0s autopkgtest [20:04:05]: starting date and time: 2025-10-28 20:04:05+0000 0s autopkgtest [20:04:05]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:04:05]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7z3hxrpc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:liburi-perl --apt-upgrade trinityrnaseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=liburi-perl/5.34-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-16.secgroup --name adt-resolute-arm64-trinityrnaseq-20251028-200405-juju-7f2275-prod-proposed-migration-environment-15-02cacfb6-681f-4351-a3f8-0f99f7255777 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-trinityrnaseq-20251028-200405-juju-7f2275-prod-proposed-migration-environment-15-02cacfb6-681f-4351-a3f8-0f99f7255777 from image adt/ubuntu-resolute-arm64-server-20251027.img (UUID 0c8717a7-1983-4858-8ad5-6d56cfcb3438)... 62s autopkgtest [20:05:07]: testbed dpkg architecture: arm64 62s autopkgtest [20:05:07]: testbed apt version: 3.1.8ubuntu1 62s autopkgtest [20:05:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [20:05:07]: testbed release detected to be: None 63s autopkgtest [20:05:08]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [194 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [69.1 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3552 kB] 67s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 67s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [236 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [2440 B] 67s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [44.3 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 67s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1835 kB] 68s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [7312 B] 68s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.4 kB] 68s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [376 B] 69s Fetched 6057 kB in 4s (1380 kB/s) 70s Reading package lists... 71s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 71s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 71s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 71s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Reading package lists... 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s Calculating upgrade... 74s The following NEW packages will be installed: 74s util-linux-extra 74s The following packages will be upgraded: 74s apt bsdextrautils bsdutils cloud-init cloud-init-base fdisk libapt-pkg7.0 74s libblkid1 libefiboot1t64 libefivar1t64 libfdisk1 liblastlog2-2 libmount1 74s libsmartcols1 libuuid1 login mount python3-cffi-backend util-linux 74s uuid-runtime 74s 20 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 6036 kB of archives. 74s After this operation, 1866 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fdisk arm64 2.41.2-4ubuntu1 [149 kB] 75s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblkid1 arm64 2.41.2-4ubuntu1 [139 kB] 75s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libmount1 arm64 2.41.2-4ubuntu1 [173 kB] 75s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libsmartcols1 arm64 2.41.2-4ubuntu1 [96.2 kB] 75s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 mount arm64 2.41.2-4ubuntu1 [145 kB] 75s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 uuid-runtime arm64 2.41.2-4ubuntu1 [56.9 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libuuid1 arm64 2.41.2-4ubuntu1 [45.3 kB] 75s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libfdisk1 arm64 2.41.2-4ubuntu1 [173 kB] 75s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 bsdutils arm64 1:2.41.2-4ubuntu1 [93.0 kB] 75s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 util-linux arm64 2.41.2-4ubuntu1 [1082 kB] 76s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 bsdextrautils arm64 2.41.2-4ubuntu1 [94.1 kB] 76s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 login arm64 1:4.16.0-2+really2.41.2-4ubuntu1 [94.9 kB] 76s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liblastlog2-2 arm64 2.41.2-4ubuntu1 [35.7 kB] 76s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.11 [1063 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.11 [1402 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cffi-backend arm64 2.0.0-2 [110 kB] 78s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 78s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 78s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libefivar1t64 arm64 39-2 [57.3 kB] 78s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libefiboot1t64 arm64 39-2 [40.1 kB] 78s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 util-linux-extra arm64 2.41.2-4ubuntu1 [361 kB] 79s dpkg-preconfigure: unable to re-open stdin: No such file or directory 79s Fetched 6036 kB in 4s (1488 kB/s) 79s (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 ... 83387 files and directories currently installed.) 79s Preparing to unpack .../fdisk_2.41.2-4ubuntu1_arm64.deb ... 79s Unpacking fdisk (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 79s Preparing to unpack .../libblkid1_2.41.2-4ubuntu1_arm64.deb ... 79s Unpacking libblkid1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 79s Setting up libblkid1:arm64 (2.41.2-4ubuntu1) ... 79s (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 ... 83387 files and directories currently installed.) 79s Preparing to unpack .../libmount1_2.41.2-4ubuntu1_arm64.deb ... 79s Unpacking libmount1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 79s Setting up libmount1:arm64 (2.41.2-4ubuntu1) ... 79s (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 ... 83387 files and directories currently installed.) 79s Preparing to unpack .../libsmartcols1_2.41.2-4ubuntu1_arm64.deb ... 79s Unpacking libsmartcols1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 80s Setting up libsmartcols1:arm64 (2.41.2-4ubuntu1) ... 80s (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 ... 83387 files and directories currently installed.) 80s Preparing to unpack .../mount_2.41.2-4ubuntu1_arm64.deb ... 80s Unpacking mount (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 80s Preparing to unpack .../uuid-runtime_2.41.2-4ubuntu1_arm64.deb ... 80s Unpacking uuid-runtime (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 80s Preparing to unpack .../libuuid1_2.41.2-4ubuntu1_arm64.deb ... 80s Unpacking libuuid1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 80s Setting up libuuid1:arm64 (2.41.2-4ubuntu1) ... 80s (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 ... 83387 files and directories currently installed.) 80s Preparing to unpack .../libfdisk1_2.41.2-4ubuntu1_arm64.deb ... 80s Unpacking libfdisk1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 80s Preparing to unpack .../bsdutils_1%3a2.41.2-4ubuntu1_arm64.deb ... 80s Unpacking bsdutils (1:2.41.2-4ubuntu1) over (1:2.41-4ubuntu4) ... 80s Setting up bsdutils (1:2.41.2-4ubuntu1) ... 81s (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 ... 83384 files and directories currently installed.) 81s Preparing to unpack .../util-linux_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking util-linux (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Setting up util-linux (2.41.2-4ubuntu1) ... 82s fstrim.service is a disabled or a static unit not running, not starting it. 82s (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 ... 83355 files and directories currently installed.) 82s Preparing to unpack .../bsdextrautils_2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking bsdextrautils (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking login (1:4.16.0-2+really2.41.2-4ubuntu1) over (1:4.16.0-2+really2.41-4ubuntu4) ... 82s Preparing to unpack .../liblastlog2-2_2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking liblastlog2-2:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Setting up liblastlog2-2:arm64 (2.41.2-4ubuntu1) ... 83s (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 ... 83350 files and directories currently installed.) 83s Preparing to unpack .../0-libapt-pkg7.0_3.1.11_arm64.deb ... 83s Unpacking libapt-pkg7.0:arm64 (3.1.11) over (3.1.8ubuntu1) ... 83s Preparing to unpack .../1-apt_3.1.11_arm64.deb ... 83s Unpacking apt (3.1.11) over (3.1.8ubuntu1) ... 83s Preparing to unpack .../2-python3-cffi-backend_2.0.0-2_arm64.deb ... 83s Unpacking python3-cffi-backend:arm64 (2.0.0-2) over (1.17.1-3build1) ... 83s Preparing to unpack .../3-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 83s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 84s Preparing to unpack .../4-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 84s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 84s Preparing to unpack .../5-libefivar1t64_39-2_arm64.deb ... 84s Unpacking libefivar1t64:arm64 (39-2) over (38-3.1build1) ... 84s Preparing to unpack .../6-libefiboot1t64_39-2_arm64.deb ... 84s Unpacking libefiboot1t64:arm64 (39-2) over (38-3.1build1) ... 84s Selecting previously unselected package util-linux-extra. 84s Preparing to unpack .../7-util-linux-extra_2.41.2-4ubuntu1_arm64.deb ... 84s Unpacking util-linux-extra (2.41.2-4ubuntu1) ... 84s Setting up bsdextrautils (2.41.2-4ubuntu1) ... 84s Setting up libefivar1t64:arm64 (39-2) ... 84s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 85s Encountered debconf setting for cloud-init-base/datasources. 87s Setting up libfdisk1:arm64 (2.41.2-4ubuntu1) ... 87s Setting up mount (2.41.2-4ubuntu1) ... 87s Setting up uuid-runtime (2.41.2-4ubuntu1) ... 88s uuidd.service is a disabled or a static unit not running, not starting it. 88s Setting up libefiboot1t64:arm64 (39-2) ... 88s Setting up libapt-pkg7.0:arm64 (3.1.11) ... 88s Setting up util-linux-extra (2.41.2-4ubuntu1) ... 88s Setting up python3-cffi-backend:arm64 (2.0.0-2) ... 88s Setting up login (1:4.16.0-2+really2.41.2-4ubuntu1) ... 88s Setting up apt (3.1.11) ... 88s Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... 89s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 89s Setting up fdisk (2.41.2-4ubuntu1) ... 89s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 89s Processing triggers for man-db (2.13.1-1) ... 91s Processing triggers for libc-bin (2.42-0ubuntu3) ... 92s autopkgtest [20:05:37]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Solving dependencies... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s autopkgtest [20:05:40]: rebooting testbed after setup commands that affected boot 127s autopkgtest [20:06:12]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 129s autopkgtest [20:06:14]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq 155s Get:1 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (dsc) [2605 B] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (tar) [305 MB] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/universe trinityrnaseq 2.15.2+dfsg-1 (diff) [38.9 kB] 156s gpgv: Signature made Wed Aug 21 22:00:38 2024 UTC 156s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 156s gpgv: Can't check signature: No public key 156s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.2+dfsg-1.dsc: no acceptable signature found 161s autopkgtest [20:06:46]: testing package trinityrnaseq version 2.15.2+dfsg-1 162s autopkgtest [20:06:47]: build not needed 183s autopkgtest [20:07:08]: test run-tests: preparing testbed 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 184s Solving dependencies... 184s The following NEW packages will be installed: 184s adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 184s ca-certificates-java dconf-gsettings-backend dconf-service default-jre 184s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 184s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 184s fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2 jaligner 184s java-common javascript-common jellyfish junit4 kallisto libapache-pom-java 184s libasan8 libasound2-data libasound2t64 libatinject-jsr330-api-java 184s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 184s libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java 184s libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0 184s libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.88-dev 184s libcairo-gobject2 libcairo2 libclone-perl libcolord2 184s libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java 184s libcommons-collections4-java libcommons-compress-java libcommons-io-java 184s libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java 184s libcommons-math3-java libcommons-parent-java libcups2t64 libdatrie1 184s libdconf1 libdeflate0 libdrm-amdgpu1 libencode-locale-perl libepoxy0 184s liberror-prone-java libezmorph-java libfile-listing-perl libfontconfig1 184s libfreemarker-java libgatk-native-bindings-java libgbm1 libgcc-15-dev 184s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5 184s libgif7 libgkl-java libgl1 libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0 184s libgomp1 libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common 184s libguava-java libhamcrest-java libharfbuzz0b libhtml-parser-perl 184s libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 184s libhtsjdk-java libhttp-cookies-perl libhttp-date-perl libhttp-message-perl 184s libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0 184s libhwloc15 libice6 libicu76 libio-html-perl libio-socket-ssl-perl libitm1 184s libjaxen-java libjbig0 libjbzip2-java libjellyfish-2.0-2 libjoptsimple-java 184s libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3 184s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables 184s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax 184s libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify 184s libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker 184s libjs-underscore libjson-java libjsr305-java libjung-free-java liblapack3 184s liblcms2-2 liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0 184s liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto16 184s libmbedtls21 libmbedx509-7 libmongodb-java libncbi-ngs3 libncbi-vdb3 184s libnet-http-perl libnet-ssleay-perl libngs-java libngs-jni libnspr4 libnss3 184s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 184s libpaper2 libpcsclite1 libpicard-java libpixman-1-0 libprotobuf32t64 184s librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni 184s libsnappy1v5 libstaden-read14t64 libstdc++-15-dev libtbb12 libtbbbind-2-5 184s libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl 184s libtk8.6 libtry-tiny-perl libtsan2 libubsan1 liburi-perl libvulkan1 184s libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 libwww-perl 184s libwww-robotrules-perl libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-present0 184s libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 184s libxcomposite1 libxcursor1 libxdamage1 libxerces2-java libxfixes3 libxft2 184s libxi6 libxinerama1 libxml-commons-external-java 184s libxml-commons-resolver1.1-java libxom-java libxrandr2 libxrender1 184s libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 mesa-libgallium 184s ncbi-blast+ ncbi-data ncbi-vdb-data node-bootstrap-sass node-html5shiv 184s node-normalize.css openjdk-21-jre openjdk-21-jre-headless pandoc pandoc-data 184s parafly perl-openssl-defaults python3-hisat2 python3-htseq python3-numpy 184s python3-numpy-dev python3-pysam r-base-core r-bioc-annotate 184s r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics 184s r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings 184s r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger 184s r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter 184s r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments 184s r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq 184s r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics 184s r-bioc-qvalue r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer 184s r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray 184s r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils 184s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-argparse r-cran-askpass 184s r-cran-backports r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-bit 184s r-cran-bit64 r-cran-bitops r-cran-blob r-cran-broom r-cran-bslib 184s r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli r-cran-clipr 184s r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-commonmark 184s r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 184s r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dtplyr 184s r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 184s r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython 184s r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs 184s r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics 184s r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive 184s r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable 184s r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv 184s r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband 184s r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr 184s r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle 184s r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass 184s r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime 184s r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar 184s r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png 184s r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps 184s r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer 184s r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl 184s r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr 184s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi 184s r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny 184s r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr 184s r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping 184s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse 184s r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid 184s r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 184s r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools 184s subread trimmomatic trinityrnaseq trinityrnaseq-examples unzip x11-common 184s xdg-utils zip zlib1g-dev 185s 0 upgraded, 451 newly installed, 0 to remove and 0 not upgraded. 185s Need to get 890 MB of archives. 185s After this operation, 2190 MB of additional disk space will be used. 185s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 185s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 185s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 185s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 185s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 186s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf2.0-common all 2.44.4+dfsg-1 [8584 B] 186s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 186s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 186s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 186s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 186s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 186s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 186s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 186s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 186s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgdk-pixbuf-2.0-0 arm64 2.44.4+dfsg-1 [149 kB] 186s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 gtk-update-icon-cache arm64 4.20.2+ds-1 [54.4 kB] 186s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 186s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 adwaita-icon-theme all 49.0-1 [581 kB] 186s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 at-spi2-common all 2.57.1-1 [9432 B] 186s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6build1 [132 kB] 186s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-5ubuntu2 [287 kB] 186s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-program-options1.83.0 arm64 1.83.0-5ubuntu2 [325 kB] 186s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-thread1.83.0 arm64 1.83.0-5ubuntu2 [277 kB] 186s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libprotobuf32t64 arm64 3.21.12-14build1 [867 kB] 186s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 berkeley-express arm64 1.5.3+dfsg-3build6 [209 kB] 186s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 ca-certificates-java all 20240118 [11.6 kB] 186s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libdconf1 arm64 0.49.0-1 [40.6 kB] 186s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-service arm64 0.49.0-1 [27.1 kB] 186s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 dconf-gsettings-backend arm64 0.49.0-1 [21.9 kB] 186s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 java-common all 0.76 [6852 B] 186s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 186s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libnspr4 arm64 2:4.36-1ubuntu2 [115 kB] 186s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libnss3 arm64 2:3.114-1 [1453 kB] 186s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcsclite1 arm64 2.3.3-1 [24.7 kB] 186s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre-headless arm64 21.0.9+10-1 [45.9 MB] 188s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B] 188s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libatk1.0-0t64 arm64 2.57.1-1 [55.5 kB] 188s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 188s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libatspi2.0-0t64 arm64 2.57.1-1 [84.7 kB] 188s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libatk-bridge2.0-0t64 arm64 2.57.1-1 [66.0 kB] 188s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 188s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 188s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 188s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 188s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 188s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 188s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 188s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 188s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 188s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo-gobject2 arm64 1.18.4-1build1 [128 kB] 188s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolord2 arm64 1.4.7-3build1 [148 kB] 188s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common-data arm64 0.8-16ubuntu3 [31.1 kB] 188s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common3 arm64 0.8-16ubuntu3 [24.5 kB] 188s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-client3 arm64 0.8-16ubuntu3 [28.4 kB] 188s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libcups2t64 arm64 2.4.12-0ubuntu3 [269 kB] 188s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libepoxy0 arm64 1.5.10-2 [236 kB] 188s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 188s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 188s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.15.0-2.3ubuntu1 [191 kB] 188s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 188s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.13-4 [19.1 kB] 188s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 188s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.56.3-2 [237 kB] 188s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [50.2 kB] 188s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [27.7 kB] 188s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-client0 arm64 1.24.0-1build1 [28.9 kB] 188s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-cursor0 arm64 1.24.0-1build1 [11.1 kB] 188s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libwayland-egl1 arm64 1.24.0-1build1 [6500 B] 188s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcomposite1 arm64 1:0.4.6-1 [6626 B] 188s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB] 188s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcursor1 arm64 1:1.2.3-1 [22.2 kB] 188s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B] 188s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B] 188s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB] 188s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-3-common all 3.24.50-1ubuntu2 [1425 kB] 188s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libgtk-3-0t64 arm64 3.24.50-1ubuntu2 [3229 kB] 188s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libglvnd0 arm64 1.7.0-1build2 [59.2 kB] 188s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libx11-xcb1 arm64 2:1.8.12-1build1 [8216 B] 188s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-dri3-0 arm64 1.17.0-2build1 [8120 B] 188s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-glx0 arm64 1.17.0-2build1 [27.8 kB] 188s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-present0 arm64 1.17.0-2build1 [6560 B] 188s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-xfixes0 arm64 1.17.0-2build1 [11.4 kB] 188s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 188s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.127-1ubuntu1 [23.9 kB] 188s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-randr0 arm64 1.17.0-2build1 [20.2 kB] 188s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-sync1 arm64 1.17.0-2build1 [10.4 kB] 188s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 libxshmfence1 arm64 1.3.3-1 [5378 B] 188s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 mesa-libgallium arm64 25.2.3-1ubuntu1 [12.1 MB] 189s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libgbm1 arm64 25.2.3-1ubuntu1 [34.4 kB] 189s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libvulkan1 arm64 1.4.321.0-1 [169 kB] 189s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1-mesa-dri arm64 25.2.3-1ubuntu1 [34.9 kB] 189s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx-mesa0 arm64 25.2.3-1ubuntu1 [110 kB] 189s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 libglx0 arm64 1.7.0-1build2 [34.5 kB] 189s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libgl1 arm64 1.7.0-1build2 [104 kB] 189s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2-data all 1.2.14-1ubuntu1 [21.2 kB] 189s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 libasound2t64 arm64 1.2.14-1ubuntu1 [394 kB] 189s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libgif7 arm64 5.2.2-1ubuntu2 [36.1 kB] 189s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 189s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtst6 arm64 2:1.2.5-1 [13.2 kB] 189s Get:100 http://ftpmaster.internal/ubuntu resolute/main arm64 openjdk-21-jre arm64 21.0.9+10-1 [224 kB] 189s Get:101 http://ftpmaster.internal/ubuntu resolute/main arm64 default-jre arm64 2:1.21-76 [918 B] 189s Get:102 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 189s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 189s Get:104 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 190s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 hisat2 arm64 2.2.1-5 [3961 kB] 190s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 jaligner all 1.0+dfsg-11 [136 kB] 190s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 javascript-common all 12+nmu1 [4828 B] 190s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 190s Get:109 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 190s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjellyfish-2.0-2 arm64 2.3.1-4build2 [65.4 kB] 190s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 jellyfish arm64 2.3.1-4build2 [715 kB] 190s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhamcrest-java all 2.2-2 [117 kB] 190s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 junit4 all 4.13.2-5 [348 kB] 190s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 kallisto arm64 0.48.0+dfsg-4build1 [256 kB] 190s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapache-pom-java all 33-2 [5874 B] 190s Get:116 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-5ubuntu1 [2922 kB] 191s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5076 B] 191s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 191s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-lang3-java all 3.17.0-1 [603 kB] 191s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfreemarker-java all 2.3.32-2.1 [1517 kB] 191s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB] 191s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjoptsimple-java all 5.0.4-7 [73.2 kB] 191s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-codec-java all 1.18.0-1 [303 kB] 191s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 191s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB] 191s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB] 191s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB] 191s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB] 191s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 libslf4j-java all 1.7.32-2 [141 kB] 191s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB] 191s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 191s Get:132 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 191s Get:133 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-5ubuntu1 [28.1 kB] 191s Get:134 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-5ubuntu1 [1316 kB] 191s Get:135 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-5ubuntu1 [2689 kB] 192s Get:136 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-5ubuntu1 [1176 kB] 192s Get:137 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-5ubuntu1 [1639 kB] 192s Get:138 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-5ubuntu1 [2601 kB] 192s Get:139 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-5ubuntu1 [2545 kB] 192s Get:140 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost1.88-dev arm64 1.88.0-1.4ubuntu2 [11.3 MB] 193s Get:141 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-dev arm64 1.88.0.0ubuntu1 [4542 B] 193s Get:142 http://ftpmaster.internal/ubuntu resolute/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-5ubuntu2 [260 kB] 193s Get:143 http://ftpmaster.internal/ubuntu resolute/main arm64 libclone-perl arm64 0.47-1 [10.4 kB] 193s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-collections3-java all 3.2.2-3 [526 kB] 193s Get:145 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-beanutils-java all 1.10.1-1.1 [224 kB] 193s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-collections4-java all 4.4-2 [670 kB] 193s Get:147 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-io-java all 2.19.0-1 [491 kB] 193s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-compress-java all 1.27.1-2 [610 kB] 193s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 193s Get:150 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-math3-java all 3.6.1-4 [2029 kB] 194s Get:151 http://ftpmaster.internal/ubuntu resolute/main arm64 libencode-locale-perl all 1.05-3 [11.6 kB] 194s Get:152 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjsr305-java all 0.1~+svn49-12 [27.0 kB] 194s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 libguava-java all 32.0.1-1 [2692 kB] 194s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] 194s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 libezmorph-java all 1.0.6-4 [76.0 kB] 194s Get:156 http://ftpmaster.internal/ubuntu resolute/main arm64 libtimedate-perl all 2.3300-2 [34.0 kB] 194s Get:157 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-date-perl all 6.06-1 [10.2 kB] 194s Get:158 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-listing-perl all 6.16-1 [11.3 kB] 194s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 194s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB] 194s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjaxen-java all 1.1.6-5 [213 kB] 194s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] 194s Get:163 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB] 194s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxerces2-java all 2.12.2-1 [1430 kB] 194s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 libxom-java all 1.3.9-1 [174 kB] 194s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjson-java all 3.1.0+dfsg-2 [141 kB] 194s Get:167 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 194s Get:168 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 194s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 194s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 194s Get:171 http://ftpmaster.internal/ubuntu resolute/universe arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1259 kB] 194s Get:172 http://ftpmaster.internal/ubuntu resolute/universe arm64 libncbi-ngs3 arm64 3.2.1+dfsg-4ubuntu5 [147 kB] 194s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 libngs-jni arm64 3.2.1+dfsg-4ubuntu5 [4808 B] 194s Get:174 http://ftpmaster.internal/ubuntu resolute/universe arm64 libngs-java arm64 3.2.1+dfsg-4ubuntu5 [91.1 kB] 194s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 librhino-java all 1.7.15-1 [1354 kB] 194s Get:176 http://ftpmaster.internal/ubuntu resolute/main arm64 libsnappy1v5 arm64 1.2.2-1 [30.5 kB] 194s Get:177 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsnappy-jni arm64 1.1.10.7-1 [6672 B] 194s Get:178 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsnappy-java all 1.1.10.7-1 [83.6 kB] 194s Get:179 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1829 kB] 194s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB] 194s Get:181 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-tagset-perl all 3.24-1 [14.1 kB] 194s Get:182 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 liburi-perl all 5.34-2 [100 kB] 195s Get:183 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-parser-perl arm64 3.83-1build1 [85.3 kB] 195s Get:184 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-tree-perl all 5.07-3 [200 kB] 195s Get:185 http://ftpmaster.internal/ubuntu resolute/main arm64 libio-html-perl all 1.004-3 [15.9 kB] 195s Get:186 http://ftpmaster.internal/ubuntu resolute/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 195s Get:187 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-message-perl all 7.00-2ubuntu1 [75.9 kB] 195s Get:188 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-cookies-perl all 6.11-1 [18.2 kB] 195s Get:189 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-negotiate-perl all 6.01-2 [12.4 kB] 195s Get:190 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 195s Get:191 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 195s Get:192 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu76 arm64 76.1-4ubuntu2 [11.2 MB] 196s Get:193 http://ftpmaster.internal/ubuntu resolute/main arm64 perl-openssl-defaults arm64 7build3 [6628 B] 196s Get:194 http://ftpmaster.internal/ubuntu resolute/main arm64 libnet-ssleay-perl arm64 1.94-3 [307 kB] 196s Get:195 http://ftpmaster.internal/ubuntu resolute/main arm64 libio-socket-ssl-perl all 2.089-1 [200 kB] 196s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 196s Get:197 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 196s Get:198 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB] 196s Get:199 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-d3 all 3.5.17-4 [132 kB] 196s Get:200 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 196s Get:201 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 196s Get:202 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 197s Get:203 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 197s Get:204 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 197s Get:205 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 197s Get:206 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 197s Get:207 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 197s Get:208 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 197s Get:209 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 197s Get:210 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 197s Get:211 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 197s Get:212 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjung-free-java all 2.1.1-3 [1478 kB] 198s Get:213 http://ftpmaster.internal/ubuntu resolute/main arm64 liblua5.4-0 arm64 5.4.8-1 [171 kB] 198s Get:214 http://ftpmaster.internal/ubuntu resolute/main arm64 libnet-http-perl all 6.23-1 [22.3 kB] 198s Get:215 http://ftpmaster.internal/ubuntu resolute/main arm64 libtry-tiny-perl all 0.32-1 [21.2 kB] 198s Get:216 http://ftpmaster.internal/ubuntu resolute/main arm64 libwww-robotrules-perl all 6.02-1 [12.6 kB] 198s Get:217 http://ftpmaster.internal/ubuntu resolute/main arm64 libwww-perl all 6.78-1 [139 kB] 198s Get:218 http://ftpmaster.internal/ubuntu resolute/main arm64 liblwp-protocol-https-perl all 6.14-1 [9040 B] 198s Get:219 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 198s Get:220 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 198s Get:221 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpicard-java all 3.3.0+dfsg-2 [1765 kB] 199s Get:222 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 199s Get:223 http://ftpmaster.internal/ubuntu resolute/universe arm64 libstaden-read14t64 arm64 1.15.0-1.1build2 [248 kB] 199s Get:224 http://ftpmaster.internal/ubuntu resolute/universe arm64 libtbbbind-2-5 arm64 2022.1.0-1 [14.3 kB] 199s Get:225 http://ftpmaster.internal/ubuntu resolute/universe arm64 libtbbmalloc2 arm64 2022.1.0-1 [39.0 kB] 199s Get:226 http://ftpmaster.internal/ubuntu resolute/universe arm64 libtbb12 arm64 2022.1.0-1 [72.1 kB] 199s Get:227 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 199s Get:228 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 199s Get:229 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 199s Get:230 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 199s Get:231 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 199s Get:232 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB] 200s Get:233 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-blast+ arm64 2.16.0+ds-7 [15.4 MB] 202s Get:234 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB] 202s Get:235 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 202s Get:236 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 202s Get:237 http://ftpmaster.internal/ubuntu resolute/universe arm64 pandoc-data all 3.1.11.1-3build1 [78.8 kB] 202s Get:238 http://ftpmaster.internal/ubuntu resolute/universe arm64 pandoc arm64 3.1.11.1+ds-4 [28.0 MB] 206s Get:239 http://ftpmaster.internal/ubuntu resolute/universe arm64 parafly arm64 0.1.0-5 [15.7 kB] 206s Get:240 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-hisat2 all 2.2.1-5 [12.7 kB] 206s Get:241 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build2 [4334 kB] 207s Get:242 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-htseq arm64 2.0.9+dfsg-1build3 [451 kB] 207s Get:243 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu2 [175 kB] 207s Get:244 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-28ubuntu7 [176 kB] 207s Get:245 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 207s Get:246 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.1-1 [28.7 MB] 212s Get:247 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 212s Get:248 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biobase arm64 2.66.0-2 [2331 kB] 213s Get:249 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB] 213s Get:250 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-iranges arm64 2.40.1-3 [2301 kB] 213s Get:251 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1 [853 kB] 213s Get:252 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 214s Get:253 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit64 arm64 4.6.0-1-4 [495 kB] 214s Get:254 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 214s Get:255 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 214s Get:256 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 214s Get:257 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 214s Get:258 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 214s Get:259 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB] 214s Get:260 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 214s Get:261 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 214s Get:262 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 214s Get:263 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 214s Get:264 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 214s Get:265 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 214s Get:266 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 215s Get:267 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB] 215s Get:268 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 215s Get:269 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB] 215s Get:270 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB] 215s Get:271 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB] 215s Get:272 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB] 215s Get:273 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 215s Get:274 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] 215s Get:275 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-png arm64 0.1-8-1build2 [40.1 kB] 215s Get:276 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 215s Get:277 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB] 215s Get:278 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB] 215s Get:279 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB] 215s Get:280 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] 217s Get:281 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB] 218s Get:282 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB] 218s Get:283 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB] 219s Get:284 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB] 219s Get:285 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB] 220s Get:286 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xml arm64 3.99-0.18-1build1 [1746 kB] 220s Get:287 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] 220s Get:288 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB] 220s Get:289 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 220s Get:290 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 220s Get:291 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 220s Get:292 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 220s Get:293 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 220s Get:294 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 220s Get:295 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 220s Get:296 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 220s Get:297 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 220s Get:298 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 220s Get:299 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build1 [902 kB] 220s Get:300 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 220s Get:301 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 220s Get:302 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbplyr all 2.5.0+dfsg-1 [1233 kB] 220s Get:303 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-filelock arm64 1.0.3-1 [29.7 kB] 221s Get:304 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocfilecache all 2.14.0+dfsg-2 [300 kB] 221s Get:305 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB] 221s Get:306 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-formatr all 1.14-2 [152 kB] 221s Get:307 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lambda.r all 1.2.4-2build1 [119 kB] 221s Get:308 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB] 221s Get:309 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB] 221s Get:310 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-snow all 1:0.4.4-2 [97.6 kB] 221s Get:311 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB] 221s Get:312 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bh all 1.84.0-1 [5962 B] 221s Get:313 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biocparallel arm64 1.40.0-2 [1333 kB] 221s Get:314 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB] 221s Get:315 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB] 221s Get:316 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB] 221s Get:317 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB] 221s Get:318 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-httr2 all 1.1.1-1 [752 kB] 222s Get:319 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB] 222s Get:320 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xml2 arm64 1.4.0-1ubuntu1 [326 kB] 222s Get:321 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-biomart all 2.62.1+dfsg-1 [444 kB] 222s Get:322 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 222s Get:323 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 222s Get:324 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 222s Get:325 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB] 222s Get:326 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 222s Get:327 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-s4arrays arm64 1.6.0+dfsg-2 [698 kB] 222s Get:328 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-sparsearray arm64 1.6.2+dfsg-2 [1369 kB] 222s Get:329 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-delayedarray arm64 0.32.0+dfsg-2 [2064 kB] 222s Get:330 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicranges arm64 1.58.0+dfsg-2 [2083 kB] 222s Get:331 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB] 223s Get:332 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-locfit arm64 1.5-9.12-1 [514 kB] 223s Get:333 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 223s Get:334 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 223s Get:335 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 223s Get:336 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 223s Get:337 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-3-1 [3324 kB] 223s Get:338 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 223s Get:339 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 223s Get:340 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 223s Get:341 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 223s Get:342 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 223s Get:343 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 223s Get:344 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 223s Get:345 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 223s Get:346 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.21-1 [99.7 kB] 223s Get:347 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 223s Get:348 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 223s Get:349 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 14.6.0-1-1 [858 kB] 223s Get:350 