16.034 3.923 3.518 4.023 18.601 2.932333 4.175333 1.379333 8.966667 3.183333 5.966667 2.515333 5.916667 4.880333 0.597 8.657333 0 26.49267 5.907333 2.795333 2.091333 5.972667 0.3683333 1.362 3.392 2.201333 1.082 2.298667 0 0 1.805 10.182 4.613333 3.583333 3.766667 6.506333 4.885 7.344667 4.728667 4.943333 0.911 2.479333 2.582 1.481667 47.94667 7.661333 5.132 0 2.759333 3.599 1.101667 3.284667 4.356 2.819 0 3.673667 0 0.774 0.7583333 7.471 2.833333 4.525 1.016667 8.528 0 1.173667 2.414 0.3263333 5.924 1.954333 2.116667 2.037 0 0 3.214 2.062 2.919667 2.585333 7.372333 3.673333 7.599 3.048 3.431333 2.400667 3.17 4.567333 0 0 3.38 16.083 9.191667 7.766333 4.954667 2.839333 0.05333333 3.975 16.31167 5.980333 3.139667 4.509333 1.766333 2.267 2.893333 4.752333 0 1.525 6.575 3.54 0 3.08 8.722 0.969 2.136333 1.796333 0 3.779333 1.799 7.809 2.693333 2.451 4.770333 0.7883333 1.826 0.914 0.831 2.901 0 
2852s num discordant:  0 
2852s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
2852s sampleA_mean:  15.838 2.068 4.080333 21.39933 36.11867 7.282667 7.963667 2.713333 7.685 16.51667 6.167 5.415 40.988 88.57 10.53633 102.2703 31.261 15.04567 28.64033 72.55133 96.61333 103.6867 30.97967 20.01233 224.904 68.104 141.0787 509.7623 2.398333 5.762333 4.654333 76.15267 16.54033 46.17067 37.21967 0.1093333 18.96267 4.281667 2.433333 121.0697 803.1917 503.5693 7.252667 40.83233 98.448 55.26267 25.78433 539.652 9.434667 57.26933 526.2243 11.583 4.244 655.8127 1.292667 279.6767 3.451 291.1757 7.212667 0.4346667 478.7223 504.111 26.51267 11.22367 558.1363 2.550333 88.20633 31.92667 0.713 14.71933 31.501 15.54567 96.77733 409.1913 125.9483 81.319 5.627 3.200667 5.017333 11.52 26.208 337.399 35.44767 40.27 2.219333 733.6827 20.97667 24.615 45.412 9.896333 13.98533 78.96333 3.586667 22.74167 300.087 5.474667 25.605 2.280333 578.8703 47.34533 5.682 31.97667 1.577 1.460333 43.50567 915.841 354.6413 33.57133 23.127 903.1557 3.420333 3.078667 115.4593 23.33733 50.11167 20.36667 1275.026 188.4693 0.838 113.9973 641.1777 2.243333 43.09833 37.152 443.633 48.562 40.25467 3.595333 7.980667 6.745333 16.528 12.94133 697.2287 34.135 7.059 6.515667 763.5533 33.62067 17.48067 25.208 23.04333 23.94067 28.26467 6.546 5.016 2.696667 16.27833 620.406 0.8066667 3.139 81.34233 12.993 110.725 2.330333 7.909333 8.791 0.248 106.1753 11.312 65.027 237.8803 16.899 4.745 37.27233 22.51133 850.6397 15.09333 89.987 2.177333 1.919333 27.29 15.92433 29.55 2.154 87.317 425.357 225.8327 18.754 18.317 51.407 6.812333 159.4173 47.036 16.303 13.46667 209.5917 18.76 19.92833 87.42633 5.630333 11.438 5.733 3.043 9.969333 18.88733 1.991 642.0663 223.9227 25.55733 2.811 9.642 71.78533 57.46833 8.043333 103.9153 6.919333 5.557333 691.0767 91.49933 670.486 55.73 0.6643333 22.68433 10.216 26.715 1.911333 26.67967 16.556 24.758 27.48633 4.766333 30.828 7.844 3.468 37.25567 56.797 5.931333 17.19067 15.01 4.531333 29.18933 0.7683333 15.18033 171.0287 14.063 19.11967 21.51767 66.65833 23.09367 15.73033 4.59 64.82733 4.156333 22.31233 17.96533 8.807333 4.371 24.63167 3.941333 6.819 6.559667 30.80767 39.67767 10.30533 17.221 6.455667 5.615667 13.08133 5.802333 75.469 74.79833 10.95167 27.83967 11.227 27.59267 9.507333 22.752 86.883 103.2833 26.75667 6.980333 0.485 6.527333 8.162667 7.039 42.57533 22.93933 11.29367 759.571 22.17067 15.08833 12.98 6.496333 4.341667 62.50533 18.30367 39.57833 27.94767 241.785 6.674 5.177333 12.39433 393.3037 0 28.057 50.469 9.735667 216.0503 7.163 11.22367 7.412333 2.534667 7.107 13.78833 20.135 79.21967 8.316667 12.753 18.62433 142.0663 20.37167 5.895 37.255 49.835 31.32 11.286 497.7577 18.233 47.42233 16.40367 0 26.291 8.497 0.3666667 2.592667 52.084 21.116 44.93767 2.163667 50.97333 6.929 35.29633 12.36433 20.74967 6.300667 27.23133 32.849 20.992 443.3597 1.469333 8.631333 13.65367 7.48 20.261 9.557333 28.45833 11.93267 3.857 2.900667 1.688667 23.67567 8.077 30.424 260.666 321.257 7.354 22.627 84.312 20.16567 9.613667 19.73 118.9327 22.996 2.723 44.996 28.33667 7.310333 55.59767 1.288 19.921 33.50367 1.162333 5.364667 7.884667 9.824333 14.78033 77.21567 14.94733 40.34367 20.71867 8.578333 9.767333 8.002 6.524 1.448333 9.773333 4.963667 44.07433 14.06433 11.817 10.38333 33.01633 13.22967 15.64 12.40267 0.9146667 28.43467 17.692 25.32233 14.22267 18.33267 4.676 1.302333 18.30633 8.393333 25.40433 7.050333 17.85933 35.802 8.403667 1.160333 3.424 21.69333 5.720333 15.57933 5.558333 14.91467 27.77367 6.066 21.06767 8.173 9.616 39.729 11.59067 1.715333 7.555333 30.75333 25.361 14.16 13.58 10.12033 8.866333 1.252 7.216333 18.23433 7.672667 6.910667 17.332 1.363333 18.94267 1.444 11.994 5.740333 12.76533 6.380333 2.411 7.431333 57.61633File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2852s  7.394333 8.791667 6.248333 11.097 42.16967 11.758 11.36067 13.23767 44.679 11.21733 9.744667 18.93367 33.10033 6.863 3.162667 5.332667 6.204 5.416333 5.603 1.695333 1.992333 7.083333 2.976667 5.581333 3.762 2.682667 7.585333 12.14267 33.815 20.36133 3.09 6.592 0 10.85033 21.88733 25.089 8.395 13.50467 0 3.979 3.541667 1.574667 6.983667 1.122 5.264 0 2.605 2.844 16.06567 3.109667 9.471667 2.818 8.198 10.201 5.596333 4.926 2.745 11.89067 8.805333 6.861667 53.09233 6.067667 9.752333 3.294667 1.897333 6.752667 6.521 0.4176667 7.621667 12.883 2.715 8.293333 5.057 21.32033 2.14 7.601333 7.766333 11.40267 0.01 1.981333 4.058 0 3.292 5.421333 13.88733 7.325667 23.38367 7.168667 3.765 3.418667 15.09267 6.567 1.281667 4.638 8.889333 8.351333 12.67933 6.625333 0.7146667 4.064333 1.351667 2.922 8.038333 2.310667 4.196 6.512667 0.2473333 18.91833 0 3.822 5.686333 1.769667 2.474333 2.517333 4.053 1.851 3.090333 8.223667 1.407667 1.994667 6.754333 8.255667 7.337333 0.5473333 7.195333 0.622 2.883333 1.492667 1.089 3.425333 1.649667 16.116 0.9123333 4.009 4.765 3.273 4.325333 161.101 0.409 3.733667 8.773 5.060667 0.676 4.989667 2.194 0.939 3.122667 4.695333 3.219333 4.572333 1.547 3.696333 2.800667 0 3.179 6.813333 1.576667 3.493 36.09 6.893667 0 2.414667 0 2.275333 0.7693333 1.980333 1.637333 4.387 12.75533 3.293333 0 3.403333 2.337333 2.877333 11.126 1.776 2.663333 1.344 3.021333 3.398 2.692333 7.756333 6.45 3.077333 1.544333 2.347333 4.451333 2.448333 0.4253333 2.577667 3.570667 3.319667 8.963667 3.992 0.989 2.259667 4.385333 5.633333 3.945667 2.578333 2.573667 2.623333 2.777667 1.844333 4.611667 2.285667 4.123667 1.800333 1.324 2.962333 3.988333 1.305 0.8176667 1.929667 1.56 4.080333 5.287333 0 8.504333 4.444667 1.784333 4.52 4.893667 0.7723333 2.242667 0 2.252333 2.192 1.807333 0.604 1.697667 0 2.529667 3.511333 0 0.4806667 2.396667 1.870667 0.9256667 0 2.706333 1.130667 0.8176667 1.452333 0 1.141667 2.325 0 2.881333 2.617 1.002 2.705667 2.246 6.169 1.383 1.010333 0.9066667 1.125333 1.184333 4.289667 0 0 0 0 5.855667 0.67 1.916 0 5.097667 4.041 3.683667 1.665 4.773 0 3.556333 2.746333 14.30567 1.322 2.482667 0 1.733333 0 2.415333 3.810667 0 1.562333 3.535667 3.218333 1.622667 1.277333 1.723 1.461667 1.577333 3.201 
2852s sampleB_mean:  2001.57 205.6727 348.3133 1524.761 2415.454 437.971 472.5113 149.84 339.544 736.2793 266.1853 208.1393 1440.661 2830.628 285.4657 2786.993 809.747 370.6363 686.1263 1611.849 1997.885 1889.849 566.031 344.6643 3005.897 856.342 1374.611 4325.944 112.4467 90.55133 105.6647 759.8243 253.343 768.1787 394.7987 161.9667 211.0497 317.0973 382.0493 2237.994 4759.337 3179.415 118.7197 562.3953 875.9707 953.5553 378.7327 3396.666 146.4013 556.5843 3330.022 144.7763 73.643 3693.07 67.006 2471.048 120.2137 2047.901 79.82167 177.154 3249.388 3216.203 574.6353 142.302 2922.537 156.2033 476.768 300.4817 136.4467 140.0233 240.971 267.5577 485.2353 2374.126 606.0663 630.4883 130.9923 125.4973 132.7817 192.3193 265.6093 2883.64 421.1887 310.312 151.719 3620.716 140.997 166.0277 241.776 135.609 164.205 439.0257 87.15567 171.3853 1235.974 140.1517 255.2837 68.593 3756.434 298.0877 141.5657 279.329 83.61967 60.04567 269.2717 4427.58 4198.375 193.8653 199.6 4251.336 58.96367 105.0843 760.6557 167.053 267.723 165.0047 5398.857 1094.26 104.978 461.5343 2990.729 65.65667 341.4467 609.5917 2376.446 692.2687 332.1813 71.08433 87.31133 90.86167 120.8233 116.6347 4895.859 320.243 109.1813 165.4787 3709.705 189.6917 263.798 366.0723 189.5857 166.8767 194.996 84.91167 96.602 42.12067 177.3257 3616.512 80.36 126.504 401.21 194.1133 511.8627 119.8297 118.3287 97.3 82.68433 731.863 177.183 699.6877 925.7747 133.069 120.4613 218.6657 155.4747 3423.331 253.0167 683.449 81.26567 59.379 212.3977 133.1023 127.811 39.998 365.2543 2436.015 1012.972 105.6257 98.13967 321.7517 166.5273 927.6743 203.65 1604.347 143.3147 1034.454 132.628 79.65933 434.556 55.55933 160.1683 96.957 117.851 58.79033 138.4137 80.46333 2890.802 1049.838 160.4317 57.69533 90.957 280.2643 290.862 303.0437 444.0447 92.061 38.85333 3650.525 357.7387 3849.83 274.3337 84.001 150.3183 195.2947 178.71 72.596 178.5933 385.176 193.4727 189.0233 79.68 175.8867 92.43267 64.25433 260.6683 366.123 131.585 132.4173 117.2697 82.67333 259.148 96.94267 90.116 878.6043 75.75133 120.8867 96.142 287.485 216.949 88.38 60.63 255.8583 87.65567 161.1673 115.1327 40.32533 51.73767 127.943 31.73 85.78933 183.3313 125.2547 254.1857 140.2763 123.721 103.81 93.48367 91.18133 58.06633 428.623 1621.57 127.5543 168.0607 240.6073 149.819 109.6237 194.3873 404.5893 443.3713 213.8997 67.408 76.24933 85.55767 69.18967 123.938 162.5713 220.7547 59.23867 5152.482 184.3507 62.39367 74.99667 48.27933 76.57167 382.3843 150.3003 153.0033 162.3163 1082.98 59.629 133.338 53.59967 1642.015 22.75467 218.8733 286.777 91.509 842.3293 293.9087 74.632 136.346 43.412 69.947 88.725 116.5553 496.8353 67.72533 134.7907 83.573 568.8347 101.0153 61.29533 229.5497 351.08 148.7563 132.2 3067.808 107.4287 252.983 143.607 251.767 199.317 72.854 36.6 71.74267 224.5063 95.749 207.045 423.253 232.1147 49.419 136.5493 71.93733 145.5417 33.62833 195.6537 151.599 87.012 1780.032 68.608 90.91333 108.7427 57.40167 140.8457 96.76 186.8647 68.66267 83.324 32.967 36.13033 143.433 53.67167 124.6713 1395.183 1547.523 41.93 110.8577 473.3597 102.0507 62.05533 78.48367 460.2323 136.4563 69.599 231.7267 174.409 80.51633 303.08 30.70733 118.1207 143.872 61.53933 34.301 76.68167 84.66667 96.91167 323.664 138.9263 161.956 79.32433 77.97333 45.994 48.91 35.42167 127.1577 67.53533 47.35667 177.785 69.52233 53.655 71.949 183.9787 84.28567 89.57667 63.03733 61.21367 188.4637 127.9993 114.4257 71.81167 88.05067 65.56833 130.8803 188.329 51.723 100.6683 36.76567 77.092 142.4753 71.28167 28.55333 34.95467 311.329 39.086 78.28033 56.562 77.38367 123.1273 57.43267 90.31267 50.22033 63.84367 280.2713 53.014 36.53367 29.627 151.883 98.33933 76.47533 126.4583 55.85733 53.52367 36.72267 36.70233 159.7823 40.14733 27.296 68.32067 41.03967 176.0977 59.38567 120.206 38.799 61.12667 79.551 22.85467 51.13867 230.7707 47.69067 61.486 30.21933 47.47333 178.2697 150.4293 76.577 62.81267 191.3687 73.193 68.67667 100.608 137.8557 30.35033 29.26867 27.176 43.65367 37.65433 186.3597 19.45267 30.54067 27.671 31.70567 48.22433 57.43367 27.28933 43.97967 183.6017 131.6793 84.57567 37.55767 48.224 7.787333 48.89833 106.615 149.342 42.95633 62.27133 7.434333 93.36767 33.21433 84.23433 37.29667 27.11633 44.01933 19.23067 33.399 35.499 84.252 44.45533 49.472 67.063 32.39667 55.77667 40.13033 58.25633 39.59267 106.4977 49.36433 79.067 356.891 45.60867 42.28633 14.628 21.83433 65.255 35.098 19.80633 31.972 50.84367 33.473 79.87367 34.77567 91.86567 22.669 31.336 52.33733 50.05667 18.93767 49.82833 27.94833 86.78467 33.73067 27.93333 69.843 42.60033 329.1877 31.52433 28.714 32.58033 61.76067 33.70267 20.92033 46.144 34.46367 58.12767 61.23533 25.97433 73.018 30.03567 14.83167 16.267 38.139 31.73667 56.93233 98.03267 19.36667 107.6573 20.285 15.205 21.914 27.04033 33.19833 30.23233 17.84967 13.23833 16.67967 117.513 12.861 18.55533 37.849 49.72933 77.94767 28.44433 30.596 17.43 28.15867 20.05633 15.25033 15.277 18.50433 95.334 24.30433 26.188 34.77033 18.09167 22.413 885.105 18.61167 70.27367 78.66133 26.27467 31.89 65.14467 16.95033 23.73133 15.02733 106.1883 29.242 37.429 19.614 26.23633 22.274 30.69133 20.35933 27.944 17.502 13.99333 166.674 28.39433 3.268 38.715 18.48833 17.236 17.31067 12.443 13.41633 21.34167 66.67867 13.36767 31.383 18.03233 23.945 15.656 80.966 35.44867 15.33767 13.94367 46.892 16.01333 17.96033 38.17233 62.73233 28.101 28.76267 12.703 32.61467 39.09833 13.18233 17.898 16.27233 14.817 62.61533 16.55367 29.174 13.60433 18.28267 41.99133 35.23233 15.10167 20.55233 17.09767 19.04733 14.40533 22.38467 20.926 22.969 20.43233 11.96033 20.87567 15.90267 10.317 21.75 21.75767 15.269 22.439 25.09 14.14033 37.68333 22.49467 11.87167 29.889 26.32667 21.54967 17.53033 23.57 19.42067 12.63367 9.565333 15.508 11.406 26.512 17.607 14.73 25.41533 13.284 22.467 48.44967 13.124 12.082 32.57833 13.01133 16.799 10.03867 20.102 22.88133 16.668 40.46467 17.52867 18.108 19.44067 13.56067 9.561333 29.66167 11.82467 12.414 16.34867 11.65033 13.48967 23.23533 17.859 18.481 15.03767 3.817667 38.401 11.25967 14.066 7.422 25.72733 29.10133 17.881 11.77733 20.93267 32.58667 15.16033 26.44433 72.94233 14.34133 24.97333 3.745333 13.629 12.603 10.763 42.748 3.536 25.30367 16.31933 17.09167 15.84367 8.590333 16.32567 15.533 25.56867 19.31367 
2852s num discordant:  0 
2852s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2852s sampleA_mean:  322.6313 2373.043 328.0923 2550.414 768.306 12470.43 620.017 510.9113 1781.496 440.9727 3211.031 514.415 224.469 876.8277 95.89333 4624.974 1636.976 512.042 198.0453 177.0987 1506.715 621.286 189.5647 707.8263 339.8283 411.447 871.6373 646.6133 1101.219 324.8553 1098.868 645.4617 217.5877 493.2167 850.5097 347.4017 834.608 501.203 222.09 429.5973 244.213 615.4837 173.88 1003.238 306.1523 474.0487 1192.947 1494.298 565.0517 374.99 3078.184 689.711 204.598 623.5437 900.1817 856.7063 166.336 378.627 237.177 646.864 211.7417 132.9247 198.031 578.1793 257.3087 109.0163 97.24867 88.61667 153.4527 151.8027 194.2893 75.79967 138.8203 661.7387 116.0807 149.5763 189.876 194.0203 188.654 272.869 276.1017 92.354 506.512 112.6127 189.338 215.8967 103.6453 202.739 499.6263 278.7853 175.2467 63.519 37.50533 103.0963 160.284 161.0497 53.598 100.247 2633.716 91.645 112.168 54.95833 131.159 214.853 374.3023 72.98133 59.07767 46.03533 55.41567 39.40267 583.86 45.62033 63.24267 114.2777 55.17567 80.30267 106.367 94.455 51.208 58.90833 82.208 36.49633 31.404 50.66867 66.74667 43.62667 103.33 541.9867 13.208 29.69867 99.289 30.70067 72.57967 46.59433 170.258 69.91033 50.351 39.44033 83.27833 41.25767 75.16967 39.745 227.2843 28.455 42.52533 52.59533 82.00433 40.44433 33.46233 137.7607 28.618 32.245 35.30367 63.80367 134.6853 24.83067 38.06967 75.28167 18.93167 25.087 43.80133 7.618667 40.18733 25.539 124.9103 27.874 92.552 36.466 19.68333 48.025 81.69967 25.74867 68.14433 29.06367 37.18267 72.777 63.05533 57.61033 22.32333 58.47233 50.767 20.62167 59.28433 79.93733 22.33433 76.51933 28.191 31.40267 43.573 19.09633 55.27767 63.71067 48.78233 23.51433 48.16367 147.841 27.69933 45.16833 67.73133 24.891 23.021 29.71933 31.79067 69.305 52.69467 31.779 122.654 26.44133 31.89567 36.90167 18.868 62.14133 19.622 23.01233 27.838 116.5107 78.60667 56.21533 23.8 18.83133 101.7453 26.81733 28.387 49.08533 32.10933 33.90867 45.292 57.80667 72.11233 39.1 24.45867 19.95933 22.708 23.05967 35.719 64.68467 48.198 58.21167 64.09967 23.75833 11.958 14.43033 93.41733 41.316 22.16333 22.89067 37.25433 22.77433 23.558 28.69233 21.97633 14.56467 43.359 25.653 37.281 19.54733 44.44267 45.90233 27.504 36.46133 17.79667 23.64233 10.555 26.64367 24.61133 40.67867 13.03933 70.339 13.487 28.572 45.92167 34.59267 16.99367 24.47467 23.85167 37.914 28.30367 33.908 30.64067 62.26333 34.511 51.61667 21.27433 23.06333 22.96933 32.872 17.955 18.41033 133.2117 11.50733 9.291 15.83533 11.65967 16.25467 15.14 33.81667 38.27767 44.84 19.36833 30.82967 15.25267 29.75367 28.19233 22.45533 21.40767 20.10433 16.872 18.279 29.146 5.414333 18.92167 17.03133 6.829667 20.381 17.45867 19.253 42.82367 35.64 
2852s sampleB_mean:  0 8.807333 1.413333 16.70467 11.541 312.258 19.323 17.62467 78.223 21.142 176.0093 28.83167 15.272 59.789 6.833333 341.9077 131.954 41.31433 17.10933 18.75567 165.372 70.838 21.17867 84.293 40.62 51.37267 107.8423 84.69133 143.015 42.12067 162.736 98.93967 33.19 77.04167 173.185 72.11933 149.042 107.4767 40.211 60.698 24.36067 3.97 11.974 231.01 60.63 62.01667 230.7603 361.5717 3.203 63.14733 644.6073 91.85267 31.336 149.0183 190.2367 147.5103 8.328333 50.806 52.02367 126.507 47.04433 22.66633 35.05467 5.375333 52.632 14.771 20.43633 4.436 22.414 21.67633 15.897 14.72967 21.66667 126.2827 23.35133 30.432 43.86567 27.23467 25.96333 61.038 49.04333 11.42567 113.391 3.546 5.980333 43.19967 13.34567 35.93933 52.72333 38.81867 36.80733 4.816667 6.593 15.84233 5.957333 34.63 7.705667 21.97267 603.3247 15.47833 20.231 11.08667 21.75133 47.94933 84.23433 15.958 13.23833 3.929667 11.73133 1.620333 126.723 6.119333 6.474667 24.79367 5.855333 15.00967 21.74967 7.766333 7.976 7.353333 14.15433 2.201333 7.205333 0.6883333 15.63733 4.916 21.066 101.151 0 1.439333 22.53 6.552 1.932 6.709 21.36367 4.875667 2.48 4.478333 8.861667 3.745333 15.06367 7.033333 53.09067 3.039667 0 10.64267 0 7.920333 2.116667 34.28533 3.831 6.818 3.374 14.63867 12.223 1.628667 3.003333 7.897667 1.101667 5.451 5.966667 0 6.937333 4.024 21.018 6.301667 8.839667 6.506333 3.384 4.954667 19.603 3.431333 1.799 1.569 8.477667 14.62267 5.157 6.500333 1.63 8.693333 10.157 1.082 5.139 14.45 1.765 8.006333 2.819 6.082333 2.462333 0.4836667 3.485333 10.28 10.15367 5.055333 7.749 41.35533 0.692 9.145 5.873 2.909667 2.511 2.893333 7.386333 13.05267 5.417 1.487333 19.24567 4.422333 6.758333 8.017333 2.849667 9.771667 2.936333 4.993333 0.8023333 0.08 0.05333333 12.1 2.193667 4.229333 25.41533 5.261333 4.762667 5.657333 2.181667 2.136333 10.16333 2.217667 16.907 4.943333 1.362 3.54 4.677 4.158333 3.098 10.456 8.646 12.014 9.295333 0 2.343667 1.481667 14.763 3.833667 0.8846667 3.947333 6.111 2.732667 4.627333 6.918667 2.95 2.289 5.704667 5.972667 1.766333 0 6.405333 2.344 3.367 8.528 3.412667 3.727667 2.445 3.223333 2.001 2.058 0 16.79133 1.764667 5.310333 10.56633 5.351 2.097 0 4.567333 8.735 3.839 1.942 7.471 16.31167 1.925667 7.252 3.862 5.472667 0 3.237667 2.384 0.911 31.983 2.312667 0 2.121667 2.345 1.519333 2.622333 2.112667 8.592 4.294667 0 1.783333 3.487 1.833667 4.401 2.345 3.301 0 0 1.173667 0 0 3.405667 1.633667 0.3683333 0 3.381 4.706333 10.319 6.860333 
2852s num discordant:  0 
2852s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
2852s sampleA_mean:  4.98 16.50567 117.2063 112.322 62.58133 37.23367 40.96933 28.62567 210.276 110.7323 73.97767 77.55333 94.08633 56.147 95.99433 311.829 220.5287 24.33867 534.2237 138.353 105.9497 53.11833 658.8357 407.2907 1020.23 65.965 773.7893 825.1763 59.968 124.4243 55.75367 501.0717 135.901 30.499 2661.226 191.8153 0 36.84367 36.99433 81.05967 53.687 88.495 132.8633 62.68467 50.429 189.9813 12.544 2.172 21.54267 83.305 180.8457 53.33433 12.42267 58.24233 14.554 17.029 104.7537 341.9023 47.89667 48.72833 25.096 57.313 3.969667 42.797 49.103 193.8337 3.122 17.875 9.165333 39.58367 68.49367 54.28 17.60767 24.273 16.69733 42.71533 6.042667 21.25867 9.605 15.418 39.777 56.695 19.86033 115.6623 23.53367 15.26033 35.78433 30.00467 41.80933 11.277 5.607667 336.3973 16.22733 7.374 199.8083 41.83033 7.538 22.84267 21.14433 342.208 3.966667 8.516333 133.0233 23.71433 24.02367 14.411 10.63267 63.41767 20.959 35.43333 24.38833 14.56933 5.832 57.13467 31.04633 103.5143 25.39133 41.856 40.53433 32.75133 29.33233 36.41067 24.772 7.960667 5.097667 12.85033 29.44033 45.89833 28.28467 6.926 70.13033 16.53733 8.362 22.77967 10.23233 6.981333 15.28167 12.023 8.268 13.52433 25.25367 12.36 75.059 40.92067 31.838 56.92767 31.61067 15.914 15.559 7.083 21.88967 91.47333 12.771 16.38067 21.31667 2.752667 6.314 88.60033 2.792667 10.30967 43.318 17.12667 20.27767 40.359 8.47 7.979667 23.029 238.9387 5.342333 10.49233 10.16833 7.825667 5.777667 8.79 65.86733 21.02533 11.38633 49.53233 11.90333 12.81233 21.765 18.746 28.07033 7.526667 9.187667 5.772333 12.13567 21.686 5.464 19.21233 2.727 2.539333 15.31167 5.664333 27.34567 18.06167 6.437333 5.960667 46.84667 35.59733 3.51 3.596 5.197667 16.75833 37.02633 54.65067 12.438 64.78933 21.776 22.86533 4.820333 17.25667 7.951 3.046667 7.603667 32.918 22.029 20.79733 16.17933 11.03933 14.33467 6.225667 24.662 7.807333 29.746 23.46733 10.73033 14.50533 6.306667 8.48 8.792667 8.809 22.12067 0.8883333 11.28667 3.531333 6.174667 14.356 7.113667 5.639333 3.158 7.839333 5.134333 6.934 74.98367 12.918 3.201 0 0 5.177333 1.752333 7.395 78.08667 1.506333 19.07367 7.025 9.925 3.503 3.788 0 13.76033 7.259 5.081 9.197667 8.591 7.501667 7.014667 10.31933 2.409667 2.654667 3.867 0 4.912333 2.723333 8.232 2.349 1.934333 6.318 23.97033 6.052333 23.34367 0.2506667 3.773667 3.633333 0.5686667 2.518667 7.901333 2.414667 2.742667 2.105667 5.981333 0.093 7.077333 2.653333 2.888 7.560667 2.993667 10.41 9.876 6.688 1.734 2.503 9.321667 4.237 5.407667 4.064667 2.677333 3.311333 4.158 0 7.296333 6.958667 1.742333 19.63133 2.967333 0.4486667 0 8.351 4.931333 3.471667 10.97667 2.231667 7.922333 3.617 3.082 2.362667 1.651333 10.806 5.76 6.261 3.743 3.945333 3.012 4.701 2.98 2.387667 1.848333 2.767667 1.224333 1.755667 2.625667 1.870667 1.814333 0.4626667 0 1.403333 13.32033 4.514333 5.397667 2.188333 2.961333 7.176667 3.138333 4.864 0 5.445 0 1.448333 1.803333 12.06 1.584 2.361 3.174667 0 2.965333 19.41933 2.893667 0.829 3.214 1.168333 2.242 8.255667 4.021333 1.874 3.013 5.335333 1.322667 1.187667 2.536333 0.733 2.772 7.399 0.5746667 2.15 
2852s sampleB_mean:  1440.661 584.575 3506.467 2786.993 843.2847 461.5343 501.3557 317.4807 2415.454 1202.982 805.275 809.747 968.2863 562.3953 878.6043 2830.628 2047.901 203.078 4004.8 953.5553File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2852s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2852s  686.1263 339.544 4216.251 2355.907 5398.857 317.8843 3709.705 3756.434 266.1853 513.784 222.0223 2001.57 807.5603 378.7327 13329.63 1242.884 174.965 208.1393 279.329 786.1327 256.6427 574.6353 641.6557 303.08 573.2667 926.6357 137.7833 58.96367 255.2837 401.8723 1012.972 371.2327 166.8767 310.312 148.789 286.777 468.317 1524.761 265.6093 224.5063 166.0277 255.8583 59.23867 255.0223 290.862 731.863 91.739 116.6347 177.154 320.243 585.796 205.6727 156.2033 145.604 151.719 263.0527 90.957 168.2893 109.3147 194.1133 157.5777 387.0143 121.5623 720.0863 132.4173 124.6713 178.71 125.2547 158.383 110.8993 99.863 1576.856 194.3873 143.872 1109.48 195.216 303.0437 301.9357 213.8997 1834.421 102.0507 127.5543 1082.98 120.8867 150.3003 179.874 92.061 477.213 143.3147 160.5167 148.7563 91.18133 91.509 232.1147 163.1987 496.8353 156.0383 278.7393 682.0817 219.6953 161.1673 148.6807 163.021 98.33933 87.65567 70.221 151.599 178.2697 145.137 41.78967 311.44 119.8297 51.73767 918.9367 69.18967 31.73 143.0897 96.804 67.408 57.44367 174.6973 101.4477 332.2983 161.4237 263.5397 253.0167 160.1683 117.851 108.837 64.25433 109.0193 405.776 118.1207 109.6677 83.61967 29.627 71.81167 437.7257 76.24933 53.655 193.3587 85.78933 138.9263 188.56 96.91167 192.615 113.004 4759.337 24.80467 48.96533 46.842 60.90233 251.767 41.93 285.3807 293.9087 64.15933 195.2947 63.62167 96.94267 141.0183 82.68433 126.6913 71.949 54.097 51.723 84.001 141.442 36.76567 107.2877 36.6 32.39667 130.4127 47.31267 174.409 91.49033 56.05633 50.22033 216.4093 136.4563 37.96133 27.192 27.296 76.82 191.0543 230.7707 311.329 250.7013 90.427 97.60633 68.67667 317.6723 44.69833 29.675 127.1577 170.7463 127.9993 125.7047 93.09033 68.608 106.615 61.53933 176.0977 29.00467 120.0493 169.1617 55.476 216.4057 41.517 39.086 44.98367 49.09733 112.8043 19.95267 84.252 36.53367 28.425 73.193 61.76067 59.38567 30.93667 34.05967 40.13033 43.94933 381.953 52.36933 31.46 19.80633 24.882 30.54067 33.473 28.775 356.891 18.20933 75.443 58.12767 41.50267 20.82433 24.244 18.23433 76.899 27.29533 54.54667 61.80233 65.255 31.52433 27.23833 48.14767 16.15667 28.39433 30.03567 6.507333 33.73067 31.73667 42.92033 86.78467 28.30833 129.8027 106.4977 27.607 93.36633 19.36667 24.241 19.99067 18.004 26.27467 34.77567 20.92033 22.782 28.15867 24.384 12.004 28.714 33.19833 23.60467 32.58033 15.938 40.12533 49.72933 68.356 19.23067 11.60833 44.13267 15.87267 21.00233 27.04033 72.35433 18.612 20.046 3.268 33.75167 80.966 38.715 178.6527 12.202 16.761 31.383 54.89133 20.212 14.948 73.018 17.502 70.27367 18.62033 31.89 17.43 27.84133 68.52333 28.421 25.473 15.33767 20.05633 35.44867 18.50433 16.92567 30.69133 15.13667 17.09767 17.607 16.162 19.71067 19.42067 17.881 4.691 14.14033 18.108 65.14467 23.30167 21.03667 14.85333 45.46433 32.61467 14.73 20.91 15.228 23.73133 26.512 11.83367 11.96033 62.73233 11.77833 13.698 12.84233 20.102 13.354 183.9787 21.75767 16.799 13.157 13.01133 10.317 42.515 17.93933 10.60267 16.80767 26.071 24.89367 22.072 15.71033 11.25967 15.253 39.66833 9.569333 14.066 
2852s num discordant:  0 
2852s touch test_edgeR
2852s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
2852s Got 9 samples, and got: 10 data fields.