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-deseq2 arm64 1.46.0+dfsg-2 [1237 kB] 224s Get:351 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hwriter all 1.3.2.1-1 [106 kB] 224s Get:352 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bitops arm64 1.0-9-1 [30.2 kB] 224s Get:353 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rhtslib arm64 3.2.0+dfsg-2 [1429 kB] 224s Get:354 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rsamtools arm64 2.22.0+dfsg-2 [3668 kB] 224s Get:355 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 224s Get:356 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-geneplotter all 1.84.0+dfsg-2 [1508 kB] 224s Get:357 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 224s Get:358 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genefilter arm64 1.88.0-2 [1241 kB] 224s Get:359 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-dexseq all 1.52.0+dfsg-2 [453 kB] 224s Get:360 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-limma arm64 3.62.2+dfsg-1 [1968 kB] 224s Get:361 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-edger arm64 4.4.2+dfsg-1 [1114 kB] 224s Get:362 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicalignments arm64 1.42.0-2 [2164 kB] 225s Get:363 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcurl arm64 1.98-1.16+dfsg-1 [806 kB] 225s Get:364 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rjson arm64 0.2.23-1 [104 kB] 225s Get:365 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 225s Get:366 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-restfulr arm64 0.0.15-1 [380 kB] 225s Get:367 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-rtracklayer arm64 1.66.0-3 [5216 kB] 225s Get:368 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB] 225s Get:369 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-txdbmaker all 1.2.1+ds-2 [875 kB] 225s Get:370 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-genelendatabase all 1.42.0-3 [100 MB] 231s Get:371 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-go.db all 3.20.0-2 [16.5 MB] 232s Get:372 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-biasedurn arm64 2.0.12-1 [278 kB] 232s Get:373 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-goseq all 1.58.0-2 [1911 kB] 232s Get:374 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 232s Get:375 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reshape2 arm64 1.4.4-2build1 [110 kB] 232s Get:376 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-bioc-qvalue all 2.38.0-2 [2811 kB] 232s Get:377 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-findpython all 1.0.9-1 [25.3 kB] 232s Get:378 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-argparse all 2.2.5+dfsg-1 [143 kB] 232s Get:379 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 232s Get:380 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB] 232s Get:381 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 232s Get:382 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-htmltools arm64 0.5.8.1-1 [373 kB] 232s Get:383 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 232s Get:384 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fs arm64 1.6.5+dfsg-1 [244 kB] 232s Get:385 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sass arm64 0.4.9+dfsg-1 [957 kB] 232s Get:386 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB] 232s Get:387 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ps arm64 1.9.0-1 [407 kB] 232s Get:388 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-processx arm64 3.8.6-1 [363 kB] 232s Get:389 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-callr all 3.7.6-1 [458 kB] 232s Get:390 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rematch all 2.0.0-1 [18.3 kB] 232s Get:391 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cellranger all 1.1.0-3 [102 kB] 232s Get:392 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-clipr all 0.8.0-1 [53.5 kB] 232s Get:393 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cluster arm64 2.1.8.1-1 [569 kB] 233s Get:394 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-commonmark arm64 1.9.5-1 [130 kB] 233s Get:395 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB] 233s Get:396 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 233s Get:397 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dtplyr all 1.3.1-1 [364 kB] 233s Get:398 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 233s Get:399 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 233s Get:400 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastcluster arm64 1.3.0-1build1 [191 kB] 233s Get:401 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fontawesome all 0.5.3-1 [1331 kB] 233s Get:402 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-forcats all 1.0.0-1 [369 kB] 233s Get:403 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gargle all 1.5.2-1 [737 kB] 233s Get:404 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB] 233s Get:405 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-uuid arm64 1.2-1-1 [48.7 kB] 233s Get:406 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-googledrive all 2.1.1-3 [1238 kB] 234s Get:407 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ids all 1.0.1-2 [124 kB] 234s Get:408 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 234s Get:409 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-googlesheets4 all 1.1.1-1 [520 kB] 234s Get:410 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB] 234s Get:411 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-goplot all 1.0.2-2 [2427 kB] 234s Get:412 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tzdb arm64 0.5.0-1 [530 kB] 234s Get:413 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vroom arm64 1.6.5-1 [832 kB] 234s Get:414 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-readr arm64 2.1.5-1 [756 kB] 234s Get:415 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-haven arm64 2.5.5-1 [355 kB] 234s Get:416 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB] 234s Get:417 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 234s Get:418 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-later arm64 1.4.1+dfsg-1 [141 kB] 234s Get:419 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-promises arm64 1.3.2+dfsg-1 [290 kB] 234s Get:420 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-httpuv arm64 1.6.15+dfsg-1 [489 kB] 234s Get:421 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-kernsmooth arm64 2.23-26-1 [93.3 kB] 234s Get:422 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 234s Get:423 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.50+dfsg-1 [840 kB] 234s Get:424 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timechange arm64 0.3.0-2 [175 kB] 234s Get:425 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lubridate arm64 1.9.4+dfsg-1 [1009 kB] 234s Get:426 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 234s Get:427 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-systemfonts arm64 1.2.1-1 [302 kB] 234s Get:428 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-textshaping arm64 0.3.7-2 [91.8 kB] 234s Get:429 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ragg arm64 1.3.3-1 [496 kB] 234s Get:430 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-readxl arm64 1.4.5-1 [342 kB] 234s Get:431 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tinytex all 0.56-1 [148 kB] 234s Get:432 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-modernizr all 3.13.0-0.1 [101 kB] 234s Get:433 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB] 234s Get:434 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 234s Get:435 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB] 234s Get:436 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rmarkdown all 2.29+dfsg-1 [1501 kB] 234s Get:437 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rstudioapi all 0.17.1-1 [299 kB] 234s Get:438 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reprex all 2.1.1-1 [468 kB] 234s Get:439 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-selectr all 0.4-2-2build1 [416 kB] 235s Get:440 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rvest all 1.0.5-1 [301 kB] 235s Get:441 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyverse all 2.0.0+dfsg-2 [85.2 kB] 235s Get:442 http://ftpmaster.internal/ubuntu resolute/universe arm64 bowtie arm64 1.3.1-3 [1346 kB] 235s Get:443 http://ftpmaster.internal/ubuntu resolute/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB] 235s Get:444 http://ftpmaster.internal/ubuntu resolute/universe arm64 rsem arm64 1.3.3+dfsg-3build1 [36.0 MB] 236s Get:445 http://ftpmaster.internal/ubuntu resolute/universe arm64 salmon arm64 1.10.2+ds1-1build2 [3239 kB] 236s Get:446 http://ftpmaster.internal/ubuntu resolute/universe arm64 samtools arm64 1.21-1 [609 kB] 236s Get:447 http://ftpmaster.internal/ubuntu resolute/universe arm64 subread arm64 2.0.8+dfsg-1 [553 kB] 236s Get:448 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjbzip2-java all 0.9.1-8 [42.4 kB] 236s Get:449 http://ftpmaster.internal/ubuntu resolute/universe arm64 trimmomatic all 0.39+dfsg-2 [758 kB] 236s Get:450 http://ftpmaster.internal/ubuntu resolute/universe arm64 trinityrnaseq arm64 2.15.2+dfsg-1 [1733 kB] 236s Get:451 http://ftpmaster.internal/ubuntu resolute/universe arm64 trinityrnaseq-examples arm64 2.15.2+dfsg-1 [299 MB] 260s Preconfiguring packages ... 260s Fetched 890 MB in 1min 14s (12.0 MB/s) 260s Selecting previously unselected package python3-numpy-dev:arm64. 260s (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 ... 83457 files and directories currently installed.) 260s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 260s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 260s Selecting previously unselected package libblas3:arm64. 260s Preparing to unpack .../001-libblas3_3.12.1-6build1_arm64.deb ... 260s Unpacking libblas3:arm64 (3.12.1-6build1) ... 260s Selecting previously unselected package libgfortran5:arm64. 260s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 260s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 260s Selecting previously unselected package liblapack3:arm64. 260s Preparing to unpack .../003-liblapack3_3.12.1-6build1_arm64.deb ... 260s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 260s Selecting previously unselected package python3-numpy. 260s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 260s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 260s Selecting previously unselected package libgdk-pixbuf2.0-common. 261s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.44.4+dfsg-1_all.deb ... 261s Unpacking libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 261s Selecting previously unselected package libjpeg-turbo8:arm64. 261s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 261s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 261s Selecting previously unselected package libjpeg8:arm64. 261s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_arm64.deb ... 261s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 261s Selecting previously unselected package libdeflate0:arm64. 261s Preparing to unpack .../008-libdeflate0_1.23-2_arm64.deb ... 261s Unpacking libdeflate0:arm64 (1.23-2) ... 261s Selecting previously unselected package libjbig0:arm64. 261s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 261s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 261s Selecting previously unselected package liblerc4:arm64. 261s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 261s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 261s Selecting previously unselected package libsharpyuv0:arm64. 261s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_arm64.deb ... 261s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 261s Selecting previously unselected package libwebp7:arm64. 261s Preparing to unpack .../012-libwebp7_1.5.0-0.1_arm64.deb ... 261s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 261s Selecting previously unselected package libtiff6:arm64. 261s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 261s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 261s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 261s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.44.4+dfsg-1_arm64.deb ... 261s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.44.4+dfsg-1) ... 261s Selecting previously unselected package gtk-update-icon-cache. 261s Preparing to unpack .../015-gtk-update-icon-cache_4.20.2+ds-1_arm64.deb ... 261s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 261s 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. 261s Unpacking gtk-update-icon-cache (4.20.2+ds-1) ... 261s Selecting previously unselected package hicolor-icon-theme. 261s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 261s Unpacking hicolor-icon-theme (0.18-2) ... 261s Selecting previously unselected package adwaita-icon-theme. 261s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 261s Unpacking adwaita-icon-theme (49.0-1) ... 261s Selecting previously unselected package at-spi2-common. 261s Preparing to unpack .../018-at-spi2-common_2.57.1-1_all.deb ... 261s Unpacking at-spi2-common (2.57.1-1) ... 261s Selecting previously unselected package libbamtools2.5.2:arm64. 261s Preparing to unpack .../019-libbamtools2.5.2_2.5.2+dfsg-6build1_arm64.deb ... 261s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-6build1) ... 261s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 261s Preparing to unpack .../020-libboost-filesystem1.83.0_1.83.0-5ubuntu2_arm64.deb ... 261s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-5ubuntu2) ... 261s Selecting previously unselected package libboost-program-options1.83.0:arm64. 261s Preparing to unpack .../021-libboost-program-options1.83.0_1.83.0-5ubuntu2_arm64.deb ... 261s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-5ubuntu2) ... 261s Selecting previously unselected package libboost-thread1.83.0:arm64. 261s Preparing to unpack .../022-libboost-thread1.83.0_1.83.0-5ubuntu2_arm64.deb ... 261s Unpacking libboost-thread1.83.0:arm64 (1.83.0-5ubuntu2) ... 262s Selecting previously unselected package libprotobuf32t64:arm64. 262s Preparing to unpack .../023-libprotobuf32t64_3.21.12-14build1_arm64.deb ... 262s Unpacking libprotobuf32t64:arm64 (3.21.12-14build1) ... 262s Selecting previously unselected package berkeley-express. 262s Preparing to unpack .../024-berkeley-express_1.5.3+dfsg-3build6_arm64.deb ... 262s Unpacking berkeley-express (1.5.3+dfsg-3build6) ... 262s Selecting previously unselected package ca-certificates-java. 262s Preparing to unpack .../025-ca-certificates-java_20240118_all.deb ... 262s Unpacking ca-certificates-java (20240118) ... 262s Selecting previously unselected package libdconf1:arm64. 262s Preparing to unpack .../026-libdconf1_0.49.0-1_arm64.deb ... 262s Unpacking libdconf1:arm64 (0.49.0-1) ... 262s Selecting previously unselected package dconf-service. 262s Preparing to unpack .../027-dconf-service_0.49.0-1_arm64.deb ... 262s Unpacking dconf-service (0.49.0-1) ... 262s Selecting previously unselected package dconf-gsettings-backend:arm64. 262s Preparing to unpack .../028-dconf-gsettings-backend_0.49.0-1_arm64.deb ... 262s Unpacking dconf-gsettings-backend:arm64 (0.49.0-1) ... 262s Selecting previously unselected package java-common. 262s Preparing to unpack .../029-java-common_0.76_all.deb ... 262s Unpacking java-common (0.76) ... 262s Selecting previously unselected package liblcms2-2:arm64. 262s Preparing to unpack .../030-liblcms2-2_2.16-2_arm64.deb ... 262s Unpacking liblcms2-2:arm64 (2.16-2) ... 262s Selecting previously unselected package libnspr4:arm64. 262s 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.../036-libatk1.0-0t64_2.57.1-1_arm64.deb ... 263s Unpacking libatk1.0-0t64:arm64 (2.57.1-1) ... 264s Selecting previously unselected package libxi6:arm64. 264s Preparing to unpack .../037-libxi6_2%3a1.8.2-1_arm64.deb ... 264s Unpacking libxi6:arm64 (2:1.8.2-1) ... 264s Selecting previously unselected package libatspi2.0-0t64:arm64. 264s Preparing to unpack .../038-libatspi2.0-0t64_2.57.1-1_arm64.deb ... 264s Unpacking libatspi2.0-0t64:arm64 (2.57.1-1) ... 264s Selecting previously unselected package libatk-bridge2.0-0t64:arm64. 264s Preparing to unpack .../039-libatk-bridge2.0-0t64_2.57.1-1_arm64.deb ... 264s Unpacking libatk-bridge2.0-0t64:arm64 (2.57.1-1) ... 264s Selecting previously unselected package fonts-dejavu-mono. 264s Preparing to unpack .../040-fonts-dejavu-mono_2.37-8_all.deb ... 264s Unpacking fonts-dejavu-mono (2.37-8) ... 264s Selecting previously unselected package fonts-dejavu-core. 264s Preparing to unpack .../041-fonts-dejavu-core_2.37-8_all.deb ... 264s Unpacking fonts-dejavu-core (2.37-8) ... 264s Selecting previously unselected package fontconfig-config. 264s Preparing to unpack .../042-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 264s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 264s Selecting previously unselected package libfontconfig1:arm64. 264s Preparing to unpack .../043-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 264s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 264s Selecting previously unselected package libpixman-1-0:arm64. 264s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_arm64.deb ... 264s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 264s Selecting previously unselected package libxcb-render0:arm64. 264s Preparing to unpack .../045-libxcb-render0_1.17.0-2build1_arm64.deb ... 264s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 264s Selecting previously unselected package libxcb-shm0:arm64. 264s Preparing to unpack .../046-libxcb-shm0_1.17.0-2build1_arm64.deb ... 264s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 264s Selecting previously unselected package libxrender1:arm64. 264s Preparing to unpack .../047-libxrender1_1%3a0.9.12-1_arm64.deb ... 264s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 264s Selecting previously unselected package libcairo2:arm64. 264s Preparing to unpack .../048-libcairo2_1.18.4-1build1_arm64.deb ... 264s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 264s Selecting previously unselected package libcairo-gobject2:arm64. 264s Preparing to unpack .../049-libcairo-gobject2_1.18.4-1build1_arm64.deb ... 264s Unpacking libcairo-gobject2:arm64 (1.18.4-1build1) ... 264s Selecting previously unselected package libcolord2:arm64. 264s Preparing to unpack .../050-libcolord2_1.4.7-3build1_arm64.deb ... 264s Unpacking libcolord2:arm64 (1.4.7-3build1) ... 264s Selecting previously unselected package libavahi-common-data:arm64. 264s Preparing to unpack .../051-libavahi-common-data_0.8-16ubuntu3_arm64.deb ... 264s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu3) ... 264s Selecting previously unselected package libavahi-common3:arm64. 264s Preparing to unpack .../052-libavahi-common3_0.8-16ubuntu3_arm64.deb ... 264s Unpacking libavahi-common3:arm64 (0.8-16ubuntu3) ... 265s Selecting previously unselected package libavahi-client3:arm64. 265s Preparing to unpack .../053-libavahi-client3_0.8-16ubuntu3_arm64.deb ... 265s Unpacking libavahi-client3:arm64 (0.8-16ubuntu3) ... 265s Selecting previously unselected package libcups2t64:arm64. 265s Preparing to unpack .../054-libcups2t64_2.4.12-0ubuntu3_arm64.deb ... 265s Unpacking libcups2t64:arm64 (2.4.12-0ubuntu3) ... 265s Selecting previously unselected package libepoxy0:arm64. 265s Preparing to unpack .../055-libepoxy0_1.5.10-2_arm64.deb ... 265s Unpacking libepoxy0:arm64 (1.5.10-2) ... 265s Selecting previously unselected package libgraphite2-3:arm64. 265s Preparing to unpack .../056-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 265s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 265s Selecting previously unselected package libharfbuzz0b:arm64. 265s Preparing to unpack .../057-libharfbuzz0b_12.1.0-1_arm64.deb ... 265s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 265s Selecting previously unselected package fontconfig. 265s Preparing to unpack .../058-fontconfig_2.15.0-2.3ubuntu1_arm64.deb ... 265s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 265s Selecting previously unselected package libthai-data. 265s Preparing to unpack .../059-libthai-data_0.1.29-2build1_all.deb ... 265s Unpacking libthai-data (0.1.29-2build1) ... 265s Selecting previously unselected package libdatrie1:arm64. 265s Preparing to unpack .../060-libdatrie1_0.2.13-4_arm64.deb ... 265s Unpacking libdatrie1:arm64 (0.2.13-4) ... 265s Selecting previously unselected package libthai0:arm64. 265s Preparing to unpack .../061-libthai0_0.1.29-2build1_arm64.deb ... 265s Unpacking libthai0:arm64 (0.1.29-2build1) ... 265s Selecting previously unselected package libpango-1.0-0:arm64. 265s Preparing to unpack .../062-libpango-1.0-0_1.56.3-2_arm64.deb ... 265s Unpacking libpango-1.0-0:arm64 (1.56.3-2) ... 265s Selecting previously unselected package libpangoft2-1.0-0:arm64. 265s Preparing to unpack .../063-libpangoft2-1.0-0_1.56.3-2_arm64.deb ... 265s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-2) ... 265s Selecting previously unselected package libpangocairo-1.0-0:arm64. 265s Preparing to unpack .../064-libpangocairo-1.0-0_1.56.3-2_arm64.deb ... 265s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-2) ... 265s Selecting previously unselected package libwayland-client0:arm64. 265s Preparing to unpack .../065-libwayland-client0_1.24.0-1build1_arm64.deb ... 265s Unpacking libwayland-client0:arm64 (1.24.0-1build1) ... 265s Selecting previously unselected package libwayland-cursor0:arm64. 265s Preparing to unpack .../066-libwayland-cursor0_1.24.0-1build1_arm64.deb ... 265s Unpacking libwayland-cursor0:arm64 (1.24.0-1build1) ... 265s Selecting previously unselected package libwayland-egl1:arm64. 265s Preparing to unpack .../067-libwayland-egl1_1.24.0-1build1_arm64.deb ... 265s Unpacking libwayland-egl1:arm64 (1.24.0-1build1) ... 265s Selecting previously unselected package libxcomposite1:arm64. 265s Preparing to unpack .../068-libxcomposite1_1%3a0.4.6-1_arm64.deb ... 265s Unpacking libxcomposite1:arm64 (1:0.4.6-1) ... 265s Selecting previously unselected package libxfixes3:arm64. 265s Preparing to unpack .../069-libxfixes3_1%3a6.0.0-2build1_arm64.deb ... 265s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ... 265s Selecting previously unselected package libxcursor1:arm64. 265s Preparing to unpack .../070-libxcursor1_1%3a1.2.3-1_arm64.deb ... 265s Unpacking libxcursor1:arm64 (1:1.2.3-1) ... 265s Selecting previously unselected package libxdamage1:arm64. 265s Preparing to unpack .../071-libxdamage1_1%3a1.1.6-1build1_arm64.deb ... 265s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ... 265s Selecting previously unselected package libxinerama1:arm64. 265s Preparing to unpack .../072-libxinerama1_2%3a1.1.4-3build1_arm64.deb ... 265s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ... 265s Selecting previously unselected package libxrandr2:arm64. 265s Preparing to unpack .../073-libxrandr2_2%3a1.5.4-1_arm64.deb ... 265s Unpacking libxrandr2:arm64 (2:1.5.4-1) ... 265s Selecting previously unselected package libgtk-3-common. 265s Preparing to unpack .../074-libgtk-3-common_3.24.50-1ubuntu2_all.deb ... 265s Unpacking libgtk-3-common (3.24.50-1ubuntu2) ... 265s Selecting previously unselected package libgtk-3-0t64:arm64. 265s Preparing to unpack .../075-libgtk-3-0t64_3.24.50-1ubuntu2_arm64.deb ... 265s Unpacking libgtk-3-0t64:arm64 (3.24.50-1ubuntu2) ... 266s Selecting previously unselected package libglvnd0:arm64. 266s Preparing to unpack .../076-libglvnd0_1.7.0-1build2_arm64.deb ... 266s Unpacking libglvnd0:arm64 (1.7.0-1build2) ... 266s Selecting previously unselected package libx11-xcb1:arm64. 266s Preparing to unpack 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.../082-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 266s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 266s Selecting previously unselected package libdrm-amdgpu1:arm64. 266s Preparing to unpack .../083-libdrm-amdgpu1_2.4.127-1ubuntu1_arm64.deb ... 266s Unpacking libdrm-amdgpu1:arm64 (2.4.127-1ubuntu1) ... 266s Selecting previously unselected package libxcb-randr0:arm64. 266s Preparing to unpack .../084-libxcb-randr0_1.17.0-2build1_arm64.deb ... 266s Unpacking libxcb-randr0:arm64 (1.17.0-2build1) ... 266s Selecting previously unselected package libxcb-sync1:arm64. 266s Preparing to unpack .../085-libxcb-sync1_1.17.0-2build1_arm64.deb ... 266s Unpacking libxcb-sync1:arm64 (1.17.0-2build1) ... 266s Selecting previously unselected package libxshmfence1:arm64. 266s Preparing to unpack .../086-libxshmfence1_1.3.3-1_arm64.deb ... 266s Unpacking libxshmfence1:arm64 (1.3.3-1) ... 266s Selecting previously unselected package mesa-libgallium:arm64. 266s Preparing to unpack .../087-mesa-libgallium_25.2.3-1ubuntu1_arm64.deb ... 266s Unpacking mesa-libgallium:arm64 (25.2.3-1ubuntu1) ... 266s Selecting previously unselected package libgbm1:arm64. 266s Preparing to unpack .../088-libgbm1_25.2.3-1ubuntu1_arm64.deb ... 266s Unpacking libgbm1:arm64 (25.2.3-1ubuntu1) ... 266s Selecting previously unselected package libvulkan1:arm64. 267s Preparing to unpack .../089-libvulkan1_1.4.321.0-1_arm64.deb ... 267s Unpacking libvulkan1:arm64 (1.4.321.0-1) ... 267s Selecting previously unselected package libgl1-mesa-dri:arm64. 267s Preparing to unpack .../090-libgl1-mesa-dri_25.2.3-1ubuntu1_arm64.deb ... 267s Unpacking libgl1-mesa-dri:arm64 (25.2.3-1ubuntu1) ... 267s Selecting previously unselected package libglx-mesa0:arm64. 267s Preparing to unpack .../091-libglx-mesa0_25.2.3-1ubuntu1_arm64.deb ... 267s Unpacking libglx-mesa0:arm64 (25.2.3-1ubuntu1) ... 267s Selecting previously unselected package libglx0:arm64. 267s Preparing to unpack .../092-libglx0_1.7.0-1build2_arm64.deb ... 267s Unpacking libglx0:arm64 (1.7.0-1build2) ... 267s Selecting previously unselected package libgl1:arm64. 267s Preparing to unpack .../093-libgl1_1.7.0-1build2_arm64.deb ... 267s Unpacking libgl1:arm64 (1.7.0-1build2) ... 267s Selecting previously unselected package libasound2-data. 267s Preparing to unpack .../094-libasound2-data_1.2.14-1ubuntu1_all.deb ... 267s Unpacking libasound2-data (1.2.14-1ubuntu1) ... 267s Selecting previously unselected package libasound2t64:arm64. 267s Preparing to unpack .../095-libasound2t64_1.2.14-1ubuntu1_arm64.deb ... 267s Unpacking libasound2t64:arm64 (1.2.14-1ubuntu1) ... 267s Selecting previously unselected package libgif7:arm64. 267s Preparing to unpack .../096-libgif7_5.2.2-1ubuntu2_arm64.deb ... 267s Unpacking libgif7:arm64 (5.2.2-1ubuntu2) ... 267s Selecting previously unselected package x11-common. 267s Preparing to unpack .../097-x11-common_1%3a7.7+24ubuntu1_all.deb ... 267s Unpacking x11-common (1:7.7+24ubuntu1) ... 267s Selecting previously unselected package libxtst6:arm64. 267s Preparing to unpack .../098-libxtst6_2%3a1.2.5-1_arm64.deb ... 267s Unpacking libxtst6:arm64 (2:1.2.5-1) ... 267s Selecting previously unselected package openjdk-21-jre:arm64. 267s Preparing to unpack .../099-openjdk-21-jre_21.0.9+10-1_arm64.deb ... 267s Unpacking openjdk-21-jre:arm64 (21.0.9+10-1) ... 267s Selecting previously unselected package default-jre. 267s Preparing to unpack .../100-default-jre_2%3a1.21-76_arm64.deb ... 267s Unpacking default-jre (2:1.21-76) ... 267s Selecting previously unselected package fonts-font-awesome. 267s Preparing to unpack .../101-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 267s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 267s Selecting previously unselected package fonts-glyphicons-halflings. 267s Preparing to unpack .../102-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 267s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 267s Selecting previously unselected package fonts-mathjax. 267s Preparing to unpack .../103-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 267s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 267s Selecting previously unselected package hisat2. 267s Preparing to unpack .../104-hisat2_2.2.1-5_arm64.deb ... 267s Unpacking hisat2 (2.2.1-5) ... 267s Selecting previously unselected package jaligner. 267s Preparing to unpack .../105-jaligner_1.0+dfsg-11_all.deb ... 267s Unpacking jaligner (1.0+dfsg-11) ... 267s Selecting previously unselected package javascript-common. 267s Preparing to unpack .../106-javascript-common_12+nmu1_all.deb ... 267s Unpacking javascript-common (12+nmu1) ... 268s Selecting previously unselected package libhtscodecs2:arm64. 268s Preparing to unpack .../107-libhtscodecs2_1.6.1-2_arm64.deb ... 268s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 268s Selecting previously unselected package libhts3t64:arm64. 268s Preparing to unpack .../108-libhts3t64_1.21+ds-1_arm64.deb ... 268s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 268s Selecting previously unselected package libjellyfish-2.0-2:arm64. 268s Preparing to unpack .../109-libjellyfish-2.0-2_2.3.1-4build2_arm64.deb ... 268s Unpacking libjellyfish-2.0-2:arm64 (2.3.1-4build2) ... 268s Selecting previously unselected package jellyfish. 268s Preparing to unpack .../110-jellyfish_2.3.1-4build2_arm64.deb ... 268s Unpacking jellyfish (2.3.1-4build2) ... 268s Selecting previously unselected package libhamcrest-java. 268s Preparing to unpack .../111-libhamcrest-java_2.2-2_all.deb ... 268s Unpacking libhamcrest-java (2.2-2) ... 268s Selecting previously unselected package junit4. 268s Preparing to unpack .../112-junit4_4.13.2-5_all.deb ... 268s Unpacking junit4 (4.13.2-5) ... 268s Selecting previously unselected package kallisto. 268s Preparing to unpack .../113-kallisto_0.48.0+dfsg-4build1_arm64.deb ... 268s Unpacking kallisto (0.48.0+dfsg-4build1) ... 268s Selecting previously unselected package libapache-pom-java. 268s Preparing to unpack .../114-libapache-pom-java_33-2_all.deb ... 268s Unpacking libapache-pom-java (33-2) ... 268s Selecting previously unselected package libasan8:arm64. 268s Preparing to unpack .../115-libasan8_15.2.0-5ubuntu1_arm64.deb ... 268s Unpacking libasan8:arm64 (15.2.0-5ubuntu1) ... 268s Selecting previously unselected package libatinject-jsr330-api-java. 268s Preparing to unpack .../116-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ... 268s Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ... 268s Selecting previously unselected package libcommons-parent-java. 268s Preparing to unpack .../117-libcommons-parent-java_56-1_all.deb ... 268s Unpacking libcommons-parent-java (56-1) ... 268s Selecting previously unselected package libcommons-lang3-java. 268s Preparing to unpack .../118-libcommons-lang3-java_3.17.0-1_all.deb ... 268s Unpacking libcommons-lang3-java (3.17.0-1) ... 268s Selecting previously unselected package libfreemarker-java. 268s Preparing to unpack .../119-libfreemarker-java_2.3.32-2.1_all.deb ... 268s Unpacking libfreemarker-java (2.3.32-2.1) ... 268s Selecting previously unselected package libgoogle-gson-java. 268s Preparing to unpack .../120-libgoogle-gson-java_2.10.1-1_all.deb ... 268s Unpacking libgoogle-gson-java (2.10.1-1) ... 268s Selecting previously unselected package libjoptsimple-java. 268s Preparing to unpack .../121-libjoptsimple-java_5.0.4-7_all.deb ... 268s Unpacking libjoptsimple-java (5.0.4-7) ... 268s Selecting previously unselected package libcommons-codec-java. 268s Preparing to unpack .../122-libcommons-codec-java_1.18.0-1_all.deb ... 268s Unpacking libcommons-codec-java (1.18.0-1) ... 268s Selecting previously unselected package libcommons-logging-java. 268s Preparing to unpack .../123-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 268s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 268s Selecting previously unselected package libhttpcore-java. 268s 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(2.19.0-2) ... 269s Selecting previously unselected package libbarclay-java. 269s Preparing to unpack .../130-libbarclay-java_5.0.0+dfsg-1_all.deb ... 269s Unpacking libbarclay-java (5.0.0+dfsg-1) ... 269s Selecting previously unselected package libgomp1:arm64. 269s Preparing to unpack .../131-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libitm1:arm64. 269s Preparing to unpack .../132-libitm1_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libitm1:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package liblsan0:arm64. 269s Preparing to unpack .../133-liblsan0_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking liblsan0:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libtsan2:arm64. 269s Preparing to unpack .../134-libtsan2_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libtsan2:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libubsan1:arm64. 269s Preparing to unpack .../135-libubsan1_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libubsan1:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libhwasan0:arm64. 269s Preparing to unpack .../136-libhwasan0_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libhwasan0:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libgcc-15-dev:arm64. 269s Preparing to unpack .../137-libgcc-15-dev_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libgcc-15-dev:arm64 (15.2.0-5ubuntu1) ... 269s Selecting previously unselected package libstdc++-15-dev:arm64. 269s Preparing to unpack .../138-libstdc++-15-dev_15.2.0-5ubuntu1_arm64.deb ... 269s Unpacking libstdc++-15-dev:arm64 (15.2.0-5ubuntu1) ... 270s Selecting previously unselected package libboost1.88-dev:arm64. 270s Preparing to unpack .../139-libboost1.88-dev_1.88.0-1.4ubuntu2_arm64.deb ... 270s Unpacking libboost1.88-dev:arm64 (1.88.0-1.4ubuntu2) ... 271s Selecting previously unselected package libboost-dev:arm64. 271s Preparing to unpack .../140-libboost-dev_1.88.0.0ubuntu1_arm64.deb ... 271s Unpacking libboost-dev:arm64 (1.88.0.0ubuntu1) ... 271s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 271s Preparing to unpack .../141-libboost-iostreams1.83.0_1.83.0-5ubuntu2_arm64.deb ... 271s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-5ubuntu2) ... 271s Selecting previously unselected package libclone-perl:arm64. 271s Preparing to unpack .../142-libclone-perl_0.47-1_arm64.deb ... 271s Unpacking libclone-perl:arm64 (0.47-1) ... 271s Selecting previously unselected package libcommons-collections3-java. 271s Preparing to unpack .../143-libcommons-collections3-java_3.2.2-3_all.deb ... 271s Unpacking libcommons-collections3-java (3.2.2-3) ... 271s Selecting previously unselected package libcommons-beanutils-java. 271s Preparing to unpack .../144-libcommons-beanutils-java_1.10.1-1.1_all.deb ... 271s Unpacking libcommons-beanutils-java (1.10.1-1.1) ... 271s Selecting previously unselected package libcommons-collections4-java. 271s Preparing to unpack .../145-libcommons-collections4-java_4.4-2_all.deb ... 271s Unpacking libcommons-collections4-java (4.4-2) ... 271s Selecting previously unselected package libcommons-io-java. 271s Preparing to unpack .../146-libcommons-io-java_2.19.0-1_all.deb ... 271s Unpacking libcommons-io-java (2.19.0-1) ... 271s Selecting previously unselected package libcommons-compress-java. 271s Preparing to unpack .../147-libcommons-compress-java_1.27.1-2_all.deb ... 271s Unpacking libcommons-compress-java (1.27.1-2) ... 271s Selecting previously unselected package libcommons-jexl2-java. 272s Preparing to unpack .../148-libcommons-jexl2-java_2.1.1-6_all.deb ... 272s Unpacking libcommons-jexl2-java (2.1.1-6) ... 272s Selecting previously unselected package libcommons-math3-java. 272s Preparing to unpack .../149-libcommons-math3-java_3.6.1-4_all.deb ... 272s Unpacking libcommons-math3-java (3.6.1-4) ... 272s Selecting previously unselected package libencode-locale-perl. 272s Preparing to unpack .../150-libencode-locale-perl_1.05-3_all.deb ... 272s Unpacking libencode-locale-perl (1.05-3) ... 272s Selecting previously unselected package libjsr305-java. 272s Preparing to unpack .../151-libjsr305-java_0.1~+svn49-12_all.deb ... 272s Unpacking libjsr305-java (0.1~+svn49-12) ... 272s Selecting previously unselected package libguava-java. 272s Preparing to unpack .../152-libguava-java_32.0.1-1_all.deb ... 272s Unpacking libguava-java (32.0.1-1) ... 272s Selecting previously unselected package liberror-prone-java. 272s Preparing to unpack .../153-liberror-prone-java_2.18.0-1_all.deb ... 272s Unpacking liberror-prone-java (2.18.0-1) ... 272s Selecting previously unselected package libezmorph-java. 272s Preparing to unpack .../154-libezmorph-java_1.0.6-4_all.deb ... 272s Unpacking libezmorph-java (1.0.6-4) ... 272s Selecting previously unselected package libtimedate-perl. 272s Preparing to unpack .../155-libtimedate-perl_2.3300-2_all.deb ... 272s Unpacking libtimedate-perl (2.3300-2) ... 272s Selecting previously unselected package libhttp-date-perl. 272s Preparing to unpack .../156-libhttp-date-perl_6.06-1_all.deb ... 272s Unpacking libhttp-date-perl (6.06-1) ... 272s Selecting previously unselected package libfile-listing-perl. 272s Preparing to unpack .../157-libfile-listing-perl_6.16-1_all.deb ... 272s Unpacking libfile-listing-perl (6.16-1) ... 272s Selecting previously unselected package libgatk-native-bindings-java. 272s Preparing to unpack .../158-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ... 272s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ... 272s Selecting previously unselected package libgetopt-java. 272s Preparing to unpack .../159-libgetopt-java_1.0.14+dfsg-6_all.deb ... 272s Unpacking libgetopt-java (1.0.14+dfsg-6) ... 272s Selecting previously unselected package libjaxen-java. 272s Preparing to unpack .../160-libjaxen-java_1.1.6-5_all.deb ... 272s Unpacking libjaxen-java (1.1.6-5) ... 272s Selecting previously unselected package libxml-commons-external-java. 272s Preparing to unpack .../161-libxml-commons-external-java_1.4.01-6_all.deb ... 272s Unpacking libxml-commons-external-java (1.4.01-6) ... 272s Selecting previously unselected package libxml-commons-resolver1.1-java. 272s Preparing to unpack .../162-libxml-commons-resolver1.1-java_1.2-11_all.deb ... 272s Unpacking libxml-commons-resolver1.1-java (1.2-11) ... 272s Selecting previously unselected package libxerces2-java. 272s Preparing to unpack .../163-libxerces2-java_2.12.2-1_all.deb ... 272s Unpacking libxerces2-java (2.12.2-1) ... 272s Selecting previously unselected package libxom-java. 272s Preparing to unpack .../164-libxom-java_1.3.9-1_all.deb ... 272s Unpacking libxom-java (1.3.9-1) ... 272s Selecting previously unselected package libjson-java. 272s Preparing to unpack .../165-libjson-java_3.1.0+dfsg-2_all.deb ... 272s Unpacking libjson-java (3.1.0+dfsg-2) ... 272s Selecting previously unselected package libmbedcrypto16:arm64. 272s Preparing to unpack .../166-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 272s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 272s Selecting previously unselected package libmbedx509-7:arm64. 272s Preparing to unpack .../167-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 272s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 273s Selecting previously unselected package libmbedtls21:arm64. 273s Preparing to unpack .../168-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 273s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 273s Selecting previously unselected package ncbi-vdb-data. 273s Preparing to unpack .../169-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 273s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 273s Selecting previously unselected package libncbi-vdb3:arm64. 273s Preparing to unpack .../170-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... 273s Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 273s Selecting previously unselected package libncbi-ngs3:arm64. 273s Preparing to unpack .../171-libncbi-ngs3_3.2.1+dfsg-4ubuntu5_arm64.deb ... 273s Unpacking libncbi-ngs3:arm64 (3.2.1+dfsg-4ubuntu5) ... 273s Selecting previously unselected package libngs-jni:arm64. 273s Preparing to unpack .../172-libngs-jni_3.2.1+dfsg-4ubuntu5_arm64.deb ... 273s Unpacking libngs-jni:arm64 (3.2.1+dfsg-4ubuntu5) ... 273s Selecting previously unselected package libngs-java:arm64. 273s Preparing to unpack .../173-libngs-java_3.2.1+dfsg-4ubuntu5_arm64.deb ... 273s Unpacking libngs-java:arm64 (3.2.1+dfsg-4ubuntu5) ... 273s Selecting previously unselected package librhino-java. 273s Preparing to unpack .../174-librhino-java_1.7.15-1_all.deb ... 273s Unpacking librhino-java (1.7.15-1) ... 273s Selecting previously unselected package libsnappy1v5:arm64. 273s Preparing to unpack .../175-libsnappy1v5_1.2.2-1_arm64.deb ... 273s Unpacking libsnappy1v5:arm64 (1.2.2-1) ... 273s Selecting previously unselected package libsnappy-jni. 273s Preparing to unpack .../176-libsnappy-jni_1.1.10.7-1_arm64.deb ... 273s Unpacking libsnappy-jni (1.1.10.7-1) ... 273s Selecting previously unselected package libsnappy-java. 273s Preparing to unpack .../177-libsnappy-java_1.1.10.7-1_all.deb ... 273s Unpacking libsnappy-java (1.1.10.7-1) ... 273s Selecting previously unselected package libhtsjdk-java. 273s Preparing to unpack .../178-libhtsjdk-java_4.1.3+dfsg-2_all.deb ... 273s Unpacking libhtsjdk-java (4.1.3+dfsg-2) ... 273s Selecting previously unselected package libgkl-java. 273s Preparing to unpack .../179-libgkl-java_0.8.11+dfsg-2build1_all.deb ... 273s Unpacking libgkl-java (0.8.11+dfsg-2build1) ... 273s Selecting previously unselected package libhtml-tagset-perl. 273s Preparing to unpack .../180-libhtml-tagset-perl_3.24-1_all.deb ... 273s Unpacking libhtml-tagset-perl (3.24-1) ... 273s Selecting previously unselected package liburi-perl. 273s Preparing to unpack .../181-liburi-perl_5.34-2_all.deb ... 273s Unpacking liburi-perl (5.34-2) ... 273s Selecting previously unselected package libhtml-parser-perl:arm64. 273s Preparing to unpack .../182-libhtml-parser-perl_3.83-1build1_arm64.deb ... 273s Unpacking libhtml-parser-perl:arm64 (3.83-1build1) ... 273s Selecting previously unselected package libhtml-tree-perl. 273s Preparing to unpack .../183-libhtml-tree-perl_5.07-3_all.deb ... 273s Unpacking libhtml-tree-perl (5.07-3) ... 273s Selecting previously unselected package libio-html-perl. 273s Preparing to unpack .../184-libio-html-perl_1.004-3_all.deb ... 273s Unpacking libio-html-perl (1.004-3) ... 273s Selecting previously unselected package liblwp-mediatypes-perl. 273s Preparing to unpack .../185-liblwp-mediatypes-perl_6.04-2_all.deb ... 273s Unpacking liblwp-mediatypes-perl (6.04-2) ... 273s Selecting previously unselected package libhttp-message-perl. 274s Preparing to unpack .../186-libhttp-message-perl_7.00-2ubuntu1_all.deb ... 274s Unpacking libhttp-message-perl (7.00-2ubuntu1) ... 274s Selecting previously unselected package libhttp-cookies-perl. 274s Preparing to unpack .../187-libhttp-cookies-perl_6.11-1_all.deb ... 274s Unpacking libhttp-cookies-perl (6.11-1) ... 274s Selecting previously unselected package libhttp-negotiate-perl. 274s Preparing to unpack .../188-libhttp-negotiate-perl_6.01-2_all.deb ... 274s Unpacking libhttp-negotiate-perl (6.01-2) ... 274s Selecting previously unselected package libhwloc15:arm64. 274s Preparing to unpack .../189-libhwloc15_2.12.2-1_arm64.deb ... 274s Unpacking libhwloc15:arm64 (2.12.2-1) ... 274s Selecting previously unselected package libice6:arm64. 274s Preparing to unpack .../190-libice6_2%3a1.1.1-1_arm64.deb ... 274s Unpacking libice6:arm64 (2:1.1.1-1) ... 274s Selecting previously unselected package libicu76:arm64. 274s Preparing to unpack .../191-libicu76_76.1-4ubuntu2_arm64.deb ... 274s Unpacking libicu76:arm64 (76.1-4ubuntu2) ... 274s Selecting previously unselected package perl-openssl-defaults:arm64. 274s Preparing to unpack .../192-perl-openssl-defaults_7build3_arm64.deb ... 274s Unpacking perl-openssl-defaults:arm64 (7build3) ... 274s Selecting previously unselected package libnet-ssleay-perl:arm64. 274s Preparing to unpack .../193-libnet-ssleay-perl_1.94-3_arm64.deb ... 274s Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... 274s Selecting previously unselected package libio-socket-ssl-perl. 274s Preparing to unpack .../194-libio-socket-ssl-perl_2.089-1_all.deb ... 274s Unpacking libio-socket-ssl-perl (2.089-1) ... 274s Selecting previously unselected package libjs-bootstrap. 274s Preparing to unpack .../195-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 274s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 274s Selecting previously unselected package libjs-popper.js. 274s Preparing to unpack .../196-libjs-popper.js_1.16.1+ds-6_all.deb ... 274s Unpacking libjs-popper.js (1.16.1+ds-6) ... 274s Selecting previously unselected package libjs-bootstrap4. 274s Preparing to unpack .../197-libjs-bootstrap4_4.6.2+dfsg-1_all.deb ... 274s Unpacking libjs-bootstrap4 (4.6.2+dfsg-1) ... 274s Selecting previously unselected package libjs-d3. 274s Preparing to unpack .../198-libjs-d3_3.5.17-4_all.deb ... 274s Unpacking libjs-d3 (3.5.17-4) ... 274s Selecting previously unselected package libjs-es5-shim. 275s Preparing to unpack .../199-libjs-es5-shim_4.6.7-2_all.deb ... 275s Unpacking libjs-es5-shim (4.6.7-2) ... 275s Selecting previously unselected package libjs-highlight.js. 275s Preparing to unpack .../200-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 275s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 275s Selecting previously unselected package libjs-jquery. 275s Preparing to unpack .../201-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 275s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 275s Selecting previously unselected package libjs-jquery-datatables. 275s Preparing to unpack .../202-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 275s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 275s Selecting previously unselected package libjs-sifter.js. 275s Preparing to unpack .../203-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 275s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 275s Selecting previously unselected package libjs-microplugin.js. 275s Preparing to unpack .../204-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 275s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 275s Selecting previously unselected package libjs-jquery-selectize.js. 275s Preparing to unpack .../205-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 275s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 275s Selecting previously unselected package libjs-jquery-ui. 275s Preparing to unpack .../206-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 275s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 275s Selecting previously unselected package libjs-json. 275s Preparing to unpack .../207-libjs-json_0~20221030+~1.0.8-1_all.deb ... 