2852s Header: wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
2852s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2852s 
2852s $VAR1 = {
2852s           'wt_ph8_3' => 7,
2852s           'wt_GSNO_2' => 6,
2852s           'wt_37_2' => 1,
2852s           'wt_GSNO_3' => 4,
2852s           'wt_ph8_2' => 9,
2852s           'wt_37_1' => 3,
2852s           'wt_ph8_1' => 8,
2852s           'wt_37_3' => 2,
2852s           'wt_GSNO_1' => 5
2852s         };
2852s $VAR1 = {
2852s           'wt_37' => [
2852s                        'wt_37_1',
2852s                        'wt_37_2',
2852s                        'wt_37_3'
2852s                      ],
2852s           'wt_ph8' => [
2852s                         'wt_ph8_1',
2852s                         'wt_ph8_2',
2852s                         'wt_ph8_3'
2852s                       ],
2852s           'wt_GSNO' => [
2852s                          'wt_GSNO_1',
2852s                          'wt_GSNO_2',
2852s                          'wt_GSNO_3'
2852s                        ]
2852s         };
2852s Contrasts to perform are: $VAR1 = [
2852s           [
2852s             'wt_37',
2852s             'wt_GSNO'
2852s           ],
2852s           [
2852s             'wt_37',
2852s             'wt_ph8'
2852s           ],
2852s           [
2852s             'wt_GSNO',
2852s             'wt_ph8'
2852s           ]
2852s         ];
2852s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.Rscript
2852s Loading required package: edgeR
2852s Loading required package: limma
2853s Loading required package: DESeq2
2853s Loading required package: S4Vectors
2853s Loading required package: stats4
2853s Loading required package: BiocGenerics
2853s 
2853s Attaching package: ‘BiocGenerics’
2853s 
2853s The following object is masked from ‘package:limma’:
2853s 
2853s     plotMA
2853s 
2853s The following objects are masked from ‘package:stats’:
2853s 
2853s     IQR, mad, sd, var, xtabs
2853s 
2853s The following objects are masked from ‘package:base’:
2853s 
2853s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2853s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2853s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2853s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2853s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2853s     table, tapply, union, unique, unsplit, which.max, which.min
2853s 
2853s 
2853s Attaching package: ‘S4Vectors’
2853s 
2853s The following object is masked from ‘package:utils’:
2853s 
2853s     findMatches
2853s 
2853s The following objects are masked from ‘package:base’:
2853s 
2853s     expand.grid, I, unname
2853s 
2853s Loading required package: IRanges
2854s Loading required package: GenomicRanges
2854s Loading required package: GenomeInfoDb
2855s Loading required package: SummarizedExperiment
2855s Loading required package: MatrixGenerics
2855s Loading required package: matrixStats
2855s 
2855s Attaching package: ‘MatrixGenerics’
2855s 
2855s The following objects are masked from ‘package:matrixStats’:
2855s 
2855s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2855s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2855s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2855s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2855s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2855s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2855s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2855s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2855s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2855s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2855s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2855s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2855s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2855s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2855s     rowWeightedSds, rowWeightedVars
2855s 
2855s Loading required package: Biobase
2855s Welcome to Bioconductor
2855s 
2855s     Vignettes contain introductory material; view with
2855s     'browseVignettes()'. To cite Bioconductor, see
2855s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2855s 
2855s 
2855s Attaching package: ‘Biobase’
2855s 
2855s The following object is masked from ‘package:MatrixGenerics’:
2855s 
2855s     rowMedians
2855s 
2855s The following objects are masked from ‘package:matrixStats’:
2855s 
2855s     anyMissing, rowMedians
2855s 
2860s converting counts to integer mode
2860s estimating size factors
2860s estimating dispersions
2860s gene-wise dispersion estimates
2861s mean-dispersion relationship
2861s final dispersion estimates
2861s fitting model and testing
2864s null device 
2864s           1 
2864s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.Rscript
2864s Loading required package: edgeR
2864s Loading required package: limma
2865s Loading required package: DESeq2
2865s Loading required package: S4Vectors
2865s Loading required package: stats4
2865s Loading required package: BiocGenerics
2865s 
2865s Attaching package: ‘BiocGenerics’
2865s 
2865s The following object is masked from ‘package:limma’:
2865s 
2865s     plotMA
2865s 
2865s The following objects are masked from ‘package:stats’:
2865s 
2865s     IQR, mad, sd, var, xtabs
2865s 
2865s The following objects are masked from ‘package:base’:
2865s 
2865s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2865s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2865s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2865s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2865s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2865s     table, tapply, union, unique, unsplit, which.max, which.min
2865s 
2865s 
2865s Attaching package: ‘S4Vectors’
2865s 
2865s The following object is masked from ‘package:utils’:
2865s 
2865s     findMatches
2865s 
2865s The following objects are masked from ‘package:base’:
2865s 
2865s     expand.grid, I, unname
2865s 
2865s Loading required package: IRanges
2866s Loading required package: GenomicRanges
2866s Loading required package: GenomeInfoDb
2867s Loading required package: SummarizedExperiment
2867s Loading required package: MatrixGenerics
2867s Loading required package: matrixStats
2867s 
2867s Attaching package: ‘MatrixGenerics’
2867s 
2867s The following objects are masked from ‘package:matrixStats’:
2867s 
2867s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2867s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2867s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2867s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2867s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2867s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2867s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2867s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2867s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2867s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2867s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2867s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2867s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2867s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2867s     rowWeightedSds, rowWeightedVars
2867s 
2867s Loading required package: Biobase
2867s Welcome to Bioconductor
2867s 
2867s     Vignettes contain introductory material; view with
2867s     'browseVignettes()'. To cite Bioconductor, see
2867s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2867s 
2867s 
2867s Attaching package: ‘Biobase’
2867s 
2867s The following object is masked from ‘package:MatrixGenerics’:
2867s 
2867s     rowMedians
2867s 
2867s The following objects are masked from ‘package:matrixStats’:
2867s 
2867s     anyMissing, rowMedians
2867s 
2871s converting counts to integer mode
2872s estimating size factors
2872s estimating dispersions
2872s gene-wise dispersion estimates
2873s mean-dispersion relationship
2873s final dispersion estimates
2873s fitting model and testing
2876s null device 
2876s           1 
2876s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.Rscript
2876s Loading required package: edgeR
2876s Loading required package: limma
2877s Loading required package: DESeq2
2877s Loading required package: S4Vectors
2877s Loading required package: stats4
2877s Loading required package: BiocGenerics
2877s 
2877s Attaching package: ‘BiocGenerics’
2877s 
2877s The following object is masked from ‘package:limma’:
2877s 
2877s     plotMA
2877s 
2877s The following objects are masked from ‘package:stats’:
2877s 
2877s     IQR, mad, sd, var, xtabs
2877s 
2877s The following objects are masked from ‘package:base’:
2877s 
2877s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2877s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2877s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2877s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2877s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2877s     table, tapply, union, unique, unsplit, which.max, which.min
2877s 
2878s 
2878s Attaching package: ‘S4Vectors’
2878s 
2878s The following object is masked from ‘package:utils’:
2878s 
2878s     findMatches
2878s 
2878s The following objects are masked from ‘package:base’:
2878s 
2878s     expand.grid, I, unname
2878s 
2878s Loading required package: IRanges
2879s Loading required package: GenomicRanges
2879s Loading required package: GenomeInfoDb
2879s Loading required package: SummarizedExperiment
2879s Loading required package: MatrixGenerics
2879s Loading required package: matrixStats
2880s 
2880s Attaching package: ‘MatrixGenerics’
2880s 
2880s The following objects are masked from ‘package:matrixStats’:
2880s 
2880s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2880s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2880s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2880s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2880s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2880s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2880s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2880s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2880s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2880s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2880s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2880s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2880s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2880s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2880s     rowWeightedSds, rowWeightedVars
2880s 
2880s Loading required package: Biobase
2880s Welcome to Bioconductor
2880s 
2880s     Vignettes contain introductory material; view with
2880s     'browseVignettes()'. To cite Bioconductor, see
2880s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2880s 
2880s 
2880s Attaching package: ‘Biobase’
2880s 
2880s The following object is masked from ‘package:MatrixGenerics’:
2880s 
2880s     rowMedians
2880s 
2880s The following objects are masked from ‘package:matrixStats’:
2880s 
2880s     anyMissing, rowMedians
2880s 
2884s converting counts to integer mode
2884s estimating size factors
2884s estimating dispersions
2885s gene-wise dispersion estimates
2885s mean-dispersion relationship
2885s final dispersion estimates
2886s fitting model and testing
2889s null device 
2889s           1 
2889s cd DESeq2_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2889s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \
2889s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2889s 
2889s 
2889s ** Found 1783 features as differentially expressed.
2889s 
2889s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  -s ../samples.txt --order_columns_by_samples_file --sample_clust none 
2889s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2889s Loading required package: BiocGenerics
2889s 
2889s Attaching package: ‘BiocGenerics’
2889s 
2889s The following objects are masked from ‘package:stats’:
2889s 
2889s     IQR, mad, sd, var, xtabs
2889s 
2889s The following objects are masked from ‘package:base’:
2889s 
2889s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2889s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2889s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2889s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2889s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2889s     table, tapply, union, unique, unsplit, which.max, which.min
2889s 
2889s Welcome to Bioconductor
2889s 
2889s     Vignettes contain introductory material; view with
2889s     'browseVignettes()'. To cite Bioconductor, see
2889s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2889s 
2890s [1] "Reading matrix file."
2890s 
2890s Attaching package: ‘fastcluster’
2890s 
2890s The following object is masked from ‘package:stats’:
2890s 
2890s     hclust
2890s 
2891s for plotting:: min.raw: -0.674993513119273 max.raw: 1
2891s Warning messages:
2891s 1: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
2891s   Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
2891s 2: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
2891s   Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram.
2891s null device 
2891s           1 
2892s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2892s null device 
2892s           1 
2892s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
2892s sampleA_mean:  4954.434 1326.5 1046.9File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2892s  470.179 1833.283 1037.645 5637.134 1407.266 1371.045 1262.588 982.539 11423.35 1681.385 6030.232 1816.62 335.7477 2191.464 20787.35 1013.064 4776.171 15024.4 522.8673 838.8547 2460.887 3549.085 887.2083 559.8297 484.398 499.8527 4784.861 1120.621 620.238 1445.705 2059.192 562.1487 533.844 5797.692 810.3883 502.9777 1707.219 4182.673 1532.142 637.4673 2891.881 1718.763 581.2863 545.5957 333.5833 4713.887 1066.12 647.4437 772.306 363.4713 480.5827 400.0377 923.62 1512.754 252.8977 1272.664 2616.495 5395.606 2602.336 3468.578 2442.782 4913.275 296.1627 1326.869 567.2883 1229.376 409.7437 198.9307 1939.628 665.289 1265.232 1088.069 1315.006 335.2157 1640.267 373.2207 1291.39 244.753 604.7417 742.0153 508.1423 350.3023 579.459 876.645 301.1237 629 872.2057 1319.258 941.4197 1753.538 323.5933 338.9207 323.2733 425.4187 2635.243 350.1547 180.1727 2002.536 530.7697 182.1447 1099.802 490.2657 134.168 564.1773 574.8767 203.246 912.636 494.789 933.0403 762.2617 482.3557 407.805 579.619 249.8873 198.8237 298.6353 178.6107 210.486 2688.784 599.1197 2207.998 231.4073 731.256 388.648 310.3963 744.858 711.3287 676.234 393.785 104.2153 335.4993 335.637 1125.723 148.374 854.0897 207.4947 584.709 219.039 435.0017 85.82433 127.1483 211.844 481.5627 209.749 914.4587 719.3537 241.211 162.433 150.8137 218.991 322.1607 991.437 122.234 300.3533 419.6373 1214.03 693.0703 1412.697 2446.14 197.342 583.6803 330.6623 387.8127 122.4237 114.123 99.45067 6660.051 1815.027 262.1497 201.4867 356.783 571.859 1547.728 124.028 134.0677 340.5557 323.746 510.4197 456.1583 177.4467 310.3323 617.054 354.781 505.6607 339.0793 167.1063 781.6647 97.82467 2465.916 199.325 446.9747 122.591 136.2463 356.3497 455.3783 192.5983 234.695 256.9907 272.6143 294.269 243.326 690.4453 221.959 172.982 154.4447 563.9263 119.932 183.172 112.757 432.0453 216.15 303.8613 71.71033 594.819 352.3153 156.591 189.715 161.9753 114.485 176.9843 318.1197 240.267 220.177 322.742 369.791 721.5107 342.712 210.2437 152.1197 111.007 783.8573 2952.358 371.817 196.6567 160.8853 313.843 62.65367 80.98433 146.7767 60.22767 328.3217 334.935 123.246 110.791 207.939 334.361 252.697 89.249 407.6713 320.023 169.0567 421.348 156.8307 118.5347 239.7997 86.67367 144.7257 168.189 133.1057 112.5293 62.56033 109.0817 306.508 250.2393 135.433 442.0453 307.9013 69.89367 228.911 99.03533 134.6873 94.07567 75.336 83.207 324.5383 115.132 78.31633 83.07667 172.4453 79.282 79.07433 354.898 1557.898 67.469 42.552 87.49733 160.1673 363.302 4534.064 207.397 299.966 122.177 1606.153 104.0613 93.672 81.80933 97.23167 52.74467 86.386 110.5993 703.739 57.64267 91.61633 55.68233 76.27033 155.7297 280.7067 105.6967 158.1847 398.1303 58.232 526.9727 94.133 603.3643 59.60267 85.95367 114.563 361.8817 164.921 67.206 78.67633 87.15633 31.766 73.085 108.859 100.0123 94.69467 3561.451 33.26767 32.351 1172.149 112.884 91.79433 76.09067 84.972 280.1693 93.57967 84.25 551.5827 64.34933 39.99867 41.339 84.98533 340.941 98.302 31.38733 74.26433 44.71033 47.17133 38.966 37.59833 279.711 246.2103 66.88467 77.01533 80.43867 197.0237 73.806 69.21367 69.92267 64.40333 84.101 46.65767 405.356 69.72667 204.481 306.441 35.384 31.01767 62.81 47.40267 38.21567 144.1087 89.883 103.086 51.06833 56.34967 112.7063 30.17067 32 26.93367 37.93767 40.988 37.304 38.01367 34.95267 67.623 44.67767 95.708 176.214 58.726 38.414 39.204 21.82767 31.13533 53.25667 20.93567 52.91967 32.60533 51.916 422.5397 85.27667 66.12467 49.19267 43.95233 56.22233 30.96067 78.667 71.85 74.20533 32.07433 16.46033 131.435 65.34533 56.78633 171.2653 47.775 27.49133 64.515 158.4163 54.81767 52.662 50.27133 23.42167 40.022 9.429667 69.90667 38.41333 29.75167 115.2073 24.04867 5495.505 23.232 35.23567 89.08767 163.5027 15.402 168.4167 71.55767 84.52867 31.93633 33.50367 52.49167 38.44933 14.64167 34.237 28.112 10.73367 209.263 42.42 8.473333 15.47467 36.76933 41.489 88.74833 20.16567 56.72833 24.90267 40.90567 16.558 20.61433 43.001 36.44033 40.95667 22.18367 14.82667 23.62733 14.972 19.56433 21.19933 23.66867 16.59667 66.32833 67.70667 16.92233 26.74467 9.629333 23.34767 68.59733 32.359 
2892s sampleB_mean:  175.7007 98.97567 27.41467 10.76867 63.97333 47.461 68.49367 33.63533 28.87167 9.133333 33.35533 534.2237 10.849 173.6673 3.202333 21.376 98.61433 336.3973 18.23967 543.417 661.7387 28.62567 39.777 73.97767 84.42267 55.41567 32.483 24.33867 18.18567 299.0663 43.62667 12.49967 139.4193 313.6673 52.09567 47.52733 900.1817 63.963 9.088 218.998 658.8357 225.2773 2.778333 125.8543 296.743 27.60133 72.053 36.39433 338.805 183.983 49.48767 68.979 12.30667 39.797 24.273 79.21633 281.149 15.51133 217.05 629.0693 4.127667 514.415 457.8803 563.4113 1003.238 8.580333 191.8153 23.51433 124.0153 42.68733 5.223667 297.3653 12.67333 250.9827 145.798 131.764 43.422 280.8763 53.687 194.2893 5.388667 95.47967 62.58133 79.409 19.23033 102.7107 94.216 55.75367 94.08633 116.6427 117.2063 232.083 375.202 38.47567 50.10333 25.39133 72.874 623.5437 36.41067 27.94467 429.5973 110.7323 18.134 170.561 44.471 13.52433 68.27467 56.695 32.93 115.6623 58.90833 143.4493 43.57767 70.27367 58.22233 113.0753 36.231 22.41533 26.58267 32.70533 32.109 462.724 130.483 412.998 7.825667 170.8453 85.85133 29.69867 132.8633 118.5947 116.0857 68.88567 14.398 2.287 74.29867 261.706 9.605 11.05733 28.87667 122.476 9.034667 66.97833 10.49667 14.087 29.54433 105.7627 15.964 213.755 119.1803 22.455 11.277 10.44 48.99067 6.660667 223.4383 10.49233 29.063 50.429 230.2087 150.937 4.412333 582.8023 29.96067 85.73633 43.27 89.28567 3.616 2.461333 10.675 938.454 402.3693 40.96933 23.402 68.36967 87.39733 377.1183 15.837 23.18133 72.46567 38.353 126.7297 80.21667 21.00533 21.807 115.9157 80.928 118.5987 70.59233 33.283 4.512667 10.31967 7.979667 20.14333 88.46167 8.546333 14.554 58.833 92.838 26.01033 45.62033 62.40367 38.81867 55.04367 43.417 154.972 45.02367 6.052333 37.50533 120.0037 22.87333 26.18 12.85033 70.388 45.433 49.50333 10.603 131.159 56.458 30.82233 31.15267 35.82667 2.967333 39.035 73.76233 44.52567 16.50567 73.756 70.13033 80.658 71.40267 28.455 26.68733 11.71333 170.3357 424.5863 78.80367 42.91667 14.26033 74.91 4.263 15.42567 32.132 12.03667 43.231 64.78933 29.317 26.685 51.52233 72.094 52.69567 1.321667 96.276 71.137 14.82467 75.955 2.732333 28.90033 41.856 17.759 29.59733 28.625 24.22767 15.32067 11.399 19.12733 71.361 48.89067 15.437 40.53433 65.235 8.867667 40.359 19.23 31.58467 12.35967 6.437333 20.623 55.915 26.14833 14.54933 18.13133 32.75133 17.413 12.544 7.045667 260.6453 8.652333 10.51167 6.740333 36.07133 64.46467 3.101333 47.833 72.38467 19.68333 6.318 16.69133 16.16267 10.94967 22.98467 4.583667 15.947 16.40267 138.602 13.374 15.559 7.72 15.62833 27.02667 65.26833 15.246 28.212 84.71567 8.792667 73.07533 19.81633 118.617 14.42733 20.73367 26.33733 69.556 28.223 12.19033 7.913667 14.08133 5.709667 12.023 21.776 16.38067 18.174 499.6263 6.353667 7.566333 228.7547 14.411 19.28233 14.33167 14.10833 20.15033 18.108 14.04867 19.63133 15.44967 6.174667 9.647 18.931 67.14133 12.226 6.926 17.83733 7.395 10.679 9.231 3.122 58.535 14.50533 7.66 14.676 19.83467 37.02633 11.486 10.57833 8.412333 9.925 5.474333 10.23033 22.77967 13.91533 40.363 72.50367 2.032 2.410333 12.327 8.274 6.723333 21.41267 21.74733 23.04733 7.516667 6.977333 22.84267 7.087667 7.807333 0 2.177 4.98 4.895 9.294667 5.981333 15.98533 9.524 23.05433 17.25667 2.115333 8.525667 8.836 0.8883333 5.992 8.352 2.503 9.865667 5.685 10.462 1.723667 15.31167 15.28167 8.369 10.124 9.195667 5.838 17.55633 15.521 13.76033 4.789 3.596 21.67067 13.338 5.468 21.40333 11.013 6.127333 0.6243333 23.73867 13.31333 8.300333 10.828 5.664333 4.636667 0 11.173 2.327667 5.607667 9.423667 1.734333 10.288 0.1823333 5.763333 9.302667 23.191 0.4626667 29.664 13.186 4.385333 5.784 7.374 9.638667 9.153 3.51 8.232 1.195 0 18.65833 6.257667 0.093 3.68 3.465 5.190667 10.806 3.966667 6.641667 5.709333 5.354333 3.201 4.44 10.293 1.998667 4.074333 3.513333 3.158 2.341667 2.939 2.98 4.922 5.790333 0.668 5.685333 13.44 1.497 1.905667 2.409667 0 5.035 7.557333 
2892s num discordant:  0 
2892s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2892s sampleA_mean:  68.104 300.087 279.6767 558.1363 478.7223 641.1777 691.0767 620.406 98.85333 526.2243 96.61333 20.01233 103.6867 539.652 1406.461 850.6397 96.77733 260.666 251.019 876.482 954.153 536.193 1005.984 1005.984 655.8127 733.6827 360.2233 2.696667 45.76333 4.654333 72.55133 866.6187 35.44767 915.841 1220.149 113.178 81.319 5.762333 551.9577 967.4877 213.4847 950.0057 38.978 903.1557 861.8193 1117.319 15.838 20.97667 509.7623 555.952 1690.757 884.0843 93.42833 21.39933 17.37067 409.1913 98.448 2042.114 114.5207 1385.135 1784.069 16.51667 1545.514 1681.069 57.579 86.883 226.9223 443.633 504.111 33.62067 1094.775 15.04567 13.98533 866.9083 898.047 697.2287 121.0697 57.26933 128.1763 7.951667 425.357 1834.914 2466.545 1313.1 37.21967 1584.902 443.3597 642.0663 2590.581 224.904 56.797 223.9227 37.25567 11.583 603.456 9.434667 70.24967 393.3037 39.57833 33.57133 103.9153 62.50533 824.9103 759.571 7.212667 10.53633 18.754 76.41333 16.528 40.61467 4.244 3.078667 237.8803 1593.583 2.713333 118.9327 31.501 660.21 94.847 94.089 188.4693 39.67767 337.399 7.282667 1666.136 25.208 37.255 354.6413 22.92133 35.529 759.148 20.36667 141.697 75.48133 100.1173 71.78533 2166.993 2.398333 503.5693 27.52967 27.29 251.833 5.017333 29.18933 1796.241 28.45833 18.96267 23.04333 670.486 29.55 63.58333 325.5413 27.48633 6.167 560.8327 43.09833 14.91467 7.601333 18.88733 22.627 67.08167 5775.202 617.7277 42.57533 44.93767 47.34533 4.080333 1846.256 25.55733 15.73033 18.30633 6.546 17.221 64.19 35.29633 17.48067 27.59267 483.664 321.257 66.65833 497.7577 46.75733 65.027 51.407 10.30533 50.14667 40.23433 756.3963 77.21567 123.0927 6.496333 9.969333 6.745333 20.37167 16.54033 134.6073 15.08833 9.613667 74.00233 5.682 302.136 40.12067 37.942 42.16667 5.627 6.515667 31.92667 5.016 129.326 110.725 91.49933 2.280333 15.92433 27.23133 3.586667 47.651 30.828 2.177333 9.896333 43.50567 6.300667 14.33333 17.96533 22.74167 48.27367 3.595333 18.233 23.33733 16.27833 11.52 23.09367 34.16433 5.802333 7.963667 7.685 7.412333 28.839 18.592 4.745 15.54567 6.455667 1.292667 3.139 1.919333 275.3867 40.25467 5.474667 7.980667 20.135 12.30833 15.18033 66.73133 3.451 7.059 225.547 5.557333 7.909333 6.527333 73.59667 474.4033 14.71933 46.23067 1.460333 50.11167 9.824333 2.900667 48.562 2.592667 22.68433 8.791 73.27533 13.78833 61.43567 8.807333 8.292 27.61367 109.3627 25.71133 28.26467 18.317 15.46533 19.73 18.67133 49.835 22.375 11.312 33.815 30.97967 27.77367 7.083333 7.252667 12.40267 46.17067 9.274 2.154 6.248333 4.531333 0.838 4.766333 6.812333 6.929 44.97967 93.21667 59.43533 43.83633 5.733 25.73033 34.33067 112.283 10.12033 4.361 4.281667 49.788 29.26167 35.802 11.93267 17.59867 36.11867 25.40433 43.001 18.33267 13.64567 9.767333 7.869333 8.866333 23.127 46.73367 20.81133 24.63167 11.286 33.21467 1.991 8.002 13.58 15.25233 8.395 7.107 21.67167 5.895 2.068 266.444 3.200667 2.811 2.682667 25.089 0.8066667 7.48 8.631333 4.59 20.71867 17.53667 37.152 11.98267 6.686 87.024 14.93733 25.32233 15.94867 22.31833 3.516 3.293333 5.558333 9.773333 5.931333 2.433333 16.116 6.863 1001.993 1.851 21.32033 27.14367 12.79833 16.64833 30.75333 48.976 8.316667 16.899 9.616 7.782667 3.762 16.66533 7.766333 6.250667 21.06767 7.700667 15.01 31.12967 26.40167 7.226333 4.341667 5.364667 11.22367 17.85933 27.53867 0.713 27.83967 5.615667 8.077 6.204 13.22967 12.36433 12.753 74.79833 16.73 18.23433 15.57933 14.558 25.646 20.261 4.926 11.40267 22.93933 21.74467 14.18933 4064.721 2.723 2.534667 1.695333 7.884667 10.471 5.415 12.443 11.227 5.740333 2.800667 10.85033 5.603 5.421333 12.44167 16.40367 16.303 1.688667 1.288 24.758 9.105333 14.83533 2.243333 1.574667 3.424 12.394 13.71433 6.524 8.028 7.310333 95.166 12.388 12.76533 1956.885 275.0887 20.74967 1.160333 6.091333 5.630333 8.791667 7.585333 11.59067 7.711667 11.22367 13.106 12.90733 1.577 7.039 6.559667 22.17067 9.378667 9.510333 7.844 13.917 2.194 3.109667 12.14267 26.291 20.36133 6.380333 13.65367 9.436667 2.411 7.672667 34.157 6.778333 13.50467 9.471667 6.625333 7.621667 8.497 6.067667 8.578333 3.294667 63.63933 0.9146667 4.676 6.567 11.91033 10.12333 8.805333 2.818 3.857 3.09 17.75767 6.066 16.556 0.1093333 2.14 6.829333 8.293333 9.299667 10.72933 6.861667 1.363333 5.416333 3.468 19.73733 5.332667 9.694667 7.431333 11.94067 7.325667 11.36067 39.729 11.994 4.053 2.163667 17.19233 11.758 3.493 3.822 9.557333 4.963667 12.01933 3.301333 2.976667 0 3.165 0 0.01 23.38367 16.47133 2.758667 1.911333 6.521 3.736333 5.177333 4.482333 6.512667 26.67367 5.422333 0 15.47733 8.411333 10.216 10.201 1.302333 11.24533 5.581333 15.75333 0 6.813333 3.489667 1.897333 3.27 17.23067 1.407667 9.507333 3.680333 4.765 2.550333 7.337333 11.46067 0.248 8.343667 8.839 6.395 0 8.445667 6.326 4.196667 4.638 5.633333 4.293333 4.009 3.051 2.745 7.881333 0.6643333 4.127333 1.252 1.547 4.223333 2.578333 2.219333 0.409 6.606667 0.7683333 5.001333 0.4346667 2.605 4.484 3.268333 7.634333 2.517333 2.330333 1.184333 1.56 9.374333 1.870667 3.162667 21.42967 4.126 2.467333 1.384 3.090333 5.019333 9.984333 4.196 1.153667 2.692333 8.218333 3.043 1.351667 1.169 0 12.573 5.509667 1.637333 8.504333 3.979 3.021333 7.756333 35.02267 0.3906667 1.469333 1.980333 8.773 1.122 4.744333 10.61867 2.577667 3.393667 8.025 3.570667 2.448333 2.844 2.242667 4.724667 3.077333 3.682667 8.963667 0 19.30967 35.57467 1.344 8.003 4.41 2.335333 2.011 11.52467 4.52 0 3.484667 3.398 0 3.328 2.678 0.724 0.9123333 2.573667 2.944667 4.695333 
2892s sampleB_mean: File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2892s  1492.051 2827.345 7779.492 7520.41 5346.478 7181.47 9939.373 11165.49 2550.414 6944.853 1331.648 1076.978 1438.471 6464.644 10849.9 6705.697 971.4367 4978.607 2449.757 6887.084 7405.14 3982.392 8614.152 8614.152 4540.328 5036.385 4624.974 324.8553 440.9727 193.995 1007.03 5515.698 722.7793 6156.043 8313.711 1781.496 973.0083 155.6753 3325.992 5874.642 1506.715 8726.054 347.4017 5974.238 4809.412 7596.105 501.0717 303.273 3398.294 3104.744 11956.17 5589.41 1192.947 341.9023 217.5877 2649.173 819.1427 12136.75 876.8277 10695.83 8625.824 721.2523 9160.812 10005.84 512.042 880.4753 2510.784 2806.072 3101.543 318.3057 7921.826 147.2877 340.8923 5311.835 7137.863 5150.462 1183.775 644.756 850.5097 322.6313 3135.76 11807.78 12803.12 8077.68 337.5617 9231.562 2899.79 4181.758 14596.83 1237.565 498.566 1388.008 636.1717 188.059 3043.903 227.1767 493.2167 2813.865 381.4813 286.7303 803.7297 820.1 5402.498 5955.872 98.27667 224.959 176.1237 395.6523 210.5073 510.9113 88.77667 363.4697 1147.187 7646.521 135.6287 954.507 297.5633 3606.195 501.203 592.331 1232.959 437.8937 1727.754 304.1167 7998.991 434.5497 568.9407 2636.168 177.0987 277.6277 4659.391 237.9167 624.4283 369.4417 464.656 437.7077 12057.81 136.0917 2069.238 374.99 347.1993 1538.062 183.432 568.3683 7391.381 464.25 165.5147 227.959 3497.592 178.331 366.6233 1485.8 318.668 59.968 4052.112 365.9053 307.597 204.598 234.8707 257.8713 497.3057 31019.62 3477.406 221.5063 330.2803 309.0137 204.688 10466.26 229.8227 126.265 728.6047 124.821 209.5997 303.588 265.4807 361.7567 248.7967 2983.166 1573.052 365.304 2478.864 306.1523 744.834 346.0203 254.0923 223.6213 259.974 3680.324 617.5097 566.3103 96.888 76.629 115.6383 169.5693 159.9217 794.7277 102.4913 141.1233 434.0653 190.3363 1314.765 244.213 198.0453 228.616 148.3807 240.9067 205.964 133.1137 784.5 473.468 383.3883 91.93733 171.415 396.4167 107.6607 219.043 221.3943 132.997 130.7987 242.2357 58.786 198.031 153.6373 151.089 297.5293 92.04867 134.7863 146.225 201.1477 139.8577 332.1927 383.105 87.30767 189.81 53.11833 327.728 204.0893 160.6447 177.6103 196.2657 163.2497 65.022 293.4293 79.23 1190.783 243.0527 129.359 79.78767 171.2443 186.3673 106.9733 288.2643 85.369 118.4783 1374.415 41.92667 132.86 138.7943 324.095 1924.887 93.961 199.25 66.28233 208.997 165.6487 56.084 404.8233 199.5333 145.871 92.801 376.801 112.8707 261.1813 44.52667 71.07333 146.7367 502.0593 217.828 130.4647 92.66933 88.84733 108.0163 84.19433 317.4007 162.353 166.719 264.5573 155.6507 219.1713 51.48067 55.56067 110.12 241.8647 109.0163 38.50333 65.14433 102.4957 381.073 82.77467 175.727 65.82467 506.512 434.0367 451.6893 279.8187 79.15267 109.1297 189.876 446.5917 104.7473 565.0517 160.461 217.945 120.016 221.9553 92.14267 102.8277 210.276 150.83 251.6407 125.6427 142.4997 63.51467 49.84633 101.2043 125.9207 244.312 138.8203 102.9103 139.4217 147.5143 88.20067 72.04033 205.7273 138.9953 91.96267 72.27033 91.36867 72.229 54.28 1437.071 67.97633 42.94067 64.48933 313.5353 94.084 53.67933 98.42267 57.92467 94.855 88.724 329.0943 54.17467 92.354 391.7213 114.7247 147.9097 117.3687 188.654 615.4837 57.289 78.15767 94.036 98.59367 176.1103 359.4497 48.662 6554.638 59.07767 177.7223 111.3283 71.95633 112.4907 205.2823 272.869 62.202 80.658 92.10033 67.32633 136.3853 92.673 92.91767 578.1793 114.413 55.31033 75.13167 160.033 143.6177 63.519 58.84033 33.64933 54.697 89.19033 123.7103 60.909 126.6667 71.83833 52.40167 68.93667 92.58367 61.75633 98.25867 654.0063 70.82967 185.3687 83.32767 84.09433 189.338 97.67333 86.666 86.82867 143.2053 97.74133 106.367 23095.85 64.96333 31.92033 26.105 69.31567 51.40267 36.84367 55.42833 100.9357 49.55567 66.58633 60.39433 284.8557 40.88467 59.70833 91.34767 558.288 27.42533 23.09333 108.9977 44.59133 63.39167 25.16133 374.3023 36.129 63.275 80.30267 29.19933 37.13833 61.927 629.935 82.208 65.265 12433.72 1768.526 97.91867 29.412 30.305 28.11233 67.40867 57.38933 56.87433 37.373 47.69867 70.48667 74.47967 21.31667 59.309 65.641 101.2333 51.208 40.01867 44.65167 75.314 38.35733 52.62167 118.5717 105.9517 89.473 57.89033 58.72433 50.94033 20.836 36.83567 180.145 38.239 70.23367 53.35367 36.76167 39.14833 37.861 48.09067 51.20733 17.67167 269.8203 61.049 45.43467 40.58467 59.017 52.59533 40.58733 81.03933 46.01667 32.39167 72.092 44.57067 104.9537 58.52433 33.96833 63.80367 95.03067 39.439 43.553 74.76 33.71767 31.81733 22.795 89.41967 24.105 44.80233 42.02167 49.809 49.184 60.34067 170.7703 77.42067 24.42933 323.135 71.77333 83.02567 22.759 19.01033 43.199 24.998 58.53467 28.618 23.031 41.25767 16.98933 9.080667 16.39933 275.1827 65.63533 37.18267 19.87967 31.64467 50.351 42.55233 50.66867 134.3513 170.258 28.99667 8.385 64.17467 56.735 49.53233 45.68133 63.43233 59.187 31.359 63.14133 17.20333 34.963 79.93733 17.666 21.26833 69.73067 17.978 38.56967 28.08767 46.573 17.60767 80.83067 147.841 18.746 33.274 43.21967 35.30367 101.7453 72.57967 25.818 18.67167 39.557 79.05433 21.37133 21.925 19.069 25.20967 31.30167 12.13567 31.40267 16.692 27.15533 52.68633 28.28967 16.69733 40.14133 33.96667 12.81233 38.21633 9.165333 16.98933 38.06967 134.6853 62.14133 26.59233 16.53733 47.25833 22.82667 50.767 125.1613 13.12667 133.2117 18.98967 82.00433 45.292 13.31667 42.533 48.78233 37.97 58.21167 21.58933 69.305 15.914 8.173667 55.27767 44.84 122.654 24.348 14.71567 37.642 343.3797 51.753 37.89133 139.358 17.79667 11.03933 12.07167 51.325 10.06533 23.01233 45.16833 20.69233 23.021 43.66433 15.776 37.33167 13.166 19.56367 24.04433 30.44067 22.33433 63.401 11.09467 92.552 200.7123 10.878 34.98133 49.08533 18.31433 70.339 76.51933 29.65133 35.64 37.25433 14.291 29.38867 20.035 23.558 23.8 17.76433 22.41933 16.55933 130.2143 
2892s num discordant:  0 
2892s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
2893s sampleA_mean:  4954.434 1326.5 12222.46 2602.336 1751.765 887.2083 1445.705 1046.9 470.179 5495.505 2002.536 3549.085 637.4673 4784.861 5797.692 15024.4 36600.33 1833.283 1407.266 1371.045 521.84 1262.588 982.539 2635.243 1681.385 6030.232 944.0123 1816.62 335.7477 2191.464 1265.232 20787.35 4191.816 1013.064 4913.275 3468.578 1512.754 499.8527 1593.001 1718.763 559.8297 4713.887 1272.664 1291.39 1348.496 562.1487 647.4437 1233.492 1933.215 1656.826 1939.628 620.238 371.296 1707.219 999.5363 335.2157 1532.142 326.0873 2891.881 5395.606 1088.069 1091.041 772.306 1640.267 1037.645 810.3883 387.8127 176.112 363.4713 1120.621 2237.79 116.9527 258.5643 252.8977 5645.434 2017.126 5637.134 335.637 933.0403 178.6107 1753.538 1031.742 198.9307 923.62 925.3123 1179.723 388.648 564.1773 296.1627 581.2863 1434.927 531.0443 244.753 405.4877 154.4447 502.9777 425.4187 494.789 435.0017 594.819 876.645 590.469 2446.14 825.5967 533.844 393.785 234.695 460.3903 838.8547 405.9907 665.289 770.6237 567.2883 521.2813 1198.79 335.4993 1756.628 581.914 617.5563 194.6923 104.2153 734.0483 337.406 872.2057 762.2617 298.6353 233.2683 482.3557 1547.728 1707.261 322.1607 610.589 210.486 508.1423 854.0897 1125.723 664.8137 300.2583 480.5827 1412.697 244.4597 604.7417 209.749 114.123 337.767 563.9263 159.0503 568.889 1030.087 344.3147 146.7767 272.6143 122.4237 356.3497 150.8137 1315.006 182.1447 199.325 133.8673 437.1223 168.438 3088.486 991.437 122.591 99.45067 1229.376 407.805 350.3023 323.746 316.5037 719.3537 97.82467 349.218 100.0037 310.3323 219.039 432.0453 1099.802 499.693 89.41233 85.82433 156.591 176.9843 2769.091 147.324 89.249 240.267 519.577 310.3963 1023.96 721.5107 378.0157 109.0817 210.2437 407.6713 389.129 1606.153 562.891 207.397 114.485 201.4867 132.971 125.2723 207.939 120.7347 189.715 128.0267 294.269 164.5937 300.3533 3561.451 466.314 241.211 198.061 368.628 127.1483 471.4763 156.8307 1505.046 603.3643 328.3217 94.07567 71.71033 2036.308 116.1613 160.8853 103.573 177.4467 63.90033 60.22767 324.5383 115.35 161.1783 172.982 354.7773 122.177 212.7377 164.083 183.172 291.7607 62.56033 95.84833 421.348 80.98433 78.31633 105.1747 971.5327 192.5983 1557.898 81.80933 2465.916 250.2393 132.1053 169.0567 94.133 206.046 425.4893 304.6523 173.3993 104.0613 407.7717 84.98533 52.74467 363.302 91.99833 168.189 129.574 280.7067 59.607 98.94267 136.4807 124.4867 278.785 93.672 154.7137 66.11467 181.09 98.85333 236.6537 751.6327 55.68233 87.15633 78.67633 781.6647 62.65367 76.27033 305.3177 105.6967 93.57967 87.49733 135.433 354.898 280.1693 60.025 171.9977 204.4367 86.272 38.966 90.65667 4534.064 74.26433 40.38733 56.42633 51.06833 113.344 73.156 233.2737 66.544 47.17133 46.29267 54.279 214.102 53.23867 77.01533 66.88467 97.46133 62.81 44.27933 35.384 86.26767 64.515 496.4993 260.459 144.1087 93.98167 114.1953 38.21567 84.101 69.30367 194.3693 47.40267 27.49133 33.614 158.4977 37.746 51.68567 95.708 58.726 6075.931 51.916 32.07433 65.08533 630.4887 47.12267 101.362 56.34967 44.67767 471.7457 26.77667 50.39 35.92467 31.01767 42.52667 69.90667 37.93767 30.31033 40.76933 32.60533 82.45067 187.0867 71.55767 71.85 171.2653 40.022 50.27133 42.259 49.19267 131.435 56.78633 58.77867 45.27567 34.524 70.90433 269.428 27.86967 142.1963 16.066 38.467 38.41333 51.49667 33.66067 34.55067 163.5027 52.054 32.87767 10.913 141.5087 7.951667 56.986 115.2073 51.36633 41.489 209.263 42.42 24.04867 56.72833 43.001 20.61433 52.49167 19.379 45.48233 26.72567 42.69267 69.761 48.80533 32.359 40.90567 26.74467 84.52867 27.07933 32.296 19.36133 31.80833 28.112 92.064 35.653 23.66867 59.42133 132.0313 38.71367 45.49933 13.46233 20.89067 36.44033 66.32833 26.93367 191.9503 30.83533 73.985 23.675 23.51567 19.87867 59.42267 27.10933 23.62733 27.92067 27.69867 86.196 22.18367 31.895 43.59833 27.188 67.70667 23.94367 68.59733 14.442 26.41767 26.73867 23.232 22.01133 19.07933 27.52167 44.083 20.94233 13.58767 36.69767 28.092 20.15333 13.02633 27.81033 16.59667 20.281 22.07333 25.49633 14.06933 16.92233 422.5397 45.54267 20.21567 11.48267 
2893s sampleB_mean:  175.0553 46.38933 644.6073 28.83167 11.541 11.73133 39.02467 21.734 14.071 10.731 60.698 54.76233 9.523667 176.7203 190.2367 126.2827 312.258 18.24467 61.93367 20.785 15.272 5.897667 38.35033 149.0183 34.85667 71.58533 40.62 3.02 17.87533 67.15133 70.315 1576.856 162.736 20.73967 231.01 143.0547 120.2997 10.32667 84.69133 167.6013 38.834 184.242 122.321 15.897 62.01667 41.809 18.007 131.954 91.85267 70.838 191.4833 5.31 11.974 199.414 52.632 18.10167 216.263 34.29367 107.587 4.892333 85.388 78.63867 52.029 172.0003 154.1127 97.40133 32.09667 10.14033 18.10667 4.916 176.0093 6.833333 20.43633 13.45833 1058.536 263.582 585.796File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2893s  31.756 82.944 17.35367 290.869 146.7283 5.075 94.25133 167.5307 120.642 51.789 44.774 21.86767 69.84367 147.5103 59.39767 4.303333 68.43533 6.593 2.201 62.69867 7.353333 18.98533 21.75133 96.643 19.323 327.4777 138.9923 99.03833 46.20633 6.119333 86.94433 157.5777 33.76633 5.982333 76.85 5.055333 34.63 112.516 2.999 288.293 81.38067 35.93933 11.08667 10.803 1.413333 44.574 151.9077 60.149 29.81633 22.66633 78.18267 296.326 274.274 17.25433 119.8197 33.16933 111.2203 10.01733 239.1367 138.5447 8.328333 81.65333 4.947333 33.99767 135.326 6.52 5.291 57.83967 71.425 29.81667 98.93967 236.2837 48.44967 9.162667 14.93967 7.044667 45.153 13.40767 252.1407 31.26267 11.36967 18.47767 64.78833 24.10267 8.807333 228.12 5.435 11.37767 252.5313 80.735 68.39567 40.80033 66.14267 131.7207 10.11133 81.69867 7.705667 36.04767 31.115 62.152 262.4237 5.957333 11.83333 16.697 25.95767 33.04933 692.4403 29.03533 5.086333 46.24133 68.06833 1.439333 247.8637 64.61967 60.40333 9.454333 3.039667 77.499 52.96867 129.8027 92.249 22.379 12.202 37.04267 21.17867 22.86333 42.20867 4.436 31.045 15.958 60.023 15.18533 55.72533 52.72333 114.7383 52.859 43.10367 77.462 28.43733 103.8797 3.080667 300.8857 32.20767 46.83533 4.922 14.63133 456.8783 26.55867 19.13967 1.620333 41.19767 12.78767 12.457 44.73367 24.55133 33.53433 27.607 81.672 3.384 22.53 29.20433 41.53733 49.06433 9.876 20.181 77.08667 16.686 11.56533 20.32033 161.046 46.35533 221.51 6.152333 192.615 50.52767 28.67333 24.19267 13.001 27.23467 38.81867 72.39567 41.26233 14.93967 79.67267 11.13 3.457 72.445 21.33367 37.84833 25.094 57.499 9.053333 15.63733 23.92933 21.97267 38.40433 16.52467 36.59667 3.929667 29.328 16.70467 53.45667 131.0337 8.892333 10.136 2.519 0.8923333 14.59467 17.05033 58.95767 19.338 15.72 16.72967 30.64367 10.47367 10.048 12.56167 26.382 41.21667 4.478333 6.782 15.84233 1.982 14.317 7.813 6.818 3.424 26.43 3.546 47.94933 15.178 10.08733 6.808667 9.956333 49.04333 9.581333 15.967 10.61567 19.69133 11.71167 2.343667 2.932 13.70767 3.776 96.05 65.05167 22.72933 11.88467 25.736 7.134 9.684333 12.49533 41.753 9.795333 3.111 5.698 24.952 7.286 11.101 23.3 3.721 603.3247 9.442 2.596 15.82633 144.8737 10.034 8.861667 9.696333 9.568 63.54133 6.056667 8.024 5.451 6.028 8.245667 4.551667 5.482333 5.053 5.855333 6.225333 12.136 44.787 6.153 15.87967 6.163 2.558333 9.387667 6.709 9.898 23.79767 5.819667 13.348 10.75867 6.474667 15.06367 60.65633 5.932 34.28533 0 2.289 0.77 3.487 1.628667 4.229333 30.05333 9.460667 6.930333 0 5.704667 0 3.947333 0.8253333 10.76167 1.601 9.86 5.672667 4.175333 2.356667 6.886 2.932333 12.28333 2.445 4.818333 4.023 6.758333 16.034 4.762667 1.994333 4.880333 0 18.601 0 6.506333 2.312667 5.966667 5.907333 24.11533 7.766333 4.525 8.966667 26.49267 8.657333 3.518 2.201333 3.392 5.916667 2.695333 0.388 47.94667 7.344667 3.183333 0 1.805 3.583333 3.923 0 3.766667 2.298667 6.937333 1.362 5.132 5.972667 10.182 3.599 16.083 4.885 7.661333 0 2.759333 2.819 0.3263333 4.613333 4.606 2.479333 8.528 0.597 0.3683333 2.795333 1.379333 4.356 0 2.091333 2.582 1.481667 3.673667 0.774 1.082 3.048 25.345 4.943333 1.016667 1.101667 
2893s num discordant:  0 
2893s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