275s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 275s Selecting previously unselected package libjs-prettify. 275s Preparing to unpack .../208-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 275s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 275s Selecting previously unselected package libjs-underscore. 275s Preparing to unpack .../209-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 275s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 275s Selecting previously unselected package libjs-sphinxdoc. 275s Preparing to unpack .../210-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 275s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 275s Selecting previously unselected package libjung-free-java. 275s Preparing to unpack .../211-libjung-free-java_2.1.1-3_all.deb ... 275s Unpacking libjung-free-java (2.1.1-3) ... 275s Selecting previously unselected package liblua5.4-0:arm64. 275s Preparing to unpack .../212-liblua5.4-0_5.4.8-1_arm64.deb ... 275s Unpacking liblua5.4-0:arm64 (5.4.8-1) ... 275s Selecting previously unselected package libnet-http-perl. 275s Preparing to unpack .../213-libnet-http-perl_6.23-1_all.deb ... 275s Unpacking libnet-http-perl (6.23-1) ... 275s Selecting previously unselected package libtry-tiny-perl. 275s Preparing to unpack .../214-libtry-tiny-perl_0.32-1_all.deb ... 275s Unpacking libtry-tiny-perl (0.32-1) ... 275s Selecting previously unselected package libwww-robotrules-perl. 276s Preparing to unpack .../215-libwww-robotrules-perl_6.02-1_all.deb ... 276s Unpacking libwww-robotrules-perl (6.02-1) ... 276s Selecting previously unselected package libwww-perl. 276s Preparing to unpack .../216-libwww-perl_6.78-1_all.deb ... 276s Unpacking libwww-perl (6.78-1) ... 276s Selecting previously unselected package liblwp-protocol-https-perl. 276s Preparing to unpack .../217-liblwp-protocol-https-perl_6.14-1_all.deb ... 276s Unpacking liblwp-protocol-https-perl (6.14-1) ... 276s Selecting previously unselected package libpaper2:arm64. 276s Preparing to unpack .../218-libpaper2_2.2.5-0.3_arm64.deb ... 276s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 276s Selecting previously unselected package libpaper-utils. 276s Preparing to unpack .../219-libpaper-utils_2.2.5-0.3_arm64.deb ... 276s Unpacking libpaper-utils (2.2.5-0.3) ... 276s Selecting previously unselected package libpicard-java. 276s Preparing to unpack .../220-libpicard-java_3.3.0+dfsg-2_all.deb ... 276s Unpacking libpicard-java (3.3.0+dfsg-2) ... 276s Selecting previously unselected package libsm6:arm64. 276s Preparing to unpack .../221-libsm6_2%3a1.2.6-1_arm64.deb ... 276s Unpacking libsm6:arm64 (2:1.2.6-1) ... 276s Selecting previously unselected package libstaden-read14t64:arm64. 276s Preparing to unpack .../222-libstaden-read14t64_1.15.0-1.1build2_arm64.deb ... 276s Unpacking libstaden-read14t64:arm64 (1.15.0-1.1build2) ... 276s Selecting previously unselected package libtbbbind-2-5:arm64. 276s Preparing to unpack .../223-libtbbbind-2-5_2022.1.0-1_arm64.deb ... 276s Unpacking libtbbbind-2-5:arm64 (2022.1.0-1) ... 276s Selecting previously unselected package libtbbmalloc2:arm64. 276s Preparing to unpack .../224-libtbbmalloc2_2022.1.0-1_arm64.deb ... 276s Unpacking libtbbmalloc2:arm64 (2022.1.0-1) ... 276s Selecting previously unselected package libtbb12:arm64. 276s Preparing to unpack .../225-libtbb12_2022.1.0-1_arm64.deb ... 276s Unpacking libtbb12:arm64 (2022.1.0-1) ... 276s Selecting previously unselected package libtcl8.6:arm64. 276s Preparing to unpack .../226-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 276s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 276s Selecting previously unselected package libxft2:arm64. 276s Preparing to unpack .../227-libxft2_2.3.6-1build1_arm64.deb ... 276s Unpacking libxft2:arm64 (2.3.6-1build1) ... 276s Selecting previously unselected package libxss1:arm64. 276s Preparing to unpack .../228-libxss1_1%3a1.2.3-1build3_arm64.deb ... 276s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 276s Selecting previously unselected package libtk8.6:arm64. 276s Preparing to unpack .../229-libtk8.6_8.6.17-1_arm64.deb ... 276s Unpacking libtk8.6:arm64 (8.6.17-1) ... 276s Selecting previously unselected package libxt6t64:arm64. 276s Preparing to unpack .../230-libxt6t64_1%3a1.2.1-1.3_arm64.deb ... 276s Unpacking libxt6t64:arm64 (1:1.2.1-1.3) ... 277s Selecting previously unselected package ncbi-data. 277s Preparing to unpack .../231-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... 277s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... 277s Selecting previously unselected package ncbi-blast+. 277s Preparing to unpack .../232-ncbi-blast+_2.16.0+ds-7_arm64.deb ... 277s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 277s Selecting previously unselected package node-bootstrap-sass. 277s Preparing to unpack .../233-node-bootstrap-sass_3.4.3-2_all.deb ... 277s Unpacking node-bootstrap-sass (3.4.3-2) ... 277s Selecting previously unselected package node-html5shiv. 277s Preparing to unpack .../234-node-html5shiv_3.7.3+dfsg-5_all.deb ... 277s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 277s Selecting previously unselected package node-normalize.css. 277s Preparing to unpack .../235-node-normalize.css_8.0.1-5_all.deb ... 277s Unpacking node-normalize.css (8.0.1-5) ... 277s Selecting previously unselected package pandoc-data. 277s Preparing to unpack .../236-pandoc-data_3.1.11.1-3build1_all.deb ... 277s Unpacking pandoc-data (3.1.11.1-3build1) ... 277s Selecting previously unselected package pandoc. 277s Preparing to unpack .../237-pandoc_3.1.11.1+ds-4_arm64.deb ... 277s Unpacking pandoc (3.1.11.1+ds-4) ... 278s Selecting previously unselected package parafly. 278s Preparing to unpack .../238-parafly_0.1.0-5_arm64.deb ... 278s Unpacking parafly (0.1.0-5) ... 278s Selecting previously unselected package python3-hisat2. 278s Preparing to unpack .../239-python3-hisat2_2.2.1-5_all.deb ... 278s Unpacking python3-hisat2 (2.2.1-5) ... 278s Selecting previously unselected package python3-pysam. 278s Preparing to unpack .../240-python3-pysam_0.23.0+ds-1build2_arm64.deb ... 278s Unpacking python3-pysam (0.23.0+ds-1build2) ... 279s Selecting previously unselected package python3-htseq. 279s Preparing to unpack .../241-python3-htseq_2.0.9+dfsg-1build3_arm64.deb ... 279s Unpacking python3-htseq (2.0.9+dfsg-1build3) ... 279s Selecting previously unselected package zip. 279s Preparing to unpack .../242-zip_3.0-15ubuntu2_arm64.deb ... 279s Unpacking zip (3.0-15ubuntu2) ... 279s Selecting previously unselected package unzip. 279s Preparing to unpack .../243-unzip_6.0-28ubuntu7_arm64.deb ... 279s Unpacking unzip (6.0-28ubuntu7) ... 279s Selecting previously unselected package xdg-utils. 279s Preparing to unpack .../244-xdg-utils_1.2.1-2ubuntu1_all.deb ... 279s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 279s Selecting previously unselected package r-base-core. 279s Preparing to unpack .../245-r-base-core_4.5.1-1_arm64.deb ... 279s Unpacking r-base-core (4.5.1-1) ... 279s Selecting previously unselected package r-bioc-biocgenerics. 279s Preparing to unpack .../246-r-bioc-biocgenerics_0.52.0-2_all.deb ... 279s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 279s Selecting previously unselected package r-bioc-biobase. 279s Preparing to unpack .../247-r-bioc-biobase_2.66.0-2_arm64.deb ... 279s Unpacking r-bioc-biobase (2.66.0-2) ... 279s Selecting previously unselected package r-bioc-s4vectors. 279s Preparing to unpack .../248-r-bioc-s4vectors_0.44.0+dfsg-2_arm64.deb ... 279s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ... 280s Selecting previously unselected package r-bioc-iranges. 280s Preparing to unpack .../249-r-bioc-iranges_2.40.1-3_arm64.deb ... 280s Unpacking r-bioc-iranges (2.40.1-3) ... 280s Selecting previously unselected package r-cran-dbi. 280s Preparing to unpack .../250-r-cran-dbi_1.2.3-1_all.deb ... 280s Unpacking r-cran-dbi (1.2.3-1) ... 280s Selecting previously unselected package r-cran-bit. 280s Preparing to unpack .../251-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 280s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 280s Selecting previously unselected package r-cran-bit64. 280s Preparing to unpack .../252-r-cran-bit64_4.6.0-1-4_arm64.deb ... 280s Unpacking r-cran-bit64 (4.6.0-1-4) ... 280s Selecting previously unselected package r-cran-rlang. 280s Preparing to unpack .../253-r-cran-rlang_1.1.5-3_arm64.deb ... 280s Unpacking r-cran-rlang (1.1.5-3) ... 280s Selecting previously unselected package r-cran-cli. 280s Preparing to unpack .../254-r-cran-cli_3.6.4-1_arm64.deb ... 280s Unpacking r-cran-cli (3.6.4-1) ... 280s Selecting previously unselected package r-cran-glue. 280s Preparing to unpack .../255-r-cran-glue_1.8.0-1_arm64.deb ... 280s Unpacking r-cran-glue (1.8.0-1) ... 280s Selecting previously unselected package r-cran-lifecycle. 280s Preparing to unpack .../256-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 280s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 280s Selecting previously unselected package r-cran-vctrs. 280s Preparing to unpack .../257-r-cran-vctrs_0.6.5-1_arm64.deb ... 280s Unpacking r-cran-vctrs (0.6.5-1) ... 280s Selecting previously unselected package r-cran-blob. 280s Preparing to unpack .../258-r-cran-blob_1.2.4-1_all.deb ... 280s Unpacking r-cran-blob (1.2.4-1) ... 280s Selecting previously unselected package r-cran-fastmap. 280s Preparing to unpack .../259-r-cran-fastmap_1.2.0-1_arm64.deb ... 280s Unpacking r-cran-fastmap (1.2.0-1) ... 280s Selecting previously unselected package r-cran-cachem. 280s Preparing to unpack .../260-r-cran-cachem_1.1.0-1_arm64.deb ... 280s Unpacking r-cran-cachem (1.1.0-1) ... 280s Selecting previously unselected package r-cran-memoise. 280s Preparing to unpack .../261-r-cran-memoise_2.0.1-1_all.deb ... 280s Unpacking r-cran-memoise (2.0.1-1) ... 280s Selecting previously unselected package r-cran-pkgconfig. 280s Preparing to unpack .../262-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 280s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 280s Selecting previously unselected package r-cran-plogr. 281s Preparing to unpack .../263-r-cran-plogr_0.2.0-3build1_all.deb ... 281s Unpacking r-cran-plogr (0.2.0-3build1) ... 281s Selecting previously unselected package r-cran-cpp11. 281s Preparing to unpack .../264-r-cran-cpp11_0.5.2-1_all.deb ... 281s Unpacking r-cran-cpp11 (0.5.2-1) ... 281s Selecting previously unselected package r-cran-rsqlite. 281s Preparing to unpack .../265-r-cran-rsqlite_2.3.9-1_arm64.deb ... 281s Unpacking r-cran-rsqlite (2.3.9-1) ... 281s Selecting previously unselected package r-cran-curl. 281s Preparing to unpack .../266-r-cran-curl_6.2.1+dfsg-1ubuntu1_arm64.deb ... 281s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 281s Selecting previously unselected package r-cran-jsonlite. 281s Preparing to unpack .../267-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 281s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 281s Selecting previously unselected package r-cran-mime. 281s Preparing to unpack .../268-r-cran-mime_0.12-2_arm64.deb ... 281s Unpacking r-cran-mime (0.12-2) ... 281s Selecting previously unselected package r-cran-sys. 281s Preparing to unpack .../269-r-cran-sys_3.4.3-1_arm64.deb ... 281s Unpacking r-cran-sys (3.4.3-1) ... 281s Selecting previously unselected package r-cran-askpass. 281s Preparing to unpack .../270-r-cran-askpass_1.2.1-1_arm64.deb ... 281s Unpacking r-cran-askpass (1.2.1-1) ... 281s Selecting previously unselected package r-cran-openssl. 281s Preparing to unpack .../271-r-cran-openssl_2.3.2+dfsg-1_arm64.deb ... 281s Unpacking r-cran-openssl (2.3.2+dfsg-1) ... 281s Selecting previously unselected package r-cran-r6. 281s Preparing to unpack .../272-r-cran-r6_2.6.1-1_all.deb ... 281s Unpacking r-cran-r6 (2.6.1-1) ... 281s Selecting previously unselected package r-cran-httr. 281s Preparing to unpack .../273-r-cran-httr_1.4.7+dfsg-1_all.deb ... 281s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 281s Selecting previously unselected package r-cran-png. 281s Preparing to unpack .../274-r-cran-png_0.1-8-1build2_arm64.deb ... 281s Unpacking r-cran-png (0.1-8-1build2) ... 281s Selecting previously unselected package zlib1g-dev:arm64. 281s Preparing to unpack .../275-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_arm64.deb ... 281s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 281s Selecting previously unselected package r-bioc-zlibbioc. 281s Preparing to unpack .../276-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ... 281s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ... 281s Selecting previously unselected package r-bioc-xvector. 281s Preparing to unpack .../277-r-bioc-xvector_0.46.0-2_arm64.deb ... 281s Unpacking r-bioc-xvector (0.46.0-2) ... 281s Selecting previously unselected package r-bioc-ucsc.utils. 281s Preparing to unpack .../278-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ... 281s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ... 281s Selecting previously unselected package r-bioc-genomeinfodbdata. 281s Preparing to unpack .../279-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ... 281s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ... 282s Selecting previously unselected package r-bioc-genomeinfodb. 282s Preparing to unpack .../280-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ... 282s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 282s Selecting previously unselected package r-cran-crayon. 282s Preparing to unpack .../281-r-cran-crayon_1.5.3-1_all.deb ... 282s Unpacking r-cran-crayon (1.5.3-1) ... 282s Selecting previously unselected package r-bioc-biostrings. 282s Preparing to unpack .../282-r-bioc-biostrings_2.74.1+dfsg-2_arm64.deb ... 282s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ... 282s Selecting previously unselected package r-bioc-keggrest. 282s Preparing to unpack .../283-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ... 282s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ... 282s Selecting previously unselected package r-bioc-annotationdbi. 282s Preparing to unpack .../284-r-bioc-annotationdbi_1.68.0-2_all.deb ... 282s Unpacking r-bioc-annotationdbi (1.68.0-2) ... 282s Selecting previously unselected package r-cran-xml. 282s Preparing to unpack .../285-r-cran-xml_3.99-0.18-1build1_arm64.deb ... 282s Unpacking r-cran-xml (3.99-0.18-1build1) ... 282s Selecting previously unselected package r-cran-xtable. 282s Preparing to unpack .../286-r-cran-xtable_1%3a1.8-4-2_all.deb ... 282s Unpacking r-cran-xtable (1:1.8-4-2) ... 282s Selecting previously unselected package r-bioc-annotate. 282s Preparing to unpack .../287-r-bioc-annotate_1.84.0+dfsg-2_all.deb ... 282s Unpacking r-bioc-annotate (1.84.0+dfsg-2) ... 282s Selecting previously unselected package r-cran-generics. 282s Preparing to unpack .../288-r-cran-generics_0.1.3-1_all.deb ... 282s Unpacking r-cran-generics (0.1.3-1) ... 282s Selecting previously unselected package r-cran-magrittr. 282s Preparing to unpack .../289-r-cran-magrittr_2.0.3-1_arm64.deb ... 282s Unpacking r-cran-magrittr (2.0.3-1) ... 282s Selecting previously unselected package r-cran-utf8. 282s Preparing to unpack .../290-r-cran-utf8_1.2.4-1_arm64.deb ... 282s Unpacking r-cran-utf8 (1.2.4-1) ... 282s Selecting previously unselected package r-cran-pillar. 282s Preparing to unpack .../291-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 282s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 282s Selecting previously unselected package r-cran-fansi. 282s Preparing to unpack .../292-r-cran-fansi_1.0.6-2_arm64.deb ... 282s Unpacking r-cran-fansi (1.0.6-2) ... 282s Selecting previously unselected package r-cran-tibble. 282s Preparing to unpack .../293-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 282s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 283s Selecting previously unselected package r-cran-withr. 283s Preparing to unpack .../294-r-cran-withr_3.0.2+dfsg-1_all.deb ... 283s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 283s Selecting previously unselected package r-cran-tidyselect. 283s Preparing to unpack .../295-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 283s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 283s Selecting previously unselected package r-cran-dplyr. 283s Preparing to unpack .../296-r-cran-dplyr_1.1.4-4_arm64.deb ... 283s Unpacking r-cran-dplyr (1.1.4-4) ... 283s Selecting previously unselected package r-cran-purrr. 283s Preparing to unpack .../297-r-cran-purrr_1.0.4-1_arm64.deb ... 283s Unpacking r-cran-purrr (1.0.4-1) ... 283s Selecting previously unselected package r-cran-stringi. 283s Preparing to unpack .../298-r-cran-stringi_1.8.4-1build1_arm64.deb ... 283s Unpacking r-cran-stringi (1.8.4-1build1) ... 283s Selecting previously unselected package r-cran-stringr. 283s Preparing to unpack .../299-r-cran-stringr_1.5.1-1_all.deb ... 283s Unpacking r-cran-stringr (1.5.1-1) ... 283s Selecting previously unselected package r-cran-tidyr. 283s Preparing to unpack .../300-r-cran-tidyr_1.3.1-1_arm64.deb ... 283s Unpacking r-cran-tidyr (1.3.1-1) ... 283s Selecting previously unselected package r-cran-dbplyr. 283s Preparing to unpack .../301-r-cran-dbplyr_2.5.0+dfsg-1_all.deb ... 283s Unpacking r-cran-dbplyr (2.5.0+dfsg-1) ... 283s Selecting previously unselected package r-cran-filelock. 283s Preparing to unpack .../302-r-cran-filelock_1.0.3-1_arm64.deb ... 283s Unpacking r-cran-filelock (1.0.3-1) ... 283s Selecting previously unselected package r-bioc-biocfilecache. 283s Preparing to unpack .../303-r-bioc-biocfilecache_2.14.0+dfsg-2_all.deb ... 283s Unpacking r-bioc-biocfilecache (2.14.0+dfsg-2) ... 283s Selecting previously unselected package r-bioc-biocio. 283s Preparing to unpack .../304-r-bioc-biocio_1.16.0+dfsg-2_all.deb ... 283s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ... 283s Selecting previously unselected package r-cran-formatr. 283s Preparing to unpack .../305-r-cran-formatr_1.14-2_all.deb ... 283s Unpacking r-cran-formatr (1.14-2) ... 283s Selecting previously unselected package r-cran-lambda.r. 283s Preparing to unpack .../306-r-cran-lambda.r_1.2.4-2build1_all.deb ... 283s Unpacking r-cran-lambda.r (1.2.4-2build1) ... 283s Selecting previously unselected package r-cran-futile.options. 283s Preparing to unpack .../307-r-cran-futile.options_1.0.1-3build1_all.deb ... 283s Unpacking r-cran-futile.options (1.0.1-3build1) ... 283s Selecting previously unselected package r-cran-futile.logger. 283s Preparing to unpack .../308-r-cran-futile.logger_1.4.3-4build1_all.deb ... 283s Unpacking r-cran-futile.logger (1.4.3-4build1) ... 283s Selecting previously unselected package r-cran-snow. 284s Preparing to unpack .../309-r-cran-snow_1%3a0.4.4-2_all.deb ... 284s Unpacking r-cran-snow (1:0.4.4-2) ... 284s Selecting previously unselected package r-cran-codetools. 284s Preparing to unpack .../310-r-cran-codetools_0.2-20-1_all.deb ... 284s Unpacking r-cran-codetools (0.2-20-1) ... 284s Selecting previously unselected package r-cran-bh. 284s Preparing to unpack .../311-r-cran-bh_1.84.0-1_all.deb ... 284s Unpacking r-cran-bh (1.84.0-1) ... 284s Selecting previously unselected package r-bioc-biocparallel. 284s Preparing to unpack .../312-r-bioc-biocparallel_1.40.0-2_arm64.deb ... 284s Unpacking r-bioc-biocparallel (1.40.0-2) ... 284s Selecting previously unselected package r-cran-hms. 284s Preparing to unpack .../313-r-cran-hms_1.1.3-1_all.deb ... 284s Unpacking r-cran-hms (1.1.3-1) ... 284s Selecting previously unselected package r-cran-prettyunits. 284s Preparing to unpack .../314-r-cran-prettyunits_1.2.0-1_all.deb ... 284s Unpacking r-cran-prettyunits (1.2.0-1) ... 284s Selecting previously unselected package r-cran-progress. 284s Preparing to unpack .../315-r-cran-progress_1.2.3-1_all.deb ... 284s Unpacking r-cran-progress (1.2.3-1) ... 284s Selecting previously unselected package r-cran-rappdirs. 284s Preparing to unpack .../316-r-cran-rappdirs_0.3.3-1_arm64.deb ... 284s Unpacking r-cran-rappdirs (0.3.3-1) ... 284s Selecting previously unselected package r-cran-httr2. 284s Preparing to unpack .../317-r-cran-httr2_1.1.1-1_all.deb ... 284s Unpacking r-cran-httr2 (1.1.1-1) ... 284s Selecting previously unselected package r-cran-digest. 284s Preparing to unpack .../318-r-cran-digest_0.6.37-1_arm64.deb ... 284s Unpacking r-cran-digest (0.6.37-1) ... 284s Selecting previously unselected package r-cran-xml2. 284s Preparing to unpack .../319-r-cran-xml2_1.4.0-1ubuntu1_arm64.deb ... 284s Unpacking r-cran-xml2 (1.4.0-1ubuntu1) ... 284s Selecting previously unselected package r-bioc-biomart. 284s Preparing to unpack .../320-r-bioc-biomart_2.62.1+dfsg-1_all.deb ... 284s Unpacking r-bioc-biomart (2.62.1+dfsg-1) ... 284s Selecting previously unselected package r-cran-lattice. 284s Preparing to unpack .../321-r-cran-lattice_0.22-7-1_arm64.deb ... 284s Unpacking r-cran-lattice (0.22-7-1) ... 284s Selecting previously unselected package r-cran-matrix. 284s Preparing to unpack .../322-r-cran-matrix_1.7-3-1_arm64.deb ... 284s Unpacking r-cran-matrix (1.7-3-1) ... 284s Selecting previously unselected package r-cran-matrixstats. 284s Preparing to unpack .../323-r-cran-matrixstats_1.5.0-1_arm64.deb ... 284s Unpacking r-cran-matrixstats (1.5.0-1) ... 284s Selecting previously unselected package r-bioc-matrixgenerics. 285s Preparing to unpack .../324-r-bioc-matrixgenerics_1.18.1-1_all.deb ... 285s Unpacking r-bioc-matrixgenerics (1.18.1-1) ... 285s Selecting previously unselected package r-cran-abind. 285s Preparing to unpack .../325-r-cran-abind_1.4-8-1_all.deb ... 285s Unpacking r-cran-abind (1.4-8-1) ... 285s Selecting previously unselected package r-bioc-s4arrays. 285s Preparing to unpack .../326-r-bioc-s4arrays_1.6.0+dfsg-2_arm64.deb ... 285s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ... 285s Selecting previously unselected package r-bioc-sparsearray. 285s Preparing to unpack .../327-r-bioc-sparsearray_1.6.2+dfsg-2_arm64.deb ... 285s Unpacking r-bioc-sparsearray (1.6.2+dfsg-2) ... 285s Selecting previously unselected package r-bioc-delayedarray. 285s Preparing to unpack .../328-r-bioc-delayedarray_0.32.0+dfsg-2_arm64.deb ... 285s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ... 285s Selecting previously unselected package r-bioc-genomicranges. 285s Preparing to unpack .../329-r-bioc-genomicranges_1.58.0+dfsg-2_arm64.deb ... 285s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ... 285s Selecting previously unselected package r-bioc-summarizedexperiment. 285s Preparing to unpack .../330-r-bioc-summarizedexperiment_1.36.0+dfsg-2_all.deb ... 285s Unpacking r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 285s Selecting previously unselected package r-cran-locfit. 285s Preparing to unpack .../331-r-cran-locfit_1.5-9.12-1_arm64.deb ... 285s Unpacking r-cran-locfit (1.5-9.12-1) ... 285s Selecting previously unselected package r-cran-gtable. 285s Preparing to unpack .../332-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 285s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 285s Selecting previously unselected package r-cran-isoband. 285s Preparing to unpack .../333-r-cran-isoband_0.2.7-1_arm64.deb ... 285s Unpacking r-cran-isoband (0.2.7-1) ... 285s Selecting previously unselected package r-cran-mass. 285s Preparing to unpack .../334-r-cran-mass_7.3-65-1_arm64.deb ... 285s Unpacking r-cran-mass (7.3-65-1) ... 285s Selecting previously unselected package r-cran-nlme. 285s Preparing to unpack .../335-r-cran-nlme_3.1.168-1_arm64.deb ... 285s Unpacking r-cran-nlme (3.1.168-1) ... 285s Selecting previously unselected package r-cran-mgcv. 285s Preparing to unpack .../336-r-cran-mgcv_1.9-3-1_arm64.deb ... 285s Unpacking r-cran-mgcv (1.9-3-1) ... 285s Selecting previously unselected package r-cran-farver. 286s Preparing to unpack .../337-r-cran-farver_2.1.2-1_arm64.deb ... 286s Unpacking r-cran-farver (2.1.2-1) ... 286s Selecting previously unselected package r-cran-labeling. 286s Preparing to unpack .../338-r-cran-labeling_0.4.3-1_all.deb ... 286s Unpacking r-cran-labeling (0.4.3-1) ... 286s Selecting previously unselected package r-cran-colorspace. 286s Preparing to unpack .../339-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 286s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 286s Selecting previously unselected package r-cran-munsell. 286s Preparing to unpack .../340-r-cran-munsell_0.5.1-1_all.deb ... 286s Unpacking r-cran-munsell (0.5.1-1) ... 286s Selecting previously unselected package r-cran-rcolorbrewer. 286s Preparing to unpack .../341-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 286s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 286s Selecting previously unselected package r-cran-viridislite. 286s Preparing to unpack .../342-r-cran-viridislite_0.4.2-2_all.deb ... 286s Unpacking r-cran-viridislite (0.4.2-2) ... 286s Selecting previously unselected package r-cran-scales. 286s Preparing to unpack .../343-r-cran-scales_1.3.0-1_all.deb ... 286s Unpacking r-cran-scales (1.3.0-1) ... 286s Selecting previously unselected package r-cran-ggplot2. 286s Preparing to unpack .../344-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 286s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 286s Selecting previously unselected package r-cran-littler. 286s Preparing to unpack .../345-r-cran-littler_0.3.21-1_arm64.deb ... 286s Unpacking r-cran-littler (0.3.21-1) ... 286s Selecting previously unselected package r-cran-pkgkitten. 286s Preparing to unpack .../346-r-cran-pkgkitten_0.2.4-1_all.deb ... 286s Unpacking r-cran-pkgkitten (0.2.4-1) ... 286s Selecting previously unselected package r-cran-rcpp. 286s Preparing to unpack .../347-r-cran-rcpp_1.1.0-1_arm64.deb ... 286s Unpacking r-cran-rcpp (1.1.0-1) ... 286s Selecting previously unselected package r-cran-rcpparmadillo. 286s Preparing to unpack .../348-r-cran-rcpparmadillo_14.6.0-1-1_arm64.deb ... 286s Unpacking r-cran-rcpparmadillo (14.6.0-1-1) ... 286s Selecting previously unselected package r-bioc-deseq2. 286s Preparing to unpack .../349-r-bioc-deseq2_1.46.0+dfsg-2_arm64.deb ... 286s Unpacking r-bioc-deseq2 (1.46.0+dfsg-2) ... 286s Selecting previously unselected package r-cran-hwriter. 286s Preparing to unpack .../350-r-cran-hwriter_1.3.2.1-1_all.deb ... 286s Unpacking r-cran-hwriter (1.3.2.1-1) ... 287s Selecting previously unselected package r-cran-bitops. 287s Preparing to unpack .../351-r-cran-bitops_1.0-9-1_arm64.deb ... 287s Unpacking r-cran-bitops (1.0-9-1) ... 287s Selecting previously unselected package r-bioc-rhtslib. 287s Preparing to unpack .../352-r-bioc-rhtslib_3.2.0+dfsg-2_arm64.deb ... 287s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ... 287s Selecting previously unselected package r-bioc-rsamtools. 287s Preparing to unpack .../353-r-bioc-rsamtools_2.22.0+dfsg-2_arm64.deb ... 287s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ... 287s Selecting previously unselected package r-cran-statmod. 287s Preparing to unpack .../354-r-cran-statmod_1.5.0-1_arm64.deb ... 287s Unpacking r-cran-statmod (1.5.0-1) ... 287s Selecting previously unselected package r-bioc-geneplotter. 287s Preparing to unpack .../355-r-bioc-geneplotter_1.84.0+dfsg-2_all.deb ... 287s Unpacking r-bioc-geneplotter (1.84.0+dfsg-2) ... 287s Selecting previously unselected package r-cran-survival. 287s Preparing to unpack .../356-r-cran-survival_3.8-3-1_arm64.deb ... 287s Unpacking r-cran-survival (3.8-3-1) ... 287s Selecting previously unselected package r-bioc-genefilter. 287s Preparing to unpack .../357-r-bioc-genefilter_1.88.0-2_arm64.deb ... 287s Unpacking r-bioc-genefilter (1.88.0-2) ... 287s Selecting previously unselected package r-bioc-dexseq. 287s Preparing to unpack .../358-r-bioc-dexseq_1.52.0+dfsg-2_all.deb ... 287s Unpacking r-bioc-dexseq (1.52.0+dfsg-2) ... 287s Selecting previously unselected package r-bioc-limma. 287s Preparing to unpack .../359-r-bioc-limma_3.62.2+dfsg-1_arm64.deb ... 287s Unpacking r-bioc-limma (3.62.2+dfsg-1) ... 287s Selecting previously unselected package r-bioc-edger. 287s Preparing to unpack .../360-r-bioc-edger_4.4.2+dfsg-1_arm64.deb ... 287s Unpacking r-bioc-edger (4.4.2+dfsg-1) ... 287s Selecting previously unselected package r-bioc-genomicalignments. 287s Preparing to unpack .../361-r-bioc-genomicalignments_1.42.0-2_arm64.deb ... 287s Unpacking r-bioc-genomicalignments (1.42.0-2) ... 287s Selecting previously unselected package r-cran-rcurl. 287s Preparing to unpack .../362-r-cran-rcurl_1.98-1.16+dfsg-1_arm64.deb ... 287s Unpacking r-cran-rcurl (1.98-1.16+dfsg-1) ... 287s Selecting previously unselected package r-cran-rjson. 287s Preparing to unpack .../363-r-cran-rjson_0.2.23-1_arm64.deb ... 287s Unpacking r-cran-rjson (0.2.23-1) ... 287s Selecting previously unselected package r-cran-yaml. 287s Preparing to unpack .../364-r-cran-yaml_2.3.10-1_arm64.deb ... 287s Unpacking r-cran-yaml (2.3.10-1) ... 287s Selecting previously unselected package r-cran-restfulr. 288s Preparing to unpack .../365-r-cran-restfulr_0.0.15-1_arm64.deb ... 288s Unpacking r-cran-restfulr (0.0.15-1) ... 288s Selecting previously unselected package r-bioc-rtracklayer. 288s Preparing to unpack .../366-r-bioc-rtracklayer_1.66.0-3_arm64.deb ... 288s Unpacking r-bioc-rtracklayer (1.66.0-3) ... 288s Selecting previously unselected package r-bioc-genomicfeatures. 288s Preparing to unpack .../367-r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ... 288s Unpacking r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 288s Selecting previously unselected package r-bioc-txdbmaker. 288s Preparing to unpack .../368-r-bioc-txdbmaker_1.2.1+ds-2_all.deb ... 288s Unpacking r-bioc-txdbmaker (1.2.1+ds-2) ... 288s Selecting previously unselected package r-bioc-genelendatabase. 288s Preparing to unpack .../369-r-bioc-genelendatabase_1.42.0-3_all.deb ... 288s Unpacking r-bioc-genelendatabase (1.42.0-3) ... 288s Selecting previously unselected package r-bioc-go.db. 288s Preparing to unpack .../370-r-bioc-go.db_3.20.0-2_all.deb ... 288s Unpacking r-bioc-go.db (3.20.0-2) ... 289s Selecting previously unselected package r-cran-biasedurn. 289s Preparing to unpack .../371-r-cran-biasedurn_2.0.12-1_arm64.deb ... 289s Unpacking r-cran-biasedurn (2.0.12-1) ... 289s Selecting previously unselected package r-bioc-goseq. 289s Preparing to unpack .../372-r-bioc-goseq_1.58.0-2_all.deb ... 289s Unpacking r-bioc-goseq (1.58.0-2) ... 289s Selecting previously unselected package r-cran-plyr. 289s Preparing to unpack .../373-r-cran-plyr_1.8.9-1_arm64.deb ... 289s Unpacking r-cran-plyr (1.8.9-1) ... 289s Selecting previously unselected package r-cran-reshape2. 289s Preparing to unpack .../374-r-cran-reshape2_1.4.4-2build1_arm64.deb ... 289s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 289s Selecting previously unselected package r-bioc-qvalue. 289s Preparing to unpack .../375-r-bioc-qvalue_2.38.0-2_all.deb ... 289s Unpacking r-bioc-qvalue (2.38.0-2) ... 289s Selecting previously unselected package r-cran-findpython. 289s Preparing to unpack .../376-r-cran-findpython_1.0.9-1_all.deb ... 289s Unpacking r-cran-findpython (1.0.9-1) ... 289s Selecting previously unselected package r-cran-argparse. 289s Preparing to unpack .../377-r-cran-argparse_2.2.5+dfsg-1_all.deb ... 289s Unpacking r-cran-argparse (2.2.5+dfsg-1) ... 289s Selecting previously unselected package r-cran-backports. 289s Preparing to unpack .../378-r-cran-backports_1.5.0-2_arm64.deb ... 289s Unpacking r-cran-backports (1.5.0-2) ... 289s Selecting previously unselected package r-cran-base64enc. 289s Preparing to unpack .../379-r-cran-base64enc_0.1-3-3_arm64.deb ... 289s Unpacking r-cran-base64enc (0.1-3-3) ... 289s Selecting previously unselected package r-cran-broom. 289s Preparing to unpack .../380-r-cran-broom_1.0.7+dfsg-1_all.deb ... 289s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 289s Selecting previously unselected package r-cran-htmltools. 289s Preparing to unpack .../381-r-cran-htmltools_0.5.8.1-1_arm64.deb ... 289s Unpacking r-cran-htmltools (0.5.8.1-1) ... 289s Selecting previously unselected package r-cran-jquerylib. 289s Preparing to unpack .../382-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 289s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 289s Selecting previously unselected package r-cran-fs. 290s Preparing to unpack .../383-r-cran-fs_1.6.5+dfsg-1_arm64.deb ... 290s Unpacking r-cran-fs (1.6.5+dfsg-1) ... 290s Selecting previously unselected package r-cran-sass. 290s Preparing to unpack .../384-r-cran-sass_0.4.9+dfsg-1_arm64.deb ... 290s Unpacking r-cran-sass (0.4.9+dfsg-1) ... 290s Selecting previously unselected package r-cran-bslib. 290s Preparing to unpack .../385-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ... 290s Unpacking r-cran-bslib (0.9.0+dfsg-3build1) ... 290s Selecting previously unselected package r-cran-ps. 290s Preparing to unpack .../386-r-cran-ps_1.9.0-1_arm64.deb ... 290s Unpacking r-cran-ps (1.9.0-1) ... 290s Selecting previously unselected package r-cran-processx. 290s Preparing to unpack .../387-r-cran-processx_3.8.6-1_arm64.deb ... 290s Unpacking r-cran-processx (3.8.6-1) ... 290s Selecting previously unselected package r-cran-callr. 290s Preparing to unpack .../388-r-cran-callr_3.7.6-1_all.deb ... 290s Unpacking r-cran-callr (3.7.6-1) ... 290s Selecting previously unselected package r-cran-rematch. 290s Preparing to unpack .../389-r-cran-rematch_2.0.0-1_all.deb ... 290s Unpacking r-cran-rematch (2.0.0-1) ... 290s Selecting previously unselected package r-cran-cellranger. 290s Preparing to unpack .../390-r-cran-cellranger_1.1.0-3_all.deb ... 290s Unpacking r-cran-cellranger (1.1.0-3) ... 290s Selecting previously unselected package r-cran-clipr. 290s Preparing to unpack .../391-r-cran-clipr_0.8.0-1_all.deb ... 290s Unpacking r-cran-clipr (0.8.0-1) ... 290s Selecting previously unselected package r-cran-cluster. 290s Preparing to unpack .../392-r-cran-cluster_2.1.8.1-1_arm64.deb ... 290s Unpacking r-cran-cluster (2.1.8.1-1) ... 290s Selecting previously unselected package r-cran-commonmark. 290s Preparing to unpack .../393-r-cran-commonmark_1.9.5-1_arm64.deb ... 290s Unpacking r-cran-commonmark (1.9.5-1) ... 290s Selecting previously unselected package r-cran-conflicted. 290s Preparing to unpack .../394-r-cran-conflicted_1.2.0-1.1_all.deb ... 290s Unpacking r-cran-conflicted (1.2.0-1.1) ... 290s Selecting previously unselected package r-cran-data.table. 290s Preparing to unpack .../395-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 290s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 290s Selecting previously unselected package r-cran-dtplyr. 290s Preparing to unpack .../396-r-cran-dtplyr_1.3.1-1_all.deb ... 290s Unpacking r-cran-dtplyr (1.3.1-1) ... 290s Selecting previously unselected package r-cran-ellipsis. 290s Preparing to unpack .../397-r-cran-ellipsis_0.3.2-2_arm64.deb ... 290s Unpacking r-cran-ellipsis (0.3.2-2) ... 290s Selecting previously unselected package r-cran-evaluate. 290s Preparing to unpack .../398-r-cran-evaluate_1.0.3-1_all.deb ... 290s Unpacking r-cran-evaluate (1.0.3-1) ... 290s Selecting previously unselected package r-cran-fastcluster. 290s Preparing to unpack .../399-r-cran-fastcluster_1.3.0-1build1_arm64.deb ... 290s Unpacking r-cran-fastcluster (1.3.0-1build1) ... 290s Selecting previously unselected package r-cran-fontawesome. 290s Preparing to unpack .../400-r-cran-fontawesome_0.5.3-1_all.deb ... 290s Unpacking r-cran-fontawesome (0.5.3-1) ... 291s Selecting previously unselected package r-cran-forcats. 291s Preparing to unpack .../401-r-cran-forcats_1.0.0-1_all.deb ... 291s Unpacking r-cran-forcats (1.0.0-1) ... 291s Selecting previously unselected package r-cran-gargle. 291s Preparing to unpack .../402-r-cran-gargle_1.5.2-1_all.deb ... 291s Unpacking r-cran-gargle (1.5.2-1) ... 291s Selecting previously unselected package r-cran-ggdendro. 291s Preparing to unpack .../403-r-cran-ggdendro_0.2.0+dfsg-1_all.deb ... 291s Unpacking r-cran-ggdendro (0.2.0+dfsg-1) ... 291s Selecting previously unselected package r-cran-uuid. 291s Preparing to unpack .../404-r-cran-uuid_1.2-1-1_arm64.deb ... 291s Unpacking r-cran-uuid (1.2-1-1) ... 291s Selecting previously unselected package r-cran-googledrive. 291s Preparing to unpack .../405-r-cran-googledrive_2.1.1-3_all.deb ... 291s Unpacking r-cran-googledrive (2.1.1-3) ... 291s Selecting previously unselected package r-cran-ids. 291s Preparing to unpack .../406-r-cran-ids_1.0.1-2_all.deb ... 291s Unpacking r-cran-ids (1.0.1-2) ... 291s Selecting previously unselected package r-cran-rematch2. 291s Preparing to unpack .../407-r-cran-rematch2_2.1.2-2build1_all.deb ... 291s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 291s Selecting previously unselected package r-cran-googlesheets4. 291s Preparing to unpack .../408-r-cran-googlesheets4_1.1.1-1_all.deb ... 291s Unpacking r-cran-googlesheets4 (1.1.1-1) ... 291s Selecting previously unselected package r-cran-gridextra. 291s Preparing to unpack .../409-r-cran-gridextra_2.3-3build1_all.deb ... 291s Unpacking r-cran-gridextra (2.3-3build1) ... 291s Selecting previously unselected package r-cran-goplot. 291s Preparing to unpack .../410-r-cran-goplot_1.0.2-2_all.deb ... 291s Unpacking r-cran-goplot (1.0.2-2) ... 291s Selecting previously unselected package r-cran-tzdb. 291s Preparing to unpack .../411-r-cran-tzdb_0.5.0-1_arm64.deb ... 291s Unpacking r-cran-tzdb (0.5.0-1) ... 291s Selecting previously unselected package r-cran-vroom. 291s Preparing to unpack .../412-r-cran-vroom_1.6.5-1_arm64.deb ... 291s Unpacking r-cran-vroom (1.6.5-1) ... 291s Selecting previously unselected package r-cran-readr. 291s Preparing to unpack .../413-r-cran-readr_2.1.5-1_arm64.deb ... 291s Unpacking r-cran-readr (2.1.5-1) ... 291s Selecting previously unselected package r-cran-haven. 291s Preparing to unpack .../414-r-cran-haven_2.5.5-1_arm64.deb ... 291s Unpacking r-cran-haven (2.5.5-1) ... 292s Selecting previously unselected package r-cran-xfun. 292s Preparing to unpack .../415-r-cran-xfun_0.51+dfsg-1_arm64.deb ... 292s Unpacking r-cran-xfun (0.51+dfsg-1) ... 292s Selecting previously unselected package r-cran-highr. 292s Preparing to unpack .../416-r-cran-highr_0.11+dfsg-1_all.deb ... 292s Unpacking r-cran-highr (0.11+dfsg-1) ... 292s Selecting previously unselected package r-cran-later. 292s Preparing to unpack .../417-r-cran-later_1.4.1+dfsg-1_arm64.deb ... 292s Unpacking r-cran-later (1.4.1+dfsg-1) ... 292s Selecting previously unselected package r-cran-promises. 292s Preparing to unpack .../418-r-cran-promises_1.3.2+dfsg-1_arm64.deb ... 292s Unpacking r-cran-promises (1.3.2+dfsg-1) ... 292s Selecting previously unselected package r-cran-httpuv. 292s Preparing to unpack .../419-r-cran-httpuv_1.6.15+dfsg-1_arm64.deb ... 292s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ... 292s Selecting previously unselected package r-cran-kernsmooth. 292s Preparing to unpack .../420-r-cran-kernsmooth_2.23-26-1_arm64.deb ... 292s Unpacking r-cran-kernsmooth (2.23-26-1) ... 292s Selecting previously unselected package libjs-mathjax. 292s Preparing to unpack .../421-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 292s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 292s Selecting previously unselected package r-cran-knitr. 292s Preparing to unpack .../422-r-cran-knitr_1.50+dfsg-1_all.deb ... 292s Unpacking r-cran-knitr (1.50+dfsg-1) ... 293s Selecting previously unselected package r-cran-timechange. 293s Preparing to unpack .../423-r-cran-timechange_0.3.0-2_arm64.deb ... 293s Unpacking r-cran-timechange (0.3.0-2) ... 293s Selecting previously unselected package r-cran-lubridate. 293s Preparing to unpack .../424-r-cran-lubridate_1.9.4+dfsg-1_arm64.deb ... 293s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 293s Selecting previously unselected package r-cran-modelr. 293s Preparing to unpack .../425-r-cran-modelr_0.1.11-1_all.deb ... 293s Unpacking r-cran-modelr (0.1.11-1) ... 293s Selecting previously unselected package r-cran-systemfonts. 293s Preparing to unpack .../426-r-cran-systemfonts_1.2.1-1_arm64.deb ... 293s Unpacking r-cran-systemfonts (1.2.1-1) ... 293s Selecting previously unselected package r-cran-textshaping. 293s Preparing to unpack .../427-r-cran-textshaping_0.3.7-2_arm64.deb ... 293s Unpacking r-cran-textshaping (0.3.7-2) ... 293s Selecting previously unselected package r-cran-ragg. 293s Preparing to unpack .../428-r-cran-ragg_1.3.3-1_arm64.deb ... 293s Unpacking r-cran-ragg (1.3.3-1) ... 293s Selecting previously unselected package r-cran-readxl. 293s Preparing to unpack .../429-r-cran-readxl_1.4.5-1_arm64.deb ... 293s Unpacking r-cran-readxl (1.4.5-1) ... 293s Selecting previously unselected package r-cran-tinytex. 293s Preparing to unpack .../430-r-cran-tinytex_0.56-1_all.deb ... 293s Unpacking r-cran-tinytex (0.56-1) ... 293s Selecting previously unselected package libjs-modernizr. 293s Preparing to unpack .../431-libjs-modernizr_3.13.0-0.1_all.deb ... 293s Unpacking libjs-modernizr (3.13.0-0.1) ... 293s Selecting previously unselected package r-cran-sourcetools. 293s Preparing to unpack .../432-r-cran-sourcetools_0.1.7-1-1_arm64.deb ... 293s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 293s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 293s Preparing to unpack .../433-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 293s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 293s Selecting previously unselected package r-cran-shiny. 293s Preparing to unpack .../434-r-cran-shiny_1.10.0+dfsg-2_all.deb ... 293s Unpacking r-cran-shiny (1.10.0+dfsg-2) ... 293s Selecting previously unselected package r-cran-rmarkdown. 293s Preparing to unpack .../435-r-cran-rmarkdown_2.29+dfsg-1_all.deb ... 293s Unpacking r-cran-rmarkdown (2.29+dfsg-1) ... 293s Selecting previously unselected package r-cran-rstudioapi. 293s Preparing to unpack .../436-r-cran-rstudioapi_0.17.1-1_all.deb ... 293s Unpacking r-cran-rstudioapi (0.17.1-1) ... 293s Selecting previously unselected package r-cran-reprex. 293s Preparing to unpack .../437-r-cran-reprex_2.1.1-1_all.deb ... 293s Unpacking r-cran-reprex (2.1.1-1) ... 293s Selecting previously unselected package r-cran-selectr. 294s Preparing to unpack .../438-r-cran-selectr_0.4-2-2build1_all.deb ... 294s Unpacking r-cran-selectr (0.4-2-2build1) ... 294s Selecting previously unselected package r-cran-rvest. 294s Preparing to unpack .../439-r-cran-rvest_1.0.5-1_all.deb ... 294s Unpacking r-cran-rvest (1.0.5-1) ... 294s Selecting previously unselected package r-cran-tidyverse. 294s Preparing to unpack .../440-r-cran-tidyverse_2.0.0+dfsg-2_all.deb ... 294s Unpacking r-cran-tidyverse (2.0.0+dfsg-2) ... 294s Selecting previously unselected package bowtie. 294s Preparing to unpack .../441-bowtie_1.3.1-3_arm64.deb ... 294s Unpacking bowtie (1.3.1-3) ... 294s Selecting previously unselected package bowtie2. 294s Preparing to unpack .../442-bowtie2_2.5.4-1_arm64.deb ... 294s Unpacking bowtie2 (2.5.4-1) ... 294s Selecting previously unselected package rsem. 294s Preparing to unpack .../443-rsem_1.3.3+dfsg-3build1_arm64.deb ... 294s Unpacking rsem 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294s Unpacking trinityrnaseq (2.15.2+dfsg-1) ... 295s Selecting previously unselected package trinityrnaseq-examples. 295s Preparing to unpack .../450-trinityrnaseq-examples_2.15.2+dfsg-1_arm64.deb ... 295s Unpacking trinityrnaseq-examples (2.15.2+dfsg-1) ... 297s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 297s Setting up libjs-json (0~20221030+~1.0.8-1) ... 297s Setting up javascript-common (12+nmu1) ... 297s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 297s Setting up libxcb-dri3-0:arm64 (1.17.0-2build1) ... 297s Setting up liblcms2-2:arm64 (2.16-2) ... 297s Setting up ncbi-data (6.1.20170106+dfsg2-6) ... 297s Setting up libtbbmalloc2:arm64 (2022.1.0-1) ... 297s Setting up libboost-program-options1.83.0:arm64 (1.83.0-5ubuntu2) ... 297s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 297s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 297s Setting up libx11-xcb1:arm64 (2:1.8.12-1build1) ... 297s Setting up libslf4j-java (1.7.32-2) ... 297s Setting up libprotobuf32t64:arm64 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libnet-ssleay-perl:arm64 (1.94-3) ... 298s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 298s Setting up libice6:arm64 (2:1.1.1-1) ... 298s Setting up libhttp-date-perl (6.06-1) ... 298s Setting up parafly (0.1.0-5) ... 298s Setting up mesa-libgallium:arm64 (25.2.3-1ubuntu1) ... 298s Setting up liblapack3:arm64 (3.12.1-6build1) ... 298s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 298s Setting up python3-pysam (0.23.0+ds-1build2) ... 298s Setting up libgcc-15-dev:arm64 (15.2.0-5ubuntu1) ... 298s Setting up libatk1.0-0t64:arm64 (2.57.1-1) ... 298s Setting up libfile-listing-perl (6.16-1) ... 298s Setting up python3-hisat2 (2.2.1-5) ... 298s Setting up libgbm1:arm64 (25.2.3-1ubuntu1) ... 298s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 298s Setting up libxtst6:arm64 (2:1.2.5-1) ... 298s Setting up libxcursor1:arm64 (1:1.2.3-1) ... 298s Setting up libgl1-mesa-dri:arm64 (25.2.3-1ubuntu1) ... 298s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 298s Setting up libcommons-parent-java (56-1) ... 298s Setting up libavahi-common3:arm64 (0.8-16ubuntu3) ... 298s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 298s Setting up libnet-http-perl (6.23-1) ... 298s Setting up dconf-service (0.49.0-1) ... 298s Setting up libnss3:arm64 (2:3.114-1) ... 298s Setting up libpaper-utils (2.2.5-0.3) ... 298s Setting up libxom-java (1.3.9-1) ... 298s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 298s Setting up samtools (1.21-1) ... 298s Setting up libtbbbind-2-5:arm64 (2022.1.0-1) ... 298s Setting up libcommons-jexl2-java (2.1.1-6) ... 298s Setting up libthai0:arm64 (0.1.29-2build1) ... 298s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 298s Setting up libstdc++-15-dev:arm64 (15.2.0-5ubuntu1) ... 298s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 298s Setting up pandoc (3.1.11.1+ds-4) ... 298s Setting up jellyfish (2.3.1-4build2) ... 298s Setting up libcommons-collections4-java (4.4-2) ... 298s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 300s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 300s Setting up libcommons-lang3-java (3.17.0-1) ... 300s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 300s Setting up libwww-robotrules-perl (6.02-1) ... 300s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 300s Setting up libwayland-cursor0:arm64 (1.24.0-1build1) ... 