2893s sampleA_mean:  21.39933 88.57 72.55133 7.685 6.167 15.838 15.04567 224.904 40.988 102.2703 31.261 96.61333 103.6867 36.11867 121.0697 509.7623 28.64033 68.104 141.0787 30.97967 55.26267 803.1917 539.652 337.399 98.448 26.51267 76.15267 16.51667 655.8127 37.21967 503.5693 478.7223 46.17067 354.6413 504.111 279.6767 578.8703 10.53633 20.01233 526.2243 409.1913 733.6827 558.1363 4.654333 697.2287 5.762333 7.282667 57.26933 915.841 1275.026 291.1757 35.44767 18.96267 443.633 763.5533 2.713333 16.54033 81.319 620.406 641.1777 903.1557 7.963667 300.087 5.415 4.080333 40.83233 31.92667 125.9483 25.208 88.20633 96.77733 7.252667 4.244 11.583 7.212667 31.97667 850.6397 25.78433 425.357 115.4593 45.412 106.1753 78.96333 11.22367 188.4693 9.434667 223.9227 759.571 24.615 14.71933 31.501 209.5917 48.562 2.398333 47.34533 25.605 89.987 113.9973 691.0767 28.26467 159.4173 11.52 56.797 40.25467 33.62067 670.486 20.97667 171.0287 43.09833 26.208 497.7577 40.27 33.57133 13.98533 22.51133 15.54567 81.34233 2.068 23.04333 22.74167 110.725 50.11167 43.50567 18.76 23.33733 87.317 5.017333 12.993 642.0663 321.257 3.451 47.036 16.528 20.36667 23.127 55.73 37.27233 9.896333 443.3597 51.407 65.027 34.135 86.883 18.754 241.785 12.94133 7.980667 5.627 3.420333 393.3037 37.152 23.94067 260.666 19.92833 6.745333 57.46833 75.469 91.49933 87.42633 5.474667 17.48067 16.899 1.292667 79.21967 29.55 6.546 11.438 4.281667 13.46667 50.469 2.550333 225.8327 15.09333 5.682 39.67767 3.586667 3.078667 52.084 26.715 3.200667 66.65833 2.696667 27.29 26.67967 103.9153 9.969333 16.27833 18.317 9.642 2.280333 25.55733 55.59767 8.043333 6.919333 8.791 74.79833 22.68433 5.016 6.515667 7.059 15.73033 64.82733 15.92433 15.01 3.595333 103.2833 5.733 24.63167 37.25567 21.51767 5.557333 30.828 10.95167 27.48633 62.50533 11.312 18.88733 1.577 5.630333 11.227 7.909333 49.835 16.556 17.19067 1.460333 22.31233 15.18033 2.154 1.919333 2.177333 30.80767 17.96533 24.758 8.807333 14.063 18.233 18.30367 47.42233 2.811 17.221 2.243333 6.819 26.75667 4.745 10.216 10.30533 6.559667 4.766333 29.18933 44.93767 27.59267 44.996 19.11967 2.219333 27.83967 50.97333 4.371 18.62433 2.433333 5.802333 6.812333 7.844 9.735667 28.057 13.08133 23.09367 22.752 11.29367 21.116 3.468 5.931333 12.39433 20.261 26.291 6.455667 22.17067 3.941333 22.93933 12.98 13.65367 13.78833 20.37167 12.753 4.531333 15.08833 4.156333 4.59 7.48 27.94767 16.40367 8.497 7.039 37.255 23.67567 0.713 6.496333 6.980333 20.992 8.162667 8.316667 3.139 11.22367 9.507333 7.107 20.135 4.341667 33.01633 6.527333 18.94267 11.286 3.043 5.615667 12.36433 6.674 20.74967 1.991 31.32 28.45833 6.300667 32.849 42.16967 9.557333 84.312 6.929 2.330333 8.631333 5.895 14.94733 7.412333 0.8066667 44.07433 16.303 22.627 19.73 2.900667 1.911333 27.23133 9.613667 2.534667 77.21567 5.364667 8.077 40.34367 7.163 5.177333 30.424 11.93267 0.4346667 6.524 15.64 19.921 33.50367 28.33667 0.838 11.89067 8.403667 22.996 20.16567 2.592667 9.824333 7.354 4.963667 7.310333 9.767333 1.288 1.688667 8.578333 14.22267 14.78033 13.22967 7.884667 18.30633 11.817 18.33267 25.32233 3.857 8.002 14.06433 39.729 2.723 0.6643333 5.558333 12.40267 12.14267 0.7683333 15.57933 8.393333 17.692 9.773333 10.38333 25.40433 8.173 17.85933 28.43467 27.77367 1.469333 6.380333 35.802 21.06767 13.58 4.676 1.715333 21.69333 8.805333 7.050333 11.758 9.744667 18.23433 17.332 3.424 30.75333 11.994 14.91467 33.10033 7.083333 5.720333 7.216333 6.066 10.12033 9.616 14.16 8.866333 53.09233 7.672667 1.160333 6.248333 7.555333 1.162333 11.59067 2.411 12.76533 5.581333 3.162667 7.394333 6.910667 8.791667 0.1093333 11.36067 5.740333 0.3666667 1.695333 6.863 7.431333 11.21733 3.09 16.06567 5.416333 2.682667 44.679 10.85033 21.88733 6.204 2.976667 5.332667 11.097 0.485 18.93367 6.592 13.23767 4.926 7.585333 1.444 3.541667 20.36133 0.248 5.264 1.363333 8.395 5.603 6.067667 3.762 2.844 1.252 25.089 6.752667 7.766333 9.471667 0.9146667 3.109667 2.605 9.752333 0 0 5.596333 13.50467 10.201 6.861667 8.198 6.983667 1.302333 5.421333 8.351333 161.101 1.448333 2.715 21.32033 6.521 3.294667 2.818 2.745 5.057 1.897333 2.163667 2.14 7.621667 4.058 6.567 13.88733 12.883 7.601333 11.40267 15.09267 0 1.122 2.922 0.01 8.293333 7.325667 4.009 12.67933 1.351667 7.168667 3.765 0 8.038333 3.292 6.625333 23.38367 3.418667 0 1.574667 4.064333 4.638 3.822 18.91833 2.310667 0.4176667 4.053 1.769667 8.223667 36.09 1.281667 3.090333 6.754333 1.851 1.981333 8.255667 7.195333 7.337333 0 4.196 3.425333 0 2.800667 16.116 2.194 6.813333 8.773 5.060667 2.517333 6.512667 4.325333 1.089 0.7146667 2.474333 3.273 1.407667 1.994667 3.696333 4.572333 0.2473333 3.122667 2.883333 6.893667 4.765 3.493 3.293333 1.492667 1.649667 3.179 3.219333 0 1.576667 0 0.7693333 4.387 1.547 1.992333 1.344 4.989667 3.403333 0 1.980333 12.75533 2.347333 0.5473333 3.398 3.570667 2.877333 0.622 0 2.275333 3.733667 11.126 4.611667 0.9123333 7.756333 1.637333 0.409 2.663333 0.676 8.504333 2.337333 0.939 3.988333 2.414667 2.692333 2.448333 2.777667 3.992 1.56 3.319667 4.52 3.021333 2.577667 3.077333 4.451333 4.385333 6.45 2.578333 5.633333 0.4253333 
2893s sampleB_mean:  1524.761 2830.628 1611.849 339.544 266.1853 2001.57 370.6363 3005.897 1440.661 2786.993 809.747 1997.885 1889.849 2415.454 2237.994 4325.944 686.1263 856.342 1374.611 566.031 953.5553 4759.337 3396.666 2883.64 875.9707 574.6353 759.8243 736.2793 3693.07 394.7987 3179.415 3249.388 768.1787 4198.375 3216.203 2471.048 3756.434 285.4657 344.6643 3330.022 2374.126 3620.716 2922.537 105.6647 4895.859 90.55133 437.971 556.5843 4427.58 5398.857 2047.901 421.1887 211.0497 2376.446 3709.705 149.84 253.343 630.4883 3616.512 2990.729 4251.336 472.5113 1235.974 208.1393 348.3133 562.3953 300.4817 606.0663 366.0723 476.768 485.2353 118.7197 73.643 144.7763 79.82167 279.329 3423.331 378.7327 2436.015 760.6557 241.776 731.863 439.0257 142.302 1094.26 146.4013 1049.838 5152.482 166.0277 140.0233 240.971 1034.454 692.2687 112.4467 298.0877 255.2837 683.449 461.5343 3650.525 194.996 927.6743 192.3193 366.123 332.1813 189.6917 3849.83 140.997 878.6043 341.4467 265.6093 3067.808 310.312 193.8653 164.205 155.4747 267.5577 401.21 205.6727 189.5857 171.3853 511.8627 267.723 269.2717 132.628 167.053 365.2543 132.7817 194.1133 2890.802 1547.523 120.2137 203.65 120.8233 165.0047 199.6 274.3337 218.6657 135.609 1780.032 321.7517 699.6877 320.243 404.5893 105.6257 1082.98 116.6347 87.31133 130.9923 58.96367 1642.015 609.5917 166.8767 1395.183 79.65933 90.86167 290.862 428.623 357.7387 434.556 140.1517 263.798 133.069 67.006 496.8353 127.811 84.91167 160.1683 317.0973 143.3147 286.777 156.2033 1012.972 253.0167 141.5657 254.1857 87.15567 105.0843 224.5063 178.71 125.4973 287.485 42.12067 212.3977 178.5933 444.0447 58.79033 177.3257 98.13967 90.957 68.593 160.4317 303.08 303.0437 92.061 97.3 1621.57 150.3183 96.602 165.4787 109.1813 88.38 255.8583 133.1023 117.2697 71.08433 443.3713 96.957 127.943 260.6683 96.142 38.85333 175.8867 127.5543 189.0233 382.3843 177.183 138.4137 83.61967 55.55933 240.6073 118.3287 351.08 385.176 132.4173 60.04567 161.1673 90.116 39.998 59.379 81.26567 125.2547 115.1327 193.4727 40.32533 75.75133 107.4287 150.3003 252.983 57.69533 123.721 65.65667 85.78933 213.8997 120.4613 195.2947 140.2763 183.3313 79.68 259.148 207.045 149.819 231.7267 120.8867 151.719 168.0607 232.1147 51.73767 83.573 382.0493 58.06633 166.5273 92.43267 91.509 218.8733 91.18133 216.949 194.3873 59.23867 95.749 64.25433 131.585 53.59967 140.8457 199.317 103.81 184.3507 31.73 220.7547 74.99667 108.7427 88.725 101.0153 134.7907 82.67333 62.39367 87.65567 60.63 57.40167 162.3163 143.607 72.854 123.938 229.5497 143.433 136.4467 48.27933 67.408 87.012 69.18967 67.72533 126.504 74.632 109.6237 69.947 116.5553 76.57167 183.9787 85.55767 176.0977 132.2 117.851 93.48367 71.93733 59.629 145.5417 80.46333 148.7563 186.8647 33.62833 151.599 178.2697 96.76 473.3597 49.419 119.8297 90.91333 61.29533 138.9263 136.346 80.36 177.785 1604.347 110.8577 78.48367 32.967 72.596 195.6537 62.05533 43.412 323.664 34.301 53.67167 161.956 293.9087 133.338 124.6713 68.66267 177.154 35.42167 89.57667 118.1207 143.872 174.409 104.978 106.4977 71.28167 136.4563 102.0507 71.74267 84.66667 41.93 47.35667 80.51633 45.994 30.70733 36.13033 77.97333 71.81167 96.91167 84.28567 76.68167 188.329 53.655 88.05067 114.4257 83.324 48.91 69.52233 280.2713 69.599 84.001 56.562 63.03733 183.6017 96.94267 78.28033 51.723 127.9993 67.53533 71.949 100.6683 50.22033 77.092 188.4637 123.1273 68.608 79.551 142.4753 90.31267 126.4583 65.56833 36.53367 311.329 49.36433 36.76567 150.4293 68.67667 159.7823 68.32067 34.95467 151.883 120.206 77.38367 137.8557 27.671 39.086 36.70233 57.43267 55.85733 63.84367 76.47533 53.52367 356.891 40.14733 28.55333 30.21933 29.627 61.53933 53.014 22.85467 61.12667 48.22433 29.26867 47.69067 27.296 61.486 161.9667 76.577 38.799 36.6 19.45267 30.35033 51.13867 73.193 37.55767 84.252 37.65433 27.28933 191.3687 48.89833 106.615 43.65367 31.70567 27.176 47.47333 76.24933 100.608 48.224 62.81267 58.25633 43.97967 59.38567 33.21433 84.57567 82.68433 44.01933 41.03967 42.95633 186.3597 45.60867 57.43367 35.499 36.72267 149.342 65.255 52.33733 49.472 61.21367 44.45533 33.399 42.28633 22.75467 251.767 40.13033 62.27133 55.77667 79.067 32.39667 37.29667 130.8803 27.93333 58.12767 885.105 127.1577 33.473 91.86567 35.098 14.628 67.063 39.59267 34.77567 21.83433 423.253 22.669 31.972 27.94833 33.70267 69.843 50.84367 31.336 50.05667 61.76067 7.787333 27.11633 16.267 18.93767 79.87367 42.60033 26.188 61.23533 14.83167 31.52433 28.714 7.434333 38.139 33.73067 25.97433 329.1877 32.58033 19.23067 84.23433 30.03567 46.144 15.205 107.6573 31.73667 19.80633 17.84967 27.04033 117.513 166.674 20.92033 16.67967 37.849 13.23833 49.82833 49.72933 30.596 77.94767 20.285 56.93233 15.277 86.78467 22.274 95.334 16.95033 27.944 78.66133 26.27467 30.23233 98.03267 22.413 15.25033 73.018 33.19833 18.09167 12.861 18.55533 26.23633 37.429 19.36667 15.02733 28.15867 28.39433 34.77033 13.99333 13.36767 20.05633 18.50433 20.35933 29.242 30.69133 17.502 18.48833 17.31067 21.34167 19.614 30.54067 13.94367 65.14467 18.03233 3.268 12.443 66.67867 12.703 28.44433 16.01333 16.27233 15.656 17.43 31.383 17.236 70.27367 80.966 22.38467 24.30433 38.17233 13.41633 18.61167 15.33767 31.89 37.68333 23.945 23.73133 15.90267 38.715 17.96033 39.09833 19.04733 16.55367 15.269 14.817 29.889 46.892 17.898 28.101 32.61467 18.28267 62.73233 15.10167 41.99133 13.18233 
2893s num discordant:  0 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2893s 
2893s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2893s sampleA_mean:  768.306 1781.496 876.8277 1636.976 4624.974 512.042 12470.43 440.9727 834.608 324.8553 871.6373 2550.414 1506.715 1101.219 707.8263 3078.184 347.4017 217.5877 177.0987 493.2167 31019.62 850.5097 514.415 501.203 224.469 510.9113 339.8283 620.017 1098.868 95.89333 2373.043 1192.947 621.286 645.4617 198.0453 856.7063 411.447 3211.031 646.6133 429.5973 173.88 189.5647File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2893s  1003.238 244.213 222.09 474.0487 689.711 1494.298 306.1523 237.177 900.1817 374.99 328.0923 211.7417 623.5437 646.864 204.598 378.627 166.336 194.2893 132.9247 661.7387 257.3087 198.031 151.8027 97.24867 138.8203 109.0163 88.61667 116.0807 499.6263 103.6453 75.79967 189.876 153.4527 565.0517 194.0203 186.3673 615.4837 149.5763 202.739 188.654 92.354 63.519 506.512 215.8967 91.645 53.598 276.1017 175.2467 160.284 272.869 112.6127 278.7853 189.338 103.0963 37.50533 583.86 374.3023 161.0497 131.159 578.1793 114.7247 138.9953 72.98133 322.6313 45.62033 100.247 112.168 2633.716 54.95833 94.455 63.24267 39.40267 214.853 46.03533 55.41567 59.07767 57.289 82.208 51.208 58.90833 106.367 114.2777 80.30267 55.17567 359.4497 541.9867 66.74667 103.33 43.62667 31.404 99.289 29.69867 30.70067 52.59533 36.49633 46.59433 75.16967 227.2843 83.27833 170.258 69.91033 41.25767 39.44033 28.455 40.44433 39.745 28.618 50.351 32.245 137.7607 35.30367 13.208 63.80367 43.80133 25.087 33.46233 81.69967 72.57967 42.52533 50.66867 36.466 82.00433 40.18733 72.777 27.874 24.83067 134.6853 75.28167 38.06967 79.93733 19.68333 37.18267 124.9103 25.539 48.025 7.618667 23.51433 58.47233 24.891 31.40267 92.552 25.74867 50.767 57.61033 18.93167 56.21533 147.841 48.78233 62.14133 45.16833 22.33433 31.79067 29.71933 48.16367 23.021 29.06367 63.71067 20.62167 63.05533 26.44133 76.51933 22.32333 69.305 101.7453 31.89567 55.27767 68.14433 59.28433 122.654 28.191 36.90167 23.01233 27.69933 18.868 93.41733 19.09633 11.958 45.292 18.83133 49.08533 32.10933 27.838 31.779 52.69467 19.622 19.95933 67.73133 72.11233 26.81733 22.708 64.09967 19.45967 43.573 23.05967 37.914 57.80667 
2893s sampleB_mean:  11.541 78.223 59.789 131.954 341.9077 41.31433 312.258 21.142 149.042 42.12067 107.8423 16.70467 165.372 143.015 84.293 644.6073 72.11933 33.19 18.75567 77.04167 8202.657 173.185 28.83167 107.4767 15.272 17.62467 40.62 19.323 162.736 6.833333 8.807333 230.7603 70.838 98.93967 17.10933 147.5103 51.37267 176.0093 84.69133 60.698 11.974 21.17867 231.01 24.36067 40.211 62.01667 91.85267 361.5717 60.63 52.02367 190.2367 63.14733 1.413333 47.04433 149.0183 126.507 31.336 50.806 8.328333 15.897 22.66633 126.2827 52.632 35.05467 21.67633 20.43633 21.66667 14.771 4.436 23.35133 52.72333 13.34567 14.72967 43.86567 22.414 3.203 27.23467 44.21233 3.97 30.432 35.93933 25.96333 11.42567 4.816667 113.391 43.19967 15.47833 7.705667 49.04333 36.80733 5.957333 61.038 3.546 38.81867 5.980333 15.84233 6.593 126.723 84.23433 34.63 21.75133 5.375333 27.299 33.24633 15.958 0 6.119333 21.97267 20.231 603.3247 11.08667 7.766333 6.474667 1.620333 47.94933 3.929667 11.73133 13.23833 13.36767 14.15433 7.976 7.353333 21.74967 24.79367 15.00967 5.855333 95.334 101.151 15.63733 21.066 4.916 7.205333 22.53 1.439333 6.552 10.64267 2.201333 6.709 15.06367 53.09067 8.861667 21.36367 4.875667 3.745333 4.478333 3.039667 7.920333 7.033333 3.831 2.48 6.818 34.28533 3.374 0 14.63867 5.966667 5.451 2.116667 19.603 1.932 0 0.6883333 6.506333 0 6.937333 14.62267 6.301667 1.628667 12.223 7.897667 3.003333 14.45 3.384 8.477667 21.018 4.024 4.954667 0 5.055333 8.693333 2.909667 6.082333 8.839667 3.431333 10.157 6.500333 1.101667 12.1 41.35533 10.15367 9.771667 9.145 1.765 7.386333 2.893333 7.749 2.511 1.569 10.28 1.082 5.157 4.422333 8.006333 1.63 13.05267 25.41533 6.758333 3.485333 1.799 5.139 19.24567 2.819 8.017333 4.993333 0.692 2.849667 14.763 0.4836667 2.343667 10.16333 4.229333 5.657333 2.181667 0.8023333 1.487333 5.417 2.936333 3.54 5.873 16.907 5.261333 4.677 9.295333 4.786667 2.462333 4.158333 8.735 2.217667 
2893s num discordant:  0 
2893s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
2893s sampleA_mean:  825.1763 1020.23 311.829 2661.226 28.62567 53.11833 37.23367 658.8357 110.7323 773.7893 117.2063 534.2237 112.322 77.55333 407.2907 94.08633 210.276 135.901 191.8153 501.0717 95.99433 62.58133 220.5287 138.353 59.968 341.9023 40.96933 105.9497 88.495 189.9813 4.98 81.05967 53.687 73.97767 16.50567 36.99433 65.965 24.33867 115.6623 50.429 124.4243 55.75367 56.147 17.029 30.499 104.7537 62.68467 83.305 25.096 63.41767 21.54267 132.8633 42.797 48.72833 36.84367 56.695 336.3973 49.103 180.8457 12.544 12.42267 9.165333 14.554 40.53433 53.33433 57.313 15.418 58.24233 68.49367 47.89667 39.58367 103.5143 17.60767 9.605 19.86033 3.969667 32.75133 2.172 17.875 6.042667 25.39133 30.00467 24.273 39.777 41.856 199.8083 21.25867 31.04633 35.78433 11.277 8.516333 342.208 22.84267 45.89833 20.959 42.71533 16.69733 10.63267 21.14433 31.838 57.13467 41.83033 7.538 23.53367 24.02367 15.26033 16.22733 70.13033 91.47333 35.43333 24.772 29.33233 5.832 3.122 28.28467 7.374 5.607667 36.41067 24.38833 133.0233 31.61067 14.56933 14.411 12.023 23.71433 40.92067 12.36 15.559 7.083 13.52433 7.960667 29.44033 75.059 88.60033 15.28167 5.097667 56.92767 12.85033 43.318 8.362 6.926 3.966667 21.31667 6.314 21.88967 25.25367 8.268 10.23233 16.53733 24.662 16.38067 17.12667 12.771 15.914 40.359 20.27767 12.81233 6.981333 12.13567 22.77967 21.02533 10.30967 7.979667 10.16833 23.029 2.752667 8.47 65.86733 10.49233 5.664333 7.825667 2.792667 5.342333 18.746 3.51 21.765 49.53233 6.437333 11.38633 5.772333 238.9387 27.34567 5.960667 28.07033 20.79733 7.526667 2.727 19.21233 9.187667 3.596 8.79 11.90333 4.820333 15.31167 21.686 18.06167 16.75833 54.65067 46.84667 5.464 37.02633 17.25667 2.539333 3.046667 5.197667 21.776 14.33467 22.029 22.86533 0 11.28667 8.792667 23.46733 14.50533 7.951 5.777667 11.03933 6.225667 12.438 3.531333 32.918 16.17933 6.306667 8.809 7.603667 29.746 74.98367 10.73033 8.48 7.113667 7.839333 6.174667 78.08667 5.639333 22.12067 14.356 5.177333 5.134333 7.025 6.934 0.8883333 3.201 3.158 8.591 13.76033 12.918 7.395 3.788 10.31933 1.752333 1.506333 9.925 3.503 8.232 9.197667 7.014667 7.501667 0 5.081 4.237 2.409667 0 3.773667 3.867 7.901333 5.981333 2.654667 6.052333 2.742667 4.912333 0 2.518667 0 2.723333 3.633333 2.993667 6.318 7.077333 1.934333 0.093 9.321667 2.414667 23.97033 19.63133 5.407667 9.876 7.560667 2.888 6.688 4.064667 2.503 2.105667 2.653333 7.296333 0.2506667 3.311333 10.97667 4.158 2.967333 2.349 3.471667 1.734 4.931333 0.5686667 8.351 6.958667 2.231667 0 5.76 0 10.806 2.677333 3.945333 0.4486667 6.261 5.397667 7.922333 2.362667 4.514333 1.742333 2.98 3.743 
2893s sampleB_mean:  3756.434 5398.857 2830.628 13329.63 317.4807 339.544 461.5343 4216.251 1202.982 3709.705 3506.467 4004.8 2786.993 809.747 2355.907 968.2863 2415.454 807.5603 1242.884 2001.57 878.6043 843.2847 2047.901 953.5553 266.1853 1524.761 501.3557 686.1263 574.6353 926.6357 1440.661 786.1327 256.6427 805.275 584.575 279.329 317.8843 203.078 720.0863 573.2667 513.784 222.0223 562.3953 286.777 378.7327 468.317 303.08 401.8723 166.0277 477.213 255.2837 641.6557 255.0223 224.5063 208.1393 387.0143 1576.856 290.862 1012.972 137.7833 166.8767 177.154 148.789 682.0817 371.2327 255.8583 194.1133 310.312 585.796 265.6093 320.243 496.8353 156.2033 109.3147 121.5623 59.23867 219.6953 58.96367 116.6347 90.957 156.0383 125.2547 145.604 157.5777 278.7393 1109.48 168.2893 163.1987 178.71 110.8993 127.5543 1834.421 301.9357 178.2697 143.3147 263.0527 151.719 92.061 213.8997 263.5397 232.1147 195.216 303.0437 132.4173 150.3003 124.6713 194.3873 311.44 405.776 160.5167 163.021 161.1673 91.509 91.739 145.137 143.872 99.863 148.6807 148.7563 1082.98 160.1683 91.18133 179.874 96.804 120.8867 161.4237 101.4477 108.837 64.25433 57.44367 98.33933 151.599 332.2983 437.7257 143.0897 87.65567 253.0167 70.221 193.3587 51.73767 41.78967 102.0507 83.61967 71.81167 109.0193 174.6973 67.408 69.18967 119.8297 176.0977 109.6677 85.78933 118.1207 117.851 188.56 138.9263 96.94267 31.73 84.001 918.9367 293.9087 53.655 192.615 46.842 113.004 29.627 96.91167 285.3807 48.96533 47.31267 60.90233 76.24933 24.80467 82.68433 37.96133 141.0183 195.2947 56.05633 64.15933 51.723 4759.337 174.409 50.22033 126.6913 125.7047 71.949 36.6 107.2877 54.097 27.192 41.93 63.62167 68.67667 130.4127 141.442 91.49033 76.82 230.7707 216.4093 36.76567 191.0543 317.6723 32.39667 29.675 27.296 90.427 106.615 127.9993 97.60633 174.965 84.252 44.98367 169.1617 216.4057 44.69833 251.767 68.608 61.53933 311.329 36.53367 170.7463 93.09033 41.517 49.09733 127.1577 120.0493 381.953 55.476 39.086 61.76067 34.05967 28.425 356.891 59.38567 112.8043 73.193 30.54067 40.13033 58.12767 43.94933 19.95267 31.46 30.93667 65.255 76.899 52.36933 28.775 24.244 48.14767 33.473 18.20933 41.50267 20.82433 42.92033 61.80233 27.23833 31.52433 24.882 54.54667 15.87267 16.15667 19.80633 24.241 30.03567 34.77567 24.384 28.39433 27.607 22.782 33.73067 18.23433 26.27467 6.507333 31.73667 19.99067 15.938 129.8027 28.714 28.30833 12.004 44.13267 20.92033 106.4977 178.6527 21.00233 49.72933 32.58033 23.60467 68.356 27.04033 11.60833 28.15867 33.19833 33.75167 19.36667 18.612 73.018 20.046 12.202 86.78467 14.948 19.23067 20.212 18.004 54.89133 80.966 17.502 3.268 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2893s 28.421 31.383 68.52333 72.35433 20.05633 16.761 25.473 21.03667 70.27367 17.43 23.30167 38.715 16.92567 15.33767 
2893s num discordant:  0 
2893s touch test_DESeq2
2893s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
2893s Got 9 samples, and got: 10 data fields.
2893s Header: wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
2893s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2893s 
2893s $VAR1 = {
2893s           'wt_ph8_1' => 8,
2893s           'wt_GSNO_3' => 4,
2893s           'wt_GSNO_2' => 6,
2893s           'wt_ph8_2' => 9,
2893s           'wt_37_2' => 1,
2893s           'wt_GSNO_1' => 5,
2893s           'wt_37_1' => 3,
2893s           'wt_37_3' => 2,
2893s           'wt_ph8_3' => 7
2893s         };
2893s $VAR1 = {
2893s           'wt_ph8' => [
2893s                         'wt_ph8_1',
2893s                         'wt_ph8_2',
2893s                         'wt_ph8_3'
2893s                       ],
2893s           'wt_GSNO' => [
2893s                          'wt_GSNO_1',
2893s                          'wt_GSNO_2',
2893s                          'wt_GSNO_3'
2893s                        ],
2893s           'wt_37' => [
2893s                        'wt_37_1',
2893s                        'wt_37_2',
2893s                        'wt_37_3'
2893s                      ]
2893s         };
2893s Contrasts to perform are: $VAR1 = [
2893s           [
2893s             'wt_37',
2893s             'wt_GSNO'
2893s           ],
2893s           [
2893s             'wt_37',
2893s             'wt_ph8'
2893s           ],
2893s           [
2893s             'wt_GSNO',
2893s             'wt_ph8'
2893s           ]
2893s         ];
2893s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.voom.Rscript
2893s Loading required package: limma
2895s null device 
2895s           1 
2895s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.voom.Rscript
2895s Loading required package: limma
2896s null device 
2896s           1 
2896s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.voom.Rscript
2896s Loading required package: limma
2898s null device 
2898s           1 
2898s cd voom_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2898s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
2898s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2898s 
2898s 
2898s ** Found 1817 features as differentially expressed.
2898s 
2898s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  -s ../samples.txt
2898s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2898s Loading required package: BiocGenerics
2898s 
2898s Attaching package: ‘BiocGenerics’
2898s 
2898s The following objects are masked from ‘package:stats’:
2898s 
2898s     IQR, mad, sd, var, xtabs
2898s 
2898s The following objects are masked from ‘package:base’:
2898s 
2898s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2898s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2898s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2898s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2898s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2898s     table, tapply, union, unique, unsplit, which.max, which.min
2898s 
2898s Welcome to Bioconductor
2898s 
2898s     Vignettes contain introductory material; view with
2898s     'browseVignettes()'. To cite Bioconductor, see
2898s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2898s 
2899s 
2899s Attaching package: ‘fastcluster’
2899s 
2899s The following object is masked from ‘package:stats’:
2899s 
2899s     hclust
2899s 
2899s [1] "Reading matrix file."
2899s for plotting:: min.raw: -0.680559894057534 max.raw: 1
2899s null device 
2899s           1 
2900s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2900s null device 
2900s           1 
2901s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset 
2901s sampleA_mean:  6030.232 20787.35 1833.283 1407.266 1046.9 4776.171 2191.464 4954.434 1371.045 1037.645 1013.064 1326.5 982.539 484.398 887.2083 559.8297 2059.192 522.8673 335.7477 1681.385 1262.588 838.8547 533.844 499.8527 4182.673 1066.12 11423.35 5797.692 545.5957 1532.142 562.1487 333.5833 470.179 1120.621 810.3883 1445.705 1707.219 1512.754 2616.495 301.1237 409.7437 2460.887 2442.782 2602.336 3549.085 480.5827 604.7417 581.2863 4784.861 629 502.9777 941.4197 1319.258 4913.275 15024.4 1272.664 400.0377 323.5933 647.4437 620.238 1265.232 508.1423 134.168 1816.62 338.9207 1718.763 198.8237 530.7697 1088.069 2635.243 923.62 1753.538 425.4187 350.1547 180.1727 335.637 296.1627 178.6107 637.4673 298.6353 388.648 203.246 872.2057 564.1773 1326.869 249.8873 1939.628 933.0403 393.785 373.2207 207.4947 731.256 335.2157 579.459 104.2153 914.4587 218.991 3468.578 772.306 1291.39 456.1583 693.0703 5637.134 1640.267 665.289 494.789 599.1197 744.858 481.5627 2207.998 339.0793 252.8977 350.3023 584.709 876.645 579.619 583.6803 4713.887 419.6373 182.1447 134.0677 323.2733 2002.536 1315.006 1229.376 124.028 150.8137 119.932 167.1063 435.0017 127.1483 719.3537 567.2883 201.4867 2446.14 482.3557 177.4467 490.2657 85.82433 340.5557 148.374 742.0153 221.959 991.437 154.4447 272.6143 209.749 310.3963 2891.881 505.6607 161.9753 198.9307 455.3783 510.4197 211.844 363.4713 1214.03 762.2617 197.342 711.3287 1099.802 354.781 446.9747 313.843 1547.728 210.486 156.591 241.211 256.9907 262.1497 574.8767 219.039 123.246 912.636 1125.723 122.234 244.753 407.805 352.3153 243.9703 189.715 387.8127 676.234 300.3533 854.0897 2688.784 323.746 318.1197 243.326 183.172 99.45067 231.4073 176.9843 62.56033 690.4453 196.6567 168.189 334.935 146.7767 71.71033 303.8613 432.0453 97.82467 234.695 252.697 162.433 369.791 192.5983 330.6623 122.4237 1815.027 1412.697 152.1197 356.3497 783.8573 563.9263 5395.606 216.15 83.207 594.819 83.07667 356.783 250.2393 67.469 617.054 57.64267 114.123 60.22767 114.485 294.269 78.31633 97.23167 407.6713 136.2463 342.712 110.791 160.8853 109.0817 160.1673 86.386 310.3323 122.177 210.2437 324.5383 122.591 76.27033 87.49733 322.742 112.757 240.267 328.3217 322.1607 118.5347 320.023 239.7997 111.007 69.89367 421.348 299.966 334.361 371.817 93.672 94.07567 571.859 133.1057 199.325 104.0613 75.336 207.397 132.6493 62.65367 335.4993 33.26767 144.7257 172.982 115.132 81.80933 99.03533 91.61633 86.67367 280.7067 31.38733 76.09067 228.911 169.0567 134.6873 306.508 42.552 1557.898 64.34933 79.282 32.351 6660.051 85.95367 55.68233 110.5993 721.5107 78.67633 89.249 59.60267 108.859 38.966 52.74467 105.6967 135.433 307.9013 363.302 80.98433 112.5293 58.232 781.6647 94.69467 93.57967 220.177 67.206 114.563 94.133 79.07433 84.972 361.8817 204.481 46.65767 31.766 62.81 84.25 155.7297 77.01533 38.21567 3561.451 98.302 89.883 156.8307 91.79433 84.98533 73.806 603.3643 44.71033 47.17133 172.4453 30.17067 112.7063 66.88467 41.339 38.01367 56.34967 87.15633 67.623 398.1303 526.9727 35.384 39.99867 32.60533 74.26433 158.1847 47.40267 73.085 64.40333 69.72667 112.884 2952.358 100.0123 37.59833 176.214 47.775 51.06833 69.21367 144.1087 32.07433 34.95267 74.20533 71.85 2465.916 32 5495.505 23.42167 103.086 44.67767 131.435 20.93567 26.93367 53.25667 49.19267 69.90667 39.204 164.921 78.667 56.22233 31.13533 16.46033 52.91967 279.711 43.95233 1172.149 66.12467 21.82767 30.96067 54.81767 171.2653 31.01767 40.988 306.441 64.515 340.941 38.41333 703.739 31.93633 168.4167 65.34533 27.49133 33.50367 38.414 50.27133 280.1693 354.898 40.022 34.237 14.64167 95.708 115.173 37.93767 163.5027 405.356 197.0237 84.101 52.49167 442.0453 37.304 38.44933 85.27667 51.916 52.662 69.92267 71.55767 15.47467 29.75167 1606.153 15.402 56.78633 42.42 36.76933 20.16567 89.08767 24.04867 35.23567 551.5827 58.726 4534.064 84.52867 106.8033 115.2073 28.112 16.59667 41.489 36.44033 23.34767 14.82667 9.429667 20.02467 16.066 14.972 23.62733 19.56433 16.558 23.565 8.473333 246.2103 35.217 36.86033 88.74833 24.90267 66.32833 10.73367 33.16667 26.74467 27.81033 209.263 158.4163 23.36033 15.77833 22.18367 176.112 38.71367 40.90567 9.629333 20.61433 
2901s sampleB_mean:  173.6673 336.3973 63.97333 33.63533 27.41467 543.417 98.61433 175.7007 28.87167 47.461 18.23967 98.97567 33.35533 24.33867 55.41567 32.483 313.6673 28.62567 21.376 10.849 9.133333 39.777 47.52733 18.18567 658.8357 183.983 534.2237 900.1817 72.053 225.2773 52.09567 36.39433 10.76867 43.62667 63.963 139.4193 218.998 281.149 629.0693 55.75367 42.68733 73.97767 563.4113 514.415 84.42267 39.797 95.47967 27.60133 299.0663 94.08633 9.088 232.083 117.2063 1003.238 661.7387 217.05 24.273 38.47567 49.48767 12.49967 250.9827 79.409 13.52433 3.202333 50.10333 296.743 22.41533 110.7323 145.798 623.5437 79.21633 375.202 72.874 36.41067 27.94467 74.29867 8.580333 32.70533 2.778333 26.58267 85.85133 32.93 116.6427 68.27467 191.8153 36.231 297.3653 143.4493 68.88567 53.687 28.87667 170.8453 43.422 102.7107 14.398 213.755 48.99067 457.8803 68.979 194.2893 80.21667 150.937 68.49367 280.8763 12.67333 58.90833 130.483 132.8633 105.7627 412.998 70.59233 15.51133 19.23033 122.476 94.216 113.0753 85.73633 338.805 50.429 18.134 23.18133 25.39133 429.5973 131.764 124.0153 15.837 10.44 22.87333 33.283 66.97833 14.087 119.1803 23.51433 23.402 582.8023 70.27367 21.00533 44.471 10.49667 72.46567 9.605 62.58133 45.02367 223.4383 37.50533 38.81867 15.964 29.69867 125.8543 118.5987 35.82667 5.223667 92.838 126.7297 29.54433 12.30667 230.2087 43.57767 29.96067 118.5947 170.561 80.928 88.46167 74.91 377.1183 32.109 30.82233 22.455 62.40367 40.96933 56.695 9.034667 29.317 115.6623 261.706 10.49233 5.388667 58.22233 56.458 60.89033 31.15267 89.28567 116.0857 29.063 11.05733 462.724 38.353 73.76233 43.417 26.18 10.675 7.825667 39.035 11.399 154.972 42.91667 28.625 64.78933 32.132 10.603 49.50333 70.388 10.31967 45.62033 52.69567 11.277 70.13033 26.01033 43.27 3.616 402.3693 4.412333 26.68733 58.833 170.3357 120.0037 4.127667 45.433 20.623 131.159 18.13133 68.36967 48.89067 8.652333 115.9157 13.374 2.461333 12.03667 2.967333 55.04367 14.54933 22.98467 96.276 14.554 71.40267 26.685 14.26033 19.12733 36.07133 15.947 21.807 19.68333 28.455 55.915 8.546333 15.62833 6.740333 73.756 12.85033 44.52567 43.231 6.660667 28.90033 71.137 41.856 11.71333 8.867667 75.955 72.38467 72.094 78.80367 16.16267 12.35967 87.39733 24.22767 20.14333 16.69133 6.437333 47.833 33.48033 4.263 2.287 6.353667 29.59733 6.052333 26.14833 10.94967 19.23 15.559 17.759 65.26833 6.926 14.33167 40.359 14.82467 31.58467 71.361 10.51167 260.6453 15.44967 17.413 7.566333 938.454 20.73367 7.72 16.40267 80.658 7.913667 1.321667 14.42733 21.776 9.231 4.583667 15.246 15.437 65.235 64.46467 15.42567 15.32067 8.792667 4.512667 18.174 18.108 16.50567 12.19033 26.33733 19.81633 12.544 14.10833 69.556 40.363 10.23033 5.709667 12.327 14.04867 27.02667 14.676 6.723333 499.6263 12.226 21.74733 2.732333 19.28233 18.931 11.486 118.617 7.395 10.679 32.75133 7.087667 22.84267 7.66 9.647 9.294667 6.977333 14.08133 15.98533 84.71567 73.07533 2.032 6.174667 5.685 17.83733 28.212 8.274 12.023 9.925 13.91533 14.411 424.5863 16.38067 3.122 17.25667 11.013 7.516667 10.57833 21.41267 4.789 5.981333 13.76033 15.521 7.979667 7.807333 10.288 5.664333 23.04733 9.524 21.67067 2.503 0 8.352 8.369 11.173 8.836 28.223 17.55633 9.195667 5.992 3.596 9.865667 58.535 10.124 228.7547 15.28167 0.8883333 5.838 13.31333 21.40333 2.410333 4.98 72.50367 0.6243333 67.14133 2.327667 138.602 5.784 29.664 13.338 6.127333 7.374 8.525667 10.828 20.15033 7.045667 4.636667 8.232 3.51 23.05433 29.06 2.177 23.191 22.77967 37.02633 5.474333 9.638667 40.53433 4.895 9.153 15.31167 10.462 8.300333 8.412333 13.186 3.68 5.607667 6.318 0.4626667 5.468 6.257667 3.465 3.966667 9.302667 1.734333 5.763333 19.63133 2.115333 3.101333 4.385333 27.046 9.423667 1.195 0.668 5.190667 1.998667 0 3.158 0 5.458 1.586 2.939 2.341667 2.98 3.201 1.755667 0.093 14.50533 4.641667 4.132667 10.806 5.709333 5.685333 0 7.033 1.905667 3.141333 18.65833 23.73867 1.651333 0 3.513333 8.689333 9.475667 5.354333 2.409667 4.44 
2901s num discordant:  0 
2901s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2901s sampleA_mean:  539.652 558.1363 279.6767 526.2243 68.104 300.087 96.61333 691.0767 641.1777 103.6867 1406.461 98.85333 96.77733 620.406 478.7223 20.01233 251.019 536.193 850.6397 72.55133 967.4877 38.978 915.841 876.482 45.76333 866.6187 1005.984 1005.984 655.8127 733.6827 861.8193 81.319 213.4847 954.153 903.1557 555.952 1220.149 1784.069 551.9577 884.0843 98.448 509.7623 1117.319 20.97667 114.5207 226.9223 15.838 17.37067 57.579 2042.114 15.04567 409.1913 128.1763 5.762333 33.62067 70.24967 4.654333 950.0057 224.904 1690.757 103.9153 93.42833 360.2233 76.41333 260.666 1385.135 21.39933 504.111 39.57833 18.754 2.696667 866.9083 113.178 2466.545 1545.514 33.57133 1681.069 443.633 57.26933 16.51667 31.501 37.21967 35.44767 1094.775 11.583 40.61467 603.456 86.883 94.089 1834.914 1313.1 697.2287 237.8803 29.55 223.9227 75.48133 37.255 898.047 642.0663 2590.581 1584.902 62.50533 9.434667 121.0697 141.697 425.357 18.96267 7.212667 27.52967 15.73033 100.1173 71.78533 56.797 1593.583 13.98533 503.5693 94.847 50.14667 27.29 393.3037 44.93767 67.08167 660.21 617.7277 16.528 20.36667 25.55733 37.25567 35.29633 64.19 18.88733 28.45833 6.167 4.244 337.399 35.529 29.18933 443.3597 188.4693 1666.136 42.57533 2.713333 560.8327 129.326 39.67767 43.50567 37.942 22.92133 22.74167 7.601333 17.221 2.398333 47.34533 27.48633 63.58333 7.685 66.65833 31.92667 824.9103 1796.241 27.59267 759.571 670.486 7.282667 6.496333 15.08833 10.53633 43.09833 91.49933 5.017333 118.9327 23.33733 40.12067 42.16667 51.407 16.54033 77.21567 7.951667 6.546 123.0927 9.896333 65.027 110.725 5.557333 30.828 73.27533 22.627 15.92433 20.37167 6.300667 3.078667 2166.993 759.148 302.136 9.969333 14.71933 7.980667 17.48067 50.11167 225.547 5.802333 23.04333 16.27833 17.96533 48.27367 28.839 20.135 15.46533 251.833 354.6413 18.67133 134.6073 61.43567 74.00233 47.651 27.61367 46.75733 73.59667 10.30533 18.30633 325.5413 4.080333 1846.256 18.317 11.52 5.016 40.25467 46.23067 18.233 27.23133 40.23433 5775.202 24.63167 7.252667 2.280333 5.682 15.54567 36.11867 29.26167 14.91467 497.7577 93.21667 18.592 6.929 474.4033 3.595333 5.627 23.127 12.40267 25.71133 12.30833 13.78833 8.791 17.59867 3.451 23.09367 25.73033 49.835 15.18033 7.059 22.375 7.909333 43.83633 17.53667 6.745333 22.68433 20.71867 483.664 7.48 6.455667 3.586667 66.73133 9.767333 8.807333 10.12033 321.257 21.67167 28.26467 5.474667 7.963667 7.869333 2.154 2.177333 30.97967 14.33333 2.900667 34.33067 46.17067 11.93267 15.25233 35.802 9.613667 34.16433 756.3963 6.515667 11.312 19.73 109.3627 27.77367 1.919333 7.083333 7.107 33.21467 7.412333 25.208 43.001 3.139 44.97967 25.40433 9.824333 275.3867 2.592667 8.002 8.292 22.31833 11.98267 49.788 9.274 112.283 8.866333 17.85933 33.815 1001.993 48.562 4.745 46.73367 59.43533 1.292667 87.024 9.773333 0.838 4.281667 18.33267 6.812333 4.531333 13.64567 14.93733 8.395 25.089 16.899 31.12967 11.286 7.700667 6.527333 1.460333 6.248333 21.74467 7.782667 1.991 6.863 12.79833 15.01 5.931333 27.14367 2.811 5.733 16.64833 26.40167 20.81133 4.766333 15.57933 4.59 9.616 25.32233 12.443 16.66533 3.516 37.152 21.32033 11.40267 15.94867 48.976 2.433333 5.895 27.53867 30.75333 12.76533 4064.721 14.83533 8.631333 22.93933 8.077 5.415 6.091333 25.646 6.204 16.73 3.762 275.0887 20.261 1.851 27.83967 11.22367 5.558333 7.226333 2.068 95.166 21.06767 12.753 10.471 5.364667 12.36433 8.316667 11.22367 14.18933 2.682667 7.310333 4.341667 2.534667 9.105333 12.44167 1956.885 24.758 2.800667 22.17067 8.028 7.766333 6.686 3.200667 7.884667 18.23433 13.917 7.039 13.58 7.844 6.250667 266.444 4.361 5.740333 3.293333 5.615667 11.59067 13.71433 20.36133 2.243333 14.558 2.723 7.621667 20.74967 1.695333 16.116 11.91033 16.40367 2.411 8.497 9.510333 63.63933 10.72933 7.672667 8.578333 12.394 12.90733 5.630333 17.75767 6.380333 5.416333 6.524 34.157 3.294667 1.688667 13.22967 9.471667 4.676 7.431333 4.926 1.160333 6.778333 17.19233 9.436667 13.50467 13.106 5.332667 3.424 9.378667 74.79833 16.556 3.165 1.577 10.85033 2.194 6.625333 11.227 4.963667 0.713 6.521 11.94067 11.36067 16.303 26.291 9.694667 0.1093333 6.567 1.574667 5.421333 6.559667 7.711667 9.557333 1.288 7.325667 12.01933 11.758 5.177333 8.791667 13.65367 10.216 6.066 3.857 6.861667 2.758667 0.8066667 9.299667 3.09 0 11.994 5.422333 2.976667 2.163667 12.388 8.293333 3.109667 6.067667 6.829333 0.9146667 10.12333 12.14267 1.407667 3.468 3.979 23.38367 5.603 6.326 9.507333 26.67367 1.363333 10.201 3.493 6.512667 39.729 11.46067 8.411333 3.822 15.47733 19.73733 3.680333 1.911333 4.482333 3.736333 11.24533 15.75333 1.302333 6.395 8.805333 0 4.293333 3.27 8.445667 0.409 4.053 1.547 3.301333 6.606667 7.337333 0.248 3.051 0 7.585333 0.7683333 2.517333 2.745 2.219333 4.638 3.268333 4.765 2.330333 4.127333 2.818 1.897333 4.196667 2.605 5.581333 9.374333 6.813333 4.484 2.467333 8.839 148.8903 3.489667 2.550333 2.692333 3.090333 0.4346667 1.384 3.043 35.57467 3.162667 1.252 0.01 7.634333 5.001333 4.695333 4.126 4.009 0.3906667 0.6643333 5.633333 1.870667 4.744333 0 1.153667 5.019333 3.021333 0.724 1.344 2.011 2.448333 12.573 1.351667 4.724667 4.196 3.398 1.169 2.056667 7.756333 2.678 17.98467 1.122 8.025 35.02267 0 8.504333 5.509667 0 8.218333 0 1.184333 2.578333 0.9123333 3.328 8.963667 9.984333 2.877333 0 1.56 0 1.469333 19.30967 0 3.570667 2.844 1.863 4.313333 3.484667 6.267667 2.573667 1.102667 10.61867 3.682667 0.989 1.980333 11.52467 5.264 8.003 1.637333 4.572333 4.102333 0 21.42967 3.945667 3.773 2.242667 0.768 1.994667 3.393667 
2901s sampleB_mean:  6464.644 7520.41 7779.492 6944.853 1492.051 2827.345 1331.648 9939.373 7181.47 1438.471 10849.9 2550.414 971.4367 11165.49 5346.478 1076.978 2449.757 3982.392 6705.697 1007.03 5874.642 347.4017 6156.043 6887.084 440.9727 5515.698 8614.152 8614.152 4540.328 5036.385 4809.412 973.0083 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2901s 1506.715 7405.14 5974.238 3104.744 8313.711 8625.824 3325.992 5589.41 819.1427 3398.294 7596.105 303.273 876.8277 2510.784 501.0717 217.5877 512.042 12136.75 147.2877 2649.173 850.5097 155.6753 318.3057 493.2167 193.995 8726.054 1237.565 11956.17 803.7297 1192.947 4624.974 395.6523 4978.607 10695.83 341.9023 3101.543 381.4813 176.1237 324.8553 5311.835 1781.496 12803.12 9160.812 286.7303 10005.84 2806.072 644.756 721.2523 297.5633 337.5617 722.7793 7921.826 188.059 510.9113 3043.903 880.4753 592.331 11807.78 8077.68 5150.462 1147.187 178.331 1388.008 369.4417 568.9407 7137.863 4181.758 14596.83 9231.562 820.1 227.1767 1183.775 624.4283 3135.76 165.5147 98.27667 374.99 126.265 464.656 437.7077 498.566 7646.521 340.8923 2069.238 501.203 223.6213 347.1993 2813.865 330.2803 497.3057 3606.195 3477.406 210.5073 237.9167 229.8227 636.1717 265.4807 303.588 234.8707 464.25 59.968 88.77667 1727.754 277.6277 568.3683 2899.79 1232.959 7998.991 221.5063 135.6287 4052.112 784.5 437.8937 242.2357 198.0453 177.0987 151.089 204.598 209.5997 136.0917 309.0137 318.668 366.6233 53.11833 365.304 205.964 5402.498 7391.381 248.7967 5955.872 3497.592 304.1167 96.888 102.4913 224.959 365.9053 383.3883 183.432 954.507 146.225 244.213 228.616 346.0203 159.9217 617.5097 322.6313 124.821 566.3103 130.7987 744.834 473.468 41.92667 221.3943 376.801 257.8713 171.415 169.5693 58.786 363.4697 12057.81 4659.391 1314.765 76.629 93.961 79.78767 361.7567 208.997 1374.415 87.30767 227.959 201.1477 153.6373 297.5293 204.0893 171.2443 88.84733 1538.062 2636.168 84.19433 794.7277 261.1813 434.0653 219.043 146.7367 306.1523 324.095 254.0923 728.6047 1485.8 204.688 10466.26 92.66933 139.8577 133.1137 243.0527 199.25 134.7863 396.4167 259.974 31019.62 102.9103 55.56067 91.93733 190.3363 196.2657 210.276 120.016 307.597 2478.864 434.0367 160.6447 65.82467 1924.887 92.04867 148.3807 125.9207 110.12 217.828 186.3673 112.8707 92.801 102.8277 85.369 332.1927 109.1297 317.4007 106.9733 118.4783 162.353 132.86 279.8187 88.724 115.6383 145.871 94.855 2983.166 53.67933 163.2497 107.6607 288.2643 63.51467 44.52667 104.7473 1573.052 91.36867 130.4647 129.359 189.81 49.84633 38.50333 132.997 155.6507 198.031 56.084 189.876 241.8647 92.14267 138.9953 221.9553 141.1233 383.105 3680.324 240.9067 166.719 108.0163 502.0593 219.1713 79.23 51.48067 72.27033 147.5143 327.728 434.5497 251.6407 293.4293 506.512 150.83 165.6487 1190.783 199.5333 72.04033 71.07333 188.654 54.17467 217.945 109.0163 446.5917 101.2043 89.19033 264.5573 6554.638 404.8233 177.6103 244.312 451.6893 65.022 391.7213 94.036 381.073 160.461 125.6427 175.727 102.4957 142.4997 114.7247 91.96267 313.5353 80.658 160.033 139.4217 55.31033 138.7943 66.28233 65.14433 97.74133 67.32633 88.20067 48.662 71.95633 75.13167 98.59367 111.3283 42.94067 79.15267 112.4907 143.6177 138.8203 82.77467 83.32767 57.92467 92.10033 147.9097 55.42833 92.673 615.4837 329.0943 177.7223 86.82867 117.3687 272.869 176.1103 72.229 123.7103 205.2823 65.265 23095.85 63.39167 98.42267 143.2053 52.40167 36.84367 30.305 189.338 68.93667 70.82967 136.3853 1768.526 97.67333 59.07767 126.6667 54.697 78.15767 63.519 54.28 629.935 114.413 98.25867 51.40267 33.64933 61.75633 62.202 47.69867 106.367 64.48933 61.927 58.84033 31.92033 44.59133 59.70833 12433.72 108.9977 66.58633 101.2333 37.13833 92.91767 92.354 67.97633 69.31567 185.3687 75.314 59.309 205.7273 44.65167 578.1793 1437.071 565.0517 49.55567 57.289 71.83833 56.87433 80.30267 89.473 25.16133 84.09433 64.96333 39.14833 97.91867 26.105 359.4497 59.017 91.34767 20.836 37.861 40.01867 269.8203 43.553 36.83567 51.20733 63.275 74.47967 28.11233 72.092 57.89033 31.81733 29.19933 180.145 17.67167 27.42533 92.58367 53.35367 45.43467 42.02167 86.666 29.412 38.239 71.77333 50.94033 70.23367 70.48667 24.105 36.129 51.208 654.0063 104.9537 16.98933 21.31667 60.39433 38.35733 36.76167 100.9357 24.998 60.909 31.64467 49.809 60.34067 558.288 105.9517 44.80233 58.52433 40.58467 374.3023 40.88467 65.641 37.373 43.199 23.09333 49.184 58.53467 83.02567 42.55233 67.40867 58.72433 49.53233 44.57067 46.01667 74.76 37.18267 94.084 39.439 32.39167 41.25767 77.42067 28.99667 23.031 323.135 82.208 95.03067 52.62167 48.09067 63.80367 61.049 52.59533 118.5717 17.978 22.795 343.3797 275.1827 284.8557 25.818 38.56967 170.258 33.71767 45.68133 22.759 134.3513 170.7703 147.841 56.735 19.01033 64.17467 89.41967 28.08767 19.87967 50.66867 50.351 59.187 63.14133 63.43233 35.30367 40.58733 17.20333 21.37133 21.26833 72.57967 40.14133 24.42933 27.15533 28.618 33.96667 80.83067 18.746 19.069 101.7453 57.38933 12.81233 26.59233 25.20967 16.69733 39.557 134.6853 46.573 16.53733 31.40267 81.03933 17.666 18.67167 16.98933 31.359 50.767 34.963 38.06967 82.00433 43.21967 541.9867 79.93733 17.60767 21.58933 13.31667 9.165333 45.292 15.914 200.7123 13.12667 16.692 16.39933 62.14133 38.21633 130.2143 18.98967 21.925 17.79667 12.13567 79.05433 125.1613 23.01233 29.38867 58.21167 42.533 51.753 23.8 10.878 70.339 37.33167 122.654 8.173667 24.04433 37.97 14.291 55.27767 11.24133 37.89133 23.558 67.874 10.06533 43.66433 139.358 33.81667 37.642 24.348 11.09467 69.305 8.385 47.25833 28.28967 17.76433 20.035 63.401 48.78233 12.62967 35.64 22.82667 9.080667 11.03933 92.552 1.073 15.776 13.166 45.16467 23.05967 37.25433 24.88967 22.41933 27.504 45.16833 22.33433 22.85333 12.07167 76.51933 19.075 34.98133 14.71567 21.97667 23.06333 11.718 133.2117 26.364 18.868 19.56367 17.268 11.69767 23.021 
2901s num discordant:  0 
2901s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset 
2901s sampleA_mean:  6030.232 1681.385 1407.266 5797.692 1833.283 20787.35 1046.9 2191.464 1326.5 4954.434 5495.505 4913.275 12222.46 4191.816 2602.336 2635.243 944.0123 1512.754 1013.064 1371.045 982.539 559.8297 335.7477 637.4673 1272.664 1265.232 1751.765 1445.705 521.84 887.2083 1532.142 326.0873 1233.492 2002.536 1939.628 3549.085 1593.001 4784.861 562.1487 470.179 1262.588 810.3883 1718.763 5645.434 499.8527 1037.645 388.648 405.4877 1707.219 581.2863 3468.578 647.4437 925.3123 178.6107 258.5643 933.0403 1031.742 371.296 1348.496 393.785 116.9527 15024.4 999.5363 335.637 335.2157 1088.069 564.1773 1753.538 405.9907 533.844 460.3903 1091.041 425.4187 104.2153 4713.887 1933.215 154.4447 1640.267 387.8127 620.238 923.62 296.1627 36600.33 1816.62 2446.14 825.5967 838.8547 1291.39 194.6923 1656.826 298.6353 1179.723 521.2813 344.3147 604.7417 2017.126 159.0503 2237.79 531.0443 876.645 581.914 772.306 610.589 494.789 508.1423 872.2057 1707.261 664.8137 252.8977 337.767 1547.728 337.406 150.8137 133.8673 1030.087 568.889 482.3557 1434.927 1120.621 244.4597 234.695 233.2683 363.4713 5637.134 176.112 480.5827 1756.628 147.324 168.438 349.218 356.3497 378.0157 594.819 762.2617 2891.881 244.753 272.6143 85.82433 350.3023 1125.723 146.7767 210.486 201.4867 198.9307 114.485 156.591 182.1447 435.0017 991.437 432.0453 563.9263 176.9843 241.211 322.1607 368.628 219.039 1412.697 114.123 5395.606 209.749 407.6713 122.4237 1198.79 502.9777 71.71033 323.746 617.5563 310.3323 116.1613 99.45067 300.2583 240.267 719.3537 125.2723 854.0897 590.469 164.083 109.0817 1315.006 100.0037 89.249 89.41233 177.4467 189.715 97.82467 207.939 437.1223 122.591 770.6237 198.061 207.397 183.172 316.5037 128.0267 324.5383 91.99833 354.7773 389.129 164.5937 127.1483 60.22767 328.3217 161.1783 567.2883 63.90033 665.289 407.805 105.1747 132.971 734.0483 62.56033 1229.376 335.4993 300.3533 294.269 168.189 199.325 104.0613 78.31633 206.046 84.98533 132.1053 499.693 160.8853 210.2437 129.574 122.177 87.49733 250.2393 98.94267 236.6537 471.4763 115.35 519.577 173.3993 172.982 124.4867 181.09 2465.916 59.607 280.7067 60.025 81.80933 154.7137 562.891 291.7607 421.348 169.0567 721.5107 93.672 62.65367 310.3963 94.07567 76.27033 66.11467 55.68233 94.133 98.85333 363.302 278.785 603.3643 113.344 90.65667 105.6967 171.9977 136.4807 156.8307 40.38733 204.4367 3561.451 212.7377 214.102 93.57967 46.29267 62.81 103.573 80.98433 78.67633 305.3177 304.6523 66.544 2036.308 77.01533 53.23867 66.88467 52.74467 1557.898 120.7347 1505.046 95.84833 135.433 51.06833 471.7457 38.966 781.6647 38.21567 54.279 86.272 64.515 35.384 32.07433 32.60533 194.3693 187.0867 971.5327 50.39 56.34967 47.40267 97.46133 3088.486 1606.153 33.614 26.77667 56.42633 47.17133 71.85 27.49133 69.30367 233.2737 158.4977 144.1087 407.7717 74.26433 44.67767 73.156 31.01767 131.435 87.15633 40.76933 44.27933 630.4887 71.55767 86.26767 30.31033 50.27133 49.19267 40.022 93.98167 16.066 42.259 51.916 6075.931 751.6327 69.90667 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2901s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2901s 37.93767 101.362 34.524 35.92467 354.898 82.45067 37.746 425.4893 171.2653 280.1693 42.52667 56.986 58.77867 56.78633 47.12267 51.36633 114.1953 38.41333 26.93367 84.101 58.726 163.5027 42.42 27.86967 26.74467 52.054 70.90433 48.80533 41.489 141.5087 19.36133 34.55067 142.1963 32.87767 19.379 43.001 51.68567 42.69267 69.761 52.49167 45.27567 115.2073 7.951667 27.10933 51.49667 84.52867 4534.064 269.428 38.71367 209.263 24.04867 59.42133 36.44033 31.80833 20.94233 28.112 28.092 26.72567 31.895 32.359 36.69767 20.61433 45.48233 43.59833 38.467 132.0313 66.32833 59.42267 33.66067 20.87967 22.01133 13.58767 13.46233 14.442 19.87867 45.49933 24.69267 23.94367 496.4993 27.92067 56.72833 23.62733 73.985 12.36533 40.90567 13.02633 28.60833 14.06933 37.072 23.51567 32.296 27.81033 10.913 30.83533 18.52533 26.52667 29.40667 36.76933 28.27267 87.54867 27.07933 20.89067 41.65 13.554 18.73767 26.41767 15.976 44.083 16.59667 20.15333 23.038 45.54267 18.127 25.49633 27.188 22.07333 36.86033 12.43333 27.52167 68.59733 20.84167 