300s Setting up libhtml-parser-perl:arm64 (3.83-1build1) ... 300s Setting up libcommons-beanutils-java (1.10.1-1.1) ... 300s Setting up libgdk-pixbuf-2.0-0:arm64 (2.44.4+dfsg-1) ... 300s Setting up libsnappy-java (1.1.10.7-1) ... 300s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 300s Setting up libcommons-codec-java (1.18.0-1) ... 300s Setting up libsm6:arm64 (2:1.2.6-1) ... 300s Setting up python3-htseq (2.0.9+dfsg-1build3) ... 301s Setting up libavahi-client3:arm64 (0.8-16ubuntu3) ... 301s Setting up libio-socket-ssl-perl (2.089-1) ... 301s Setting up libhttp-message-perl (7.00-2ubuntu1) ... 301s Setting up libatk-bridge2.0-0t64:arm64 (2.57.1-1) ... 301s Setting up gtk-update-icon-cache (4.20.2+ds-1) ... 301s Setting up libhttp-negotiate-perl (6.01-2) ... 301s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 303s Regenerating fonts cache... done. 303s Setting up libxft2:arm64 (2.3.6-1build1) ... 303s Setting up libglx-mesa0:arm64 (25.2.3-1ubuntu1) ... 303s Setting up openjdk-21-jre-headless:arm64 (21.0.9+10-1) ... 303s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 303s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 303s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 303s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 303s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 303s Setting up libglx0:arm64 (1.7.0-1build2) ... 303s Setting up dconf-gsettings-backend:arm64 (0.49.0-1) ... 303s Setting up libhttp-cookies-perl (6.11-1) ... 303s Setting up libcommons-io-java (2.19.0-1) ... 303s Setting up libboost1.88-dev:arm64 (1.88.0-1.4ubuntu2) ... 303s Setting up libhtml-tree-perl (5.07-3) ... 303s Setting up libtk8.6:arm64 (8.6.17-1) ... 303s Setting up libpango-1.0-0:arm64 (1.56.3-2) ... 303s Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 303s Setting up libtbb12:arm64 (2022.1.0-1) ... 303s Setting up libcairo2:arm64 (1.18.4-1build1) ... 303s Setting up ncbi-blast+ (2.16.0+ds-7) ... 303s Setting up salmon (1.10.2+ds1-1build2) ... 303s Setting up libgl1:arm64 (1.7.0-1build2) ... 303s Setting up adwaita-icon-theme (49.0-1) ... 303s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 303s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 303s Setting up libhttpclient-java (4.5.14-1) ... 303s Setting up liblightcouch-java (0.2.0-1) ... 303s Setting up libcairo-gobject2:arm64 (1.18.4-1build1) ... 303s Setting up libboost-dev:arm64 (1.88.0.0ubuntu1) ... 303s Setting up libpangoft2-1.0-0:arm64 (1.56.3-2) ... 303s Setting up libcups2t64:arm64 (2.4.12-0ubuntu3) ... 303s Setting up libgtk-3-common (3.24.50-1ubuntu2) ... 303s Setting up libpangocairo-1.0-0:arm64 (1.56.3-2) ... 303s Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-4ubuntu5) ... 303s Setting up libngs-jni:arm64 (3.2.1+dfsg-4ubuntu5) ... 303s Setting up libcommons-compress-java (1.27.1-2) ... 303s Setting up liblog4j2-java (2.19.0-2) ... 303s Setting up r-base-core (4.5.1-1) ... 303s Creating config file /etc/R/Renviron with new version 303s Setting up r-cran-crayon (1.5.3-1) ... 303s Setting up r-cran-labeling (0.4.3-1) ... 303s Setting up r-cran-biasedurn (2.0.12-1) ... 303s Setting up r-cran-sourcetools (0.1.7-1-1) ... 303s Setting up r-cran-futile.options (1.0.1-3build1) ... 303s Setting up r-cran-lattice (0.22-7-1) ... 303s Setting up r-cran-ps (1.9.0-1) ... 303s Setting up r-cran-nlme (3.1.168-1) ... 303s Setting up r-cran-farver (2.1.2-1) ... 303s Setting up r-cran-formatr (1.14-2) ... 303s Setting up r-cran-xml (3.99-0.18-1build1) ... 303s Setting up trinityrnaseq-examples (2.15.2+dfsg-1) ... 303s Setting up r-cran-viridislite (0.4.2-2) ... 303s Setting up r-cran-locfit (1.5-9.12-1) ... 303s Setting up r-cran-cluster (2.1.8.1-1) ... 303s Setting up rsem (1.3.3+dfsg-3build1) ... 303s Setting up r-cran-statmod (1.5.0-1) ... 303s Setting up r-cran-clipr (0.8.0-1) ... 303s Setting up r-cran-commonmark (1.9.5-1) ... 303s Setting up r-cran-rjson (0.2.23-1) ... 303s Setting up libngs-java:arm64 (3.2.1+dfsg-4ubuntu5) ... 303s Setting up r-cran-r6 (2.6.1-1) ... 303s Setting up r-cran-pkgkitten (0.2.4-1) ... 303s Setting up r-cran-fastcluster (1.3.0-1build1) ... 303s Setting up r-cran-magrittr (2.0.3-1) ... 303s Setting up r-cran-rappdirs (0.3.3-1) ... 303s Setting up r-cran-filelock (1.0.3-1) ... 303s Setting up libbarclay-java (5.0.0+dfsg-1) ... 303s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ... 303s Setting up r-cran-littler (0.3.21-1) ... 303s Setting up r-cran-bh (1.84.0-1) ... 303s Setting up r-cran-fs (1.6.5+dfsg-1) ... 303s Setting up r-cran-rcpp (1.1.0-1) ... 303s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 303s Setting up r-cran-codetools (0.2-20-1) ... 303s Setting up r-cran-rematch (2.0.0-1) ... 303s Setting up r-bioc-biocgenerics (0.52.0-2) ... 303s Setting up r-cran-rlang (1.1.5-3) ... 303s Setting up r-cran-matrixstats (1.5.0-1) ... 303s Setting up r-cran-findpython (1.0.9-1) ... 303s Setting up r-bioc-matrixgenerics (1.18.1-1) ... 303s Setting up r-cran-uuid (1.2-1-1) ... 303s Setting up r-cran-xfun (0.51+dfsg-1) ... 303s Setting up r-cran-sys (3.4.3-1) ... 303s Setting up r-cran-plogr (0.2.0-3build1) ... 303s Setting up r-cran-withr (3.0.2+dfsg-1) ... 303s Setting up r-cran-backports (1.5.0-2) ... 303s Setting up r-cran-processx (3.8.6-1) ... 303s Setting up r-cran-mime (0.12-2) ... 303s Setting up r-cran-generics (0.1.3-1) ... 303s Setting up r-cran-base64enc (0.1-3-3) ... 303s Setting up r-cran-abind (1.4-8-1) ... 303s Setting up r-cran-digest (0.6.37-1) ... 303s Setting up r-cran-yaml (2.3.10-1) ... 303s Setting up r-cran-lambda.r (1.2.4-2build1) ... 303s Setting up r-cran-evaluate (1.0.3-1) ... 303s Setting up r-cran-dbi (1.2.3-1) ... 303s Setting up r-cran-highr (0.11+dfsg-1) ... 303s Setting up r-cran-prettyunits (1.2.0-1) ... 303s Setting up r-cran-fansi (1.0.6-2) ... 303s Setting up r-cran-mass (7.3-65-1) ... 303s Setting up r-cran-snow (1:0.4.4-2) ... 303s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 303s Setting up r-cran-glue (1.8.0-1) ... 303s Setting up r-cran-bit (4.6.0+dfsg-1) ... 303s Setting up r-cran-xtable (1:1.8-4-2) ... 303s Setting up r-cran-cli (3.6.4-1) ... 303s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 303s Setting up r-cran-bitops (1.0-9-1) ... 303s Setting up r-cran-bit64 (4.6.0-1-4) ... 303s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... 303s Setting up r-cran-askpass (1.2.1-1) ... 303s Setting up r-cran-fastmap (1.2.0-1) ... 303s Setting up r-cran-png (0.1-8-1build2) ... 303s Setting up r-bioc-biobase (2.66.0-2) ... 303s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 303s Setting up r-cran-rstudioapi (0.17.1-1) ... 303s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 303s Setting up r-cran-utf8 (1.2.4-1) ... 303s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 303s Setting up r-cran-stringi (1.8.4-1build1) ... 303s Setting up r-cran-hwriter (1.3.2.1-1) ... 303s Setting up r-cran-cpp11 (0.5.2-1) ... 303s Setting up r-cran-plyr (1.8.9-1) ... 303s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 303s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... 303s Setting up r-cran-isoband (0.2.7-1) ... 303s Setting up r-cran-futile.logger (1.4.3-4build1) ... 303s Setting up r-bioc-limma (3.62.2+dfsg-1) ... 303s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 303s Setting up r-cran-later (1.4.1+dfsg-1) ... 303s Setting up r-cran-matrix (1.7-3-1) ... 303s Setting up r-cran-htmltools (0.5.8.1-1) ... 303s Setting up r-cran-tinytex (0.56-1) ... 303s Setting up r-cran-kernsmooth (2.23-26-1) ... 303s Setting up r-cran-knitr (1.50+dfsg-1) ... 303s Setting up r-cran-mgcv (1.9-3-1) ... 303s Setting up r-cran-cachem (1.1.0-1) ... 303s Setting up r-cran-sass (0.4.9+dfsg-1) ... 303s Setting up r-cran-rcpparmadillo (14.6.0-1-1) ... 303s Setting up r-bioc-iranges (2.40.1-3) ... 303s Setting up r-cran-tzdb (0.5.0-1) ... 303s Setting up r-cran-argparse (2.2.5+dfsg-1) ... 303s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... 303s Setting up r-cran-restfulr (0.0.15-1) ... 303s Setting up r-cran-vctrs (0.6.5-1) ... 303s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 303s Setting up r-cran-ellipsis (0.3.2-2) ... 303s Setting up r-cran-openssl (2.3.2+dfsg-1) ... 303s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ... 303s Setting up r-cran-stringr (1.5.1-1) ... 303s Setting up r-bioc-biocparallel (1.40.0-2) ... 303s Setting up r-cran-callr (3.7.6-1) ... 303s Setting up r-cran-selectr (0.4-2-2build1) ... 303s Setting up r-bioc-edger (4.4.2+dfsg-1) ... 303s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ... 303s Setting up r-cran-xml2 (1.4.0-1ubuntu1) ... 303s Setting up r-cran-munsell (0.5.1-1) ... 303s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 303s Setting up r-cran-fontawesome (0.5.3-1) ... 303s Setting up r-cran-survival (3.8-3-1) ... 303s Setting up r-bioc-biocio (1.16.0+dfsg-2) ... 303s Setting up r-cran-forcats (1.0.0-1) ... 303s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... 303s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 303s Setting up r-cran-reshape2 (1.4.4-2build1) ... 303s Setting up r-cran-httr2 (1.1.1-1) ... 303s Setting up r-cran-systemfonts (1.2.1-1) ... 303s Setting up r-cran-ids (1.0.1-2) ... 303s Setting up r-cran-timechange (0.3.0-2) ... 303s Setting up r-cran-httr (1.4.7+dfsg-1) ... 303s Setting up r-cran-gridextra (2.3-3build1) ... 303s Setting up r-cran-hms (1.1.3-1) ... 303s Setting up r-cran-scales (1.3.0-1) ... 303s Setting up r-cran-memoise (2.0.1-1) ... 303s Setting up r-cran-promises (1.3.2+dfsg-1) ... 303s Setting up r-cran-purrr (1.0.4-1) ... 303s Setting up r-cran-blob (1.2.4-1) ... 303s Setting up r-bioc-xvector (0.46.0-2) ... 303s Setting up r-cran-dplyr (1.1.4-4) ... 303s Setting up r-cran-rsqlite (2.3.9-1) ... 303s Setting up r-cran-progress (1.2.3-1) ... 303s Setting up r-cran-lubridate (1.9.4+dfsg-1) ... 303s Setting up r-cran-gargle (1.5.2-1) ... 303s Setting up r-cran-vroom (1.6.5-1) ... 303s Setting up r-cran-conflicted (1.2.0-1.1) ... 303s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... 303s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ... 303s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 303s Setting up r-cran-cellranger (1.1.0-3) ... 303s Setting up r-cran-httpuv (1.6.15+dfsg-1) ... 303s Setting up r-cran-rematch2 (2.1.2-2build1) ... 303s Setting up r-cran-textshaping (0.3.7-2) ... 303s Setting up r-cran-rvest (1.0.5-1) ... 303s Setting up r-cran-dtplyr (1.3.1-1) ... 303s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 303s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ... 303s Setting up r-cran-ragg (1.3.3-1) ... 303s Setting up r-cran-readr (2.1.5-1) ... 303s Setting up r-cran-tidyr (1.3.1-1) ... 303s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ... 303s Setting up r-cran-googledrive (2.1.1-3) ... 303s Setting up r-cran-googlesheets4 (1.1.1-1) ... 303s Setting up r-bioc-qvalue (2.38.0-2) ... 303s Setting up r-cran-dbplyr (2.5.0+dfsg-1) ... 303s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ... 303s Setting up r-cran-readxl (1.4.5-1) ... 303s Setting up r-bioc-biocfilecache (2.14.0+dfsg-2) ... 303s Setting up r-cran-haven (2.5.5-1) ... 303s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... 303s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... 303s Setting up r-cran-shiny (1.10.0+dfsg-2) ... 303s Setting up r-cran-broom (1.0.7+dfsg-1) ... 303s Setting up r-cran-rmarkdown (2.29+dfsg-1) ... 303s Setting up r-cran-goplot (1.0.2-2) ... 303s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... 303s Setting up r-cran-reprex (2.1.1-1) ... 303s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 303s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ... 303s Setting up r-bioc-deseq2 (1.46.0+dfsg-2) ... 303s Setting up r-bioc-annotationdbi (1.68.0-2) ... 303s Setting up r-bioc-go.db (3.20.0-2) ... 303s Setting up r-cran-modelr (0.1.11-1) ... 303s Setting up r-bioc-annotate (1.84.0+dfsg-2) ... 303s Setting up r-bioc-biomart (2.62.1+dfsg-1) ... 303s Setting up r-bioc-genefilter (1.88.0-2) ... 303s Setting up r-bioc-genomicalignments (1.42.0-2) ... 303s Setting up r-bioc-geneplotter (1.84.0+dfsg-2) ... 303s Setting up r-bioc-rtracklayer (1.66.0-3) ... 303s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 303s Setting up r-cran-tidyverse (2.0.0+dfsg-2) ... 303s Setting up r-bioc-dexseq (1.52.0+dfsg-2) ... 303s Setting up r-bioc-txdbmaker (1.2.1+ds-2) ... 303s Setting up r-bioc-genelendatabase (1.42.0-3) ... 303s Setting up r-bioc-goseq (1.58.0-2) ... 303s Setting up liblwp-protocol-https-perl (6.14-1) ... 303s Setting up liberror-prone-java (2.18.0-1) ... 303s Setting up libwww-perl (6.78-1) ... 303s Setting up libguava-java (32.0.1-1) ... 303s Setting up libjung-free-java (2.1.1-3) ... 303s Processing triggers for libglib2.0-0t64:arm64 (2.86.1-1) ... 303s Setting up libgtk-3-0t64:arm64 (3.24.50-1ubuntu2) ... 303s Processing triggers for install-info (7.1.1-1ubuntu1) ... 303s Processing triggers for libc-bin (2.42-0ubuntu3) ... 303s Processing triggers for man-db (2.13.1-1) ... 305s Processing triggers for ca-certificates-java (20240118) ... 306s Adding debian:ACCVRAIZ1.pem 306s Adding debian:AC_RAIZ_FNMT-RCM.pem 306s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 306s Adding debian:ANF_Secure_Server_Root_CA.pem 306s Adding debian:Actalis_Authentication_Root_CA.pem 306s Adding debian:AffirmTrust_Commercial.pem 306s Adding debian:AffirmTrust_Networking.pem 306s Adding debian:AffirmTrust_Premium.pem 306s Adding debian:AffirmTrust_Premium_ECC.pem 306s Adding debian:Amazon_Root_CA_1.pem 306s Adding debian:Amazon_Root_CA_2.pem 306s Adding debian:Amazon_Root_CA_3.pem 306s Adding debian:Amazon_Root_CA_4.pem 306s Adding debian:Atos_TrustedRoot_2011.pem 306s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 306s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 306s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 306s Adding debian:BJCA_Global_Root_CA1.pem 306s Adding debian:BJCA_Global_Root_CA2.pem 306s Adding debian:Baltimore_CyberTrust_Root.pem 306s Adding debian:Buypass_Class_2_Root_CA.pem 306s Adding debian:Buypass_Class_3_Root_CA.pem 306s Adding debian:CA_Disig_Root_R2.pem 306s Adding debian:CFCA_EV_ROOT.pem 306s Adding debian:COMODO_Certification_Authority.pem 306s Adding debian:COMODO_ECC_Certification_Authority.pem 306s Adding debian:COMODO_RSA_Certification_Authority.pem 306s Adding debian:Certainly_Root_E1.pem 306s Adding debian:Certainly_Root_R1.pem 306s Adding debian:Certigna.pem 306s Adding debian:Certigna_Root_CA.pem 306s Adding debian:Certum_EC-384_CA.pem 306s Adding debian:Certum_Trusted_Network_CA.pem 306s Adding debian:Certum_Trusted_Network_CA_2.pem 306s Adding debian:Certum_Trusted_Root_CA.pem 306s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 306s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 306s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 306s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 306s Adding debian:Comodo_AAA_Services_root.pem 306s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 306s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 306s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 306s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 306s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 306s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 306s Adding debian:DigiCert_Assured_ID_Root_CA.pem 306s Adding debian:DigiCert_Assured_ID_Root_G2.pem 306s Adding debian:DigiCert_Assured_ID_Root_G3.pem 306s Adding debian:DigiCert_Global_Root_CA.pem 306s Adding debian:DigiCert_Global_Root_G2.pem 306s Adding debian:DigiCert_Global_Root_G3.pem 306s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 306s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 306s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 306s Adding debian:DigiCert_Trusted_Root_G4.pem 306s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 306s Adding debian:Entrust_Root_Certification_Authority.pem 306s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 306s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 306s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 306s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 306s Adding debian:GLOBALTRUST_2020.pem 306s Adding debian:GTS_Root_R1.pem 306s Adding debian:GTS_Root_R2.pem 306s Adding debian:GTS_Root_R3.pem 306s Adding debian:GTS_Root_R4.pem 306s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 306s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 306s Adding debian:GlobalSign_Root_CA.pem 306s Adding debian:GlobalSign_Root_CA_-_R3.pem 306s Adding debian:GlobalSign_Root_CA_-_R6.pem 306s Adding debian:GlobalSign_Root_E46.pem 306s Adding debian:GlobalSign_Root_R46.pem 306s Adding debian:Go_Daddy_Class_2_CA.pem 306s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 306s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 306s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 306s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 306s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 306s Adding debian:HiPKI_Root_CA_-_G1.pem 306s Adding debian:Hongkong_Post_Root_CA_3.pem 306s Adding debian:ISRG_Root_X1.pem 306s Adding debian:ISRG_Root_X2.pem 306s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 306s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 306s Adding debian:Izenpe.com.pem 306s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 306s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 306s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 306s Adding debian:NAVER_Global_Root_Certification_Authority.pem 306s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 306s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 306s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 306s Adding debian:QuoVadis_Root_CA_1_G3.pem 306s Adding debian:QuoVadis_Root_CA_2.pem 306s Adding debian:QuoVadis_Root_CA_2_G3.pem 306s Adding debian:QuoVadis_Root_CA_3.pem 306s Adding debian:QuoVadis_Root_CA_3_G3.pem 306s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 306s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 306s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 306s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 306s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 306s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 306s Adding debian:SZAFIR_ROOT_CA2.pem 306s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 306s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 306s Adding debian:SecureSign_Root_CA12.pem 306s Adding debian:SecureSign_Root_CA14.pem 306s Adding debian:SecureSign_Root_CA15.pem 306s Adding debian:SecureTrust_CA.pem 306s Adding debian:Secure_Global_CA.pem 306s Adding debian:Security_Communication_ECC_RootCA1.pem 306s Adding debian:Security_Communication_RootCA2.pem 306s Adding debian:Starfield_Class_2_CA.pem 306s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 306s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 306s Adding debian:SwissSign_Gold_CA_-_G2.pem 306s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 306s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 306s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 306s Adding debian:TWCA_CYBER_Root_CA.pem 306s Adding debian:TWCA_Global_Root_CA.pem 306s Adding debian:TWCA_Root_Certification_Authority.pem 306s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 306s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 306s Adding debian:TeliaSonera_Root_CA_v1.pem 306s Adding debian:Telia_Root_CA_v2.pem 306s Adding debian:TrustAsia_Global_Root_CA_G3.pem 306s Adding debian:TrustAsia_Global_Root_CA_G4.pem 306s Adding debian:Trustwave_Global_Certification_Authority.pem 306s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 306s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 306s Adding debian:TunTrust_Root_CA.pem 306s Adding debian:UCA_Extended_Validation_Root.pem 306s Adding debian:UCA_Global_G2_Root.pem 306s Adding debian:USERTrust_ECC_Certification_Authority.pem 306s Adding debian:USERTrust_RSA_Certification_Authority.pem 306s Adding debian:XRamp_Global_CA_Root.pem 306s Adding debian:certSIGN_ROOT_CA.pem 306s Adding debian:certSIGN_Root_CA_G2.pem 306s Adding debian:e-Szigno_Root_CA_2017.pem 306s Adding debian:ePKI_Root_Certification_Authority.pem 306s Adding debian:emSign_ECC_Root_CA_-_C3.pem 306s Adding debian:emSign_ECC_Root_CA_-_G3.pem 306s Adding debian:emSign_Root_CA_-_C1.pem 306s Adding debian:emSign_Root_CA_-_G1.pem 306s Adding debian:vTrus_ECC_Root_CA.pem 306s Adding debian:vTrus_Root_CA.pem 306s done. 306s Setting up junit4 (4.13.2-5) ... 306s Setting up default-jre-headless (2:1.21-76) ... 306s Setting up jaligner (1.0+dfsg-11) ... 306s Setting up openjdk-21-jre:arm64 (21.0.9+10-1) ... 306s Setting up libjson-java (3.1.0+dfsg-2) ... 306s Setting up libhtsjdk-java (4.1.3+dfsg-2) ... 306s Setting up libgkl-java (0.8.11+dfsg-2build1) ... 306s Setting up default-jre (2:1.21-76) ... 306s Setting up libpicard-java (3.3.0+dfsg-2) ... 306s Setting up trimmomatic (0.39+dfsg-2) ... 306s Setting up trinityrnaseq (2.15.2+dfsg-1) ... 308s autopkgtest [20:09:13]: test run-tests: [----------------------- 308s cd test_Trinity_Assembly && make test_all 308s make[1]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly' 308s ./runMe.sh 308s #!/bin/bash -ve 308s 308s ####################################################### 308s ## Run Trinity to Generate Transcriptome Assemblies ## 308s ####################################################### 308s 308s if [ -z ${TRINITY_HOME} ]; then 308s echo "Must set env var TRINITY_HOME" 308s exit 1 308s fi 308s 308s 308s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \ 308s --left reads.left.fq.gz \ 308s --right reads.right.fq.gz \ 308s --SS_lib_type RF \ 308s --CPU 1 \ 308s --no_cleanup 308s 308s 308s ______ ____ ____ ____ ____ ______ __ __ 308s | || \ | || \ | || || | | 308s | || D ) | | | _ | | | | || | | 308s |_| |_|| / | | | | | | | |_| |_|| ~ | 308s | | | \ | | | | | | | | | |___, | 308s | | | . \ | | | | | | | | | | | 308s |__| |__|\_||____||__|__||____| |__| |____/ 308s 308s Trinity-v2.15.2 308s 308s 308s 308s Left read files: $VAR1 = [ 308s 'reads.left.fq.gz' 308s ]; 308s Right read files: $VAR1 = [ 308s 'reads.right.fq.gz' 308s ]; 308s Tuesday, October 28, 2025: 20:09:13 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir 308s Tuesday, October 28, 2025: 20:09:13 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis 308s 308s 308s ---------------------------------------------------------------------------------- 308s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 308s ---------------------------------------------------------------------------------- 308s 308s --------------------------------------------------------------- 308s ------------ In silico Read Normalization --------------------- 308s -- (Removing Excess Reads Beyond 200 Coverage -- 308s --------------------------------------------------------------- 308s 308s # running normalization on reads: $VAR1 = [ 308s [ 308s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 308s ], 308s [ 308s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 308s ] 308s ]; 308s 308s 308s Tuesday, October 28, 2025: 20:09:13 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 308s -prepping seqs 308s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 308s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 308s CMD finished (0 seconds) 308s CMD finished (0 seconds) 308s CMD: touch left.fa.ok 308s CMD finished (0 seconds) 308s CMD: touch right.fa.ok 308s CMD finished (0 seconds) 308s Done converting input files. CMD: cat left.fa right.fa > both.fa 308s CMD finished (0 seconds) 308s CMD: touch both.fa.ok 308s CMD finished (0 seconds) 308s -kmer counting. 308s ------------------------------------------- 308s ----------- Jellyfish -------------------- 308s -- (building a k-mer catalog from reads) -- 308s ------------------------------------------- 308s 308s CMD: jellyfish count -t 1 -m 25 -s 100000000 both.fa 311s CMD finished (3 seconds) 311s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 311s CMD finished (0 seconds) 311s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 311s CMD finished (0 seconds) 311s CMD: touch jellyfish.K25.min2.kmers.fa.success 311s CMD finished (0 seconds) 311s -generating stats files 311s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 311s -reading Kmer occurrences... 311s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 311s -reading Kmer occurrences... 311s 311s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 311s 311s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 312s STATS_GENERATION_TIME: 1 seconds. 312s STATS_GENERATION_TIME: 1 seconds. 312s CMD finished (1 seconds) 312s CMD finished (1 seconds) 312s CMD: touch left.fa.K25.stats.ok 312s CMD finished (0 seconds) 312s CMD: touch right.fa.K25.stats.ok 312s CMD finished (0 seconds) 312s -sorting each stats file by read name. 312s 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 312s 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 312s CMD finished (0 seconds) 312s CMD finished (0 seconds) 312s CMD: touch left.fa.K25.stats.sort.ok 312s CMD finished (0 seconds) 312s CMD: touch right.fa.K25.stats.sort.ok 312s CMD finished (0 seconds) 312s -defining normalized reads 312s 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 312s -opening left.fa.K25.stats.sort 312s -opening right.fa.K25.stats.sort 312s -done opening files. 312s CMD finished (0 seconds) 312s CMD: touch pairs.K25.stats.ok 312s CMD finished (0 seconds) 312s 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 313s 30472 / 30575 = 99.66% reads selected during normalization. 313s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 313s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 313s CMD finished (1 seconds) 313s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 313s CMD finished (0 seconds) 313s -search and capture. 313s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 313s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 313s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 313s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 313s CMD: touch /tmp/autopkgtest.sYnnix/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 313s CMD finished (0 seconds) 313s CMD: touch /tmp/autopkgtest.sYnnix/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 313s CMD finished (0 seconds) 313s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 313s CMD finished (0 seconds) 313s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 313s CMD finished (0 seconds) 313s 313s 313s Normalization complete. See outputs: 313s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 313s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 314s Tuesday, October 28, 2025: 20:09:18 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok 314s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:09:19 CMD: cat /tmp/autopkgtest.sYnnix/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 314s Tuesday, October 28, 2025: 20:09:19 CMD: cat /tmp/autopkgtest.sYnnix/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 314s Tuesday, October 28, 2025: 20:09:19 CMD: touch left.fa.ok 314s Tuesday, October 28, 2025: 20:09:19 CMD: touch right.fa.ok 314s Tuesday, October 28, 2025: 20:09:19 CMD: touch left.fa.ok right.fa.ok 314s Tuesday, October 28, 2025: 20:09:19 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 314s Tuesday, October 28, 2025: 20:09:19 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok 314s ------------------------------------------- 314s ----------- Jellyfish -------------------- 314s -- (building a k-mer (25) catalog from reads) -- 314s ------------------------------------------- 314s 314s * [Tue Oct 28 20:09:19 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 316s * [Tue Oct 28 20:09:21 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 316s * [Tue Oct 28 20:09:21 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 316s ---------------------------------------------- 316s --------------- Inchworm (K=25, asm) --------------------- 316s -- (Linear contig construction from k-mers) -- 316s ---------------------------------------------- 316s 316s * [Tue Oct 28 20:09:21 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp 316s Kmer length set to: 25 316s Min assembly length set to: 25 316s Monitor turned on, set to: 1 316s -retaining tmp files 316s min entropy set to: 1 316s setting number of threads to: 1 316s -setting parallel iworm mode. 316s -reading Kmer occurrences... 317s [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. 317s done parsing 519541 Kmers, 519541 added, taking 1 seconds. 317s 317s TIMING KMER_DB_BUILDING 1 s. 317s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 317s Pruned 4252 kmers from catalog. 317s Pruning time: 0 seconds = 0 minutes. 317s 317s TIMING PRUNING 0 s. 317s -populating the kmer seed candidate list. 317s Kcounter hash size: 519541 317s Processed 515289 non-zero abundance kmers in kcounter. 317s -Not sorting list of kmers, given parallel mode in effect. 317s -beginning inchworm contig assembly. 317s Total kcounter hash size: 519541 vs. sorted list size: 515289 317s num threads set to: 1 317s Done opening file. tmp.iworm.fa.pid_6595.thread_0 318s 318s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 318s 318s TIMING CONTIG_BUILDING 1 s. 318s 318s TIMING PROG_RUNTIME 2 s. 318s * [Tue Oct 28 20:09:23 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 318s Tuesday, October 28, 2025: 20:09:23 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished 318s -------------------------------------------------------- 318s -------------------- Chrysalis ------------------------- 318s -- (Contig Clustering & de Bruijn Graph Construction) -- 318s -------------------------------------------------------- 318s 318s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 318s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 318s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 318s * [Tue Oct 28 20:09:23 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 318s * [Tue Oct 28 20:09:23 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null 318s * [Tue Oct 28 20:09:23 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 321s * [Tue Oct 28 20:09:26 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt 322s * [Tue Oct 28 20:09:27 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt 323s * [Tue Oct 28 20:09:28 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted 323s * [Tue Oct 28 20:09:28 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 323s * [Tue Oct 28 20:09:28 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out 323s * [Tue Oct 28 20:09:28 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 323s * [Tue Oct 28 20:09:28 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000 -strand -p 10 327s * [Tue Oct 28 20:09:31 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort 327s Tuesday, October 28, 2025: 20:09:32 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0 327s Tuesday, October 28, 2025: 20:09:32 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok 327s Tuesday, October 28, 2025: 20:09:32 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 327s Tuesday, October 28, 2025: 20:09:32 CMD: touch recursive_trinity.cmds.ok 327s Tuesday, October 28, 2025: 20:09:32 CMD: touch recursive_trinity.cmds.ok 327s 327s 327s -------------------------------------------------------------------------------- 327s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 327s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 327s -------------------------------------------------------------------------------- 327s 327s Tuesday, October 28, 2025: 20:09:32 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 327s Number of Commands: 36 422s 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. 422s 422s All commands completed successfully. :-) 422s 422s 422s 422s ** Harvesting all assembled transcripts into a single multi-fasta file... 422s 422s Tuesday, October 28, 2025: 20:11:07 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp 422s * [Tue Oct 28 20:11:07 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1 423s * [Tue Oct 28 20:11:08 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta 423s Tuesday, October 28, 2025: 20:11:08 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map 423s 423s 423s ############################################################################# 423s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta 423s ############################################################################# 423s 423s 423s 423s ##### Done Running Trinity ##### 423s 423s if [ $* ]; then 423s # check full-length reconstruction stats: 423s 423s ./misc_run_tests/__test_runMe_NO_normalization.sh 423s ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90 423s 423s ./test_FL.sh --query trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse 423s 423s fi 423s 423s #!/bin/bash -ve 423s 423s 423s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 423s gunzip -c reads.right.fq.gz > reads.right.fq 423s fi 423s 423s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 423s gunzip -c reads.left.fq.gz > reads.left.fq 423s fi 423s 423s 423s 423s ####################################################### 423s ## Run Trinity to Generate Transcriptome Assemblies ## 423s ####################################################### 423s 423s CPU=$(nproc || sysctl -n hw.physicalcpu) 423s 423s ## use jellyfish 423s ${TRINITY_HOME}/Trinity --seqType fq \ 423s --max_memory 2G \ 423s --left reads.left.fq \ 423s --right reads.right.fq \ 423s --SS_lib_type RF \ 423s --CPU ${CPU} \ 423s --no_normalize_reads \ 423s --output __test_trinity_wo_normalization 423s 423s 423s ______ ____ ____ ____ ____ ______ __ __ 423s | || \ | || \ | || || | | 423s | || D ) | | | _ | | | | || | | 423s |_| |_|| / | | | | | | | |_| |_|| ~ | 423s | | | \ | | | | | | | | | |___, | 423s | | | . \ | | | | | | | | | | | 423s |__| |__|\_||____||__|__||____| |__| |____/ 423s 423s Trinity-v2.15.2 423s 423s 423s 423s Left read files: $VAR1 = [ 423s 'reads.left.fq' 423s ]; 423s Right read files: $VAR1 = [ 423s 'reads.right.fq' 423s ]; 423s Tuesday, October 28, 2025: 20:11:08 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization 423s Tuesday, October 28, 2025: 20:11:08 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis 423s 423s 423s ---------------------------------------------------------------------------------- 423s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 423s ---------------------------------------------------------------------------------- 423s 423s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:11:08 CMD: cat /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 423s Tuesday, October 28, 2025: 20:11:08 CMD: cat /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa 423s Tuesday, October 28, 2025: 20:11:08 CMD: touch left.fa.ok 423s Tuesday, October 28, 2025: 20:11:08 CMD: touch right.fa.ok 423s Tuesday, October 28, 2025: 20:11:08 CMD: touch left.fa.ok right.fa.ok 423s Tuesday, October 28, 2025: 20:11:08 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 423s Tuesday, October 28, 2025: 20:11:08 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok 423s ------------------------------------------- 423s ----------- Jellyfish -------------------- 423s -- (building a k-mer (25) catalog from reads) -- 423s ------------------------------------------- 423s 423s * [Tue Oct 28 20:11:08 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 425s * [Tue Oct 28 20:11:10 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 425s * [Tue Oct 28 20:11:10 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 425s ---------------------------------------------- 425s --------------- Inchworm (K=25, asm) --------------------- 425s -- (Linear contig construction from k-mers) -- 425s ---------------------------------------------- 425s 425s * [Tue Oct 28 20:11:10 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp 425s Kmer length set to: 25 425s Min assembly length set to: 25 425s Monitor turned on, set to: 1 425s min entropy set to: 1 425s setting number of threads to: 2 425s -setting parallel iworm mode. 425s -reading Kmer occurrences... 425s [0M] Kmers parsed. [0M] Kmers parsed. 425s done parsing 520108 Kmers, 520108 added, taking 0 seconds. 425s 425s TIMING KMER_DB_BUILDING 0 s. 425s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 426s Pruned 4291 kmers from catalog. 426s Pruning time: 1 seconds = 0.0166667 minutes. 426s 426s TIMING PRUNING 1 s. 426s -populating the kmer seed candidate list. 426s Kcounter hash size: 520108 426s Processed 515817 non-zero abundance kmers in kcounter. 426s -Not sorting list of kmers, given parallel mode in effect. 426s -beginning inchworm contig assembly. 426s Total kcounter hash size: 520108 vs. sorted list size: 515817 426s num threads set to: 2 426s Done opening file. tmp.iworm.fa.pid_12954.thread_0 426s Done opening file. tmp.iworm.fa.pid_12954.thread_1 426s 426s Iworm contig assembly time: 0 seconds = 0 minutes. 426s 426s TIMING CONTIG_BUILDING 0 s. 426s 426s TIMING PROG_RUNTIME 1 s. 426s * [Tue Oct 28 20:11:11 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 426s Tuesday, October 28, 2025: 20:11:11 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished 426s -------------------------------------------------------- 426s -------------------- Chrysalis ------------------------- 426s -- (Contig Clustering & de Bruijn Graph Construction) -- 426s -------------------------------------------------------- 426s 426s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 426s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 426s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 426s * [Tue Oct 28 20:11:11 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 426s * [Tue Oct 28 20:11:11 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null 427s * [Tue Oct 28 20:11:12 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 430s * [Tue Oct 28 20:11:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt 430s * [Tue Oct 28 20:11:15 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt 433s * [Tue Oct 28 20:11:18 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted 433s * [Tue Oct 28 20:11:18 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 433s * [Tue Oct 28 20:11:18 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out 433s * [Tue Oct 28 20:11:18 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200 433s * [Tue Oct 28 20:11:18 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 436s * [Tue Oct 28 20:11:20 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort 436s Tuesday, October 28, 2025: 20:11:21 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0 436s Tuesday, October 28, 2025: 20:11:21 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok 436s Tuesday, October 28, 2025: 20:11:21 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 436s Tuesday, October 28, 2025: 20:11:21 CMD: touch recursive_trinity.cmds.ok 436s Tuesday, October 28, 2025: 20:11:21 CMD: touch recursive_trinity.cmds.ok 436s 436s 436s -------------------------------------------------------------------------------- 436s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 436s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 436s -------------------------------------------------------------------------------- 436s 436s Tuesday, October 28, 2025: 20:11:21 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 436s Number of Commands: 41 510s 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. 510s 510s All commands completed successfully. :-) 510s 510s 510s 510s ** Harvesting all assembled transcripts into a single multi-fasta file... 510s 510s Tuesday, October 28, 2025: 20:12:35 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp 510s * [Tue Oct 28 20:12:35 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2 511s * [Tue Oct 28 20:12:36 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta 511s Tuesday, October 28, 2025: 20:12:36 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map 511s 511s 511s ############################################################################# 511s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta 511s ############################################################################# 511s 511s 511s 511s 511s 511s ./misc_run_tests/__runMe_with_qual_trimming.sh 511s #!/bin/bash -ve 511s 511s 511s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 511s gunzip -c reads.right.fq.gz > reads.right.fq 511s fi 511s 511s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 511s gunzip -c reads.left.fq.gz > reads.left.fq 511s fi 511s 511s 511s 511s ####################################################### 511s ## Run Trinity to Generate Transcriptome Assemblies ## 511s ####################################################### 511s 511s CPU=$(nproc || sysctl -n hw.physicalcpu) 511s 511s ${TRINITY_HOME}/Trinity \ 511s --seqType fq \ 511s --max_memory 2G \ 511s --left reads.left.fq \ 511s --right reads.right.fq \ 511s --SS_lib_type RF \ 511s --CPU ${CPU} \ 511s --no_normalize_reads \ 511s --trimmomatic \ 511s --output __test_trinity_with_trimmomatic 511s 511s 511s ______ ____ ____ ____ ____ ______ __ __ 511s | || \ | || \ | || || | | 511s | || D ) | | | _ | | | | || | | 511s |_| |_|| / | | | | | | | |_| |_|| ~ | 511s | | | \ | | | | | | | | | |___, | 511s | | | . \ | | | | | | | | | | | 511s |__| |__|\_||____||__|__||____| |__| |____/ 511s 511s Trinity-v2.15.2 511s 511s 511s 511s Left read files: $VAR1 = [ 511s 'reads.left.fq' 511s ]; 511s Right read files: $VAR1 = [ 511s 'reads.right.fq' 511s ]; 511s Tuesday, October 28, 2025: 20:12:36 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic 511s Tuesday, October 28, 2025: 20:12:36 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis 511s 511s 511s ---------------------------------------------------------------------------------- 511s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 511s ---------------------------------------------------------------------------------- 511s 511s --------------------------------------------------------------- 511s ------ Quality Trimming Via Trimmomatic --------------------- 511s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 511s --------------------------------------------------------------- 511s 511s 511s ## Running Trimmomatic on read files: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 511s Tuesday, October 28, 2025: 20:12:36 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 512s TrimmomaticPE: Started with arguments: 512s -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 512s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 512s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 512s Quality encoding detected as phred33 512s 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%) 512s TrimmomaticPE: Completed successfully 512s Tuesday, October 28, 2025: 20:12:37 CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq 512s Tuesday, October 28, 2025: 20:12:37 CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq 512s Tuesday, October 28, 2025: 20:12:37 CMD: touch trimmomatic.ok 512s Tuesday, October 28, 2025: 20:12:37 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 512s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:12:37 CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 512s Tuesday, October 28, 2025: 20:12:37 CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa 512s Tuesday, October 28, 2025: 20:12:37 CMD: touch left.fa.ok 512s Tuesday, October 28, 2025: 20:12:37 CMD: touch right.fa.ok 512s Tuesday, October 28, 2025: 20:12:37 CMD: touch left.fa.ok right.fa.ok 512s Tuesday, October 28, 2025: 20:12:37 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 512s Tuesday, October 28, 2025: 20:12:37 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok 512s ------------------------------------------- 512s ----------- Jellyfish -------------------- 512s -- (building a k-mer (25) catalog from reads) -- 512s ------------------------------------------- 512s 512s * [Tue Oct 28 20:12:37 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 514s * [Tue Oct 28 20:12:39 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 514s * [Tue Oct 28 20:12:39 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 514s ---------------------------------------------- 514s --------------- Inchworm (K=25, asm) --------------------- 514s -- (Linear contig construction from k-mers) -- 514s ---------------------------------------------- 514s 514s * [Tue Oct 28 20:12:39 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp 514s Kmer length set to: 25 514s Min assembly length set to: 25 514s Monitor turned on, set to: 1 514s min entropy set to: 1 514s setting number of threads to: 2 514s -setting parallel iworm mode. 514s -reading Kmer occurrences... 514s [0M] Kmers parsed. 514s done parsing 318541 Kmers, 318541 added, taking 0 seconds. 514s 514s TIMING KMER_DB_BUILDING 0 s. 514s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 515s Pruned 1498 kmers from catalog. 515s Pruning time: 0 seconds = 0 minutes. 515s 515s TIMING PRUNING 0 s. 515s -populating the kmer seed candidate list. 515s Kcounter hash size: 318541 515s Processed 317043 non-zero abundance kmers in kcounter. 515s -Not sorting list of kmers, given parallel mode in effect. 515s -beginning inchworm contig assembly. 515s Total kcounter hash size: 318541 vs. sorted list size: 317043 515s num threads set to: 2 515s Done opening file. tmp.iworm.fa.pid_20283.thread_0 515s Done opening file. tmp.iworm.fa.pid_20283.thread_1 515s 515s Iworm contig assembly time: 0 seconds = 0 minutes. 