2901s sampleB_mean:  71.58533 34.85667 61.93367 190.2367 18.24467 1576.856 21.734 67.15133 46.38933 175.0553 10.731 231.01 644.6073 162.736 28.83167 149.0183 40.62 120.2997 20.73967 20.785 38.35033 38.834 17.87533 9.523667 122.321 70.315 11.541 39.02467 15.272 11.73133 216.263 34.29367 131.954 60.698 191.4833 54.76233 84.69133 176.7203 41.809 14.071 5.897667 97.40133 167.6013 1058.536 10.32667 154.1127 51.789 68.43533 199.414 69.84367 143.0547 18.007 167.5307 17.35367 20.43633 82.944 146.7283 11.974 62.01667 46.20633 6.833333 126.2827 52.632 31.756 18.10167 85.388 44.774 290.869 33.76633 99.03833 86.94433 78.63867 62.69867 10.803 184.242 91.85267 6.593 172.0003 32.09667 5.31 94.25133 21.86767 312.258 3.02 327.4777 138.9923 157.5777 15.897 11.08667 70.838 29.81633 120.642 34.63 48.44967 135.326 263.582 29.81667 176.0093 59.39767 96.643 81.38067 52.029 119.8197 7.353333 111.2203 151.9077 274.274 138.5447 13.45833 57.83967 296.326 44.574 13.40767 18.47767 236.2837 98.93967 78.18267 147.5103 4.916 33.99767 6.119333 22.66633 18.10667 585.796 10.14033 81.65333 288.293 29.03533 24.10267 81.69867 45.153 60.40333 21.75133 60.149 107.587 4.303333 14.93967 16.697 68.39567 239.1367 9.162667 33.16933 37.04267 5.075 12.202 25.95767 31.26267 18.98533 228.12 62.152 71.425 33.04933 52.859 17.25433 77.462 31.115 4.947333 5.291 4.892333 6.52 77.499 7.044667 112.516 2.201 14.63133 40.80033 35.93933 36.04767 26.55867 11.37767 8.328333 46.24133 131.7207 22.86333 10.01733 19.323 29.20433 9.454333 252.1407 7.705667 5.086333 11.83333 41.19767 31.045 10.11133 42.20867 64.78833 5.435 76.85 43.10367 22.379 41.53733 66.14267 15.958 44.73367 21.33367 81.672 52.96867 15.18533 28.43733 12.457 46.83533 33.53433 5.055333 12.78767 5.982333 80.735 20.32033 21.17867 1.413333 9.876 252.5313 2.999 55.72533 60.023 37.84833 11.36967 14.93967 11.56533 27.23467 11.13 28.67333 5.957333 19.13967 3.039667 25.094 3.384 16.72967 50.52767 15.63733 53.45667 103.8797 24.55133 68.06833 41.26233 27.607 21.97267 29.328 192.615 9.053333 57.499 12.56167 6.152333 36.59667 92.249 49.06433 77.08667 24.19267 64.61967 16.52467 14.59467 1.439333 4.922 17.05033 3.929667 8.892333 13.001 16.70467 72.445 38.40433 32.20767 26.43 15.84233 19.338 26.382 23.92933 3.080667 7.813 41.21667 52.72333 22.53 49.04333 15.72 6.808667 11.71167 1.620333 16.686 2.519 58.95767 72.39567 15.178 456.8783 15.967 9.581333 10.61567 3.457 221.51 4.436 300.8857 20.181 30.64367 3.424 63.54133 6.782 0.8923333 7.134 9.956333 4.478333 3.776 2.932 2.596 6.225333 41.753 44.787 161.046 8.024 9.696333 9.795333 19.69133 8.807333 129.8027 5.698 6.056667 6.818 10.08733 15.87967 3.111 12.49533 47.94933 24.952 22.72933 79.67267 14.317 9.568 3.546 6.028 23.79767 10.136 5.855333 2.343667 144.8737 6.153 13.70767 5.053 9.387667 9.898 2.558333 11.88467 0 6.709 9.442 603.3247 131.0337 4.551667 5.482333 8.861667 6.474667 5.451 10.47367 12.136 7.286 38.81867 6.163 10.048 8.245667 3.947333 13.348 5.819667 10.034 10.76167 25.736 0.77 0.388 9.684333 3.721 30.05333 5.672667 5.932 0 9.460667 15.06367 4.762667 1.601 5.704667 2.312667 4.229333 34.28533 6.930333 2.445 6.886 11.101 6.758333 16.034 12.28333 10.75867 0.8253333 0 0 3.487 18.601 1.982 60.65633 8.657333 9.86 4.175333 8.966667 5.916667 5.966667 0.597 5.907333 1.379333 4.023 5.972667 1.994333 2.795333 2.932333 4.818333 10.182 2.289 26.49267 2.695333 3.923 1.628667 0 4.613333 0.3683333 2.201333 0 3.583333 3.518 0.911 4.885 96.05 2.298667 2.356667 3.766667 3.183333 0 4.880333 0 2.238667 1.082 7.471 1.805 6.506333 2.091333 0 7.344667 1.954333 1.173667 3.284667 2.515333 0 11.32267 0 3.392 2.037 2.414 0.7583333 2.759333 3.673333 8.528 2.582 4.356 0.831 4.943333 0 0.774 3.599 3.673667 4.728667 2.062 2.479333 7.661333 2.833333 
2901s num discordant:  0 
2901s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
2901s sampleA_mean:  96.61333 15.04567 103.6867 88.57 224.904 7.685 72.55133 6.167 21.39933 15.838 509.7623 36.11867 68.104 803.1917 31.261 141.0787 102.2703 503.5693 539.652 655.8127 30.97967 76.15267 478.7223 28.64033 98.448 504.111 121.0697 40.988 526.2243 37.21967 558.1363 20.01233 1275.026 578.8703 279.6767 733.6827 337.399 409.1913 18.96267 291.1757 300.087 125.9483 915.841 96.77733 16.51667 88.20633 5.762333 763.5533 55.26267 903.1557 46.17067 45.412 57.26933 81.319 641.1777 16.54033 443.633 697.2287 31.92667 78.96333 31.501 40.83233 354.6413 850.6397 40.27 620.406 113.9973 20.97667 14.71933 24.615 4.654333 7.252667 10.53633 25.78433 33.57133 11.583 11.22367 9.434667 7.282667 47.34533 22.74167 7.212667 43.50567 237.8803 26.208 115.4593 50.11167 188.4693 425.357 35.44767 26.51267 2.713333 31.97667 33.62067 5.415 223.9227 110.725 209.5917 4.244 23.127 23.33733 81.34233 25.605 87.317 106.1753 29.55 225.8327 20.36667 47.036 19.92833 159.4173 87.42633 23.94067 2.398333 43.09833 28.26467 691.0767 71.78533 91.49933 12.94133 37.27233 103.9153 18.754 16.528 642.0663 40.25467 57.46833 9.896333 670.486 18.317 7.963667 7.980667 51.407 22.51133 171.0287 34.135 15.54567 55.73 16.899 11.52 89.987 27.29 25.55733 13.98533 56.797 21.51767 759.571 15.92433 4.080333 18.88733 66.65833 5.557333 64.82733 23.04333 24.63167 15.73033 5.627 30.80767 25.208 26.715 65.027 18.76 9.969333 17.48067 30.828 48.562 5.017333 19.11967 3.451 6.546 13.46667 5.630333 6.745333 16.27833 86.883 9.642 26.67967 17.96533 24.758 8.791 42.57533 27.48633 393.3037 27.59267 8.807333 443.3597 14.063 29.18933 22.68433 241.785 22.31233 7.059 39.57833 216.0503 2.696667 497.7577 15.08833 7.909333 39.67767 15.09333 103.2833 15.18033 3.595333 3.941333 75.469 15.01 5.682 17.221 4.281667 142.0663 11.438 27.94767 5.016 5.474667 12.39433 37.152 12.993 37.25567 3.586667 321.257 3.420333 23.09367 2.280333 18.62433 13.08133 12.98 11.312 2.154 31.32 52.084 62.50533 11.29367 50.469 7.844 2.068 6.496333 32.849 35.29633 44.93767 1.292667 27.83967 37.255 5.802333 20.135 20.992 6.819 6.980333 22.93933 6.515667 79.21967 22.17067 17.19067 6.919333 4.371 8.162667 260.666 26.75667 21.116 11.22367 13.78833 20.37167 10.216 2.243333 50.97333 4.59 47.42233 7.107 6.674 18.233 49.835 6.929 3.078667 28.45833 6.300667 11.93267 22.752 9.507333 118.9327 10.30533 8.316667 20.74967 7.354 8.497 33.50367 55.59767 6.812333 1.919333 5.931333 9.735667 20.16567 7.48 28.057 30.424 12.753 10.95167 18.30367 5.733 2.433333 2.219333 20.261 23.67567 16.556 6.455667 2.811 4.156333 19.73 3.139 27.23133 22.996 1.460333 9.767333 12.36433 84.312 3.200667 8.077 9.557333 16.40367 19.921 1.991 14.78033 7.039 77.21567 26.291 44.996 3.043 22.627 1.577 5.895 2.177333 2.330333 4.531333 11.286 4.745 8.002 2.550333 4.341667 4.766333 11.227 40.34367 2.900667 5.177333 9.773333 2.534667 3.468 13.65367 6.527333 7.310333 28.33667 14.06433 44.07433 17.85933 7.050333 25.40433 35.802 8.578333 12.40267 14.22267 11.817 5.615667 33.01633 0.838 7.412333 6.524 17.692 54.75267 9.613667 2.592667 6.559667 9.824333 5.364667 1.911333 8.393333 5.720333 74.79833 25.32233 15.64 8.043333 10.38333 28.43467 18.33267 16.303 4.963667 11.59067 27.77367 7.884667 8.631333 8.866333 9.616 7.555333 0.713 25.361 10.12033 15.57933 7.216333 4.676 3.857 17.332 5.740333 42.16967 6.910667 14.16 21.06767 12.76533 2.723 7.431333 13.23767 8.403667 8.173 11.097 7.672667 7.163 2.411 11.21733 18.93367 18.30633 57.61633 3.424 30.75333 6.066 1.688667 5.416333 21.69333 0.1093333 11.36067 5.332667 7.394333 14.91467 44.679 18.23433 0.6643333 39.729 6.204 14.94733 6.983667 13.22967 20.36133 33.10033 1.160333 25.089 13.50467 6.248333 6.863 0 0.7683333 7.083333 1.288 2.976667 0.3666667 0 1.469333 0.4346667 5.558333 11.994 3.762 1.695333 21.88733 6.592 10.201 3.162667 1.162333 33.815 9.744667 8.395 1.252 34.16433 3.294667 9.471667 2.163667 3.541667 6.380333 2.682667 8.791667 13.58 6.521 0.248 7.168667 1.715333 8.805333 1.363333 3.09 0.485 11.758 7.621667 0.8066667 16.06567 7.585333 11.40267 7.601333 1.448333 1.444 18.94267 10.85033 7.325667 5.596333 2.844 6.625333 2.745 8.198 9.752333 5.581333 6.861667 12.67933 1.122 13.88733 2.605 5.057 4.058 21.32033 15.09267 0.9146667 8.038333 6.067667 4.064333 8.293333 5.264 53.09233 3.418667 6.752667 6.567 3.292 0 0 23.38367 3.109667 1.897333 3.765 0 1.302333 4.196 2.922 3.822 7.766333 3.090333 12.14267 4.638 18.91833 2.14 2.715 5.421333 4.926 8.351333 4.053 8.255667 7.195333 6.754333 2.517333 1.851 1.407667 2.474333 6.512667 4.325333 3.425333 0 3.122667 1.281667 1.574667 3.273 16.116 5.603 2.883333 11.89067 1.351667 5.686333 8.223667 5.060667 1.981333 1.649667 2.818 161.101 1.994667 3.979 3.179 0 0.5473333 4.765 0 3.219333 6.893667 0.7146667 4.387 0 4.989667 4.009 1.769667 2.194 0.622 2.877333 0.4176667 6.813333 0 0.2473333 0.409 0.676 3.493 2.414667 12.75533 7.337333 4.695333 1.547 3.696333 0.9123333 4.572333 1.992333 2.800667 3.293333 0.939 3.733667 2.275333 11.126 2.310667 1.492667 8.773 1.980333 3.398 1.637333 36.09 2.692333 2.337333 3.319667 7.756333 3.403333 1.776 0 1.089 3.077333 0 2.577667 3.570667 0.4253333 0.989 2.663333 4.451333 1.344 3.992 2.347333 8.963667 1.544333 1.576667 3.021333 1.844333 0 4.123667 2.259667 0 0 5.287333 2.573667 4.611667 0 3.945667 4.385333 0 0.8176667 6.45 2.448333 2.962333 1.941667 0.7693333 2.578333 1.870667 1.324 2.192 5.509667 8.504333 
2901s sampleB_mean:  1997.885 370.6363 1889.849 2830.628 3005.897 339.544 1611.849 266.1853 1524.761 2001.57 4325.944 2415.454 856.342 4759.337 809.747 1374.611 2786.993 3179.415 3396.666 3693.07 566.031 759.8243 3249.388 686.1263 875.9707 3216.203 2237.994 1440.661 3330.022 394.7987 2922.537 344.6643 5398.857 3756.434 2471.048 3620.716 2883.64 2374.126 211.0497 2047.901 1235.974 606.0663 4427.58 485.2353 736.2793 476.768 90.55133 3709.705 953.5553 4251.336 768.1787 241.776 556.5843 630.4883 2990.729 253.343 2376.446 4895.859 300.4817 439.0257 240.971 562.3953 4198.375 3423.331 310.312 3616.512 461.5343 140.997 140.0233 166.0277 105.6647 118.7197 285.4657 378.7327 193.8653 144.7763 142.302 146.4013 437.971 298.0877 171.3853 79.82167 269.2717 925.7747 265.6093 760.6557 267.723 1094.26 2436.015 421.1887 574.6353 149.84 279.329 189.6917 208.1393 1049.838 511.8627 1034.454 73.643 199.6 167.053 401.21 255.2837 365.2543 731.863 127.811 1012.972 165.0047 203.65 79.65933 927.6743 434.556 166.8767 112.4467 341.4467 194.996 3650.525 280.2643 357.7387 116.6347 218.6657 444.0447 105.6257 120.8233 2890.802 332.1813 290.862 135.609 3849.83 98.13967 472.5113 87.31133 321.7517 155.4747 878.6043 320.243 267.5577 274.3337 133.069 192.3193 683.449 212.3977 160.4317 164.205 366.123 96.142 5152.482 133.1023 348.3133 138.4137 287.485 38.85333 255.8583 189.5857 127.943 88.38 130.9923 125.2547 366.0723 178.71 699.6877 132.628 58.79033 263.798 175.8867 692.2687 132.7817 120.8867 120.2137 84.91167 143.3147 55.55933 90.86167 177.3257 404.5893 90.957 178.5933 115.1327 193.4727 97.3File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2901s  162.5713 189.0233 1642.015 149.819 40.32533 1780.032 75.75133 259.148 150.3183 1082.98 161.1673 109.1813 153.0033 842.3293 42.12067 3067.808 62.39367 118.3287 254.1857 253.0167 443.3713 90.116 71.08433 31.73 428.623 117.2697 141.5657 123.721 317.0973 568.8347 160.1683 162.3163 96.602 140.1517 53.59967 609.5917 194.1133 260.6683 87.15567 1547.523 58.96367 216.949 68.593 83.573 91.18133 74.99667 177.183 39.998 148.7563 224.5063 382.3843 59.23867 286.777 92.43267 205.6727 48.27933 151.599 136.5493 207.045 67.006 168.0607 229.5497 58.06633 116.5553 87.012 85.78933 67.408 220.7547 165.4787 496.8353 184.3507 132.4173 92.061 51.73767 69.18967 1395.183 213.8997 95.749 74.632 88.725 101.0153 195.2947 65.65667 232.1147 60.63 252.983 69.947 59.629 107.4287 351.08 49.419 105.0843 186.8647 33.62833 68.66267 194.3873 109.6237 460.2323 140.2763 67.72533 145.5417 41.93 72.854 143.872 303.08 166.5273 59.379 131.585 91.509 102.0507 57.40167 218.8733 124.6713 134.7907 127.5543 150.3003 96.957 382.0493 151.719 140.8457 143.433 385.176 103.81 57.69533 87.65567 78.48367 126.504 195.6537 136.4563 60.04567 45.994 71.93733 473.3597 125.4973 53.67167 96.76 143.607 118.1207 80.46333 96.91167 123.938 323.664 199.317 231.7267 117.851 110.8577 83.61967 61.29533 81.26567 119.8297 82.67333 132.2 120.4613 48.91 156.2033 76.57167 79.68 240.6073 161.956 32.967 133.338 67.53533 43.412 64.25433 108.7427 85.55767 80.51633 174.409 69.52233 177.785 77.092 36.76567 100.6683 142.4753 77.97333 63.03733 71.81167 53.655 93.48367 183.9787 104.978 136.346 35.42167 127.9993 209.961 62.05533 71.74267 183.3313 84.66667 34.301 72.596 51.723 39.086 1621.57 114.4257 89.57667 303.0437 71.949 188.4637 88.05067 1604.347 47.35667 53.014 123.1273 76.68167 90.91333 53.52367 63.84367 29.627 136.4467 98.33933 55.85733 78.28033 36.70233 65.56833 83.324 68.32067 38.799 178.2697 27.296 76.47533 90.31267 61.12667 69.599 51.13867 62.81267 71.28167 50.22033 47.47333 40.14733 293.9087 22.85467 73.193 100.608 188.329 230.7707 34.95467 151.883 57.43267 36.13033 37.65433 311.329 161.9667 76.577 27.176 47.69067 77.38367 191.3687 159.7823 84.001 280.2713 43.65367 138.9263 37.29667 84.28567 84.57567 137.8557 28.55333 149.342 62.27133 30.21933 30.35033 22.75467 96.94267 27.671 30.70733 31.70567 36.6 251.767 68.608 177.154 56.562 120.206 57.43367 19.45267 106.615 48.224 55.77667 29.26867 61.53933 131.6793 68.67667 42.95633 36.72267 133.2 14.628 49.472 423.253 33.21433 79.551 27.28933 61.486 126.4583 35.098 82.68433 31.52433 36.53367 49.36433 41.03967 37.55767 76.24933 150.4293 31.972 80.36 84.252 43.97967 50.05667 31.336 127.1577 59.38567 176.0977 48.89833 42.60033 40.13033 35.499 25.97433 39.59267 32.39667 42.28633 48.22433 79.067 61.23533 27.11633 69.843 33.399 34.77567 27.94833 91.86567 61.76067 61.21367 38.139 45.60867 30.03567 79.87367 44.01933 356.891 32.58033 65.255 33.70267 33.73067 86.78467 19.23067 329.1877 44.45533 21.83433 28.714 7.434333 130.8803 56.93233 16.267 15.205 52.33733 16.67967 183.6017 46.144 107.6573 22.669 33.473 27.93333 58.25633 58.12767 17.84967 49.72933 30.596 37.849 30.23233 13.23833 12.861 33.19833 98.03267 22.413 15.277 7.787333 15.02733 20.92033 84.23433 18.09167 95.334 186.3597 28.15867 106.4977 14.83167 21.914 117.513 26.27467 49.82833 18.50433 67.063 885.105 18.55533 93.36767 20.35933 31.383 28.44433 34.77033 3.268 29.242 28.39433 73.018 21.34167 30.69133 65.14467 26.188 27.04033 16.95033 17.43 15.656 19.80633 27.944 18.48833 19.36667 18.61167 31.89 13.99333 38.715 66.67867 77.94767 106.1883 19.614 26.23633 24.30433 37.429 30.54067 22.274 13.36767 23.73133 70.27367 17.236 80.966 31.73667 20.05633 78.66133 12.443 16.01333 13.41633 166.674 17.96033 23.945 14.817 38.17233 18.03233 35.44867 25.41533 15.25033 28.101 14.14033 17.898 16.27233 13.18233 29.174 15.33767 32.61467 13.94367 16.55367 12.703 62.61533 28.76267 17.502 46.892 14.40533 26.512 22.969 13.60433 15.03767 40.46467 25.09 20.55233 22.38467 18.481 35.23233 18.28267 12.082 21.75 62.73233 39.09833 20.87567 18.62033 17.31067 15.10167 48.44967 11.96033 12.63367 20.713 37.68333 
2901s num discordant:  0 
2901s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2901s sampleA_mean:  4624.974 1506.715 1636.976 440.9727 1101.219 876.8277 12470.43 2550.414 1781.496 512.042 324.8553 871.6373 707.8263 493.2167 834.608 177.0987 217.5877 347.4017 768.306 645.4617 339.8283 850.5097 3211.031 621.286 198.0453 514.415 411.447 501.203 1098.868 3078.184 222.09 189.5647 95.89333 510.9113 620.017 646.6133 429.5973 224.469 306.1523 1192.947 474.0487 1003.238 1494.298 900.1817 856.7063 374.99 244.213 623.5437 173.88 689.711 237.177 211.7417 646.864 204.598 378.627 132.9247 257.3087 198.031 2373.043 97.24867 166.336 138.8203 109.0163 153.4527 116.0807 661.7387 194.0203 189.876 151.8027 188.654 149.5763 75.79967 328.0923 276.1017 506.512 272.869 161.0497 202.739 37.50533 92.354 215.8967 194.2893 2633.716 103.0963 278.7853 54.95833 112.168 175.2467 53.598 63.519 59.07767 103.6453 100.247 214.853 55.41567 91.645 114.2777 131.159 374.3023 72.98133 499.6263 46.03533 88.61667 45.62033 55.17567 615.4837 106.367 63.24267 80.30267 583.86 82.208 51.208 322.6313 160.284 58.90833 565.0517 112.6127 103.33 541.9867 43.62667 30.70067 39.745 75.16967 36.49633 46.59433 94.455 99.289 227.2843 170.258 189.338 137.7607 40.44433 39.40267 39.44033 578.1793 52.59533 63.80367 28.455 83.27833 32.245 25.087 69.91033 28.618 41.25767 13.208 82.00433 40.18733 29.69867 27.874 37.18267 42.52533 50.351 43.80133 19.68333 35.30367 72.777 50.66867 72.57967 81.69967 124.9103 25.539 50.767 36.466 24.83067 134.6853 7.618667 75.28167 147.841 25.74867 45.16833 31.79067 31.40267 48.78233 23.51433 33.46233 79.93733 63.05533 31.89567 63.71067 18.93167 36.90167 23.01233 28.191 29.06367 59.28433 38.06967 76.51933 18.83133 22.33433 58.47233 19.622 18.868 19.09633 68.14433 69.305 101.7453 48.16367 26.44133 22.32333 29.71933 92.552 57.61033 27.69933 23.021 56.21533 28.387 43.573 45.292 26.81733 20.62167 122.654 52.69467 48.025 72.11233 24.891 67.73133 22.708 27.838 55.27767 49.08533 24.47467 22.96933 37.281 11.958 36.46133 57.80667 58.21167 19.95933 48.198 31.779 23.05967 22.16333 23.8 23.558 28.69233 45.90233 
2901s sampleB_mean:  341.9077 165.372 131.954 21.142 143.015 59.789 312.258 16.70467 78.223 41.31433 42.12067 107.8423 84.293 77.04167 149.042 18.75567 33.19 72.11933 11.541 98.93967 40.62 173.185 176.0093 70.838 17.10933 28.83167 51.37267 107.4767 162.736 644.6073 40.211 21.17867File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2901s  6.833333 17.62467 19.323 84.69133 60.698 15.272 60.63 230.7603 62.01667 231.01 361.5717 190.2367 147.5103 63.14733 24.36067 149.0183 11.974 91.85267 52.02367 47.04433 126.507 31.336 50.806 22.66633 52.632 35.05467 8.807333 20.43633 8.328333 21.66667 14.771 22.414 23.35133 126.2827 27.23467 43.86567 21.67633 25.96333 30.432 14.72967 1.413333 49.04333 113.391 61.038 34.63 35.93933 6.593 11.42567 43.19967 15.897 603.3247 15.84233 38.81867 11.08667 20.231 36.80733 7.705667 4.816667 13.23833 13.34567 21.97267 47.94933 11.73133 15.47833 24.79367 21.75133 84.23433 15.958 52.72333 3.929667 4.436 6.119333 5.855333 3.97 21.74967 6.474667 15.00967 126.723 14.15433 7.976 0 5.957333 7.353333 3.203 3.546 21.066 101.151 4.916 6.552 7.033333 15.06367 2.201333 6.709 7.766333 22.53 53.09067 21.36367 5.980333 34.28533 7.920333 1.620333 4.478333 5.375333 10.64267 14.63867 3.039667 8.861667 6.818 5.451 4.875667 3.831 3.745333 0 0 6.937333 1.439333 6.301667 8.477667 0 2.48 5.966667 3.384 3.374 14.62267 0.6883333 1.932 19.603 21.018 4.024 10.157 6.506333 1.628667 12.223 0 7.897667 41.35533 3.431333 9.145 7.386333 6.082333 10.15367 5.055333 2.116667 14.45 5.157 6.758333 10.28 1.101667 8.017333 4.993333 2.819 1.569 5.139 3.003333 8.006333 4.229333 1.765 8.693333 2.936333 2.849667 0.4836667 1.799 13.05267 25.41533 7.749 4.422333 1.63 2.893333 8.839667 6.500333 0.692 2.511 12.1 4.762667 2.462333 10.16333 5.261333 1.082 19.24567 5.417 4.954667 16.907 2.909667 5.873 4.677 0.8023333 3.485333 5.657333 0 0 1.766333 2.343667 8.528 2.217667 12.014 3.54 8.646 1.487333 4.158333 0.8846667 2.193667 4.627333 6.918667 2.344 
2901s num discordant:  0 
2901s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
2901s sampleA_mean:  311.829 110.7323 658.8357 210.276 53.11833 77.55333 94.08633 1020.23 773.7893 112.322 825.1763 37.23367 28.62567 534.2237 407.2907 2661.226 117.2063 501.0717 220.5287 59.968 135.901 191.8153 105.9497 95.99433 138.353 124.4243 40.96933 65.965 55.75367 88.495 189.9813 24.33867 73.97767 62.58133 341.9023 62.68467 132.8633 36.84367 56.147 53.687 36.99433 81.05967 104.7537 83.305 48.72833 193.8337 53.33433 180.8457 50.429 42.797 47.89667 58.24233 57.313 49.103 21.54267 30.499 39.777 54.28 17.875 115.6623 12.42267 24.273 238.9387 4.98 336.3973 14.554 35.78433 25.096 23.53367 133.0233 30.00467 56.695 16.50567 12.544 19.86033 41.83033 199.8083 39.58367 17.029 41.80933 42.71533 3.969667 21.25867 17.60767 16.69733 23.71433 35.43333 57.13467 15.26033 68.49367 2.172 103.5143 342.208 24.38833 29.33233 14.56933 9.605 24.02367 63.41767 36.41067 31.04633 25.39133 20.959 45.89833 29.44033 10.63267 41.856 70.13033 6.926 24.772 6.981333 15.418 9.165333 21.14433 16.53733 8.362 6.042667 13.52433 32.75133 40.92067 16.22733 22.84267 75.059 56.92767 21.88967 21.31667 25.25367 28.28467 91.47333 7.960667 11.277 10.23233 15.914 31.61067 5.832 8.79 88.60033 15.28167 12.85033 17.12667 10.30967 7.374 40.359 49.53233 12.36 12.771 15.559 10.16833 23.029 65.86733 43.318 8.268 10.49233 5.097667 28.07033 11.38633 8.516333 20.27767 5.464 16.38067 18.746 21.686 3.122 31.838 3.966667 9.187667 12.023 5.342333 5.607667 35.59733 7.083 5.772333 7.825667 14.411 46.84667 21.776 21.765 54.65067 40.53433 7.526667 16.75833 18.06167 11.90333 6.314 32.918 16.17933 3.596 5.197667 5.960667 7.807333 2.752667 22.86533 12.81233 19.21233 15.31167 7.951 5.664333 22.029 25.534 8.48 12.13567 37.02633 10.73033 6.437333 8.47 22.12067 22.77967 2.539333 2.727 29.746 21.02533 8.809 14.33467 2.792667 3.51 14.356 11.03933 6.174667 3.046667 7.603667 23.46733 7.538 20.79733 12.918 27.34567 8.792667 6.934 6.306667 4.820333 9.925 11.28667 7.395 3.158 7.979667 17.25667 3.503 6.225667 0 7.501667 7.839333 5.134333 12.438 74.98367 7.113667 5.177333 3.531333 7.014667 5.639333 0.8883333 19.07367 3.201 14.50533 78.08667 3.788 13.76033 24.662 9.197667 7.025 6.052333 4.912333 5.777667 7.077333 10.31933 2.409667 8.232 7.901333 3.633333 1.506333 5.981333 3.867 8.591 7.560667 5.081 1.752333 8.047333 2.414667 0 10.41 5.407667 2.503 2.723333 9.876 2.105667 2.654667 3.773667 0 9.321667 2.518667 4.158 2.349 2.967333 7.296333 0 2.993667 3.311333 2.742667 6.318 2.888 1.734 5.546667 0 0 0.5686667 0 1.934333 23.97033 4.064667 4.931333 0.2506667 6.688 2.653333 8.351 3.471667 3.743 2.677333 7.922333 5.76 1.742333 3.082 10.97667 3.945333 6.958667 3.617 10.806 2.231667 0.4486667 19.41933 2.98 19.63133 2.767667 1.651333 0 3.012 2.625667 