515s 515s TIMING CONTIG_BUILDING 0 s. 515s 515s TIMING PROG_RUNTIME 1 s. 515s * [Tue Oct 28 20:12:40 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 515s Tuesday, October 28, 2025: 20:12:40 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished 515s -------------------------------------------------------- 515s -------------------- Chrysalis ------------------------- 515s -- (Contig Clustering & de Bruijn Graph Construction) -- 515s -------------------------------------------------------- 515s 515s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 515s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 515s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 515s * [Tue Oct 28 20:12:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 515s * [Tue Oct 28 20:12:40 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null 515s * [Tue Oct 28 20:12:40 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 518s * [Tue Oct 28 20:12:43 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt 519s * [Tue Oct 28 20:12:44 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt 521s * [Tue Oct 28 20:12:46 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted 521s * [Tue Oct 28 20:12:46 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 521s * [Tue Oct 28 20:12:46 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out 521s * [Tue Oct 28 20:12:46 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200 521s * [Tue Oct 28 20:12:46 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 523s * [Tue Oct 28 20:12:48 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort 523s Tuesday, October 28, 2025: 20:12:48 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0 523s Tuesday, October 28, 2025: 20:12:48 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok 523s Tuesday, October 28, 2025: 20:12:48 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 523s Tuesday, October 28, 2025: 20:12:48 CMD: touch recursive_trinity.cmds.ok 523s Tuesday, October 28, 2025: 20:12:48 CMD: touch recursive_trinity.cmds.ok 523s 523s 523s -------------------------------------------------------------------------------- 523s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 523s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 523s -------------------------------------------------------------------------------- 523s 523s Tuesday, October 28, 2025: 20:12:48 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 523s Number of Commands: 36 586s 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. 586s 586s All commands completed successfully. :-) 586s 586s 586s 586s ** Harvesting all assembled transcripts into a single multi-fasta file... 586s 586s Tuesday, October 28, 2025: 20:13:51 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp 586s * [Tue Oct 28 20:13:51 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2 587s * [Tue Oct 28 20:13:52 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta 587s Tuesday, October 28, 2025: 20:13:52 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map 587s 587s 587s ############################################################################# 587s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta 587s ############################################################################# 587s 587s 587s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh 587s 587s ##### Done Running Trinity ##### 587s 587s #!/bin/bash -ve 587s 587s 587s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 587s gunzip -c reads.right.fq.gz > reads.right.fq 587s fi 587s 587s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 587s gunzip -c reads.left.fq.gz > reads.left.fq 587s fi 587s 587s 587s 587s ####################################################### 587s ## Run Trinity to Generate Transcriptome Assemblies ## 587s ####################################################### 587s 587s CPU=$(nproc || sysctl -n hw.physicalcpu) 587s 587s ${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 587s 587s 587s ______ ____ ____ ____ ____ ______ __ __ 587s | || \ | || \ | || || | | 587s | || D ) | | | _ | | | | || | | 587s |_| |_|| / | | | | | | | |_| |_|| ~ | 587s | | | \ | | | | | | | | | |___, | 587s | | | . \ | | | | | | | | | | | 587s |__| |__|\_||____||__|__||____| |__| |____/ 587s 587s Trinity-v2.15.2 587s 587s 587s 587s Left read files: $VAR1 = [ 587s 'reads.left.fq' 587s ]; 587s Right read files: $VAR1 = [ 587s 'reads.right.fq' 587s ]; 587s Tuesday, October 28, 2025: 20:13:52 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm 587s Tuesday, October 28, 2025: 20:13:52 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis 587s 587s 587s ---------------------------------------------------------------------------------- 587s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 587s ---------------------------------------------------------------------------------- 587s 587s --------------------------------------------------------------- 587s ------ Quality Trimming Via Trimmomatic --------------------- 587s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 587s --------------------------------------------------------------- 587s 587s 587s ## Running Trimmomatic on read files: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 587s Tuesday, October 28, 2025: 20:13:52 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 587s TrimmomaticPE: Started with arguments: 587s -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 587s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 587s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 587s Quality encoding detected as phred33 588s 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%) 588s TrimmomaticPE: Completed successfully 588s Tuesday, October 28, 2025: 20:13:53 CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq 588s Tuesday, October 28, 2025: 20:13:53 CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq 588s Tuesday, October 28, 2025: 20:13:53 CMD: touch trimmomatic.ok 588s Tuesday, October 28, 2025: 20:13:53 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 588s --------------------------------------------------------------- 588s ------------ In silico Read Normalization --------------------- 588s -- (Removing Excess Reads Beyond 200 Coverage -- 588s --------------------------------------------------------------- 588s 588s # running normalization on reads: $VAR1 = [ 588s [ 588s 'reads.left.fq.PwU.qtrim.fq' 588s ], 588s [ 588s 'reads.right.fq.PwU.qtrim.fq' 588s ] 588s ]; 588s 588s 588s Tuesday, October 28, 2025: 20:13:53 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/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 588s -prepping seqs 588s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa 588s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa 588s CMD finished (0 seconds) 588s CMD finished (0 seconds) 588s CMD: touch left.fa.ok 588s CMD finished (0 seconds) 588s CMD: touch right.fa.ok 588s CMD finished (0 seconds) 588s Done converting input files. CMD: cat left.fa right.fa > both.fa 588s CMD finished (0 seconds) 588s CMD: touch both.fa.ok 588s CMD finished (0 seconds) 588s -kmer counting. 588s ------------------------------------------- 588s ----------- Jellyfish -------------------- 588s -- (building a k-mer catalog from reads) -- 588s ------------------------------------------- 588s 588s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 590s CMD finished (2 seconds) 590s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 590s CMD finished (0 seconds) 590s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 590s CMD finished (0 seconds) 590s CMD: touch jellyfish.K25.min2.kmers.fa.success 590s CMD finished (0 seconds) 590s -generating stats files 590s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 590s -reading Kmer occurrences... 590s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 590s -reading Kmer occurrences... 590s 590s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 590s 590s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 590s STATS_GENERATION_TIME: 0 seconds. 590s CMD finished (0 seconds) 590s STATS_GENERATION_TIME: 0 seconds. 590s CMD finished (0 seconds) 590s CMD: touch left.fa.K25.stats.ok 590s CMD finished (0 seconds) 590s CMD: touch right.fa.K25.stats.ok 590s CMD finished (0 seconds) 590s -sorting each stats file by read name. 590s 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 590s 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 591s CMD finished (0 seconds) 591s CMD finished (0 seconds) 591s CMD: touch left.fa.K25.stats.sort.ok 591s CMD finished (1 seconds) 591s CMD: touch right.fa.K25.stats.sort.ok 591s CMD finished (0 seconds) 591s -defining normalized reads 591s 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 591s -opening left.fa.K25.stats.sort 591s -opening right.fa.K25.stats.sort 591s -done opening files. 591s CMD finished (0 seconds) 591s CMD: touch pairs.K25.stats.ok 591s CMD finished (0 seconds) 591s 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 591s 27678 / 27726 = 99.83% reads selected during normalization. 591s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 591s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 591s CMD finished (0 seconds) 591s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 591s CMD finished (0 seconds) 591s -search and capture. 592s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 592s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq 592s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 592s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq 592s CMD: touch /tmp/autopkgtest.sYnnix/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 592s CMD finished (0 seconds) 592s CMD: touch /tmp/autopkgtest.sYnnix/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 592s CMD finished (0 seconds) 592s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 592s CMD finished (0 seconds) 592s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 592s CMD finished (0 seconds) 592s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads 592s 592s 592s Normalization complete. See outputs: 592s /tmp/autopkgtest.sYnnix/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 592s /tmp/autopkgtest.sYnnix/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 592s Tuesday, October 28, 2025: 20:13:57 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok 592s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:13:57 CMD: cat /tmp/autopkgtest.sYnnix/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 592s Tuesday, October 28, 2025: 20:13:57 CMD: cat /tmp/autopkgtest.sYnnix/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 592s Tuesday, October 28, 2025: 20:13:57 CMD: touch left.fa.ok 592s Tuesday, October 28, 2025: 20:13:57 CMD: touch right.fa.ok 592s Tuesday, October 28, 2025: 20:13:57 CMD: touch left.fa.ok right.fa.ok 592s Tuesday, October 28, 2025: 20:13:57 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 592s Tuesday, October 28, 2025: 20:13:57 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok 592s ------------------------------------------- 592s ----------- Jellyfish -------------------- 592s -- (building a k-mer (25) catalog from reads) -- 592s ------------------------------------------- 592s 592s * [Tue Oct 28 20:13:57 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 593s * [Tue Oct 28 20:13:58 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 593s * [Tue Oct 28 20:13:58 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 593s ---------------------------------------------- 593s --------------- Inchworm (K=25, asm) --------------------- 593s -- (Linear contig construction from k-mers) -- 593s ---------------------------------------------- 593s 593s * [Tue Oct 28 20:13:58 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp 593s Kmer length set to: 25 593s Min assembly length set to: 25 593s Monitor turned on, set to: 1 593s min entropy set to: 1 593s setting number of threads to: 2 593s -setting parallel iworm mode. 593s -reading Kmer occurrences... 594s [0M] Kmers parsed. 594s done parsing 311705 Kmers, 311705 added, taking 1 seconds. 594s 594s TIMING KMER_DB_BUILDING 1 s. 594s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 594s Pruned 1486 kmers from catalog. 594s Pruning time: 0 seconds = 0 minutes. 594s 594s TIMING PRUNING 0 s. 594s -populating the kmer seed candidate list. 594s Kcounter hash size: 311705 594s Processed 310219 non-zero abundance kmers in kcounter. 594s -Not sorting list of kmers, given parallel mode in effect. 594s -beginning inchworm contig assembly. 594s Total kcounter hash size: 311705 vs. sorted list size: 310219 594s num threads set to: 2 594s Done opening file. tmp.iworm.fa.pid_26798.thread_0 594s Done opening file. tmp.iworm.fa.pid_26798.thread_1 594s 594s Iworm contig assembly time: 0 seconds = 0 minutes. 594s 594s TIMING CONTIG_BUILDING 0 s. 594s 594s TIMING PROG_RUNTIME 1 s. 594s * [Tue Oct 28 20:13:59 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 594s Tuesday, October 28, 2025: 20:13:59 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished 594s -------------------------------------------------------- 594s -------------------- Chrysalis ------------------------- 594s -- (Contig Clustering & de Bruijn Graph Construction) -- 594s -------------------------------------------------------- 594s 594s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 594s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 594s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 594s * [Tue Oct 28 20:13:59 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 594s * [Tue Oct 28 20:13:59 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null 596s * [Tue Oct 28 20:14:00 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 598s * [Tue Oct 28 20:14:03 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt 599s * [Tue Oct 28 20:14:04 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt 601s * [Tue Oct 28 20:14:06 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted 601s * [Tue Oct 28 20:14:06 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 601s * [Tue Oct 28 20:14:06 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out 601s * [Tue Oct 28 20:14:06 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200 601s * [Tue Oct 28 20:14:06 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/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 604s * [Tue Oct 28 20:14:09 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort 604s Tuesday, October 28, 2025: 20:14:09 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0 604s Tuesday, October 28, 2025: 20:14:09 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok 604s Tuesday, October 28, 2025: 20:14:09 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 604s Tuesday, October 28, 2025: 20:14:09 CMD: touch recursive_trinity.cmds.ok 604s Tuesday, October 28, 2025: 20:14:09 CMD: touch recursive_trinity.cmds.ok 604s 604s 604s -------------------------------------------------------------------------------- 604s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 604s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 604s -------------------------------------------------------------------------------- 604s 604s Tuesday, October 28, 2025: 20:14:09 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 604s Number of Commands: 39 670s succeeded(1) 2.5641% completed. succeeded(2) 5.12821% completed. succeeded(3) 7.69231% completed. succeeded(4) 10.2564% completed. succeeded(5) 12.8205% completed. succeeded(6) 15.3846% completed. succeeded(7) 17.9487% completed. succeeded(8) 20.5128% completed. succeeded(9) 23.0769% completed. succeeded(10) 25.641% completed. succeeded(11) 28.2051% completed. succeeded(12) 30.7692% completed. succeeded(13) 33.3333% completed. succeeded(14) 35.8974% completed. succeeded(15) 38.4615% completed. succeeded(16) 41.0256% completed. succeeded(17) 43.5897% completed. succeeded(18) 46.1538% completed. succeeded(19) 48.7179% completed. succeeded(20) 51.2821% completed. succeeded(21) 53.8462% completed. succeeded(22) 56.4103% completed. succeeded(23) 58.9744% completed. succeeded(24) 61.5385% completed. succeeded(25) 64.1026% completed. succeeded(26) 66.6667% completed. succeeded(27) 69.2308% completed. succeeded(28) 71.7949% completed. succeeded(29) 74.359% completed. succeeded(30) 76.9231% completed. succeeded(31) 79.4872% completed. succeeded(32) 82.0513% completed. succeeded(33) 84.6154% completed. succeeded(34) 87.1795% completed. succeeded(35) 89.7436% completed. succeeded(36) 92.3077% completed. succeeded(37) 94.8718% completed. succeeded(38) 97.4359% completed. succeeded(39) 100% completed. 670s 670s All commands completed successfully. :-) 670s 670s 670s 670s ** Harvesting all assembled transcripts into a single multi-fasta file... 670s 670s Tuesday, October 28, 2025: 20:15:15 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp 670s * [Tue Oct 28 20:15:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2 671s * [Tue Oct 28 20:15:16 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta 671s Tuesday, October 28, 2025: 20:15:16 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map 671s 671s 671s ############################################################################# 671s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta 671s ############################################################################# 671s 671s 671s 671s ##### Done Running Trinity ##### 671s 671s exit 0 671s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh 671s #!/bin/bash -ve 671s 671s ${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 671s 671s 671s ______ ____ ____ ____ ____ ______ __ __ 671s | || \ | || \ | || || | | 671s | || D ) | | | _ | | | | || | | 671s |_| |_|| / | | | | | | | |_| |_|| ~ | 671s | | | \ | | | | | | | | | |___, | 671s | | | . \ | | | | | | | | | | | 671s |__| |__|\_||____||__|__||____| |__| |____/ 671s 671s Trinity-v2.15.2 671s 671s 671s 671s Left read files: $VAR1 = [ 671s 'reads.left.fq.gz' 671s ]; 671s Right read files: $VAR1 = [ 671s 'reads.right.fq.gz' 671s ]; 671s Tuesday, October 28, 2025: 20:15:16 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard 671s Tuesday, October 28, 2025: 20:15:16 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis 671s 671s 671s ---------------------------------------------------------------------------------- 671s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 671s ---------------------------------------------------------------------------------- 671s 671s --------------------------------------------------------------- 671s ------------ In silico Read Normalization --------------------- 671s -- (Removing Excess Reads Beyond 200 Coverage -- 671s --------------------------------------------------------------- 671s 671s # running normalization on reads: $VAR1 = [ 671s [ 671s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 671s ], 671s [ 671s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 671s ] 671s ]; 671s 671s 671s Tuesday, October 28, 2025: 20:15:16 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 671s -prepping seqs 671s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 671s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 671s CMD finished (0 seconds) 671s CMD finished (0 seconds) 671s CMD: touch left.fa.ok 671s CMD finished (0 seconds) 671s CMD: touch right.fa.ok 671s CMD finished (0 seconds) 671s Done converting input files. CMD: cat left.fa right.fa > both.fa 671s CMD finished (0 seconds) 671s CMD: touch both.fa.ok 671s CMD finished (0 seconds) 672s -kmer counting. 672s ------------------------------------------- 672s ----------- Jellyfish -------------------- 672s -- (building a k-mer catalog from reads) -- 672s ------------------------------------------- 672s 672s CMD: jellyfish count -t 1 -m 25 -s 100000000 both.fa 674s CMD finished (3 seconds) 674s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 674s CMD finished (0 seconds) 674s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 674s CMD finished (0 seconds) 674s CMD: touch jellyfish.K25.min2.kmers.fa.success 674s CMD finished (0 seconds) 674s -generating stats files 674s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 674s -reading Kmer occurrences... 674s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 674s -reading Kmer occurrences... 674s 674s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 674s 674s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 675s STATS_GENERATION_TIME: 1 seconds. 675s STATS_GENERATION_TIME: 1 seconds. 675s CMD finished (1 seconds) 675s CMD finished (1 seconds) 675s CMD: touch left.fa.K25.stats.ok 675s CMD finished (0 seconds) 675s CMD: touch right.fa.K25.stats.ok 675s CMD finished (0 seconds) 675s -sorting each stats file by read name. 675s 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 675s 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 675s CMD finished (0 seconds) 675s CMD finished (0 seconds) 675s CMD: touch left.fa.K25.stats.sort.ok 675s CMD finished (0 seconds) 675s CMD: touch right.fa.K25.stats.sort.ok 675s CMD finished (0 seconds) 675s -defining normalized reads 675s 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 675s -opening left.fa.K25.stats.sort 675s -opening right.fa.K25.stats.sort 675s -done opening files. 675s CMD finished (0 seconds) 675s CMD: touch pairs.K25.stats.ok 675s CMD finished (0 seconds) 675s 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 675s 30472 / 30575 = 99.66% reads selected during normalization. 675s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 675s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 675s CMD finished (0 seconds) 675s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 675s CMD finished (0 seconds) 675s -search and capture. 676s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 676s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 676s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 676s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 676s CMD: touch /tmp/autopkgtest.sYnnix/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 676s CMD finished (0 seconds) 676s CMD: touch /tmp/autopkgtest.sYnnix/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 676s CMD finished (0 seconds) 676s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 676s CMD finished (0 seconds) 676s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 676s CMD finished (0 seconds) 676s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads 676s 676s 676s Normalization complete. See outputs: 676s /tmp/autopkgtest.sYnnix/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 676s /tmp/autopkgtest.sYnnix/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 676s Tuesday, October 28, 2025: 20:15:21 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok 676s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:15:21 CMD: cat /tmp/autopkgtest.sYnnix/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 676s Tuesday, October 28, 2025: 20:15:21 CMD: cat /tmp/autopkgtest.sYnnix/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 676s Tuesday, October 28, 2025: 20:15:21 CMD: touch left.fa.ok 676s Tuesday, October 28, 2025: 20:15:21 CMD: touch right.fa.ok 676s Tuesday, October 28, 2025: 20:15:21 CMD: touch left.fa.ok right.fa.ok 676s Tuesday, October 28, 2025: 20:15:21 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 676s Tuesday, October 28, 2025: 20:15:21 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok 676s ------------------------------------------- 676s ----------- Jellyfish -------------------- 676s -- (building a k-mer (25) catalog from reads) -- 676s ------------------------------------------- 676s 676s * [Tue Oct 28 20:15:21 2025] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 679s * [Tue Oct 28 20:15:24 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 679s * [Tue Oct 28 20:15:24 2025] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 679s ---------------------------------------------- 679s --------------- Inchworm (K=25, asm) --------------------- 679s -- (Linear contig construction from k-mers) -- 679s ---------------------------------------------- 679s 679s * [Tue Oct 28 20:15:24 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp 679s Kmer length set to: 25 679s Min assembly length set to: 25 679s Monitor turned on, set to: 1 679s min entropy set to: 1 679s setting number of threads to: 1 679s -setting parallel iworm mode. 679s -reading Kmer occurrences... 679s [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. 679s done parsing 519541 Kmers, 519541 added, taking 0 seconds. 679s 679s TIMING KMER_DB_BUILDING 0 s. 679s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 680s Pruned 4252 kmers from catalog. 680s Pruning time: 1 seconds = 0.0166667 minutes. 680s 680s TIMING PRUNING 1 s. 680s -populating the kmer seed candidate list. 680s Kcounter hash size: 519541 680s Processed 515289 non-zero abundance kmers in kcounter. 680s -Not sorting list of kmers, given parallel mode in effect. 680s -beginning inchworm contig assembly. 680s Total kcounter hash size: 519541 vs. sorted list size: 515289 680s num threads set to: 1 680s Done opening file. tmp.iworm.fa.pid_33824.thread_0 680s 680s Iworm contig assembly time: 0 seconds = 0 minutes. 680s 680s TIMING CONTIG_BUILDING 0 s. 680s 680s TIMING PROG_RUNTIME 1 s. 680s * [Tue Oct 28 20:15:25 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 680s Tuesday, October 28, 2025: 20:15:25 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished 680s -------------------------------------------------------- 680s -------------------- Chrysalis ------------------------- 680s -- (Contig Clustering & de Bruijn Graph Construction) -- 680s -------------------------------------------------------- 680s 680s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 680s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 680s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 680s * [Tue Oct 28 20:15:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 680s * [Tue Oct 28 20:15:25 2025] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null 681s * [Tue Oct 28 20:15:26 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 684s * [Tue Oct 28 20:15:29 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt 684s * [Tue Oct 28 20:15:29 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt 685s * [Tue Oct 28 20:15:30 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted 685s * [Tue Oct 28 20:15:30 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 685s * [Tue Oct 28 20:15:30 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out 685s * [Tue Oct 28 20:15:30 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200 685s * [Tue Oct 28 20:15:30 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000 -strand -p 10 689s * [Tue Oct 28 20:15:34 2025] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort 689s Tuesday, October 28, 2025: 20:15:34 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0 690s Tuesday, October 28, 2025: 20:15:34 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok 690s Tuesday, October 28, 2025: 20:15:34 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 690s Tuesday, October 28, 2025: 20:15:35 CMD: touch recursive_trinity.cmds.ok 690s Tuesday, October 28, 2025: 20:15:35 CMD: touch recursive_trinity.cmds.ok 690s 690s 690s -------------------------------------------------------------------------------- 690s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 690s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 690s -------------------------------------------------------------------------------- 690s 690s Tuesday, October 28, 2025: 20:15:35 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 690s Number of Commands: 36 691s CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 691s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 691s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 691s bt2 index files: $VAR1 = []; 691s Note - bowtie-build indices do not yet exist. Indexing genome now. 691s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 691s CMD: touch /tmp/autopkgtest.sYnnix/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 691s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 692s 9900 reads; of these: 692s 9900 (100.00%) were unpaired; of these: 692s 5 (0.05%) aligned 0 times 692s 5821 (58.80%) aligned exactly 1 time 692s 4074 (41.15%) aligned >1 times 692s 99.95% overall alignment rate 692s CMD: touch /tmp/autopkgtest.sYnnix/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 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 692s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 692s CMD: samtools index /tmp/autopkgtest.sYnnix/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 692s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 692s CMD: samtools index /tmp/autopkgtest.sYnnix/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 692s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 692s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 692s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 692s 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 692s 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 692s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 692s 692s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 692s 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 692s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 692s 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 692s 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 692s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 692s -processing jaccard pair sensor 693s 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 693s [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 693s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 700s succeeded(1) 2.77778% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 700s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 700s bt2 index files: $VAR1 = []; 700s Note - bowtie-build indices do not yet exist. Indexing genome now. 700s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 700s CMD: touch /tmp/autopkgtest.sYnnix/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 700s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 700s 6 reads; of these: 700s 6 (100.00%) were unpaired; of these: 700s 0 (0.00%) aligned 0 times 700s 6 (100.00%) aligned exactly 1 time 700s 0 (0.00%) aligned >1 times 700s 100.00% overall alignment rate 700s CMD: touch /tmp/autopkgtest.sYnnix/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 700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 700s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 700s CMD: samtools index /tmp/autopkgtest.sYnnix/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 700s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 700s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 700s 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 700s 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 700s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 700s 700s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 700s 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 700s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 700s 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 700s 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 700s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 700s -processing jaccard pair sensor 700s 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 700s 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 700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 701s succeeded(2) 5.55556% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 701s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 701s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 701s bt2 index files: $VAR1 = []; 701s Note - bowtie-build indices do not yet exist. Indexing genome now. 701s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 702s CMD: touch /tmp/autopkgtest.sYnnix/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 702s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 702s 29 reads; of these: 702s 29 (100.00%) were unpaired; of these: 702s 0 (0.00%) aligned 0 times 702s 29 (100.00%) aligned exactly 1 time 702s 0 (0.00%) aligned >1 times 702s 100.00% overall alignment rate 702s CMD: touch /tmp/autopkgtest.sYnnix/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 702s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 702s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 702s CMD: samtools index /tmp/autopkgtest.sYnnix/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 702s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 702s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 702s 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 702s 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 702s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 702s 702s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 702s 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 702s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 702s 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 702s 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 702s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 702s -processing jaccard pair sensor 702s 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 702s 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 702s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 703s succeeded(3) 8.33333% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 703s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 704s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 704s bt2 index files: $VAR1 = []; 704s Note - bowtie-build indices do not yet exist. Indexing genome now. 704s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 704s CMD: touch /tmp/autopkgtest.sYnnix/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 704s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 704s 33 reads; of these: 704s 33 (100.00%) were unpaired; of these: 704s 0 (0.00%) aligned 0 times 704s 33 (100.00%) aligned exactly 1 time 704s 0 (0.00%) aligned >1 times 704s 100.00% overall alignment rate 704s CMD: touch /tmp/autopkgtest.sYnnix/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 704s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 704s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 704s CMD: samtools index /tmp/autopkgtest.sYnnix/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 704s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 704s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 704s 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 704s 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 704s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 704s 704s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 704s 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 704s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 704s 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 704s 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 704s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 704s -processing jaccard pair sensor 704s 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 704s 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 704s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 706s succeeded(4) 11.1111% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 706s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 706s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 706s bt2 index files: $VAR1 = []; 706s Note - bowtie-build indices do not yet exist. Indexing genome now. 706s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 706s CMD: touch /tmp/autopkgtest.sYnnix/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 706s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 706s 9 reads; of these: 706s 9 (100.00%) were unpaired; of these: 706s 0 (0.00%) aligned 0 times 706s 9 (100.00%) aligned exactly 1 time 706s 0 (0.00%) aligned >1 times 706s 100.00% overall alignment rate 706s CMD: touch /tmp/autopkgtest.sYnnix/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 706s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 706s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 706s CMD: samtools index /tmp/autopkgtest.sYnnix/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 706s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 706s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 706s 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 706s 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 706s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 706s 706s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 706s 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 706s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 706s 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 706s 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 706s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 706s -processing jaccard pair sensor 706s 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 706s 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 706s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 708s succeeded(5) 13.8889% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 708s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 708s bt2 index files: $VAR1 = []; 708s Note - bowtie-build indices do not yet exist. Indexing genome now. 708s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 708s CMD: touch /tmp/autopkgtest.sYnnix/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 708s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 708s 8 reads; of these: 708s 8 (100.00%) were unpaired; of these: 708s 0 (0.00%) aligned 0 times 708s 8 (100.00%) aligned exactly 1 time 708s 0 (0.00%) aligned >1 times 708s 100.00% overall alignment rate 708s CMD: touch /tmp/autopkgtest.sYnnix/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 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 708s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 708s CMD: samtools index /tmp/autopkgtest.sYnnix/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 708s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 708s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 708s 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 708s 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 708s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 708s 708s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 708s 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 708s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 708s 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 708s 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 708s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 708s -processing jaccard pair sensor 708s 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 708s 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 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 710s succeeded(6) 16.6667% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 710s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 710s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 710s bt2 index files: $VAR1 = []; 710s Note - bowtie-build indices do not yet exist. Indexing genome now. 710s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 710s CMD: touch /tmp/autopkgtest.sYnnix/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 710s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 711s 4987 reads; of these: 711s 4987 (100.00%) were unpaired; of these: 711s 2 (0.04%) aligned 0 times 711s 2643 (53.00%) aligned exactly 1 time 711s 2342 (46.96%) aligned >1 times 711s 99.96% overall alignment rate 711s CMD: touch /tmp/autopkgtest.sYnnix/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 711s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 711s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 711s CMD: samtools index /tmp/autopkgtest.sYnnix/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 711s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 711s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 711s 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 711s 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 711s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 711s 711s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 711s 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 711s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 711s 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 711s 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 711s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 711s -processing jaccard pair sensor 712s 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 712s [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 712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 716s succeeded(7) 19.4444% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 716s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 716s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 716s bt2 index files: $VAR1 = []; 716s Note - bowtie-build indices do not yet exist. Indexing genome now. 716s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 716s CMD: touch /tmp/autopkgtest.sYnnix/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 716s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 716s 15 reads; of these: 716s 15 (100.00%) were unpaired; of these: 716s 0 (0.00%) aligned 0 times 716s 15 (100.00%) aligned exactly 1 time 716s 0 (0.00%) aligned >1 times 716s 100.00% overall alignment rate 716s CMD: touch /tmp/autopkgtest.sYnnix/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 716s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 716s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 716s CMD: samtools index /tmp/autopkgtest.sYnnix/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 716s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 716s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 716s 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 716s 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 716s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 716s 716s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 716s 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 716s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 716s 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 716s 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 716s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 716s -processing jaccard pair sensor 716s 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 716s 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 716s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 718s succeeded(8) 22.2222% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 718s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 718s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 718s bt2 index files: $VAR1 = []; 718s Note - bowtie-build indices do not yet exist. Indexing genome now. 718s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 718s CMD: touch /tmp/autopkgtest.sYnnix/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 718s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 718s 17 reads; of these: 718s 17 (100.00%) were unpaired; of these: 718s 0 (0.00%) aligned 0 times 718s 17 (100.00%) aligned exactly 1 time 718s 0 (0.00%) aligned >1 times 718s 100.00% overall alignment rate 718s CMD: touch /tmp/autopkgtest.sYnnix/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 718s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 718s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 718s CMD: samtools index /tmp/autopkgtest.sYnnix/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 718s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 718s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 718s 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 718s 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 718s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 718s 718s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 718s 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 718s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 718s 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 718s 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 718s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 718s -processing jaccard pair sensor 718s 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 718s 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 718s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 720s succeeded(9) 25% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 720s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 720s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 720s bt2 index files: $VAR1 = []; 720s Note - bowtie-build indices do not yet exist. Indexing genome now. 720s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 720s CMD: touch /tmp/autopkgtest.sYnnix/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 720s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 721s 7052 reads; of these: 721s 7052 (100.00%) were unpaired; of these: 721s 4 (0.06%) aligned 0 times 721s 5120 (72.60%) aligned exactly 1 time 721s 1928 (27.34%) aligned >1 times 721s 99.94% overall alignment rate 721s CMD: touch /tmp/autopkgtest.sYnnix/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 721s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 721s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 721s CMD: samtools index /tmp/autopkgtest.sYnnix/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 721s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 721s CMD: samtools index /tmp/autopkgtest.sYnnix/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 721s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 721s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 721s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 721s 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 721s 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 721s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 721s 721s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 721s 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 721s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 721s 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 721s 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 722s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 722s -processing jaccard pair sensor 722s 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 722s [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 722s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 732s succeeded(10) 27.7778% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 732s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 732s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 732s bt2 index files: $VAR1 = []; 732s Note - bowtie-build indices do not yet exist. Indexing genome now. 732s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 732s CMD: touch /tmp/autopkgtest.sYnnix/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 732s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 732s 7 reads; of these: 732s 7 (100.00%) were unpaired; of these: 732s 3 (42.86%) aligned 0 times 732s 4 (57.14%) aligned exactly 1 time 732s 0 (0.00%) aligned >1 times 732s 57.14% overall