2901s sampleB_mean:  2830.628 1202.982 4216.251 2415.454 339.544 809.747 968.2863 5398.857 3709.705 2786.993 3756.434 461.5343 317.4807 4004.8 2355.907 13329.63 3506.467 2001.57 2047.901 266.1853 807.5603 1242.884 686.1263 878.6043 953.5553 513.784 501.3557 317.8843 222.0223 574.6353 926.6357 203.078 805.275 843.2847 1524.761 303.08 641.6557 208.1393 562.3953 256.6427 279.329 786.1327 468.317 401.8723 224.5063 731.863 371.2327 1012.972 573.2667 255.0223 265.6093 310.312 255.8583 290.862 255.2837 378.7327 157.5777 205.6727 116.6347 720.0863 166.8767 145.604 4759.337 1440.661 1576.856 148.789 178.71 166.0277 132.4173 1082.98 125.2547 387.0143 584.575 137.7833 121.5623 195.216 1109.48 320.243 286.777 158.383 263.0527 59.23867 168.2893 156.2033 151.719 120.8867 160.5167 232.1147 124.6713 585.796 58.96367 496.8353 1834.421 148.7563 161.1673 91.18133 109.3147 150.3003 477.213 148.6807 163.1987 156.0383 143.3147 178.2697 151.599 92.061 278.7393 311.44 41.78967 163.021 31.73 194.1133 177.154 213.8997 119.8297 51.73767 90.957 57.44367 219.6953 161.4237 194.3873 301.9357 332.2983 253.0167 109.0193 83.61967 174.6973 145.137 405.776 98.33933 110.8993 69.18967 117.851 160.1683 91.509 41.93 437.7257 143.0897 70.221 85.78933 53.655 143.872 188.56 195.2947 101.4477 118.1207 108.837 46.842 113.004 285.3807 193.3587 67.408 48.96533 87.65567 126.6913 64.15933 127.5543 138.9263 36.76567 109.6677 82.68433 141.442 91.739 263.5397 102.0507 54.097 96.804 24.80467 99.863 136.4563 64.25433 51.723 60.90233 179.874 216.4093 90.427 141.0183 230.7707 682.0817 71.949 76.82 91.49033 63.62167 71.81167 170.7463 93.09033 27.192 27.296 50.22033 29.00467 29.627 97.60633 96.94267 107.2877 130.4127 44.69833 47.31267 127.9993 94.78533 39.086 84.001 191.0543 55.476 56.05633 96.91167 112.8043 918.9367 32.39667 36.6 120.0493 293.9087 49.09733 106.615 76.24933 37.96133 73.193 68.608 28.425 29.675 127.1577 169.1617 303.0437 125.7047 52.36933 174.409 44.98367 43.94933 41.517 68.67667 41.50267 84.252 28.775 30.93667 192.615 317.6723 20.82433 61.53933 174.965 31.52433 34.05967 40.13033 311.329 381.953 61.76067 30.54067 36.53367 27.23833 59.38567 19.95267 75.443 31.46 216.4057 356.891 24.244 76.899 176.0977 61.80233 58.12767 27.607 33.73067 251.767 28.714 48.14767 16.15667 42.92033 34.77567 19.99067 18.20933 24.384 30.03567 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2901s 65.255 32.58033 54.54667 33.473 31.139 20.92033 19.80633 40.12533 21.00233 11.60833 31.73667 49.72933 28.15867 28.39433 24.241 18.23433 44.13267 26.27467 20.046 86.78467 12.202 33.75167 24.882 15.938 18.612 22.782 129.8027 23.60467 19.23067 19.744 6.507333 3.268 18.004 31.383 28.30833 106.4977 27.04033 20.212 19.36667 68.356 33.19833 54.89133 14.948 15.33767 72.35433 70.27367 28.421 38.715 31.89 73.018 20.05633 80.966 18.62033 68.52333 17.502 16.761 183.9787 16.92567 178.6527 17.09767 27.84133 14.14033 35.44867 19.71067 
2901s num discordant:  0 
2901s touch test_voom
2901s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save
2901s CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R
2902s Loading required package: BiocGenerics
2902s 
2902s Attaching package: ‘BiocGenerics’
2902s 
2902s The following objects are masked from ‘package:stats’:
2902s 
2902s     IQR, mad, sd, var, xtabs
2902s 
2902s The following objects are masked from ‘package:base’:
2902s 
2902s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2902s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2902s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2902s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2902s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2902s     table, tapply, union, unique, unsplit, which.max, which.min
2902s 
2902s Welcome to Bioconductor
2902s 
2902s     Vignettes contain introductory material; view with
2902s     'browseVignettes()'. To cite Bioconductor, see
2902s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2902s 
2903s [1] "Reading matrix file."
2903s 
2903s Attaching package: ‘fastcluster’
2903s 
2903s The following object is masked from ‘package:stats’:
2903s 
2903s     hclust
2903s 
2903s for plotting:: min.raw: 0.647032826340685 max.raw: 1
2903s null device 
2903s           1 
2910s for plotting:: min.raw: 0 max.raw: 15.3986319455363
2910s null device 
2910s           1 
2920s touch test_PtR_heatmap
2920s ./validate_results.pl
2920s DESeq2_outdir/diffExpr.P0.001_C2.matrix, count: 1784 DE features OK.
2920s edgeR_outdir/diffExpr.P0.001_C2.matrix, count: 2061 DE features OK.
2920s voom_outdir/diffExpr.P0.001_C2.matrix, count: 1818 DE features OK.
2920s make[2]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
2920s Running example in Spombe_example...
2920s make[2]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
2920s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_genes.counts.matrix --method edgeR -s samples.txt --dispersion 0.01 --output edgeR_genes
2920s Got 4 samples, and got: 5 data fields.
2920s $VAR1 = {
2920s           'plateau' => [
2920s                          'plat_rep1'
2920s                        ],
2920s           'heatshock' => [
2920s                            'hs_rep1'
2920s                          ],
2920s           'log_growth' => [
2920s                             'log_rep1'
2920s                           ],
2920s           'diauxic_shift' => [
2920s                                'ds_rep1'
2920s                              ]
2920s         };
2920s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.diauxic_shift.vs.heatshock.EdgeR.Rscript
2920s Header: ds_rep1	hs_rep1	log_rep1	plat_rep1
2920s Next: TRINITY_DN5555_c0_g1	0.00	0.00	0.00	0.00
2920s 
2920s $VAR1 = {
2920s           'ds_rep1' => 1,
2920s           'hs_rep1' => 2,
2920s           'plat_rep1' => 4,
2920s           'log_rep1' => 3
2920s         };
2920s Contrasts to perform are: $VAR1 = [
2920s           [
2920s             'diauxic_shift',
2920s             'heatshock'
2920s           ],
2920s           [
2920s             'diauxic_shift',
2920s             'log_growth'
2920s           ],
2920s           [
2920s             'diauxic_shift',
2920s             'plateau'
2920s           ],
2920s           [
2920s             'heatshock',
2920s             'log_growth'
2920s           ],
2920s           [
2920s             'heatshock',
2920s             'plateau'
2920s           ],
2920s           [
2920s             'log_growth',
2920s             'plateau'
2920s           ]
2920s         ];
2920s Loading required package: edgeR
2920s Loading required package: limma
2921s null device 
2921s           1 
2921s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.diauxic_shift.vs.log_growth.EdgeR.Rscript
2921s Loading required package: edgeR
2921s Loading required package: limma
2921s null device 
2921s           1 
2921s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.diauxic_shift.vs.plateau.EdgeR.Rscript
2922s Loading required package: edgeR
2922s Loading required package: limma
2922s null device 
2922s           1 
2922s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_log_growth.heatshock.vs.log_growth.EdgeR.Rscript
2922s Loading required package: edgeR
2922s Loading required package: limma
2923s null device 
2923s           1 
2923s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_plateau.heatshock.vs.plateau.EdgeR.Rscript
2923s Loading required package: edgeR
2923s Loading required package: limma
2923s null device 
2923s           1 
2923s CMD: Rscript Trinity_genes.counts.matrix.log_growth_vs_plateau.log_growth.vs.plateau.EdgeR.Rscript
2923s Loading required package: edgeR
2923s Loading required package: limma
2924s null device 
2924s           1 
2924s cd edgeR_genes && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl -m ../Trinity_genes.TMM.EXPR.matrix \
2924s         -s ../samples.txt  --examine_GO_enrichment --GO_annots ../Trinotate_report.xls.gene_ontology --gene_lengths ../Trinity_genes.lengths && \
2924s            /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2924s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.count_matrix 
2924s Loading required package: BiasedUrn
2924s Loading required package: geneLenDataBase
2936s 
2936s Loading required package: AnnotationDbi
2936s Loading required package: stats4
2936s Loading required package: BiocGenerics
2937s 
2937s Attaching package: ‘BiocGenerics’
2937s 
2937s The following objects are masked from ‘package:stats’:
2937s 
2937s     IQR, mad, sd, var, xtabs
2937s 
2937s The following objects are masked from ‘package:base’:
2937s 
2937s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2937s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2937s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2937s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2937s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2937s     table, tapply, union, unique, unsplit, which.max, which.min
2937s 
2937s Loading required package: Biobase
2937s Welcome to Bioconductor
2937s 
2937s     Vignettes contain introductory material; view with
2937s     'browseVignettes()'. To cite Bioconductor, see
2937s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2937s 
2937s Loading required package: IRanges
2937s Loading required package: S4Vectors
2937s 
2937s Attaching package: ‘S4Vectors’
2937s 
2937s The following object is masked from ‘package:geneLenDataBase’:
2937s 
2937s     unfactor
2937s 
2937s The following object is masked from ‘package:utils’:
2937s 
2937s     findMatches
2937s 
2937s The following objects are masked from ‘package:base’:
2937s 
2937s     expand.grid, I, unname
2937s 
2938s Processing category: custom_list
2938s Using manually entered categories.
2938s Calculating the p-values...
2938s 'select()' returned 1:1 mapping between keys and columns
2938s 
2938s 
2938s Done.
2938s 
2938s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.count_matrix 
2938s Loading required package: BiasedUrn
2938s Loading required package: geneLenDataBase
2950s 
2951s Loading required package: AnnotationDbi
2951s Loading required package: stats4
2951s Loading required package: BiocGenerics
2951s 
2951s Attaching package: ‘BiocGenerics’
2951s 
2951s The following objects are masked from ‘package:stats’:
2951s 
2951s     IQR, mad, sd, var, xtabs
2951s 
2951s The following objects are masked from ‘package:base’:
2951s 
2951s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2951s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2951s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2951s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2951s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2951s     table, tapply, union, unique, unsplit, which.max, which.min
2951s 
2951s Loading required package: Biobase
2951s Welcome to Bioconductor
2951s 
2951s     Vignettes contain introductory material; view with
2951s     'browseVignettes()'. To cite Bioconductor, see
2951s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2951s 
2951s Loading required package: IRanges
2951s Loading required package: S4Vectors
2951s 
2951s Attaching package: ‘S4Vectors’
2951s 
2951s The following object is masked from ‘package:geneLenDataBase’:
2951s 
2951s     unfactor
2951s 
2951s The following object is masked from ‘package:utils’:
2951s 
2951s     findMatches
2951s 
2951s The following objects are masked from ‘package:base’:
2951s 
2951s     expand.grid, I, unname
2951s 
2952s Processing category: custom_list
2952s Using manually entered categories.
2952s Calculating the p-values...
2952s 'select()' returned 1:1 mapping between keys and columns
2952s 
2952s 
2952s Done.
2952s 
2952s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.count_matrix 
2952s Loading required package: BiasedUrn
2952s Loading required package: geneLenDataBase
2964s 
2964s Loading required package: AnnotationDbi
2964s Loading required package: stats4
2964s Loading required package: BiocGenerics
2964s 
2964s Attaching package: ‘BiocGenerics’
2964s 
2964s The following objects are masked from ‘package:stats’:
2964s 
2964s     IQR, mad, sd, var, xtabs
2964s 
2964s The following objects are masked from ‘package:base’:
2964s 
2964s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2964s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2964s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2964s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2964s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2964s     table, tapply, union, unique, unsplit, which.max, which.min
2964s 
2964s Loading required package: Biobase
2964s Welcome to Bioconductor
2964s 
2964s     Vignettes contain introductory material; view with
2964s     'browseVignettes()'. To cite Bioconductor, see
2964s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2964s 
2964s Loading required package: IRanges
2964s Loading required package: S4Vectors
2964s 
2964s Attaching package: ‘S4Vectors’
2964s 
2964s The following object is masked from ‘package:geneLenDataBase’:
2964s 
2964s     unfactor
2964s 
2964s The following object is masked from ‘package:utils’:
2964s 
2964s     findMatches
2964s 
2964s The following objects are masked from ‘package:base’:
2964s 
2964s     expand.grid, I, unname
2964s 
2965s Processing category: custom_list
2965s Using manually entered categories.
2965s Calculating the p-values...
2965s 'select()' returned 1:1 mapping between keys and columns
2965s 
2965s 
2965s Done.
2965s 
2965s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.count_matrix 
2966s Loading required package: BiasedUrn
2966s Loading required package: geneLenDataBase
2977s 
2977s Loading required package: AnnotationDbi
2977s Loading required package: stats4
2977s Loading required package: BiocGenerics
2977s 
2977s Attaching package: ‘BiocGenerics’
2977s 
2977s The following objects are masked from ‘package:stats’:
2977s 
2977s     IQR, mad, sd, var, xtabs
2977s 
2977s The following objects are masked from ‘package:base’:
2977s 
2977s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2977s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2977s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2977s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2977s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2977s     table, tapply, union, unique, unsplit, which.max, which.min
2977s 
2977s Loading required package: Biobase
2977s Welcome to Bioconductor
2977s 
2977s     Vignettes contain introductory material; view with
2977s     'browseVignettes()'. To cite Bioconductor, see
2977s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2977s 
2977s Loading required package: IRanges
2977s Loading required package: S4Vectors
2977s 
2977s Attaching package: ‘S4Vectors’
2977s 
2977s The following object is masked from ‘package:geneLenDataBase’:
2977s 
2977s     unfactor
2977s 
2977s The following object is masked from ‘package:utils’:
2977s 
2977s     findMatches
2977s 
2977s The following objects are masked from ‘package:base’:
2977s 
2977s     expand.grid, I, unname
2977s 
2978s Processing category: custom_list
2978s Using manually entered categories.
2978s Calculating the p-values...
2979s 'select()' returned 1:1 mapping between keys and columns
2979s 
2979s 
2979s Done.
2979s 
2979s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 
2979s Loading required package: BiasedUrn
2979s Loading required package: geneLenDataBase
2991s 
2991s Loading required package: AnnotationDbi
2991s Loading required package: stats4
2991s Loading required package: BiocGenerics
2991s 
2991s Attaching package: ‘BiocGenerics’
2991s 
2991s The following objects are masked from ‘package:stats’:
2991s 
2991s     IQR, mad, sd, var, xtabs
2991s 
2991s The following objects are masked from ‘package:base’:
2991s 
2991s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2991s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2991s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2991s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2991s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
2991s     table, tapply, union, unique, unsplit, which.max, which.min
2991s 
2991s Loading required package: Biobase
2991s Welcome to Bioconductor
2991s 
2991s     Vignettes contain introductory material; view with
2991s     'browseVignettes()'. To cite Bioconductor, see
2991s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2991s 
2991s Loading required package: IRanges
2991s Loading required package: S4Vectors
2991s 
2991s Attaching package: ‘S4Vectors’
2991s 
2991s The following object is masked from ‘package:geneLenDataBase’:
2991s 
2991s     unfactor
2991s 
2991s The following object is masked from ‘package:utils’:
2991s 
2991s     findMatches
2991s 
2991s The following objects are masked from ‘package:base’:
2991s 
2991s     expand.grid, I, unname
2991s 
2994s Warning message:
2994s In pcls(G) : initial point very close to some inequality constraints
2994s Processing category: custom_list
2994s Using manually entered categories.
2994s Calculating the p-values...
2995s 'select()' returned 1:1 mapping between keys and columns
2996s 
2996s 
2996s Done.
2996s 
2996s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 
2996s Loading required package: BiasedUrn
2996s Loading required package: geneLenDataBase
3006s 
3006s Loading required package: AnnotationDbi
3006s Loading required package: stats4
3006s Loading required package: BiocGenerics
3006s 
3006s Attaching package: ‘BiocGenerics’
3006s 
3006s The following objects are masked from ‘package:stats’:
3006s 
3006s     IQR, mad, sd, var, xtabs
3006s 
3006s The following objects are masked from ‘package:base’:
3006s 
3006s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3006s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3006s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3006s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3006s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3006s     table, tapply, union, unique, unsplit, which.max, which.min
3006s 
3006s Loading required package: Biobase
3007s Welcome to Bioconductor
3007s 
3007s     Vignettes contain introductory material; view with
3007s     'browseVignettes()'. To cite Bioconductor, see
3007s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3007s 
3007s Loading required package: IRanges
3007s Loading required package: S4Vectors
3007s 
3007s Attaching package: ‘S4Vectors’
3007s 
3007s The following object is masked from ‘package:geneLenDataBase’:
3007s 
3007s     unfactor
3007s 
3007s The following object is masked from ‘package:utils’:
3007s 
3007s     findMatches
3007s 
3007s The following objects are masked from ‘package:base’:
3007s 
3007s     expand.grid, I, unname
3007s 
3010s Processing category: custom_list
3010s Using manually entered categories.
3010s Calculating the p-values...
3011s 'select()' returned 1:1 mapping between keys and columns
3011s 
3011s 
3011s Done.
3011s 
3011s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 
3011s Loading required package: BiasedUrn
3011s Loading required package: geneLenDataBase
3021s 
3021s Loading required package: AnnotationDbi
3021s Loading required package: stats4
3021s Loading required package: BiocGenerics
3021s 
3021s Attaching package: ‘BiocGenerics’
3021s 
3021s The following objects are masked from ‘package:stats’:
3021s 
3021s     IQR, mad, sd, var, xtabs
3021s 
3021s The following objects are masked from ‘package:base’:
3021s 
3021s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3021s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3021s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3021s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3021s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3021s     table, tapply, union, unique, unsplit, which.max, which.min
3021s 
3021s Loading required package: Biobase
3021s Welcome to Bioconductor
3021s 
3021s     Vignettes contain introductory material; view with
3021s     'browseVignettes()'. To cite Bioconductor, see
3021s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3021s 
3021s Loading required package: IRanges
3021s Loading required package: S4Vectors
3021s 
3021s Attaching package: ‘S4Vectors’
3021s 
3021s The following object is masked from ‘package:geneLenDataBase’:
3021s 
3021s     unfactor
3021s 
3021s The following object is masked from ‘package:utils’:
3021s 
3021s     findMatches
3021s 
3021s The following objects are masked from ‘package:base’:
3021s 
3021s     expand.grid, I, unname
3021s 
3025s Warning message:
3025s In pcls(G) : initial point very close to some inequality constraints
3025s Processing category: custom_list
3025s Using manually entered categories.
3025s Calculating the p-values...
3026s 'select()' returned 1:1 mapping between keys and columns
3027s 
3027s 
3027s Done.
3027s 
3027s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.count_matrix 
3027s Loading required package: BiasedUrn
3027s Loading required package: geneLenDataBase
3037s 
3037s Loading required package: AnnotationDbi
3037s Loading required package: stats4
3037s Loading required package: BiocGenerics
3037s 
3037s Attaching package: ‘BiocGenerics’
3037s 
3037s The following objects are masked from ‘package:stats’:
3037s 
3037s     IQR, mad, sd, var, xtabs
3037s 
3037s The following objects are masked from ‘package:base’:
3037s 
3037s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3037s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3037s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3037s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3037s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3037s     table, tapply, union, unique, unsplit, which.max, which.min
3037s 
3037s Loading required package: Biobase
3037s Welcome to Bioconductor
3037s 
3037s     Vignettes contain introductory material; view with
3037s     'browseVignettes()'. To cite Bioconductor, see
3037s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3037s 
3037s Loading required package: IRanges
3037s Loading required package: S4Vectors
3037s 
3037s Attaching package: ‘S4Vectors’
3037s 
3037s The following object is masked from ‘package:geneLenDataBase’:
3037s 
3037s     unfactor
3037s 
3037s The following object is masked from ‘package:utils’:
3037s 
3037s     findMatches
3037s 
3037s The following objects are masked from ‘package:base’:
3037s 
3037s     expand.grid, I, unname
3037s 
3038s Warning message:
3038s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3038s   Iteration limit reached without full convergence - check carefully
3038s Processing category: custom_list
3038s Using manually entered categories.
3038s Calculating the p-values...
3039s 'select()' returned 1:1 mapping between keys and columns
3039s 
3039s 
3039s Done.
3039s 
3039s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.count_matrix 
3039s Loading required package: BiasedUrn
3039s Loading required package: geneLenDataBase
3050s 
3051s Loading required package: AnnotationDbi
3051s Loading required package: stats4
3051s Loading required package: BiocGenerics
3051s 
3051s Attaching package: ‘BiocGenerics’
3051s 
3051s The following objects are masked from ‘package:stats’:
3051s 
3051s     IQR, mad, sd, var, xtabs
3051s 
3051s The following objects are masked from ‘package:base’:
3051s 
3051s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3051s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3051s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3051s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3051s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3051s     table, tapply, union, unique, unsplit, which.max, which.min
3051s 
3051s Loading required package: Biobase
3051s Welcome to Bioconductor
3051s 
3051s     Vignettes contain introductory material; view with
3051s     'browseVignettes()'. To cite Bioconductor, see
3051s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3051s 
3051s Loading required package: IRanges
3051s Loading required package: S4Vectors
3051s 
3051s Attaching package: ‘S4Vectors’
3051s 
3051s The following object is masked from ‘package:geneLenDataBase’:
3051s 
3051s     unfactor
3051s 
3051s The following object is masked from ‘package:utils’:
3051s 
3051s     findMatches
3051s 
3051s The following objects are masked from ‘package:base’:
3051s 
3051s     expand.grid, I, unname
3051s 
3052s Warning message:
3052s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3052s   Iteration limit reached without full convergence - check carefully
3052s Processing category: custom_list
3052s Using manually entered categories.
3052s Calculating the p-values...
3053s 'select()' returned 1:1 mapping between keys and columns
3053s 
3053s 
3053s Done.
3053s 
3053s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset --background Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.count_matrix 
3053s Loading required package: BiasedUrn
3053s Loading required package: geneLenDataBase
3065s 
3065s Loading required package: AnnotationDbi
3065s Loading required package: stats4
3065s Loading required package: BiocGenerics
3065s 
3065s Attaching package: ‘BiocGenerics’
3065s 
3065s The following objects are masked from ‘package:stats’:
3065s 
3065s     IQR, mad, sd, var, xtabs
3065s 
3065s The following objects are masked from ‘package:base’:
3065s 
3065s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3065s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3065s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3065s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3065s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3065s     table, tapply, union, unique, unsplit, which.max, which.min
3065s 
3065s Loading required package: Biobase
3065s Welcome to Bioconductor
3065s 
3065s     Vignettes contain introductory material; view with
3065s     'browseVignettes()'. To cite Bioconductor, see
3065s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3065s 
3065s Loading required package: IRanges
3065s Loading required package: S4Vectors
3065s 
3065s Attaching package: ‘S4Vectors’
3065s 
3065s The following object is masked from ‘package:geneLenDataBase’:
3065s 
3065s     unfactor
3065s 
3065s The following object is masked from ‘package:utils’:
3065s 
3065s     findMatches
3065s 
3065s The following objects are masked from ‘package:base’:
3065s 
3065s     expand.grid, I, unname
3065s 
3066s Processing category: custom_list
3066s Using manually entered categories.
3066s Calculating the p-values...
3066s 'select()' returned 1:1 mapping between keys and columns
3067s 
3067s 
3067s Done.
3067s 
3067s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.count_matrix 
3067s Loading required package: BiasedUrn
3067s Loading required package: geneLenDataBase
3078s 
3079s Loading required package: AnnotationDbi
3079s Loading required package: stats4
3079s Loading required package: BiocGenerics
3079s 
3079s Attaching package: ‘BiocGenerics’
3079s 
3079s The following objects are masked from ‘package:stats’:
3079s 
3079s     IQR, mad, sd, var, xtabs
3079s 
3079s The following objects are masked from ‘package:base’:
3079s 
3079s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3079s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3079s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3079s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3079s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3079s     table, tapply, union, unique, unsplit, which.max, which.min
3079s 
3079s Loading required package: Biobase
3079s Welcome to Bioconductor
3079s 
3079s     Vignettes contain introductory material; view with
3079s     'browseVignettes()'. To cite Bioconductor, see
3079s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3079s 
3079s Loading required package: IRanges
3079s Loading required package: S4Vectors
3079s 
3079s Attaching package: ‘S4Vectors’
3079s 
3079s The following object is masked from ‘package:geneLenDataBase’:
3079s 
3079s     unfactor
3079s 
3079s The following object is masked from ‘package:utils’:
3079s 
3079s     findMatches
3079s 
3079s The following objects are masked from ‘package:base’:
3079s 
3079s     expand.grid, I, unname
3079s 
3080s Processing category: custom_list
3080s Using manually entered categories.
3080s Calculating the p-values...
3080s 'select()' returned 1:1 mapping between keys and columns
3080s 
3080s 
3080s Done.
3080s 
3080s 
3080s 
3080s ** Found 25 features as differentially expressed.
3080s 
3080s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save  -s ../samples.txt
3080s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3080s Loading required package: BiocGenerics
3080s 
3080s Attaching package: ‘BiocGenerics’
3080s 
3080s The following objects are masked from ‘package:stats’:
3080s 
3080s     IQR, mad, sd, var, xtabs
3080s 
3080s The following objects are masked from ‘package:base’:
3080s 
3080s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3080s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3080s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3080s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3080s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
3080s     table, tapply, union, unique, unsplit, which.max, which.min
3080s 
3080s Welcome to Bioconductor
3080s 
3080s     Vignettes contain introductory material; view with
3080s     'browseVignettes()'. To cite Bioconductor, see
3080s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3080s 
3081s 
3081s Attaching package: ‘fastcluster’
3081s 
3081s The following object is masked from ‘package:stats’:
3081s 
3081s     hclust
3081s 
3081s [1] "Reading matrix file."
3082s for plotting:: min.raw: -0.790731955608766 max.raw: 1
3082s null device 
3082s           1 
3082s for plotting:: min.raw: -9.76652141391246 max.raw: 9.76652141391246
3082s null device 
3082s           1 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3082s sampleA_mean:  351.239 
3082s sampleB_mean: no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3082s  10243.92 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3082s sampleA_mean:  24474.99 
3082s sampleB_mean:  655.981 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3082s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3082s sampleA_mean:  55553.11 9045.287 7701.044 14784.77 3821.721 6809.755 5432.001 5230.464 5420.566 11308.68 3399.73 7103.994 7754.294 8095.973 3638.996 4829.911 6463.777 5768.825 4014.476 4247.003 
3082s sampleB_mean:  296.91 747.095 126.015 319.249 55.433 375.614 535.795 440.221 397.102 1596.57 221.609 176.425 409.173 810.001 115.22 165.063 1510.474 763.865 412.434 854.558 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3082s sampleA_mean:  2036.649 135.207 
3082s sampleB_mean:  11080.21 1620.935 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3082s sampleA_mean:  7754.294 
3082s sampleB_mean:  252.38 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3082s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3082s sampleA_mean:  9466.084 
3082s sampleB_mean:  470.915 
3082s num discordant:  0 
3082s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3082s ./validate_results.pl 
3082s touch test
3082s make[2]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
3082s make[1]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
3082s Running example in test_align_and_estimate_abundance...
3082s make[1]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3082s Running example in PAIRED_END_ABUNDANCE_ESTIMATION...
3082s make[2]: Entering directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3082s ../align_and_estimate_tester.pl RSEM "samples.txt" "../../test_DATA/Trinity.fasta"
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3082s no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3082s no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3082s no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3082s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3082s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3082s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3082s no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3082s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3082s no DE entries reported here.
3082s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3082s edgeR_genes/diffExpr.P0.001_C2.matrix, count: 26 DE features OK.
3082s edgeR_genes/Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.DE.subset.GOseq.enriched, count: 112 DE features OK.
3082s edgeR_genes/Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset.GOseq.enriched, count: 46 DE features OK.
3082s CMD: ln -sf ../../test_DATA/Trinity.fasta .
3082s CMD: /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz --SS_lib_type RF --seqType fq --trinity_mode --est_method RSEM --output_dir RSEM-heatshock --aln_method bowtie2 --coordsort_bam 
3082s CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta > /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map
3082s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.started
3082s CMD: bowtie2-build /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2
3082s Settings:
3082s   Output files: "/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.*.bt2"
3082s   Line rate: 6 (line is 64 bytes)
3082s   Lines per side: 1 (side is 64 bytes)
3082s   Offset rate: 4 (one in 16)
3082s   FTable chars: 10
3082s   Strings: unpacked
3082s   Max bucket size: default
3082s   Max bucket size, sqrt multiplier: default
3082s   Max bucket size, len divisor: 4
3082s   Difference-cover sample period: 1024
3082s   Endianness: little
3082s   Actual local endianness: little
3082s   Sanity checking: disabled
3082s   Assertions: disabled
3082s   Random seed: 0
3082s   Sizeofs: void*:8, int:4, long:8, size_t:8
3082s Input files DNA, FASTA:
3082s   /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3082s Reading reference sizes
3082s Building a SMALL index
3082s   Time reading reference sizes: 00:00:00
3082s Calculating joined length
3082s Writing header
3082s Reserving space for joined string
3082s Joining reference sequences
3082s   Time to join reference sequences: 00:00:00
3082s bmax according to bmaxDivN setting: 54360
3082s Using parameters --bmax 40770 --dcv 1024
3082s   Doing ahead-of-time memory usage test
3082s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3082s Constructing suffix-array element generator
3082s Building DifferenceCoverSample
3082s   Building sPrime
3082s   Building sPrimeOrder
3082s   V-Sorting samples
3082s   V-Sorting samples time: 00:00:00
3082s   Allocating rank array
3082s   Ranking v-sort output
3082s   Ranking v-sort output time: 00:00:00
3082s   Invoking Larsson-Sadakane on ranks
3082s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3082s   Sanity-checking and returning
3082s Building samples
3082s Reserving space for 12 sample suffixes
3082s Generating random suffixes
3082s QSorting 12 sample offsets, eliminating duplicates
3082s QSorting sample offsets, eliminating duplicates time: 00:00:00
3082s Multikey QSorting 12 samples
3082s   (Using difference cover)
3082s   Multikey QSorting samples time: 00:00:00
3082s Calculating bucket sizes
3082s Splitting and merging
3082s   Splitting and merging time: 00:00:00
3082s Split 2, merged 6; iterating...
3082s Splitting and merging
3082s   Splitting and merging time: 00:00:00
3082s Split 1, merged 2; iterating...
3082s Splitting and merging
3082s   Splitting and merging time: 00:00:00
3082s Split 1, merged 0; iterating...
3082s Splitting and merging
3082s   Splitting and merging time: 00:00:00
3082s Avg bucket size: 27179.5 (target: 40769)
3082s Converting suffix-array elements to index image
3082s Allocating ftab, absorbFtab
3082s Entering Ebwt loop
3082s Getting block 1 of 8
3082s   Reserving size (40770) for bucket 1
3082s   Calculating Z arrays for bucket 1
3082s   Entering block accumulator loop for bucket 1:
3082s   bucket 1: 10%
3082s   bucket 1: 20%
3082s   bucket 1: 30%
3082s   bucket 1: 40%
3082s   bucket 1: 50%
3082s   bucket 1: 60%
3082s   bucket 1: 70%
3082s   bucket 1: 80%
3082s   bucket 1: 90%
3082s   bucket 1: 100%
3082s   Sorting block of length 34231 for bucket 1
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 34232 for bucket 1
3082s Getting block 2 of 8
3082s   Reserving size (40770) for bucket 2
3082s   Calculating Z arrays for bucket 2
3082s   Entering block accumulator loop for bucket 2:
3082s   bucket 2: 10%
3082s   bucket 2: 20%
3082s   bucket 2: 30%
3082s   bucket 2: 40%
3082s   bucket 2: 50%
3082s   bucket 2: 60%
3082s   bucket 2: 70%
3082s   bucket 2: 80%
3082s   bucket 2: 90%
3082s   bucket 2: 100%
3082s   Sorting block of length 39793 for bucket 2
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 39794 for bucket 2
3082s Getting block 3 of 8
3082s   Reserving size (40770) for bucket 3
3082s   Calculating Z arrays for bucket 3
3082s   Entering block accumulator loop for bucket 3:
3082s   bucket 3: 10%
3082s   bucket 3: 20%
3082s   bucket 3: 30%
3082s   bucket 3: 40%
3082s   bucket 3: 50%
3082s   bucket 3: 60%
3082s   bucket 3: 70%
3082s   bucket 3: 80%
3082s   bucket 3: 90%
3082s   bucket 3: 100%
3082s   Sorting block of length 9793 for bucket 3
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 9794 for bucket 3
3082s Getting block 4 of 8
3082s   Reserving size (40770) for bucket 4
3082s   Calculating Z arrays for bucket 4
3082s   Entering block accumulator loop for bucket 4:
3082s   bucket 4: 10%
3082s   bucket 4: 20%
3082s   bucket 4: 30%
3082s   bucket 4: 40%
3082s   bucket 4: 50%
3082s   bucket 4: 60%
3082s   bucket 4: 70%
3082s   bucket 4: 80%
3082s   bucket 4: 90%
3082s   bucket 4: 100%
3082s   Sorting block of length 31901 for bucket 4
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 31902 for bucket 4
3082s Getting block 5 of 8
3082s   Reserving size (40770) for bucket 5
3082s   Calculating Z arrays for bucket 5
3082s   Entering block accumulator loop for bucket 5:
3082s   bucket 5: 10%
3082s   bucket 5: 20%
3082s   bucket 5: 30%
3082s   bucket 5: 40%
3082s   bucket 5: 50%
3082s   bucket 5: 60%
3082s   bucket 5: 70%
3082s   bucket 5: 80%
3082s   bucket 5: 90%
3082s   bucket 5: 100%
3082s   Sorting block of length 10600 for bucket 5
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 10601 for bucket 5
3082s Getting block 6 of 8
3082s   Reserving size (40770) for bucket 6
3082s   Calculating Z arrays for bucket 6
3082s   Entering block accumulator loop for bucket 6:
3082s   bucket 6: 10%
3082s   bucket 6: 20%
3082s   bucket 6: 30%
3082s   bucket 6: 40%
3082s   bucket 6: 50%
3082s   bucket 6: 60%
3082s   bucket 6: 70%
3082s   bucket 6: 80%
3082s   bucket 6: 90%
3082s   bucket 6: 100%
3082s   Sorting block of length 40652 for bucket 6
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 40653 for bucket 6
3082s Getting block 7 of 8
3082s   Reserving size (40770) for bucket 7
3082s   Calculating Z arrays for bucket 7
3082s   Entering block accumulator loop for bucket 7:
3082s   bucket 7: 10%
3082s   bucket 7: 20%
3082s   bucket 7: 30%
3082s   bucket 7: 40%
3082s   bucket 7: 50%
3082s   bucket 7: 60%
3082s   bucket 7: 70%
3082s   bucket 7: 80%
3082s   bucket 7: 90%
3082s   bucket 7: 100%
3082s   Sorting block of length 18337 for bucket 7
3082s   (Using difference cover)
3082s   Sorting block time: 00:00:00
3082s Returning block of 18338 for bucket 7
3082s Getting block 8 of 8
3082s   Reserving size (40770) for bucket 8
3083s   Calculating Z arrays for bucket 8
3083s   Entering block accumulator loop for bucket 8:
3083s   bucket 8: 10%
3083s   bucket 8: 20%
3083s   bucket 8: 30%
3083s   bucket 8: 40%
3083s   bucket 8: 50%
3083s   bucket 8: 60%
3083s   bucket 8: 70%
3083s   bucket 8: 80%
3083s   bucket 8: 90%
3083s   bucket 8: 100%
3083s   Sorting block of length 32129 for bucket 8
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 32130 for bucket 8
3083s Exited Ebwt loop
3083s fchr[A]: 0
3083s fchr[C]: 59864
3083s fchr[G]: 108205
3083s fchr[T]: 157829
3083s fchr[$]: 217443
3083s Exiting Ebwt::buildToDisk()
3083s Returning from initFromVector
3083s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp
3083s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp
3083s Re-opening _in1 and _in2 as input streams
3083s Returning from Ebwt constructor
3083s Headers:
3083s     len: 217443
3083s     bwtLen: 217444
3083s     sz: 54361
3083s     bwtSz: 54361
3083s     lineRate: 6
3083s     offRate: 4
3083s     offMask: 0xfffffff0
3083s     ftabChars: 10
3083s     eftabLen: 20
3083s     eftabSz: 80
3083s     ftabLen: 1048577
3083s     ftabSz: 4194308
3083s     offsLen: 13591
3083s     offsSz: 54364
3083s     lineSz: 64
3083s     sideSz: 64
3083s     sideBwtSz: 48
3083s     sideBwtLen: 192
3083s     numSides: 1133
3083s     numLines: 1133
3083s     ebwtTotLen: 72512
3083s     ebwtTotSz: 72512
3083s     color: 0
3083s     reverse: 0
3083s Total time for call to driver() for forward index: 00:00:00
3083s Reading reference sizes
3083s   Time reading reference sizes: 00:00:00
3083s Calculating joined length
3083s Writing header
3083s Reserving space for joined string
3083s Joining reference sequences
3083s   Time to join reference sequences: 00:00:00
3083s   Time to reverse reference sequence: 00:00:00
3083s bmax according to bmaxDivN setting: 54360
3083s Using parameters --bmax 40770 --dcv 1024
3083s   Doing ahead-of-time memory usage test
3083s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3083s Constructing suffix-array element generator
3083s Building DifferenceCoverSample
3083s   Building sPrime
3083s   Building sPrimeOrder
3083s   V-Sorting samples
3083s   V-Sorting samples time: 00:00:00
3083s   Allocating rank array
3083s   Ranking v-sort output
3083s   Ranking v-sort output time: 00:00:00
3083s   Invoking Larsson-Sadakane on ranks
3083s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3083s   Sanity-checking and returning
3083s Building samples
3083s Reserving space for 12 sample suffixes
3083s Generating random suffixes
3083s QSorting 12 sample offsets, eliminating duplicates
3083s QSorting sample offsets, eliminating duplicates time: 00:00:00
3083s Multikey QSorting 12 samples
3083s   (Using difference cover)
3083s   Multikey QSorting samples time: 00:00:00
3083s Calculating bucket sizes
3083s Splitting and merging
3083s   Splitting and merging time: 00:00:00
3083s Split 1, merged 6; iterating...
3083s Splitting and merging
3083s   Splitting and merging time: 00:00:00
3083s Avg bucket size: 31062.4 (target: 40769)
3083s Converting suffix-array elements to index image
3083s Allocating ftab, absorbFtab
3083s Entering Ebwt loop
3083s Getting block 1 of 7
3083s   Reserving size (40770) for bucket 1
3083s   Calculating Z arrays for bucket 1
3083s   Entering block accumulator loop for bucket 1:
3083s   bucket 1: 10%
3083s   bucket 1: 20%
3083s   bucket 1: 30%
3083s   bucket 1: 40%
3083s   bucket 1: 50%
3083s   bucket 1: 60%
3083s   bucket 1: 70%
3083s   bucket 1: 80%
3083s   bucket 1: 90%
3083s   bucket 1: 100%
3083s   Sorting block of length 37058 for bucket 1
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 37059 for bucket 1
3083s Getting block 2 of 7
3083s   Reserving size (40770) for bucket 2
3083s   Calculating Z arrays for bucket 2
3083s   Entering block accumulator loop for bucket 2:
3083s   bucket 2: 10%
3083s   bucket 2: 20%
3083s   bucket 2: 30%
3083s   bucket 2: 40%
3083s   bucket 2: 50%
3083s   bucket 2: 60%
3083s   bucket 2: 70%
3083s   bucket 2: 80%
3083s   bucket 2: 90%
3083s   bucket 2: 100%
3083s   Sorting block of length 17846 for bucket 2
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 17847 for bucket 2
3083s Getting block 3 of 7
3083s   Reserving size (40770) for bucket 3
3083s   Calculating Z arrays for bucket 3
3083s   Entering block accumulator loop for bucket 3:
3083s   bucket 3: 10%
3083s   bucket 3: 20%
3083s   bucket 3: 30%
3083s   bucket 3: 40%
3083s   bucket 3: 50%
3083s   bucket 3: 60%
3083s   bucket 3: 70%
3083s   bucket 3: 80%
3083s   bucket 3: 90%
3083s   bucket 3: 100%
3083s   Sorting block of length 39327 for bucket 3
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 39328 for bucket 3
3083s Getting block 4 of 7
3083s   Reserving size (40770) for bucket 4
3083s   Calculating Z arrays for bucket 4
3083s   Entering block accumulator loop for bucket 4:
3083s   bucket 4: 10%
3083s   bucket 4: 20%
3083s   bucket 4: 30%
3083s   bucket 4: 40%
3083s   bucket 4: 50%
3083s   bucket 4: 60%
3083s   bucket 4: 70%
3083s   bucket 4: 80%
3083s   bucket 4: 90%
3083s   bucket 4: 100%
3083s   Sorting block of length 34139 for bucket 4
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 34140 for bucket 4
3083s Getting block 5 of 7
3083s   Reserving size (40770) for bucket 5
3083s   Calculating Z arrays for bucket 5
3083s   Entering block accumulator loop for bucket 5:
3083s   bucket 5: 10%
3083s   bucket 5: 20%
3083s   bucket 5: 30%
3083s   bucket 5: 40%
3083s   bucket 5: 50%
3083s   bucket 5: 60%
3083s   bucket 5: 70%
3083s   bucket 5: 80%
3083s   bucket 5: 90%
3083s   bucket 5: 100%
3083s   Sorting block of length 31038 for bucket 5
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 31039 for bucket 5
3083s Getting block 6 of 7
3083s   Reserving size (40770) for bucket 6
3083s   Calculating Z arrays for bucket 6
3083s   Entering block accumulator loop for bucket 6:
3083s   bucket 6: 10%
3083s   bucket 6: 20%
3083s   bucket 6: 30%
3083s   bucket 6: 40%
3083s   bucket 6: 50%
3083s   bucket 6: 60%
3083s   bucket 6: 70%
3083s   bucket 6: 80%
3083s   bucket 6: 90%
3083s   bucket 6: 100%
3083s   Sorting block of length 21215 for bucket 6
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 21216 for bucket 6
3083s Getting block 7 of 7
3083s   Reserving size (40770) for bucket 7
3083s   Calculating Z arrays for bucket 7
3083s   Entering block accumulator loop for bucket 7:
3083s   bucket 7: 10%
3083s   bucket 7: 20%
3083s   bucket 7: 30%
3083s   bucket 7: 40%
3083s   bucket 7: 50%
3083s   bucket 7: 60%
3083s   bucket 7: 70%
3083s   bucket 7: 80%
3083s   bucket 7: 90%
3083s   bucket 7: 100%
3083s   Sorting block of length 36814 for bucket 7
3083s   (Using difference cover)
3083s   Sorting block time: 00:00:00
3083s Returning block of 36815 for bucket 7
3083s Exited Ebwt loop
3083s fchr[A]: 0
3083s fchr[C]: 59864
3083s fchr[G]: 108205
3083s fchr[T]: 157829
3083s fchr[$]: 217443
3083s Exiting Ebwt::buildToDisk()
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2
3083s Renaming /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp to /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2
3083s Returning from initFromVector
3083s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp
3083s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp
3083s Re-opening _in1 and _in2 as input streams
3083s Returning from Ebwt constructor
3083s Headers:
3083s     len: 217443
3083s     bwtLen: 217444
3083s     sz: 54361
3083s     bwtSz: 54361
3083s     lineRate: 6
3083s     offRate: 4
3083s     offMask: 0xfffffff0
3083s     ftabChars: 10
3083s     eftabLen: 20
3083s     eftabSz: 80
3083s     ftabLen: 1048577
3083s     ftabSz: 4194308
3083s     offsLen: 13591
3083s     offsSz: 54364
3083s     lineSz: 64
3083s     sideSz: 64
3083s     sideBwtSz: 48
3083s     sideBwtLen: 192
3083s     numSides: 1133
3083s     numLines: 1133
3083s     ebwtTotLen: 72512
3083s     ebwtTotSz: 72512
3083s     color: 0
3083s     reverse: 1
3083s Total time for backward call to driver() for mirror index: 00:00:01
3083s CMD: touch /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.rsem.prepped.started
3083s CMD: rsem-prepare-reference  --transcript-to-gene-map /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3083s rsem-synthesis-reference-transcripts /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 0 1 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3083s Transcript Information File is generated!
3083s Group File is generated!
3083s Extracted Sequences File is generated!
3083s 
3083s rsem-preref /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.transcripts.fa 1 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3083s Refs.makeRefs finished!
3083s Refs.saveRefs finished!
3083s /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.idx.fa is generated!
3083s /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.n2g.idx.fa is generated!
3083s 
3083s $VAR1 = [
3083s           {
3083s             'output_dir' => 'RSEM-heatshock',
3083s             'right' => '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz',
3083s             'left' => '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz'
3083s           }
3083s         ];
3083s CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200  -q -X 800 -x /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 -1 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz -2 /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz -p 4 | samtools view -@ 4 -F 4 -S -b | samtools sort -@ 4 -n -o bowtie2.bam 
3084s 10000 reads; of these:
3084s   10000 (100.00%) were paired; of these:
3084s     7088 (70.88%) aligned concordantly 0 times
3084s     1764 (17.64%) aligned concordantly exactly 1 time
3084s     1148 (11.48%) aligned concordantly >1 times
3084s 29.12% overall alignment rate
3084s [bam_sort_core] merging from 0 files and 4 in-memory blocks...
3084s CMD: touch bowtie2.bam.ok
3084s CMD: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem
3084s samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam
3084s samtools sort: couldn't allocate memory for bam_mem
3084s "samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam" failed! Plase check if you provide correct parameters/options for the pipeline!
3084s Error, cmd: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem died with ret: 65280 at /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl line 728.
3084s Error, cmd:
3084s /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz --right /tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz --SS_lib_type RF --seqType fq --trinity_mode --est_method RSEM --output_dir RSEM-heatshock --aln_method bowtie2 --coordsort_bam 
3084s  died with ret (512) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19.
3084s 	Process_cmd::process_cmd("/usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl -"...) called at ../align_and_estimate_tester.pl line 98
3084s make[2]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3084s make[1]: Leaving directory '/tmp/autopkgtest.zyf5Mk/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3084s make[2]: *** [Makefile:25: test_RSEM] Error 2
3084s make[1]: *** [Makefile:8: test] Error 2
3084s make: *** [Makefile:18: test] Error 2
3084s autopkgtest [00:22:19]: test run-tests: -----------------------]
3085s autopkgtest [00:22:20]: test run-tests:  - - - - - - - - - - results - - - - - - - - - -
3085s run-tests            FAIL non-zero exit status 2
3087s autopkgtest [00:22:22]: @@@@@@@@@@@@@@@@@@@@ summary
3087s run-tests            FAIL non-zero exit status 2
3093s nova [W] Skipping flock for amd64
3093s Creating nova instance adt-plucky-amd64-trinityrnaseq-20250315-233054-juju-7f2275-prod-proposed-migration-environment-2-f4af3eb7-81b6-4cd4-bb96-bbab953f2788 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)...
3093s nova [W] Timed out waiting for 2882a4cf-1984-4cd3-8bb5-953fe1b681ed to get deleted.