alignment rate 732s CMD: touch /tmp/autopkgtest.sYnnix/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 732s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 732s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 732s CMD: samtools index /tmp/autopkgtest.sYnnix/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 732s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 732s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 732s 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 732s 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 732s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 732s 732s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 732s 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 732s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 732s 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 732s 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 732s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 732s -processing jaccard pair sensor 732s 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 732s 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 732s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 733s succeeded(11) 30.5556% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 733s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 733s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 733s bt2 index files: $VAR1 = []; 733s Note - bowtie-build indices do not yet exist. Indexing genome now. 733s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 734s CMD: touch /tmp/autopkgtest.sYnnix/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 734s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 734s 28 reads; of these: 734s 28 (100.00%) were unpaired; of these: 734s 0 (0.00%) aligned 0 times 734s 28 (100.00%) aligned exactly 1 time 734s 0 (0.00%) aligned >1 times 734s 100.00% overall alignment rate 734s CMD: touch /tmp/autopkgtest.sYnnix/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 734s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 734s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 734s CMD: samtools index /tmp/autopkgtest.sYnnix/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 734s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 734s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 734s 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 734s 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 734s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 734s 734s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 734s 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 734s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 734s 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 734s 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 734s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 734s -processing jaccard pair sensor 734s 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 734s 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 734s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 735s succeeded(12) 33.3333% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 735s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 735s bt2 index files: $VAR1 = []; 735s Note - bowtie-build indices do not yet exist. Indexing genome now. 735s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 736s CMD: touch /tmp/autopkgtest.sYnnix/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 736s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 736s 24 reads; of these: 736s 24 (100.00%) were unpaired; of these: 736s 0 (0.00%) aligned 0 times 736s 24 (100.00%) aligned exactly 1 time 736s 0 (0.00%) aligned >1 times 736s 100.00% overall alignment rate 736s CMD: touch /tmp/autopkgtest.sYnnix/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 736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 736s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 736s CMD: samtools index /tmp/autopkgtest.sYnnix/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 736s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 736s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 736s 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 736s 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 736s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 736s 736s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 736s 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 736s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 736s 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 736s 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 736s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 736s -processing jaccard pair sensor 736s 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 736s 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 736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 738s succeeded(13) 36.1111% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 738s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 738s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 738s bt2 index files: $VAR1 = []; 738s Note - bowtie-build indices do not yet exist. Indexing genome now. 738s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 738s CMD: touch /tmp/autopkgtest.sYnnix/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 738s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 738s 5130 reads; of these: 738s 5130 (100.00%) were unpaired; of these: 738s 6 (0.12%) aligned 0 times 738s 4306 (83.94%) aligned exactly 1 time 738s 818 (15.95%) aligned >1 times 738s 99.88% overall alignment rate 738s CMD: touch /tmp/autopkgtest.sYnnix/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 738s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 739s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 739s CMD: samtools index /tmp/autopkgtest.sYnnix/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 739s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 739s CMD: samtools index /tmp/autopkgtest.sYnnix/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 739s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 739s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 739s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 [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 739s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 744s succeeded(14) 38.8889% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 744s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 744s bt2 index files: $VAR1 = []; 744s Note - bowtie-build indices do not yet exist. Indexing genome now. 744s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 744s CMD: touch /tmp/autopkgtest.sYnnix/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 744s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 744s 3374 reads; of these: 744s 3374 (100.00%) were unpaired; of these: 744s 1 (0.03%) aligned 0 times 744s 2870 (85.06%) aligned exactly 1 time 744s 503 (14.91%) aligned >1 times 744s 99.97% overall alignment rate 744s CMD: touch /tmp/autopkgtest.sYnnix/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 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 744s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 744s CMD: samtools index /tmp/autopkgtest.sYnnix/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 744s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 744s CMD: samtools index /tmp/autopkgtest.sYnnix/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 744s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 744s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 744s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 745s 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 745s [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 745s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 748s succeeded(15) 41.6667% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 748s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 748s bt2 index files: $VAR1 = []; 748s Note - bowtie-build indices do not yet exist. Indexing genome now. 748s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 748s CMD: touch /tmp/autopkgtest.sYnnix/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 748s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 748s 6 reads; of these: 748s 6 (100.00%) were unpaired; of these: 748s 0 (0.00%) aligned 0 times 748s 6 (100.00%) aligned exactly 1 time 748s 0 (0.00%) aligned >1 times 748s 100.00% overall alignment rate 748s CMD: touch /tmp/autopkgtest.sYnnix/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 748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 748s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 748s CMD: samtools index /tmp/autopkgtest.sYnnix/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 748s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 748s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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 748s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 748s 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.sYnnix/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.sYnnix/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 750s succeeded(16) 44.4444% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 750s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 750s bt2 index files: $VAR1 = []; 750s Note - bowtie-build indices do not yet exist. Indexing genome now. 750s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 750s CMD: touch /tmp/autopkgtest.sYnnix/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 750s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 750s 8 reads; of these: 750s 8 (100.00%) were unpaired; of these: 750s 0 (0.00%) aligned 0 times 750s 8 (100.00%) aligned exactly 1 time 750s 0 (0.00%) aligned >1 times 750s 100.00% overall alignment rate 750s CMD: touch /tmp/autopkgtest.sYnnix/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 750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 750s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 750s CMD: samtools index /tmp/autopkgtest.sYnnix/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 750s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 750s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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 750s 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 750s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 750s 750s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 750s 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 750s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 750s 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 750s 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 750s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 750s -processing jaccard pair sensor 750s 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 750s 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 750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 752s succeeded(17) 47.2222% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 752s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 752s bt2 index files: $VAR1 = []; 752s Note - bowtie-build indices do not yet exist. Indexing genome now. 752s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 752s CMD: touch /tmp/autopkgtest.sYnnix/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 752s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 752s 14 reads; of these: 752s 14 (100.00%) were unpaired; of these: 752s 0 (0.00%) aligned 0 times 752s 14 (100.00%) aligned exactly 1 time 752s 0 (0.00%) aligned >1 times 752s 100.00% overall alignment rate 752s CMD: touch /tmp/autopkgtest.sYnnix/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 752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 752s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 752s CMD: samtools index /tmp/autopkgtest.sYnnix/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 752s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 752s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 752s 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 752s 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 752s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 752s 752s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 752s 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 752s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 752s 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 752s 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 752s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 752s -processing jaccard pair sensor 752s 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 752s 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 752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 754s succeeded(18) 50% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 754s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 754s bt2 index files: $VAR1 = []; 754s Note - bowtie-build indices do not yet exist. Indexing genome now. 754s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 754s CMD: touch /tmp/autopkgtest.sYnnix/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 754s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 754s 15 reads; of these: 754s 15 (100.00%) were unpaired; of these: 754s 0 (0.00%) aligned 0 times 754s 15 (100.00%) aligned exactly 1 time 754s 0 (0.00%) aligned >1 times 754s 100.00% overall alignment rate 754s CMD: touch /tmp/autopkgtest.sYnnix/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 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 754s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 754s CMD: samtools index /tmp/autopkgtest.sYnnix/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 754s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 754s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 754s 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 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 756s succeeded(19) 52.7778% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 756s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 756s bt2 index files: $VAR1 = []; 756s Note - bowtie-build indices do not yet exist. Indexing genome now. 756s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 756s CMD: touch /tmp/autopkgtest.sYnnix/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 756s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 756s 2351 reads; of these: 756s 2351 (100.00%) were unpaired; of these: 756s 1 (0.04%) aligned 0 times 756s 1736 (73.84%) aligned exactly 1 time 756s 614 (26.12%) aligned >1 times 756s 99.96% overall alignment rate 756s CMD: touch /tmp/autopkgtest.sYnnix/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 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 757s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 757s CMD: samtools index /tmp/autopkgtest.sYnnix/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 757s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 757s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 757s 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 757s 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 757s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 757s 757s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 757s 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 757s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 757s 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 757s 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 757s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 757s -processing jaccard pair sensor 757s 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 757s [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 757s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 761s succeeded(20) 55.5556% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 761s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 761s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 761s bt2 index files: $VAR1 = []; 761s Note - bowtie-build indices do not yet exist. Indexing genome now. 761s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 761s CMD: touch /tmp/autopkgtest.sYnnix/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 761s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 761s 1875 reads; of these: 761s 1875 (100.00%) were unpaired; of these: 761s 2 (0.11%) aligned 0 times 761s 1543 (82.29%) aligned exactly 1 time 761s 330 (17.60%) aligned >1 times 761s 99.89% overall alignment rate 761s CMD: touch /tmp/autopkgtest.sYnnix/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 761s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 761s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 761s CMD: samtools index /tmp/autopkgtest.sYnnix/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 761s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 761s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 761s 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 761s 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 762s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 762s 762s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 762s 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 762s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 762s 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 762s 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 762s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 762s -processing jaccard pair sensor 762s 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 762s [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 762s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 765s succeeded(21) 58.3333% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 765s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 765s bt2 index files: $VAR1 = []; 765s Note - bowtie-build indices do not yet exist. Indexing genome now. 765s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 765s CMD: touch /tmp/autopkgtest.sYnnix/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 765s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 765s 40 reads; of these: 765s 40 (100.00%) were unpaired; of these: 765s 0 (0.00%) aligned 0 times 765s 36 (90.00%) aligned exactly 1 time 765s 4 (10.00%) aligned >1 times 765s 100.00% overall alignment rate 765s CMD: touch /tmp/autopkgtest.sYnnix/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 765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 765s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 765s CMD: samtools index /tmp/autopkgtest.sYnnix/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 765s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 765s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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.sYnnix/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.sYnnix/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 767s succeeded(22) 61.1111% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 767s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 767s bt2 index files: $VAR1 = []; 767s Note - bowtie-build indices do not yet exist. Indexing genome now. 767s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 767s CMD: touch /tmp/autopkgtest.sYnnix/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 767s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 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.sYnnix/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 767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 767s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 767s CMD: samtools index /tmp/autopkgtest.sYnnix/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 767s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 767s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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.sYnnix/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.sYnnix/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 769s succeeded(23) 63.8889% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 769s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 769s bt2 index files: $VAR1 = []; 769s Note - bowtie-build indices do not yet exist. Indexing genome now. 769s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 769s CMD: touch /tmp/autopkgtest.sYnnix/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 769s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 769s 29 reads; of these: 769s 29 (100.00%) were unpaired; of these: 769s 0 (0.00%) aligned 0 times 769s 23 (79.31%) aligned exactly 1 time 769s 6 (20.69%) aligned >1 times 769s 100.00% overall alignment rate 769s CMD: touch /tmp/autopkgtest.sYnnix/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 769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 769s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 769s CMD: samtools index /tmp/autopkgtest.sYnnix/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 769s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 769s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 770s 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 770s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 771s succeeded(24) 66.6667% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 771s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 771s bt2 index files: $VAR1 = []; 771s Note - bowtie-build indices do not yet exist. Indexing genome now. 771s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 771s CMD: touch /tmp/autopkgtest.sYnnix/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 771s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 771s 8 reads; of these: 771s 8 (100.00%) were unpaired; of these: 771s 0 (0.00%) aligned 0 times 771s 8 (100.00%) aligned exactly 1 time 771s 0 (0.00%) aligned >1 times 771s 100.00% overall alignment rate 771s CMD: touch /tmp/autopkgtest.sYnnix/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 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 771s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 772s CMD: samtools index /tmp/autopkgtest.sYnnix/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 772s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 772s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 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.sYnnix/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.sYnnix/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 773s succeeded(25) 69.4444% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 773s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 773s bt2 index files: $VAR1 = []; 773s Note - bowtie-build indices do not yet exist. Indexing genome now. 773s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 773s CMD: touch /tmp/autopkgtest.sYnnix/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 773s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 773s 81 reads; of these: 773s 81 (100.00%) were unpaired; of these: 773s 0 (0.00%) aligned 0 times 773s 78 (96.30%) aligned exactly 1 time 773s 3 (3.70%) aligned >1 times 773s 100.00% overall alignment rate 773s CMD: touch /tmp/autopkgtest.sYnnix/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 773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 773s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 773s CMD: samtools index /tmp/autopkgtest.sYnnix/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 773s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 773s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 773s 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 773s 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 773s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 773s 773s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 773s 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 773s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 773s 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 773s 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 773s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 773s -processing jaccard pair sensor 773s 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 773s 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 773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 775s succeeded(26) 72.2222% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 775s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 775s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 775s bt2 index files: $VAR1 = []; 775s Note - bowtie-build indices do not yet exist. Indexing genome now. 775s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 775s CMD: touch /tmp/autopkgtest.sYnnix/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 775s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 775s 13 reads; of these: 775s 13 (100.00%) were unpaired; of these: 775s 0 (0.00%) aligned 0 times 775s 13 (100.00%) aligned exactly 1 time 775s 0 (0.00%) aligned >1 times 775s 100.00% overall alignment rate 775s CMD: touch /tmp/autopkgtest.sYnnix/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 775s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 775s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 775s CMD: samtools index /tmp/autopkgtest.sYnnix/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 775s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 775s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 775s 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 775s 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 776s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 776s 776s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 776s 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 776s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 776s 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 776s 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 776s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 776s -processing jaccard pair sensor 776s 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 776s 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 776s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 777s succeeded(27) 75% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 777s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 777s bt2 index files: $VAR1 = []; 777s Note - bowtie-build indices do not yet exist. Indexing genome now. 777s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 777s CMD: touch /tmp/autopkgtest.sYnnix/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 777s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 777s 1556 reads; of these: 777s 1556 (100.00%) were unpaired; of these: 777s 1 (0.06%) aligned 0 times 777s 1328 (85.35%) aligned exactly 1 time 777s 227 (14.59%) aligned >1 times 777s 99.94% overall alignment rate 777s CMD: touch /tmp/autopkgtest.sYnnix/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 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 777s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 777s CMD: samtools index /tmp/autopkgtest.sYnnix/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 777s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 777s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 777s 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.sYnnix/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.sYnnix/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 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: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 778s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 781s succeeded(28) 77.7778% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 781s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 781s bt2 index files: $VAR1 = []; 781s Note - bowtie-build indices do not yet exist. Indexing genome now. 781s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 781s CMD: touch /tmp/autopkgtest.sYnnix/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 781s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 781s 20 reads; of these: 781s 20 (100.00%) were unpaired; of these: 781s 0 (0.00%) aligned 0 times 781s 20 (100.00%) aligned exactly 1 time 781s 0 (0.00%) aligned >1 times 781s 100.00% overall alignment rate 781s CMD: touch /tmp/autopkgtest.sYnnix/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 781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 781s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 781s CMD: samtools index /tmp/autopkgtest.sYnnix/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 781s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 781s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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.sYnnix/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.sYnnix/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 783s succeeded(29) 80.5556% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 783s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 784s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 784s bt2 index files: $VAR1 = []; 784s Note - bowtie-build indices do not yet exist. Indexing genome now. 784s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 784s CMD: touch /tmp/autopkgtest.sYnnix/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 784s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 784s 8656 reads; of these: 784s 8656 (100.00%) were unpaired; of these: 784s 6 (0.07%) aligned 0 times 784s 5677 (65.58%) aligned exactly 1 time 784s 2973 (34.35%) aligned >1 times 784s 99.93% overall alignment rate 784s CMD: touch /tmp/autopkgtest.sYnnix/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 784s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 785s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 785s CMD: samtools index /tmp/autopkgtest.sYnnix/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 785s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 785s CMD: samtools index /tmp/autopkgtest.sYnnix/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 785s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 785s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 785s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 786s [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 786s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 791s succeeded(30) 83.3333% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 791s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 791s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 791s bt2 index files: $VAR1 = []; 791s Note - bowtie-build indices do not yet exist. Indexing genome now. 791s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 792s CMD: touch /tmp/autopkgtest.sYnnix/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 792s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 792s 9 reads; of these: 792s 9 (100.00%) were unpaired; of these: 792s 0 (0.00%) aligned 0 times 792s 9 (100.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 100.00% overall alignment rate 792s CMD: touch /tmp/autopkgtest.sYnnix/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 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 792s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 792s CMD: samtools index /tmp/autopkgtest.sYnnix/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 792s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 792s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 792s 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 792s 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 792s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 792s 792s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 792s 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 792s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 792s 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 792s 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 792s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 792s -processing jaccard pair sensor 792s 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 792s 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 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 793s succeeded(31) 86.1111% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 793s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 793s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 793s bt2 index files: $VAR1 = []; 793s Note - bowtie-build indices do not yet exist. Indexing genome now. 793s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 794s CMD: touch /tmp/autopkgtest.sYnnix/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 794s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 794s 20 reads; of these: 794s 20 (100.00%) were unpaired; of these: 794s 0 (0.00%) aligned 0 times 794s 20 (100.00%) aligned exactly 1 time 794s 0 (0.00%) aligned >1 times 794s 100.00% overall alignment rate 794s CMD: touch /tmp/autopkgtest.sYnnix/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 794s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 794s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 794s CMD: samtools index /tmp/autopkgtest.sYnnix/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 794s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 794s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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 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.sYnnix/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.sYnnix/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 795s succeeded(32) 88.8889% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 795s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 795s bt2 index files: $VAR1 = []; 795s Note - bowtie-build indices do not yet exist. Indexing genome now. 795s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 796s CMD: touch /tmp/autopkgtest.sYnnix/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 796s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 796s 11 reads; of these: 796s 11 (100.00%) were unpaired; of these: 796s 0 (0.00%) aligned 0 times 796s 11 (100.00%) aligned exactly 1 time 796s 0 (0.00%) aligned >1 times 796s 100.00% overall alignment rate 796s CMD: touch /tmp/autopkgtest.sYnnix/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 796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 796s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 796s CMD: samtools index /tmp/autopkgtest.sYnnix/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 796s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 796s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 796s 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 796s 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 796s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 796s 796s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 796s 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 796s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 796s 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 796s 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 796s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 796s -processing jaccard pair sensor 796s 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 796s 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 796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 797s succeeded(33) 91.6667% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 797s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 797s bt2 index files: $VAR1 = []; 797s Note - bowtie-build indices do not yet exist. Indexing genome now. 797s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 797s CMD: touch /tmp/autopkgtest.sYnnix/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 797s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 798s 9 reads; of these: 798s 9 (100.00%) were unpaired; of these: 798s 0 (0.00%) aligned 0 times 798s 9 (100.00%) aligned exactly 1 time 798s 0 (0.00%) aligned >1 times 798s 100.00% overall alignment rate 798s CMD: touch /tmp/autopkgtest.sYnnix/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 798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 798s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 798s CMD: samtools index /tmp/autopkgtest.sYnnix/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 798s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 798s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 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.sYnnix/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.sYnnix/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 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.sYnnix/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.sYnnix/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 800s succeeded(34) 94.4444% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 800s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 800s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 800s bt2 index files: $VAR1 = []; 800s Note - bowtie-build indices do not yet exist. Indexing genome now. 800s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 800s CMD: touch /tmp/autopkgtest.sYnnix/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 800s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 802s 11272 reads; of these: 802s 11272 (100.00%) were unpaired; of these: 802s 2 (0.02%) aligned 0 times 802s 1241 (11.01%) aligned exactly 1 time 802s 10029 (88.97%) aligned >1 times 802s 99.98% overall alignment rate 802s CMD: touch /tmp/autopkgtest.sYnnix/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 802s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 803s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 803s CMD: samtools index /tmp/autopkgtest.sYnnix/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 803s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 803s CMD: samtools index /tmp/autopkgtest.sYnnix/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 803s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 803s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 803s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 803s 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 803s 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 803s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 803s 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.sYnnix/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.sYnnix/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 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 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 [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 806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 813s succeeded(35) 97.2222% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/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.sYnnix/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 813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 813s CMD: samtools faidx /tmp/autopkgtest.sYnnix/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 813s bt2 index files: $VAR1 = []; 813s Note - bowtie-build indices do not yet exist. Indexing genome now. 813s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/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.sYnnix/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 813s CMD: touch /tmp/autopkgtest.sYnnix/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 813s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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" 813s 18 reads; of these: 813s 18 (100.00%) were unpaired; of these: 813s 0 (0.00%) aligned 0 times 813s 18 (100.00%) aligned exactly 1 time 813s 0 (0.00%) aligned >1 times 813s 100.00% overall alignment rate 813s CMD: touch /tmp/autopkgtest.sYnnix/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 813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/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 813s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 813s CMD: samtools index /tmp/autopkgtest.sYnnix/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 813s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/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 813s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 813s 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 813s 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 813s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 813s 813s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 813s 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 813s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 813s 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 813s 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 813s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 813s -processing jaccard pair sensor 813s 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 813s 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 813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/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.sYnnix/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 814s succeeded(36) 100% completed. 814s 814s All commands completed successfully. :-) 814s 814s 814s 814s ** Harvesting all assembled transcripts into a single multi-fasta file... 814s 814s Tuesday, October 28, 2025: 20:17:39 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp 814s * [Tue Oct 28 20:17:39 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1 815s * [Tue Oct 28 20:17:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta 815s Tuesday, October 28, 2025: 20:17:40 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map 815s 815s 815s ############################################################################# 815s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta 815s ############################################################################# 815s 815s 815s 815s 815s exit 0 815s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh 815s #!/bin/bash -ve 815s 815s 815s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 815s gunzip -c reads.right.fq.gz > reads.right.fq 815s fi 815s 815s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 815s gunzip -c reads.left.fq.gz > reads.left.fq 815s fi 815s 815s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then 815s gunzip -c reads2.right.fq.gz > reads2.right.fq 815s fi 815s 815s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then 815s gunzip -c reads2.left.fq.gz > reads2.left.fq 815s fi 815s 815s 815s ####################################################### 815s ## Run Trinity to Generate Transcriptome Assemblies ## 815s ####################################################### 815s 815s CPU=$(nproc || sysctl -n hw.physicalcpu) 815s 815s ${TRINITY_HOME}/Trinity --seqType fq \ 815s --max_memory 2G \ 815s --left reads.left.fq,reads2.left.fq \ 815s --right reads.right.fq,reads2.right.fq \ 815s --SS_lib_type RF \ 815s --CPU ${CPU} \ 815s --trimmomatic \ 815s --normalize_reads \ 815s --normalize_by_read_set \ 815s --output trinity_trim_and_norm_outdir 815s 815s 815s ______ ____ ____ ____ ____ ______ __ __ 815s | || \ | || \ | || || | | 815s | || D ) | | | _ | | | | || | | 815s |_| |_|| / | | | | | | | |_| |_|| ~ | 815s | | | \ | | | | | | | | | |___, | 815s | | | . \ | | | | | | | | | | | 815s |__| |__|\_||____||__|__||____| |__| |____/ 815s 815s Trinity-v2.15.2 815s 815s 815s 815s Left read files: $VAR1 = [ 815s 'reads.left.fq', 815s 'reads2.left.fq' 815s ]; 815s Right read files: $VAR1 = [ 815s 'reads.right.fq', 815s 'reads2.right.fq' 815s ]; 816s Tuesday, October 28, 2025: 20:17:40 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir 816s Tuesday, October 28, 2025: 20:17:40 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis 816s 816s 816s ---------------------------------------------------------------------------------- 816s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 816s ---------------------------------------------------------------------------------- 816s 816s --------------------------------------------------------------- 816s ------ Quality Trimming Via Trimmomatic --------------------- 816s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 816s --------------------------------------------------------------- 816s 816s 816s ## Running Trimmomatic on read files: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 816s Tuesday, October 28, 2025: 20:17:41 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 816s TrimmomaticPE: Started with arguments: 816s -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.sYnnix/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 816s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 816s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 816s Quality encoding detected as phred33 817s 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%) 817s TrimmomaticPE: Completed successfully 817s Tuesday, October 28, 2025: 20:17:41 CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq 817s Tuesday, October 28, 2025: 20:17:41 CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq 817s Tuesday, October 28, 2025: 20:17:41 CMD: touch trimmomatic.ok 817s Tuesday, October 28, 2025: 20:17:41 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 817s 817s ## Running Trimmomatic on read files: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq 817s Tuesday, October 28, 2025: 20:17:41 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.sYnnix/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 817s TrimmomaticPE: Started with arguments: 817s -threads 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.sYnnix/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 817s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 817s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 817s Quality encoding detected as phred33 817s 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%) 817s TrimmomaticPE: Completed successfully 817s Tuesday, October 28, 2025: 20:17:42 CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq 817s Tuesday, October 28, 2025: 20:17:42 CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq 817s Tuesday, October 28, 2025: 20:17:42 CMD: touch trimmomatic.ok 817s Tuesday, October 28, 2025: 20:17:42 CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim & 817s --------------------------------------------------------------- 817s ------------ In silico Read Normalization --------------------- 817s -- (Removing Excess Reads Beyond 200 Coverage -- 817s --------------------------------------------------------------- 817s 817s 817s ## Running in silico normalization, processing each read set separately 817s # running normalization on reads: $VAR1 = [ 817s [ 817s 'reads.left.fq.PwU.qtrim.fq' 817s ], 817s [ 817s 'reads.right.fq.PwU.qtrim.fq' 817s ] 817s ]; 817s 817s 817s Tuesday, October 28, 2025: 20:17:42 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/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 818s -prepping seqs 818s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa 818s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa 818s CMD finished (0 seconds) 818s CMD finished (0 seconds) 818s CMD: touch left.fa.ok 818s CMD finished (0 seconds) 818s CMD: touch right.fa.ok 818s CMD finished (0 seconds) 818s Done converting input files. CMD: cat left.fa right.fa > both.fa 818s CMD finished (0 seconds) 818s CMD: touch both.fa.ok 818s CMD finished (0 seconds) 818s -kmer counting. 818s ------------------------------------------- 818s ----------- Jellyfish -------------------- 818s -- (building a k-mer catalog from reads) -- 818s ------------------------------------------- 818s 818s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 819s CMD finished (1 seconds) 819s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 819s CMD finished (0 seconds) 819s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 819s CMD finished (0 seconds) 819s CMD: touch jellyfish.K25.min2.kmers.fa.success 819s CMD finished (0 seconds) 819s -generating stats files 819s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 819s -reading Kmer occurrences... 819s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 819s -reading Kmer occurrences... 819s 819s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 819s 819s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 820s STATS_GENERATION_TIME: 1 seconds. 820s STATS_GENERATION_TIME: 1 seconds. 820s CMD finished (1 seconds) 820s CMD finished (1 seconds) 820s CMD: touch left.fa.K25.stats.ok 820s CMD finished (0 seconds) 820s CMD: touch right.fa.K25.stats.ok 820s CMD finished (0 seconds) 820s -sorting each stats file by read name. 820s 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 820s 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 820s CMD finished (0 seconds) 820s CMD finished (0 seconds) 820s CMD: touch left.fa.K25.stats.sort.ok 820s CMD finished (0 seconds) 820s CMD: touch right.fa.K25.stats.sort.ok 820s CMD finished (0 seconds) 820s -defining normalized reads 820s 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 820s -opening left.fa.K25.stats.sort 820s -opening right.fa.K25.stats.sort 820s -done opening files. 820s CMD finished (0 seconds) 820s CMD: touch pairs.K25.stats.ok 820s CMD finished (0 seconds) 820s 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 821s 27678 / 27726 = 99.83% reads selected during normalization. 821s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 821s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 821s CMD finished (0 seconds) 821s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 821s CMD finished (0 seconds) 821s -search and capture. 821s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 821s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq 821s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 821s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq 821s CMD: touch /tmp/autopkgtest.sYnnix/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 821s CMD finished (0 seconds) 821s CMD: touch /tmp/autopkgtest.sYnnix/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 821s CMD finished (0 seconds) 821s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 821s CMD finished (0 seconds) 821s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 821s CMD finished (0 seconds) 821s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads 821s 821s 821s Normalization complete. See outputs: 821s /tmp/autopkgtest.sYnnix/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 821s /tmp/autopkgtest.sYnnix/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 821s Tuesday, October 28, 2025: 20:17:46 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok 821s # running normalization on reads: $VAR1 = [ 821s [ 821s 'reads2.left.fq.PwU.qtrim.fq' 821s ], 821s [ 821s 'reads2.right.fq.PwU.qtrim.fq' 821s ] 821s ]; 821s 821s 821s Tuesday, October 28, 2025: 20:17:46 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/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 821s -prepping seqs 821s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa 821s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa 821s CMD finished (0 seconds) 821s CMD finished (0 seconds) 821s CMD: touch left.fa.ok 821s CMD finished (0 seconds) 821s CMD: touch right.fa.ok 821s CMD finished (0 seconds) 821s Done converting input files. CMD: cat left.fa right.fa > both.fa 821s CMD finished (0 seconds) 821s CMD: touch both.fa.ok 821s CMD finished (0 seconds) 821s -kmer counting. 821s ------------------------------------------- 821s ----------- Jellyfish -------------------- 821s -- (building a k-mer catalog from reads) -- 821s ------------------------------------------- 821s 821s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 823s CMD finished (1 seconds) 823s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 823s CMD finished (1 seconds) 823s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 823s CMD finished (0 seconds) 823s CMD: touch jellyfish.K25.min2.kmers.fa.success 823s CMD finished (0 seconds) 823s -generating stats files 823s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 823s -reading Kmer occurrences... 823s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 823s -reading Kmer occurrences... 823s 823s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 823s 823s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 823s STATS_GENERATION_TIME: 0 seconds. 823s CMD finished (0 seconds) 823s STATS_GENERATION_TIME: 0 seconds. 823s CMD finished (0 seconds) 823s CMD: touch left.fa.K25.stats.ok 823s CMD finished (0 seconds) 823s CMD: touch right.fa.K25.stats.ok 823s CMD finished (0 seconds) 823s -sorting each stats file by read name. 823s 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 823s 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 823s CMD finished (0 seconds) 823s CMD finished (0 seconds) 823s CMD: touch left.fa.K25.stats.sort.ok 823s CMD finished (0 seconds) 823s CMD: touch right.fa.K25.stats.sort.ok 823s CMD finished (0 seconds) 823s -defining normalized reads 823s 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 823s -opening left.fa.K25.stats.sort 823s -opening right.fa.K25.stats.sort 823s -done opening files. 824s CMD finished (1 seconds) 824s CMD: touch pairs.K25.stats.ok 824s CMD finished (0 seconds) 824s 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 824s 27678 / 27726 = 99.83% reads selected during normalization. 824s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 824s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 824s CMD finished (0 seconds) 824s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 824s CMD finished (0 seconds) 824s -search and capture. 824s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 824s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq 824s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/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. 824s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq 824s CMD: touch /tmp/autopkgtest.sYnnix/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 824s CMD finished (0 seconds) 824s CMD: touch /tmp/autopkgtest.sYnnix/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 824s CMD finished (0 seconds) 824s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 824s CMD finished (0 seconds) 824s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 824s CMD finished (0 seconds) 824s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads 824s 824s 824s Normalization complete. See outputs: 824s /tmp/autopkgtest.sYnnix/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 824s /tmp/autopkgtest.sYnnix/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 825s Tuesday, October 28, 2025: 20:17:49 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok 825s # running normalization on reads: $VAR1 = [ 825s [ 825s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq', 825s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq' 825s ], 825s [ 825s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq', 825s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq' 825s ] 825s ]; 825s 825s 825s Tuesday, October 28, 2025: 20:17:49 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.sYnnix/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 825s -prepping seqs 825s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa 825s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa 825s CMD finished (0 seconds) 825s CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa 825s CMD finished (0 seconds) 825s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa 825s CMD finished (0 seconds) 825s CMD finished (0 seconds) 825s CMD: touch left.fa.ok 825s CMD finished (0 seconds) 825s CMD: touch right.fa.ok 825s CMD finished (0 seconds) 825s Done converting input files. CMD: cat left.fa right.fa > both.fa 825s CMD finished (0 seconds) 825s CMD: touch both.fa.ok 825s CMD finished (0 seconds) 825s -kmer counting. 825s ------------------------------------------- 825s ----------- Jellyfish -------------------- 825s -- (building a k-mer catalog from reads) -- 825s ------------------------------------------- 825s 825s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 826s CMD finished (1 seconds) 826s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 826s CMD finished (0 seconds) 826s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 826s CMD finished (0 seconds) 826s CMD: touch jellyfish.K25.min2.kmers.fa.success 826s CMD finished (0 seconds) 826s -generating stats files 826s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 826s -reading Kmer occurrences... 826s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 826s -reading Kmer occurrences... 827s 827s done parsing 311705 Kmers, 310319 added, taking 1 seconds. 827s 827s done parsing 311705 Kmers, 310319 added, taking 1 seconds. 828s STATS_GENERATION_TIME: 1 seconds. 828s STATS_GENERATION_TIME: 1 seconds. 828s CMD finished (2 seconds) 828s CMD finished (2 seconds) 828s CMD: touch left.fa.K25.stats.ok 828s CMD finished (0 seconds) 828s CMD: touch right.fa.K25.stats.ok 828s CMD finished (0 seconds) 828s -sorting each stats file by read name. 828s 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 828s 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 828s CMD finished (0 seconds) 828s CMD finished (0 seconds) 828s CMD: touch left.fa.K25.stats.sort.ok 828s CMD finished (0 seconds) 828s CMD: touch right.fa.K25.stats.sort.ok 828s CMD finished (0 seconds) 828s -defining normalized reads 828s 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 828s -opening left.fa.K25.stats.sort 828s -opening right.fa.K25.stats.sort 828s -done opening files. 829s CMD finished (1 seconds) 829s CMD: touch pairs.K25.stats.ok 829s CMD finished (0 seconds) 829s 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 829s 51602 / 55356 = 93.22% reads selected during normalization. 829s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles. 829s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1 829s CMD finished (0 seconds) 829s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 829s CMD finished (0 seconds) 829s -search and capture. 830s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.sYnnix/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. 830s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq 830s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq 830s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.sYnnix/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. 830s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq 830s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq 830s CMD: touch /tmp/autopkgtest.sYnnix/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 830s CMD finished (0 seconds) 830s CMD: touch /tmp/autopkgtest.sYnnix/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 830s CMD finished (0 seconds) 830s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 830s CMD finished (0 seconds) 830s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 830s CMD finished (0 seconds) 830s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads 830s 830s 830s Normalization complete. See outputs: 830s /tmp/autopkgtest.sYnnix/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 830s /tmp/autopkgtest.sYnnix/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 830s Tuesday, October 28, 2025: 20:17:55 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok 830s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:17:55 CMD: cat /tmp/autopkgtest.sYnnix/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 830s Tuesday, October 28, 2025: 20:17:55 CMD: cat /tmp/autopkgtest.sYnnix/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 830s Tuesday, October 28, 2025: 20:17:55 CMD: touch left.fa.ok 830s Tuesday, October 28, 2025: 20:17:55 CMD: touch right.fa.ok 830s Tuesday, October 28, 2025: 20:17:55 CMD: touch left.fa.ok right.fa.ok 830s Tuesday, October 28, 2025: 20:17:55 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 830s Tuesday, October 28, 2025: 20:17:55 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok 830s ------------------------------------------- 830s ----------- Jellyfish -------------------- 830s -- (building a k-mer (25) catalog from reads) -- 830s ------------------------------------------- 830s 830s * [Tue Oct 28 20:17:55 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 832s * [Tue Oct 28 20:17:57 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 832s * [Tue Oct 28 20:17:57 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 832s ---------------------------------------------- 832s --------------- Inchworm (K=25, asm) --------------------- 832s -- (Linear contig construction from k-mers) -- 832s ---------------------------------------------- 832s 832s * [Tue Oct 28 20:17:57 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp 832s Kmer length set to: 25 832s Min assembly length set to: 25 832s Monitor turned on, set to: 1 832s min entropy set to: 1 832s setting number of threads to: 2 832s -setting parallel iworm mode. 832s -reading Kmer occurrences... 832s [0M] Kmers parsed. 832s done parsing 309493 Kmers, 309493 added, taking 0 seconds. 832s 832s TIMING KMER_DB_BUILDING 0 s. 832s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 832s Pruned 1482 kmers from catalog. 832s Pruning time: 0 seconds = 0 minutes. 832s 832s TIMING PRUNING 0 s. 832s -populating the kmer seed candidate list. 832s Kcounter hash size: 309493 832s Processed 308011 non-zero abundance kmers in kcounter. 832s -Not sorting list of kmers, given parallel mode in effect. 832s -beginning inchworm contig assembly. 832s Total kcounter hash size: 309493 vs. sorted list size: 308011 832s num threads set to: 2 832s Done opening file. tmp.iworm.fa.pid_43516.thread_0 832s Done opening file. tmp.iworm.fa.pid_43516.thread_1 833s 833s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 833s 833s TIMING CONTIG_BUILDING 1 s. 833s 833s TIMING PROG_RUNTIME 1 s. 833s * [Tue Oct 28 20:17:58 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 833s Tuesday, October 28, 2025: 20:17:58 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished 833s -------------------------------------------------------- 833s -------------------- Chrysalis ------------------------- 833s -- (Contig Clustering & de Bruijn Graph Construction) -- 833s -------------------------------------------------------- 833s 833s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 833s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 833s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 833s * [Tue Oct 28 20:17:58 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 833s * [Tue Oct 28 20:17:58 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null 833s * [Tue Oct 28 20:17:58 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 840s * [Tue Oct 28 20:18:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt 841s * [Tue Oct 28 20:18:06 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt 843s * [Tue Oct 28 20:18:07 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted 843s * [Tue Oct 28 20:18:07 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 843s * [Tue Oct 28 20:18:08 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out 843s * [Tue Oct 28 20:18:08 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200 843s * [Tue Oct 28 20:18:08 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/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 847s * [Tue Oct 28 20:18:12 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort 847s Tuesday, October 28, 2025: 20:18:12 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0 848s Tuesday, October 28, 2025: 20:18:13 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok 848s Tuesday, October 28, 2025: 20:18:13 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 848s Tuesday, October 28, 2025: 20:18:13 CMD: touch recursive_trinity.cmds.ok 848s Tuesday, October 28, 2025: 20:18:13 CMD: touch recursive_trinity.cmds.ok 848s 848s 848s -------------------------------------------------------------------------------- 848s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 848s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 848s -------------------------------------------------------------------------------- 848s 848s Tuesday, October 28, 2025: 20:18:13 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 848s Number of Commands: 51 941s 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. 941s 941s All commands completed successfully. :-) 941s 941s 941s 941s ** Harvesting all assembled transcripts into a single multi-fasta file... 941s 941s Tuesday, October 28, 2025: 20:19:46 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp 941s * [Tue Oct 28 20:19:46 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2 942s * [Tue Oct 28 20:19:47 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta 942s Tuesday, October 28, 2025: 20:19:47 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map 942s 942s 942s ############################################################################# 942s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta 942s ############################################################################# 942s 942s 942s 942s 942s 942s exit 0 942s ./misc_run_tests/__runMe_include_long_reads.sh 942s 942s 942s ______ ____ ____ ____ ____ ______ __ __ 942s | || \ | || \ | || || | | 942s | || D ) | | | _ | | | | || | | 942s |_| |_|| / | | | | | | | |_| |_|| ~ | 942s | | | \ | | | | | | | | | |___, | 942s | | | . \ | | | | | | | | | | | 942s |__| |__|\_||____||__|__||____| |__| |____/ 942s 942s Trinity-v2.15.2 942s 942s 942s 942s Left read files: $VAR1 = [ 942s 'reads.left.fq.gz' 942s ]; 942s Right read files: $VAR1 = [ 942s 'reads.right.fq.gz' 942s ]; 942s Tuesday, October 28, 2025: 20:19:47 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads 942s Tuesday, October 28, 2025: 20:19:47 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis 942s 942s 942s ---------------------------------------------------------------------------------- 942s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 942s ---------------------------------------------------------------------------------- 942s 942s --------------------------------------------------------------- 942s ------------ In silico Read Normalization --------------------- 942s -- (Removing Excess Reads Beyond 200 Coverage -- 942s --------------------------------------------------------------- 942s 942s # running normalization on reads: $VAR1 = [ 942s [ 942s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 942s ], 942s [ 942s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 942s ] 942s ]; 942s 942s 942s Tuesday, October 28, 2025: 20:19:47 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --no_cleanup --left /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 942s #!/bin/bash -ve 942s 942s ####################################################### 942s ## Run Trinity to Generate Transcriptome Assemblies ## 942s ####################################################### 942s 942s CPU=$(nproc || sysctl -n hw.physicalcpu) 942s 942s ${TRINITY_HOME}/Trinity --seqType fq \ 942s --max_memory 2G \ 942s --left reads.left.fq.gz \ 942s --right reads.right.fq.gz \ 942s --SS_lib_type RF \ 942s --CPU ${CPU} \ 942s --no_cleanup \ 942s --long_reads longReads.fa \ 942s --output test_trinity_long_reads 942s -prepping seqs 942s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 942s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 942s CMD finished (0 seconds) 942s CMD finished (0 seconds) 942s CMD: touch left.fa.ok 942s CMD finished (0 seconds) 942s CMD: touch right.fa.ok 942s CMD finished (0 seconds) 942s Done converting input files. CMD: cat left.fa right.fa > both.fa 942s CMD finished (0 seconds) 942s CMD: touch both.fa.ok 942s CMD finished (0 seconds) 942s -kmer counting. 942s ------------------------------------------- 942s ----------- Jellyfish -------------------- 942s -- (building a k-mer catalog from reads) -- 942s ------------------------------------------- 942s 942s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 943s CMD finished (1 seconds) 943s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 944s CMD finished (0 seconds) 944s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 944s CMD finished (1 seconds) 944s CMD: touch jellyfish.K25.min2.kmers.fa.success 944s CMD finished (0 seconds) 944s -generating stats files 944s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 944s -reading Kmer occurrences... 944s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 944s -reading Kmer occurrences... 944s 944s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 944s 944s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 944s STATS_GENERATION_TIME: 0 seconds. 944s CMD finished (0 seconds) 944s STATS_GENERATION_TIME: 0 seconds. 944s CMD finished (0 seconds) 944s CMD: touch left.fa.K25.stats.ok 944s CMD finished (0 seconds) 944s CMD: touch right.fa.K25.stats.ok 944s CMD finished (0 seconds) 944s -sorting each stats file by read name. 944s 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 944s 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 944s CMD finished (0 seconds) 944s CMD finished (0 seconds) 944s CMD: touch left.fa.K25.stats.sort.ok 944s CMD finished (0 seconds) 944s CMD: touch right.fa.K25.stats.sort.ok 944s CMD finished (0 seconds) 944s -defining normalized reads 944s 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 944s -opening left.fa.K25.stats.sort 944s -opening right.fa.K25.stats.sort 944s -done opening files. 945s CMD finished (1 seconds) 945s CMD: touch pairs.K25.stats.ok 945s CMD finished (0 seconds) 945s 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 945s 30472 / 30575 = 99.66% reads selected during normalization. 945s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 945s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 945s CMD finished (0 seconds) 945s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 945s CMD finished (0 seconds) 945s -search and capture. 945s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 945s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 945s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 945s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 946s CMD: touch /tmp/autopkgtest.sYnnix/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 946s CMD finished (0 seconds) 946s CMD: touch /tmp/autopkgtest.sYnnix/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 946s CMD finished (0 seconds) 946s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 946s CMD finished (0 seconds) 946s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 946s CMD finished (0 seconds) 946s 946s 946s Normalization complete. See outputs: 946s /tmp/autopkgtest.sYnnix/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 946s /tmp/autopkgtest.sYnnix/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 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok 946s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:19:51 CMD: cat /tmp/autopkgtest.sYnnix/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 946s Tuesday, October 28, 2025: 20:19:51 CMD: cat /tmp/autopkgtest.sYnnix/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 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch left.fa.ok 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch right.fa.ok 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch left.fa.ok right.fa.ok 946s Tuesday, October 28, 2025: 20:19:51 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok 946s Tuesday, October 28, 2025: 20:19:51 CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 946s Tuesday, October 28, 2025: 20:19:51 CMD: cat /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 946s Tuesday, October 28, 2025: 20:19:51 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok 946s ------------------------------------------- 946s ----------- Jellyfish -------------------- 946s -- (building a k-mer (25) catalog from reads) -- 946s ------------------------------------------- 946s 946s * [Tue Oct 28 20:19:51 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 947s * [Tue Oct 28 20:19:52 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 947s * [Tue Oct 28 20:19:52 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 947s ---------------------------------------------- 947s --------------- Inchworm (K=25, asm) --------------------- 947s -- (Linear contig construction from k-mers) -- 947s ---------------------------------------------- 947s 947s * [Tue Oct 28 20:19:52 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp 947s Kmer length set to: 25 947s Min assembly length set to: 25 947s Monitor turned on, set to: 1 947s -retaining tmp files 947s min entropy set to: 1 947s setting number of threads to: 2 947s -setting parallel iworm mode. 947s -reading Kmer occurrences... 948s [0M] Kmers parsed. [0M] Kmers parsed. 948s done parsing 519541 Kmers, 519541 added, taking 1 seconds. 948s 948s TIMING KMER_DB_BUILDING 1 s. 948s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 948s Pruned 4252 kmers from catalog. 948s Pruning time: 0 seconds = 0 minutes. 948s 948s TIMING PRUNING 0 s. 948s -populating the kmer seed candidate list. 948s Kcounter hash size: 519541 948s Processed 515289 non-zero abundance kmers in kcounter. 948s -Not sorting list of kmers, given parallel mode in effect. 948s -beginning inchworm contig assembly. 948s Total kcounter hash size: 519541 vs. sorted list size: 515289 948s num threads set to: 2 948s Done opening file. tmp.iworm.fa.pid_52571.thread_0 948s Done opening file. tmp.iworm.fa.pid_52571.thread_1 948s 948s Iworm contig assembly time: 0 seconds = 0 minutes. 948s 948s TIMING CONTIG_BUILDING 0 s. 948s 948s TIMING PROG_RUNTIME 1 s. 948s * [Tue Oct 28 20:19:53 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 948s Tuesday, October 28, 2025: 20:19:53 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished 948s -------------------------------------------------------- 948s -------------------- Chrysalis ------------------------- 948s -- (Contig Clustering & de Bruijn Graph Construction) -- 948s -------------------------------------------------------- 948s 948s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 948s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 948s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 948s * [Tue Oct 28 20:19:53 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 948s * [Tue Oct 28 20:19:53 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null 949s * [Tue Oct 28 20:19:54 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 953s * [Tue Oct 28 20:19:58 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt 953s * [Tue Oct 28 20:19:58 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt 955s * [Tue Oct 28 20:20:00 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted 955s * [Tue Oct 28 20:20:00 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 955s * [Tue Oct 28 20:20:00 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out 955s * [Tue Oct 28 20:20:00 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200 955s * [Tue Oct 28 20:20:00 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 957s * [Tue Oct 28 20:20:02 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort 957s Tuesday, October 28, 2025: 20:20:02 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0 957s Tuesday, October 28, 2025: 20:20:02 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok 957s Tuesday, October 28, 2025: 20:20:02 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 957s Tuesday, October 28, 2025: 20:20:02 CMD: touch recursive_trinity.cmds.ok 957s Tuesday, October 28, 2025: 20:20:02 CMD: touch recursive_trinity.cmds.ok 957s 957s 957s -------------------------------------------------------------------------------- 957s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 957s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 957s -------------------------------------------------------------------------------- 957s 957s Tuesday, October 28, 2025: 20:20:02 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 957s Number of Commands: 38 1018s 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. 1018s 1018s All commands completed successfully. :-) 1018s 1018s 1018s 1018s ** Harvesting all assembled transcripts into a single multi-fasta file... 1018s 1018s Tuesday, October 28, 2025: 20:21:03 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp 1018s * [Tue Oct 28 20:21:03 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2 1019s * [Tue Oct 28 20:21:04 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta 1019s Tuesday, October 28, 2025: 20:21:04 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map 1019s 1019s 1019s ############################################################################# 1019s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta 1019s ############################################################################# 1019s 1019s 1019s 1019s 1019s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep LR 1019s >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(-)]} 1019s >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$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]} 1019s >c0_g1_i5 len=7194 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 6182:6204-6219 6198:6220-6729 6708:6730-6733 6712:6734-6735 6714:6736-7193] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 6182, 6198, 6708, 6712, 6714, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]} 1019s >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$|mm9chr9-NM_026942;mm9chr9-69106_Stoml1_stomatin-like_1_mm9chr9:58101074-58109646(+)]} 1019s >c0_g1_i1 len=3823 path=[1:0-2158 2137:2159-2410 2389:2411-3822] [-1, 1, 2137, 2389, -2] long_read_mappings: {PairPath [_paths=[[1, 2137, 2389], []]]=[LR$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]} 1019s >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$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]} 1019s >c0_g1_i5 len=5399 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 4143:4165-5398] [-1, 1, 1730, 1752, 2672, 4143, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]} 1019s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1019s >c0_g2_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1019s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1019s >c0_g2_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1019s >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$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]} 1019s >c0_g3_i8 len=8757 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 7602:7624-7968 7947:7969-7969 7948:7970-7982 7961:7983-7983 7962:7984-8252 8231:8253-8747 8726:8748-8756] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 7602, 7947, 7948, 7961, 7962, 8231, 8726, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]} 1019s >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$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]} 1019s >c0_g1_i5 len=2364 path=[1:0-610 589:611-1077 1056:1078-1099 1078:1100-1541 1520:1542-1621 1600:1622-1794 1773:1795-2028 2007:2029-2029 2008:2030-2363] [-1, 1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]} 1019s >c0_g2_i1 len=3966 path=[6618:0-165 147:166-1345 6761:1346-1417 1348:1418-1418 8338:1419-1442 1373:1443-2963 2894:2964-3730 6857:3731-3965] [-1, 6618, 147, 6761, 1348, 8338, 1373, 2894, 6857, -2] long_read_mappings: {PairPath [_paths=[[147, 6761, 1348, 8338, 1373, 2894, 6857], []]]=[LR$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]} 1019s >c0_g1_i2 len=3739 path=[1:0-286 265:287-289 268:290-399 3806:400-459 396:460-3738] [-1, 1, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]} 1019s >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$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]} 1019s >c0_g2_i8 len=2514 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 2227:2249-2513] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 2227, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]} 1019s >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(+)]} 1019s 1019s 1019s exit 0 1019s ./misc_run_tests/__run_PE_samples_file.sh 1019s #!/bin/bash -ve 1019s 1019s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \ 1019s --seqType fq \ 1019s --max_memory 1G \ 1019s --output trinity_test_samples_PE 1019s 1019s 1019s ______ ____ ____ ____ ____ ______ __ __ 1019s | || \ | || \ | || || | | 1019s | || D ) | | | _ | | | | || | | 1019s |_| |_|| / | | | | | | | |_| |_|| ~ | 1019s | | | \ | | | | | | | | | |___, | 1019s | | | . \ | | | | | | | | | | | 1019s |__| |__|\_||____||__|__||____| |__| |____/ 1019s 1019s Trinity-v2.15.2 1019s 1019s 1019s 1019s Left read files: $VAR1 = [ 1019s 'reads.left.fq.gz', 1019s 'reads2.left.fq.gz' 1019s ]; 1019s Right read files: $VAR1 = [ 1019s 'reads.right.fq.gz', 1019s 'reads2.right.fq.gz' 1019s ]; 1019s Tuesday, October 28, 2025: 20:21:04 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE 1019s Tuesday, October 28, 2025: 20:21:04 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis 1019s 1019s 1019s ---------------------------------------------------------------------------------- 1019s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1019s ---------------------------------------------------------------------------------- 1019s 1019s --------------------------------------------------------------- 1019s ------------ In silico Read Normalization --------------------- 1019s -- (Removing Excess Reads Beyond 200 Coverage -- 1019s --------------------------------------------------------------- 1019s 1019s # running normalization on reads: $VAR1 = [ 1019s [ 1019s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1019s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1019s ], 1019s [ 1019s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz', 1019s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz' 1019s ] 1019s ]; 1019s 1019s 1019s Tuesday, October 28, 2025: 20:21:04 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000 --left /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together --PARALLEL_STATS 1019s -prepping seqs 1019s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1019s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1019s CMD finished (0 seconds) 1019s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa 1019s CMD finished (0 seconds) 1019s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa 1019s CMD finished (0 seconds) 1019s CMD finished (0 seconds) 1019s CMD: touch left.fa.ok 1019s CMD finished (0 seconds) 1019s CMD: touch right.fa.ok 1019s CMD finished (0 seconds) 1019s Done converting input files. CMD: cat left.fa right.fa > both.fa 1019s CMD finished (0 seconds) 1019s CMD: touch both.fa.ok 1019s CMD finished (0 seconds) 1019s -kmer counting. 1019s ------------------------------------------- 1019s ----------- Jellyfish -------------------- 1019s -- (building a k-mer catalog from reads) -- 1019s ------------------------------------------- 1019s 1019s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1021s CMD finished (2 seconds) 1021s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1021s CMD finished (0 seconds) 1021s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1021s CMD finished (0 seconds) 1021s CMD: touch jellyfish.K25.min2.kmers.fa.success 1021s CMD finished (0 seconds) 1021s -generating stats files 1021s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1021s -reading Kmer occurrences... 1021s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1021s -reading Kmer occurrences... 1022s 1022s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 1022s 1022s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 1023s STATS_GENERATION_TIME: 1 seconds. 1023s STATS_GENERATION_TIME: 1 seconds. 1023s CMD finished (2 seconds) 1023s CMD finished (2 seconds) 1023s CMD: touch left.fa.K25.stats.ok 1023s CMD finished (0 seconds) 1023s CMD: touch right.fa.K25.stats.ok 1023s CMD finished (0 seconds) 1023s -sorting each stats file by read name. 1023s 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 1023s 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 1023s CMD finished (0 seconds) 1023s CMD finished (0 seconds) 1023s CMD: touch left.fa.K25.stats.sort.ok 1023s CMD finished (0 seconds) 1023s CMD: touch right.fa.K25.stats.sort.ok 1023s CMD finished (0 seconds) 1023s -defining normalized reads 1023s 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 1023s -opening left.fa.K25.stats.sort 1023s -opening right.fa.K25.stats.sort 1023s -done opening files. 1024s CMD finished (1 seconds) 1024s CMD: touch pairs.K25.stats.ok 1024s CMD finished (0 seconds) 1024s 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 1025s 56508 / 61150 = 92.41% reads selected during normalization. 1025s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1025s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1 1025s CMD finished (1 seconds) 1025s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1025s CMD finished (0 seconds) 1025s -search and capture. 1025s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1025s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1025s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture. 1025s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1025s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz 1025s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1026s CMD: touch /tmp/autopkgtest.sYnnix/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 1026s CMD finished (0 seconds) 1026s CMD: touch /tmp/autopkgtest.sYnnix/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 1026s CMD finished (0 seconds) 1026s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1026s CMD finished (0 seconds) 1026s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1026s CMD finished (0 seconds) 1026s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads 1026s 1026s 1026s Normalization complete. See outputs: 1026s /tmp/autopkgtest.sYnnix/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 1026s /tmp/autopkgtest.sYnnix/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 1026s Tuesday, October 28, 2025: 20:21:11 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok 1026s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:21:11 CMD: cat /tmp/autopkgtest.sYnnix/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 1026s Tuesday, October 28, 2025: 20:21:11 CMD: cat /tmp/autopkgtest.sYnnix/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 1026s Tuesday, October 28, 2025: 20:21:11 CMD: touch left.fa.ok 1026s Tuesday, October 28, 2025: 20:21:11 CMD: touch right.fa.ok 1026s Tuesday, October 28, 2025: 20:21:11 CMD: touch left.fa.ok right.fa.ok 1026s Tuesday, October 28, 2025: 20:21:11 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1026s Tuesday, October 28, 2025: 20:21:11 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok 1026s ------------------------------------------- 1026s ----------- Jellyfish -------------------- 1026s -- (building a k-mer (25) catalog from reads) -- 1026s ------------------------------------------- 1026s 1026s * [Tue Oct 28 20:21:11 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1028s * [Tue Oct 28 20:21:13 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1028s * [Tue Oct 28 20:21:13 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1028s ---------------------------------------------- 1028s --------------- Inchworm (K=25, asm) --------------------- 1028s -- (Linear contig construction from k-mers) -- 1028s ---------------------------------------------- 1028s 1028s * [Tue Oct 28 20:21:13 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp 1028s Kmer length set to: 25 1028s Min assembly length set to: 25 1028s Monitor turned on, set to: 1 1028s double stranded mode set 1028s min entropy set to: 1 1028s setting number of threads to: 2 1028s -setting parallel iworm mode. 1028s -reading Kmer occurrences... 1028s [0M] Kmers parsed. [0M] Kmers parsed. 1028s done parsing 515206 Kmers, 515206 added, taking 0 seconds. 1028s 1028s TIMING KMER_DB_BUILDING 0 s. 1028s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1029s Pruned 4139 kmers from catalog. 1029s Pruning time: 1 seconds = 0.0166667 minutes. 1029s 1029s TIMING PRUNING 1 s. 1029s -populating the kmer seed candidate list. 1029s Kcounter hash size: 515206 1029s Processed 511067 non-zero abundance kmers in kcounter. 1029s -Not sorting list of kmers, given parallel mode in effect. 1029s -beginning inchworm contig assembly. 1029s Total kcounter hash size: 515206 vs. sorted list size: 511067 1029s num threads set to: 2 1029s Done opening file. tmp.iworm.fa.pid_59657.thread_0 1029s Done opening file. tmp.iworm.fa.pid_59657.thread_1 1030s 1030s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 1030s 1030s TIMING CONTIG_BUILDING 1 s. 1030s 1030s TIMING PROG_RUNTIME 2 s. 1030s * [Tue Oct 28 20:21:15 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 1030s Tuesday, October 28, 2025: 20:21:15 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished 1030s -------------------------------------------------------- 1030s -------------------- Chrysalis ------------------------- 1030s -- (Contig Clustering & de Bruijn Graph Construction) -- 1030s -------------------------------------------------------- 1030s 1030s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1030s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1030s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1030s * [Tue Oct 28 20:21:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1030s * [Tue Oct 28 20:21:15 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1030s * [Tue Oct 28 20:21:15 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 1039s * [Tue Oct 28 20:21:24 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt 1040s * [Tue Oct 28 20:21:25 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt 1042s * [Tue Oct 28 20:21:27 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted 1042s * [Tue Oct 28 20:21:27 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1042s * [Tue Oct 28 20:21:27 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out 1042s * [Tue Oct 28 20:21:27 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200 1042s * [Tue Oct 28 20:21:27 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1050s * [Tue Oct 28 20:21:35 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort 1050s Tuesday, October 28, 2025: 20:21:35 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0 1050s Tuesday, October 28, 2025: 20:21:35 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok 1050s Tuesday, October 28, 2025: 20:21:35 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 1050s Tuesday, October 28, 2025: 20:21:35 CMD: touch recursive_trinity.cmds.ok 1050s Tuesday, October 28, 2025: 20:21:35 CMD: touch recursive_trinity.cmds.ok 1050s 1050s 1050s -------------------------------------------------------------------------------- 1050s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1050s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1050s -------------------------------------------------------------------------------- 1050s 1050s Tuesday, October 28, 2025: 20:21:35 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1050s Number of Commands: 61 1164s succeeded(1) 1.63934% completed. succeeded(2) 3.27869% completed. succeeded(3) 4.91803% completed. succeeded(4) 6.55738% completed. succeeded(5) 8.19672% completed. succeeded(6) 9.83607% completed. succeeded(7) 11.4754% completed. succeeded(8) 13.1148% completed. succeeded(9) 14.7541% completed. succeeded(10) 16.3934% completed. succeeded(11) 18.0328% completed. succeeded(12) 19.6721% completed. succeeded(13) 21.3115% completed. succeeded(14) 22.9508% completed. succeeded(15) 24.5902% completed. succeeded(16) 26.2295% completed. succeeded(17) 27.8689% completed. succeeded(18) 29.5082% completed. succeeded(19) 31.1475% completed. succeeded(20) 32.7869% completed. succeeded(21) 34.4262% completed. succeeded(22) 36.0656% completed. succeeded(23) 37.7049% completed. succeeded(24) 39.3443% completed. succeeded(25) 40.9836% completed. succeeded(26) 42.623% completed. succeeded(27) 44.2623% completed. succeeded(28) 45.9016% completed. succeeded(29) 47.541% completed. succeeded(30) 49.1803% completed. succeeded(31) 50.8197% completed. succeeded(32) 52.459% completed. succeeded(33) 54.0984% completed. succeeded(34) 55.7377% completed. succeeded(35) 57.377% completed. succeeded(36) 59.0164% completed. succeeded(37) 60.6557% completed. succeeded(38) 62.2951% completed. succeeded(39) 63.9344% completed. succeeded(40) 65.5738% completed. succeeded(41) 67.2131% completed. succeeded(42) 68.8525% completed. succeeded(43) 70.4918% completed. succeeded(44) 72.1311% completed. succeeded(45) 73.7705% completed. succeeded(46) 75.4098% completed. succeeded(47) 77.0492% completed. succeeded(48) 78.6885% completed. succeeded(49) 80.3279% completed. succeeded(50) 81.9672% completed. succeeded(51) 83.6066% completed. succeeded(52) 85.2459% completed. succeeded(53) 86.8852% completed. succeeded(54) 88.5246% completed. succeeded(55) 90.1639% completed. succeeded(56) 91.8033% completed. succeeded(57) 93.4426% completed. succeeded(58) 95.082% completed. succeeded(59) 96.7213% completed. succeeded(60) 98.3607% completed. succeeded(61) 100% completed. 1164s 1164s All commands completed successfully. :-) 1164s 1164s 1164s 1164s ** Harvesting all assembled transcripts into a single multi-fasta file... 1164s 1164s Tuesday, October 28, 2025: 20:23:28 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp 1164s * [Tue Oct 28 20:23:29 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2 1165s * [Tue Oct 28 20:23:30 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta 1165s Tuesday, October 28, 2025: 20:23:30 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map 1165s 1165s 1165s ############################################################################# 1165s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta 1165s ############################################################################# 1165s 1165s 1165s 1165s ./misc_run_tests/__run_SE_samples_file.sh 1165s exit 0 1165s #!/bin/bash -ve 1165s 1165s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \ 1165s --seqType fq \ 1165s --max_memory 1G \ 1165s --output trinity_test_samples_SE 1165s 1165s 1165s ______ ____ ____ ____ ____ ______ __ __ 1165s | || \ | || \ | || || | | 1165s | || D ) | | | _ | | | | || | | 1165s |_| |_|| / | | | | | | | |_| |_|| ~ | 1165s | | | \ | | | | | | | | | |___, | 1165s | | | . \ | | | | | | | | | | | 1165s |__| |__|\_||____||__|__||____| |__| |____/ 1165s 1165s Trinity-v2.15.2 1165s 1165s 1165s 1165s Single read files: $VAR1 = [ 1165s 'reads.left.fq.gz', 1165s 'reads2.left.fq.gz' 1165s ]; 1166s Tuesday, October 28, 2025: 20:23:30 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE 1166s Tuesday, October 28, 2025: 20:23:31 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis 1166s 1166s 1166s ---------------------------------------------------------------------------------- 1166s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1166s ---------------------------------------------------------------------------------- 1166s 1166s --------------------------------------------------------------- 1166s ------------ In silico Read Normalization --------------------- 1166s -- (Removing Excess Reads Beyond 200 Coverage -- 1166s --------------------------------------------------------------- 1166s 1166s # running normalization on reads: $VAR1 = [ 1166s [ 1166s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1166s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1166s ] 1166s ]; 1166s 1166s 1166s Tuesday, October 28, 2025: 20:23:31 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000 --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1166s -prepping seqs 1166s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa 1166s CMD finished (0 seconds) 1166s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa 1166s CMD finished (0 seconds) 1166s CMD: touch single.fa.ok 1166s CMD finished (0 seconds) 1166s -kmer counting. 1166s ------------------------------------------- 1166s ----------- Jellyfish -------------------- 1166s -- (building a k-mer catalog from reads) -- 1166s ------------------------------------------- 1166s 1166s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical single.fa 1167s CMD finished (1 seconds) 1167s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1167s CMD finished (0 seconds) 1167s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1167s CMD finished (0 seconds) 1167s CMD: touch jellyfish.K25.min2.kmers.fa.success 1167s CMD finished (0 seconds) 1167s -generating stats files 1167s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > single.fa.K25.stats 1167s -reading Kmer occurrences... 1167s 1167s done parsing 288470 Kmers, 288470 added, taking 0 seconds. 1168s STATS_GENERATION_TIME: 1 seconds. 1168s CMD finished (1 seconds) 1168s CMD: touch single.fa.K25.stats.ok 1168s CMD finished (0 seconds) 1168s -sorting each stats file by read name. 1168s 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 1168s CMD finished (0 seconds) 1168s CMD: touch single.fa.K25.stats.sort.ok 1168s CMD finished (0 seconds) 1168s -defining normalized reads 1168s 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 1169s 59311 / 61150 = 96.99% reads selected during normalization. 1169s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1169s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1 1169s CMD finished (1 seconds) 1169s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok 1169s CMD finished (0 seconds) 1169s -search and capture. 1169s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1169s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1169s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1170s CMD: touch /tmp/autopkgtest.sYnnix/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 1170s CMD finished (0 seconds) 1170s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1170s CMD finished (0 seconds) 1170s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads 1170s 1170s 1170s Normalization complete. See outputs: 1170s /tmp/autopkgtest.sYnnix/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 1170s Tuesday, October 28, 2025: 20:23:35 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok 1170s Tuesday, October 28, 2025: 20:23:35 CMD: cat /tmp/autopkgtest.sYnnix/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 1170s Tuesday, October 28, 2025: 20:23:35 CMD: touch single.fa.ok 1170s Tuesday, October 28, 2025: 20:23:35 CMD: touch single.fa.ok 1170s ------------------------------------------- 1170s ----------- Jellyfish -------------------- 1170s -- (building a k-mer (25) catalog from reads) -- 1170s ------------------------------------------- 1170s 1170s * [Tue Oct 28 20:23:35 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1172s * [Tue Oct 28 20:23:37 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1172s * [Tue Oct 28 20:23:37 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1172s ---------------------------------------------- 1172s --------------- Inchworm (K=25, asm) --------------------- 1172s -- (Linear contig construction from k-mers) -- 1172s ---------------------------------------------- 1172s 1172s * [Tue Oct 28 20:23:37 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp 1172s Kmer length set to: 25 1172s Min assembly length set to: 25 1172s Monitor turned on, set to: 1 1172s double stranded mode set 1172s min entropy set to: 1 1172s setting number of threads to: 2 1172s -setting parallel iworm mode. 1172s -reading Kmer occurrences... 1172s [0M] Kmers parsed. 1172s done parsing 287930 Kmers, 287930 added, taking 0 seconds. 1172s 1172s TIMING KMER_DB_BUILDING 0 s. 1173s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1173s Pruned 2078 kmers from catalog. 1173s Pruning time: 0 seconds = 0 minutes. 1173s 1173s TIMING PRUNING 0 s. 1173s -populating the kmer seed candidate list. 1173s Kcounter hash size: 287930 1173s Processed 285852 non-zero abundance kmers in kcounter. 1173s -Not sorting list of kmers, given parallel mode in effect. 1173s -beginning inchworm contig assembly. 1173s Total kcounter hash size: 287930 vs. sorted list size: 285852 1173s num threads set to: 2 1173s Done opening file. tmp.iworm.fa.pid_69994.thread_0 1173s Done opening file. tmp.iworm.fa.pid_69994.thread_1 1173s 1173s Iworm contig assembly time: 0 seconds = 0 minutes. 1173s 1173s TIMING CONTIG_BUILDING 0 s. 1173s 1173s TIMING PROG_RUNTIME 1 s. 1173s * [Tue Oct 28 20:23:38 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 1173s Tuesday, October 28, 2025: 20:23:38 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished 1173s -------------------------------------------------------- 1173s -------------------- Chrysalis ------------------------- 1173s -- (Contig Clustering & de Bruijn Graph Construction) -- 1173s -------------------------------------------------------- 1173s 1173s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1173s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1173s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1173s * [Tue Oct 28 20:23:38 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 1173s * [Tue Oct 28 20:23:38 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt 1175s * [Tue Oct 28 20:23:40 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted 1175s * [Tue Oct 28 20:23:40 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1175s * [Tue Oct 28 20:23:40 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out 1175s * [Tue Oct 28 20:23:40 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200 1175s * [Tue Oct 28 20:23:40 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1179s * [Tue Oct 28 20:23:44 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort 1179s Tuesday, October 28, 2025: 20:23:44 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0 1179s Tuesday, October 28, 2025: 20:23:44 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok 1179s Tuesday, October 28, 2025: 20:23:44 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 1179s Tuesday, October 28, 2025: 20:23:44 CMD: touch recursive_trinity.cmds.ok 1179s Tuesday, October 28, 2025: 20:23:44 CMD: touch recursive_trinity.cmds.ok 1179s 1179s 1179s -------------------------------------------------------------------------------- 1179s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1179s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1179s -------------------------------------------------------------------------------- 1179s 1179s Tuesday, October 28, 2025: 20:23:44 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1179s Number of Commands: 45 1250s 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. 1250s 1250s All commands completed successfully. :-) 1250s 1250s 1250s 1250s ** Harvesting all assembled transcripts into a single multi-fasta file... 1250s 1250s Tuesday, October 28, 2025: 20:24:55 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp 1250s * [Tue Oct 28 20:24:55 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2 1251s * [Tue Oct 28 20:24:56 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta 1251s Tuesday, October 28, 2025: 20:24:56 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map 1251s 1251s 1251s ############################################################################# 1251s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta 1251s ############################################################################# 1251s 1251s 1251s 1251s 1251s exit 0 1251s ./misc_run_tests/__runMe_use_workdir.sh 1251s #!/bin/bash -ve 1251s 1251s 1251s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 1251s gunzip -c reads.right.fq.gz > reads.right.fq 1251s fi 1251s 1251s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 1251s gunzip -c reads.left.fq.gz > reads.left.fq 1251s fi 1251s 1251s 1251s 1251s ####################################################### 1251s ## Run Trinity to Generate Transcriptome Assemblies ## 1251s ####################################################### 1251s 1251s CPU=$(nproc || sysctl -n hw.physicalcpu) 1251s 1251s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \ 1251s --left reads.left.fq \ 1251s --right reads.right.fq \ 1251s --SS_lib_type RF \ 1251s --CPU ${CPU}\ 1251s --output trinity_with_workdir \ 1251s --workdir /tmp/trinity.workdir.$$ --full_cleanup 1251s 1251s 1251s ______ ____ ____ ____ ____ ______ __ __ 1251s | || \ | || \ | || || | | 1251s | || D ) | | | _ | | | | || | | 1251s |_| |_|| / | | | | | | | |_| |_|| ~ | 1251s | | | \ | | | | | | | | | |___, | 1251s | | | . \ | | | | | | | | | | | 1251s |__| |__|\_||____||__|__||____| |__| |____/ 1251s 1251s Trinity-v2.15.2 1251s 1251s 1251s 1251s Left read files: $VAR1 = [ 1251s 'reads.left.fq' 1251s ]; 1251s Right read files: $VAR1 = [ 1251s 'reads.right.fq' 1251s ]; 1251s Tuesday, October 28, 2025: 20:24:56 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir 1251s Tuesday, October 28, 2025: 20:24:56 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis 1251s 1251s 1251s ---------------------------------------------------------------------------------- 1251s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1251s ---------------------------------------------------------------------------------- 1251s 1251s --------------------------------------------------------------- 1251s ------------ In silico Read Normalization --------------------- 1251s -- (Removing Excess Reads Beyond 200 Coverage -- 1251s --------------------------------------------------------------- 1251s 1251s # running normalization on reads: $VAR1 = [ 1251s [ 1251s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq' 1251s ], 1251s [ 1251s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq' 1251s ] 1251s ]; 1251s 1251s 1251s Tuesday, October 28, 2025: 20:24:56 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together --PARALLEL_STATS 1252s -prepping seqs 1252s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 1252s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 1252s CMD finished (1 seconds) 1252s CMD finished (1 seconds) 1252s CMD: touch left.fa.ok 1252s CMD finished (0 seconds) 1252s CMD: touch right.fa.ok 1252s CMD finished (0 seconds) 1252s Done converting input files. CMD: cat left.fa right.fa > both.fa 1252s CMD finished (0 seconds) 1252s CMD: touch both.fa.ok 1252s CMD finished (0 seconds) 1252s -kmer counting. 1252s ------------------------------------------- 1252s ----------- Jellyfish -------------------- 1252s -- (building a k-mer catalog from reads) -- 1252s ------------------------------------------- 1252s 1252s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 1253s CMD finished (1 seconds) 1253s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1253s CMD finished (0 seconds) 1253s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1253s CMD finished (0 seconds) 1253s CMD: touch jellyfish.K25.min2.kmers.fa.success 1253s CMD finished (0 seconds) 1253s -generating stats files 1253s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 1253s -reading Kmer occurrences... 1253s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 1253s -reading Kmer occurrences... 1253s 1253s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 1253s 1253s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 1254s STATS_GENERATION_TIME: 1 seconds. 1254s STATS_GENERATION_TIME: 1 seconds. 1254s CMD finished (1 seconds) 1254s CMD finished (1 seconds) 1254s CMD: touch left.fa.K25.stats.ok 1254s CMD finished (0 seconds) 1254s CMD: touch right.fa.K25.stats.ok 1254s CMD finished (0 seconds) 1254s -sorting each stats file by read name. 1254s 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 1254s 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 1254s CMD finished (0 seconds) 1254s CMD finished (0 seconds) 1254s CMD: touch left.fa.K25.stats.sort.ok 1254s CMD finished (0 seconds) 1254s CMD: touch right.fa.K25.stats.sort.ok 1254s CMD finished (0 seconds) 1254s -defining normalized reads 1254s 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 1254s -opening left.fa.K25.stats.sort 1254s -opening right.fa.K25.stats.sort 1254s -done opening files. 1254s CMD finished (0 seconds) 1254s CMD: touch pairs.K25.stats.ok 1254s CMD finished (0 seconds) 1254s 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 1254s 30472 / 30575 = 99.66% reads selected during normalization. 1254s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1254s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 1254s CMD finished (0 seconds) 1254s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1254s CMD finished (0 seconds) 1254s -search and capture. 1255s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture. 1255s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq 1255s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture. 1255s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 1255s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1255s CMD finished (0 seconds) 1255s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1255s CMD finished (0 seconds) 1255s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1255s CMD finished (0 seconds) 1255s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1255s CMD finished (0 seconds) 1255s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads 1255s 1255s 1255s Normalization complete. See outputs: 1255s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 1255s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 1255s Tuesday, October 28, 2025: 20:25:00 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok 1255s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:25:00 CMD: cat /tmp/autopkgtest.sYnnix/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 1255s Tuesday, October 28, 2025: 20:25:00 CMD: cat /tmp/autopkgtest.sYnnix/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 1255s Tuesday, October 28, 2025: 20:25:00 CMD: touch left.fa.ok 1255s Tuesday, October 28, 2025: 20:25:00 CMD: touch right.fa.ok 1255s Tuesday, October 28, 2025: 20:25:00 CMD: touch left.fa.ok right.fa.ok 1255s Tuesday, October 28, 2025: 20:25:00 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1255s Tuesday, October 28, 2025: 20:25:00 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok 1255s ------------------------------------------- 1255s ----------- Jellyfish -------------------- 1255s -- (building a k-mer (25) catalog from reads) -- 1255s ------------------------------------------- 1255s 1255s * [Tue Oct 28 20:25:00 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1257s * [Tue Oct 28 20:25:02 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1257s * [Tue Oct 28 20:25:02 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1257s ---------------------------------------------- 1257s --------------- Inchworm (K=25, asm) --------------------- 1257s -- (Linear contig construction from k-mers) -- 1257s ---------------------------------------------- 1257s 1257s * [Tue Oct 28 20:25:02 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp 1257s Kmer length set to: 25 1257s Min assembly length set to: 25 1257s Monitor turned on, set to: 1 1257s min entropy set to: 1 1257s setting number of threads to: 2 1257s -setting parallel iworm mode. 1257s -reading Kmer occurrences... 1257s [0M] Kmers parsed. [0M] Kmers parsed. 1257s done parsing 519541 Kmers, 519541 added, taking 0 seconds. 1257s 1257s TIMING KMER_DB_BUILDING 0 s. 1257s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1257s Pruned 4252 kmers from catalog. 1257s Pruning time: 0 seconds = 0 minutes. 1257s 1257s TIMING PRUNING 0 s. 1257s -populating the kmer seed candidate list. 1257s Kcounter hash size: 519541 1257s Processed 515289 non-zero abundance kmers in kcounter. 1257s -Not sorting list of kmers, given parallel mode in effect. 1257s -beginning inchworm contig assembly. 1257s Total kcounter hash size: 519541 vs. sorted list size: 515289 1257s num threads set to: 2 1257s Done opening file. tmp.iworm.fa.pid_77003.thread_0 1257s Done opening file. tmp.iworm.fa.pid_77003.thread_1 1258s 1258s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 1258s 1258s TIMING CONTIG_BUILDING 1 s. 1258s 1258s TIMING PROG_RUNTIME 1 s. 1258s * [Tue Oct 28 20:25:03 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 1258s Tuesday, October 28, 2025: 20:25:03 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished 1258s -------------------------------------------------------- 1258s -------------------- Chrysalis ------------------------- 1258s -- (Contig Clustering & de Bruijn Graph Construction) -- 1258s -------------------------------------------------------- 1258s 1258s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1258s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1258s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1258s * [Tue Oct 28 20:25:03 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1258s * [Tue Oct 28 20:25:03 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null 1259s * [Tue Oct 28 20:25:03 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 1261s * [Tue Oct 28 20:25:06 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt 1262s * [Tue Oct 28 20:25:06 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt 1263s * [Tue Oct 28 20:25:08 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted 1263s * [Tue Oct 28 20:25:08 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1263s * [Tue Oct 28 20:25:08 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out 1263s * [Tue Oct 28 20:25:08 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200 1263s * [Tue Oct 28 20:25:08 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 1265s * [Tue Oct 28 20:25:10 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort 1265s Tuesday, October 28, 2025: 20:25:10 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0 1265s Tuesday, October 28, 2025: 20:25:10 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok 1265s Tuesday, October 28, 2025: 20:25:10 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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.76854 --no_salmon > recursive_trinity.cmds 1265s Tuesday, October 28, 2025: 20:25:10 CMD: touch recursive_trinity.cmds.ok 1265s Tuesday, October 28, 2025: 20:25:10 CMD: touch recursive_trinity.cmds.ok 1265s 1265s 1265s -------------------------------------------------------------------------------- 1265s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1265s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1265s -------------------------------------------------------------------------------- 1265s 1265s Tuesday, October 28, 2025: 20:25:10 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1265s Number of Commands: 38 1332s 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. 1332s 1332s All commands completed successfully. :-) 1332s 1332s 1332s 1332s ** Harvesting all assembled transcripts into a single multi-fasta file... 1332s 1332s Tuesday, October 28, 2025: 20:26:17 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp 1332s * [Tue Oct 28 20:26:17 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2 1333s * [Tue Oct 28 20:26:18 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta 1333s 1333s 1333s ############################################################################# 1333s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta 1333s ############################################################################# 1333s 1333s 1333s Tuesday, October 28, 2025: 20:26:18 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map 1333s 1333s 1333s exit 0 1333s ./misc_run_tests/__runMe_piecemeal.sh 1333s #!/bin/bash -ve 1333s 1333s ####################################################### 1333s ## Run Trinity to Generate Transcriptome Assemblies ## 1333s ####################################################### 1333s 1333s CPU=$(nproc || sysctl -n hw.physicalcpu) 1333s 1333s # stop before inchworm (just in silico norm) 1333s ${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 1333s 1333s 1333s ______ ____ ____ ____ ____ ______ __ __ 1333s | || \ | || \ | || || | | 1333s | || D ) | | | _ | | | | || | | 1333s |_| |_|| / | | | | | | | |_| |_|| ~ | 1333s | | | \ | | | | | | | | | |___, | 1333s | | | . \ | | | | | | | | | | | 1333s |__| |__|\_||____||__|__||____| |__| |____/ 1333s 1333s Trinity-v2.15.2 1333s 1333s 1333s 1333s Left read files: $VAR1 = [ 1333s 'reads.left.fq.gz' 1333s ]; 1333s Right read files: $VAR1 = [ 1333s 'reads.right.fq.gz' 1333s ]; 1333s Tuesday, October 28, 2025: 20:26:18 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal 1333s Tuesday, October 28, 2025: 20:26:18 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis 1333s 1333s 1333s ---------------------------------------------------------------------------------- 1333s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1333s ---------------------------------------------------------------------------------- 1333s 1333s --------------------------------------------------------------- 1333s ------------ In silico Read Normalization --------------------- 1333s -- (Removing Excess Reads Beyond 200 Coverage -- 1333s --------------------------------------------------------------- 1333s 1333s # running normalization on reads: $VAR1 = [ 1333s [ 1333s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1333s ], 1333s [ 1333s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1333s ] 1333s ]; 1333s 1333s 1333s Tuesday, October 28, 2025: 20:26:18 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000 --left /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 1333s -prepping seqs 1333s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1333s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1333s CMD finished (0 seconds) 1333s CMD finished (0 seconds) 1333s CMD: touch left.fa.ok 1333s CMD finished (0 seconds) 1333s CMD: touch right.fa.ok 1333s CMD finished (0 seconds) 1333s Done converting input files. CMD: cat left.fa right.fa > both.fa 1333s CMD finished (0 seconds) 1333s CMD: touch both.fa.ok 1333s CMD finished (0 seconds) 1333s -kmer counting. 1333s ------------------------------------------- 1333s ----------- Jellyfish -------------------- 1333s -- (building a k-mer catalog from reads) -- 1333s ------------------------------------------- 1333s 1333s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1334s CMD finished (1 seconds) 1334s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1334s CMD finished (0 seconds) 1334s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1335s CMD finished (0 seconds) 1335s CMD: touch jellyfish.K25.min2.kmers.fa.success 1335s CMD finished (0 seconds) 1335s -generating stats files 1335s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1335s -reading Kmer occurrences... 1335s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1335s -reading Kmer occurrences... 1335s 1335s done parsing 100964 Kmers, 100964 added, taking 1 seconds. 1335s 1335s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 1335s STATS_GENERATION_TIME: 0 seconds. 1335s CMD finished (1 seconds) 1335s STATS_GENERATION_TIME: 0 seconds. 1335s CMD finished (0 seconds) 1335s CMD: touch left.fa.K25.stats.ok 1335s CMD finished (0 seconds) 1335s CMD: touch right.fa.K25.stats.ok 1335s CMD finished (0 seconds) 1335s -sorting each stats file by read name. 1335s 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 1335s 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 1335s CMD finished (0 seconds) 1335s CMD finished (0 seconds) 1335s CMD: touch left.fa.K25.stats.sort.ok 1335s CMD finished (0 seconds) 1335s CMD: touch right.fa.K25.stats.sort.ok 1335s CMD finished (0 seconds) 1335s -defining normalized reads 1335s 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 1335s -opening left.fa.K25.stats.sort 1335s -opening right.fa.K25.stats.sort 1335s -done opening files. 1336s CMD finished (1 seconds) 1336s CMD: touch pairs.K25.stats.ok 1336s CMD finished (0 seconds) 1336s 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 1336s 30472 / 30575 = 99.66% reads selected during normalization. 1336s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1336s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 1336s CMD finished (0 seconds) 1336s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1336s CMD finished (0 seconds) 1336s -search and capture. 1336s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 1336s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1336s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 1336s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1337s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1337s CMD finished (0 seconds) 1337s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1337s CMD finished (0 seconds) 1337s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1337s CMD finished (0 seconds) 1337s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1337s CMD finished (0 seconds) 1337s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads 1337s 1337s 1337s Normalization complete. See outputs: 1337s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 1337s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 1337s Tuesday, October 28, 2025: 20:26:22 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok 1337s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:26:22 CMD: cat /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa 1337s Tuesday, October 28, 2025: 20:26:22 CMD: cat /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 1337s Tuesday, October 28, 2025: 20:26:22 CMD: touch left.fa.ok 1337s Tuesday, October 28, 2025: 20:26:22 CMD: touch right.fa.ok 1337s Tuesday, October 28, 2025: 20:26:22 CMD: touch left.fa.ok right.fa.ok 1337s Tuesday, October 28, 2025: 20:26:22 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1337s Tuesday, October 28, 2025: 20:26:22 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok 1337s WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm. 1337s 1337s # stop before chrysalis 1337s ${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 1337s 1337s 1337s ______ ____ ____ ____ ____ ______ __ __ 1337s | || \ | || \ | || || | | 1337s | || D ) | | | _ | | | | || | | 1337s |_| |_|| / | | | | | | | |_| |_|| ~ | 1337s | | | \ | | | | | | | | | |___, | 1337s | | | . \ | | | | | | | | | | | 1337s |__| |__|\_||____||__|__||____| |__| |____/ 1337s 1337s Trinity-v2.15.2 1337s 1337s 1337s 1337s Left read files: $VAR1 = [ 1337s 'reads.left.fq.gz' 1337s ]; 1337s Right read files: $VAR1 = [ 1337s 'reads.right.fq.gz' 1337s ]; 1337s 1337s 1337s ---------------------------------------------------------------------------------- 1337s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1337s ---------------------------------------------------------------------------------- 1337s 1337s --------------------------------------------------------------- 1337s ------------ In silico Read Normalization --------------------- 1337s -- (Removing Excess Reads Beyond 200 Coverage -- 1337s --------------------------------------------------------------- 1337s 1337s # running normalization on reads: $VAR1 = [ 1337s [ 1337s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1337s ], 1337s [ 1337s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1337s ] 1337s ]; 1337s 1337s 1337s ------------------------------------------- 1337s ----------- Jellyfish -------------------- 1337s -- (building a k-mer (25) catalog from reads) -- 1337s ------------------------------------------- 1337s 1337s * [Tue Oct 28 20:26:22 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1338s * [Tue Oct 28 20:26:23 2025] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1339s * [Tue Oct 28 20:26:24 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1339s ---------------------------------------------- 1339s --------------- Inchworm (K=25, asm) --------------------- 1339s -- (Linear contig construction from k-mers) -- 1339s ---------------------------------------------- 1339s 1339s * [Tue Oct 28 20:26:24 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp 1339s Kmer length set to: 25 1339s Min assembly length set to: 25 1339s Monitor turned on, set to: 1 1339s double stranded mode set 1339s min entropy set to: 1 1339s setting number of threads to: 2 1339s -setting parallel iworm mode. 1339s -reading Kmer occurrences... 1339s [0M] Kmers parsed. [0M] Kmers parsed. 1339s done parsing 517949 Kmers, 517949 added, taking 0 seconds. 1339s 1339s TIMING KMER_DB_BUILDING 0 s. 1339s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1339s Pruned 4114 kmers from catalog. 1339s Pruning time: 0 seconds = 0 minutes. 1339s 1339s TIMING PRUNING 0 s. 1339s -populating the kmer seed candidate list. 1339s Kcounter hash size: 517949 1339s Processed 513835 non-zero abundance kmers in kcounter. 1339s -Not sorting list of kmers, given parallel mode in effect. 1339s -beginning inchworm contig assembly. 1339s Total kcounter hash size: 517949 vs. sorted list size: 513835 1339s num threads set to: 2 1339s Done opening file. tmp.iworm.fa.pid_84028.thread_0 1339s Done opening file. tmp.iworm.fa.pid_84028.thread_1 1340s 1340s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 1340s 1340s TIMING CONTIG_BUILDING 1 s. 1340s 1340s TIMING PROG_RUNTIME 1 s. 1340s * [Tue Oct 28 20:26:25 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 1340s Tuesday, October 28, 2025: 20:26:25 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished 1340s 1340s 1340s 1340s ######################################################################### 1340s Inchworm is complete. --no_run_chrysalis was specified, so stopping here. 1340s ######################################################################### 1340s 1340s 1340s 1340s # stop before phase 2 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_distributed_trinity_exec 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1340s ], 1340s [ 1340s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1340s ] 1340s ]; 1340s 1340s 1340s -------------------------------------------------------- 1340s -------------------- Chrysalis ------------------------- 1340s -- (Contig Clustering & de Bruijn Graph Construction) -- 1340s -------------------------------------------------------- 1340s 1340s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1340s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1340s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1340s 1340s 1340s ####################################################################### 1340s Inchworm file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected. 1340s Skipping Inchworm Step, Using Previous Inchworm Assembly 1340s ####################################################################### 1340s 1340s * [Tue Oct 28 20:26:25 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1340s * [Tue Oct 28 20:26:25 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1340s * [Tue Oct 28 20:26:25 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 1344s * [Tue Oct 28 20:26:29 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt 1345s * [Tue Oct 28 20:26:30 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt 1346s * [Tue Oct 28 20:26:31 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted 1346s * [Tue Oct 28 20:26:31 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1346s * [Tue Oct 28 20:26:31 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out 1346s * [Tue Oct 28 20:26:31 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200 1346s * [Tue Oct 28 20:26:31 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1350s * [Tue Oct 28 20:26:35 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort 1350s Tuesday, October 28, 2025: 20:26:35 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0 1350s Tuesday, October 28, 2025: 20:26:35 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok 1350s Tuesday, October 28, 2025: 20:26:35 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 1350s Tuesday, October 28, 2025: 20:26:35 CMD: touch recursive_trinity.cmds.ok 1350s Tuesday, October 28, 2025: 20:26:35 CMD: touch recursive_trinity.cmds.ok 1350s 1350s 1350s ################################################################### 1350s ## Stopping here due to --no_distributed_trinity_exec in effect ## 1350s ################################################################### 1350s 1350s 1350s # finish it up 1350s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal 1350s 1350s 1350s ______ ____ ____ ____ ____ ______ __ __ 1350s | || \ | || \ | || || | | 1350s | || D ) | | | _ | | | | || | | 1350s |_| |_|| / | | | | | | | |_| |_|| ~ | 1350s | | | \ | | | | | | | | | |___, | 1350s | | | . \ | | | | | | | | | | | 1350s |__| |__|\_||____||__|__||____| |__| |____/ 1350s 1350s Trinity-v2.15.2 1350s 1350s 1350s 1350s Left read files: $VAR1 = [ 1350s 'reads.left.fq.gz' 1350s ]; 1350s Right read files: $VAR1 = [ 1350s 'reads.right.fq.gz' 1350s ]; 1350s 1350s 1350s ---------------------------------------------------------------------------------- 1350s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1350s ---------------------------------------------------------------------------------- 1350s 1350s --------------------------------------------------------------- 1350s ------------ In silico Read Normalization --------------------- 1350s -- (Removing Excess Reads Beyond 200 Coverage -- 1350s --------------------------------------------------------------- 1350s 1350s # running normalization on reads: $VAR1 = [ 1350s [ 1350s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1350s ], 1350s [ 1350s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1350s ] 1350s ]; 1350s 1350s 1350s -------------------------------------------------------- 1350s -------------------- Chrysalis ------------------------- 1350s -- (Contig Clustering & de Bruijn Graph Construction) -- 1350s -------------------------------------------------------- 1350s 1350s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1350s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1350s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1350s 1350s 1350s ####################################################################### 1350s Inchworm file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected. 1350s Skipping Inchworm Step, Using Previous Inchworm Assembly 1350s ####################################################################### 1350s 1350s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists. 1350s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists. 1350s -- 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists. 1350s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists. 1350s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists. 1350s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists. 1350s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists. 1350s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists. 1350s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists. 1350s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 , checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists. 1350s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists. 1350s 1350s 1350s -------------------------------------------------------------------------------- 1350s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1350s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1350s -------------------------------------------------------------------------------- 1350s 1350s Tuesday, October 28, 2025: 20:26:35 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1350s Number of Commands: 38 1419s 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. 1419s 1419s All commands completed successfully. :-) 1419s 1419s 1419s 1419s ** Harvesting all assembled transcripts into a single multi-fasta file... 1419s 1419s Tuesday, October 28, 2025: 20:27:44 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp 1419s * [Tue Oct 28 20:27:44 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2 1420s * [Tue Oct 28 20:27:45 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta 1420s Tuesday, October 28, 2025: 20:27:45 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map 1420s 1420s 1420s ############################################################################# 1420s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta 1420s ############################################################################# 1420s 1420s 1420s 1420s 1420s 1420s 1420s ##### Done Running Trinity ##### 1420s 1420s exit 0 1420s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh 1420s #!/bin/bash -ve 1420s 1420s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \ 1420s --seqType fq \ 1420s --max_memory 1G \ 1420s --min_kmer_cov 3 \ 1420s --output trinity_test_samples_PE_min_kmer_cov_3 1420s 1420s 1420s ______ ____ ____ ____ ____ ______ __ __ 1420s | || \ | || \ | || || | | 1420s | || D ) | | | _ | | | | || | | 1420s |_| |_|| / | | | | | | | |_| |_|| ~ | 1420s | | | \ | | | | | | | | | |___, | 1420s | | | . \ | | | | | | | | | | | 1420s |__| |__|\_||____||__|__||____| |__| |____/ 1420s 1420s Trinity-v2.15.2 1420s 1420s 1420s 1420s Left read files: $VAR1 = [ 1420s 'reads.left.fq.gz', 1420s 'reads2.left.fq.gz' 1420s ]; 1420s Right read files: $VAR1 = [ 1420s 'reads.right.fq.gz', 1420s 'reads2.right.fq.gz' 1420s ]; 1420s Tuesday, October 28, 2025: 20:27:45 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3 1420s Tuesday, October 28, 2025: 20:27:45 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis 1420s 1420s 1420s ---------------------------------------------------------------------------------- 1420s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1420s ---------------------------------------------------------------------------------- 1420s 1420s --------------------------------------------------------------- 1420s ------------ In silico Read Normalization --------------------- 1420s -- (Removing Excess Reads Beyond 200 Coverage -- 1420s --------------------------------------------------------------- 1420s 1420s # running normalization on reads: $VAR1 = [ 1420s [ 1420s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1420s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1420s ], 1420s [ 1420s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz', 1420s '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz' 1420s ] 1420s ]; 1420s 1420s 1420s Tuesday, October 28, 2025: 20:27:45 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together --PARALLEL_STATS 1421s -prepping seqs 1421s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1421s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1421s CMD finished (0 seconds) 1421s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa 1421s CMD finished (0 seconds) 1421s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa 1421s CMD finished (0 seconds) 1421s CMD finished (0 seconds) 1421s CMD: touch left.fa.ok 1421s CMD finished (0 seconds) 1421s CMD: touch right.fa.ok 1421s CMD finished (0 seconds) 1421s Done converting input files. CMD: cat left.fa right.fa > both.fa 1421s CMD finished (0 seconds) 1421s CMD: touch both.fa.ok 1421s CMD finished (0 seconds) 1421s -kmer counting. 1421s ------------------------------------------- 1421s ----------- Jellyfish -------------------- 1421s -- (building a k-mer catalog from reads) -- 1421s ------------------------------------------- 1421s 1421s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1422s CMD finished (1 seconds) 1422s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1422s CMD finished (0 seconds) 1422s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1423s CMD finished (1 seconds) 1423s CMD: touch jellyfish.K25.min2.kmers.fa.success 1423s CMD finished (0 seconds) 1423s -generating stats files 1423s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1423s -reading Kmer occurrences... 1423s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1423s -reading Kmer occurrences... 1423s 1423s done parsing 518514 Kmers, 518514 added, taking 0 seconds. 1423s 1423s done parsing 518514 Kmers, 518514 added, taking 0 seconds. 1424s STATS_GENERATION_TIME: 1 seconds. 1424s STATS_GENERATION_TIME: 1 seconds. 1424s CMD finished (1 seconds) 1424s CMD finished (1 seconds) 1424s CMD: touch left.fa.K25.stats.ok 1424s CMD finished (0 seconds) 1424s CMD: touch right.fa.K25.stats.ok 1424s CMD finished (0 seconds) 1424s -sorting each stats file by read name. 1424s 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 1424s 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 1425s CMD finished (1 seconds) 1425s CMD finished (1 seconds) 1425s CMD: touch left.fa.K25.stats.sort.ok 1425s CMD finished (0 seconds) 1425s CMD: touch right.fa.K25.stats.sort.ok 1425s CMD finished (0 seconds) 1425s -defining normalized reads 1425s 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 1425s -opening left.fa.K25.stats.sort 1425s -opening right.fa.K25.stats.sort 1425s -done opening files. 1425s CMD finished (0 seconds) 1425s CMD: touch pairs.K25.stats.ok 1425s CMD finished (0 seconds) 1425s 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 1426s 53574 / 61150 = 87.61% reads selected during normalization. 1426s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1426s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3 1426s CMD finished (1 seconds) 1426s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1426s CMD finished (0 seconds) 1426s -search and capture. 1426s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1426s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1426s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture. 1426s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1427s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1427s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz 1427s CMD: touch /tmp/autopkgtest.sYnnix/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 1427s CMD finished (0 seconds) 1427s CMD: touch /tmp/autopkgtest.sYnnix/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 1427s CMD finished (0 seconds) 1427s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1427s CMD finished (0 seconds) 1427s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 1427s CMD finished (0 seconds) 1427s -removing tmp dir /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads 1427s 1427s 1427s Normalization complete. See outputs: 1427s /tmp/autopkgtest.sYnnix/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 1427s /tmp/autopkgtest.sYnnix/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 1427s Tuesday, October 28, 2025: 20:27:52 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok 1427s Converting input files. (in parallel)Tuesday, October 28, 2025: 20:27:52 CMD: cat /tmp/autopkgtest.sYnnix/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 1427s Tuesday, October 28, 2025: 20:27:52 CMD: cat /tmp/autopkgtest.sYnnix/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 1427s Tuesday, October 28, 2025: 20:27:52 CMD: touch left.fa.ok 1427s Tuesday, October 28, 2025: 20:27:52 CMD: touch right.fa.ok 1427s Tuesday, October 28, 2025: 20:27:52 CMD: touch left.fa.ok right.fa.ok 1427s Tuesday, October 28, 2025: 20:27:52 CMD: cat left.fa right.fa > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1427s Tuesday, October 28, 2025: 20:27:52 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok 1427s ------------------------------------------- 1427s ----------- Jellyfish -------------------- 1427s -- (building a k-mer (25) catalog from reads) -- 1427s ------------------------------------------- 1427s 1427s * [Tue Oct 28 20:27:52 2025] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1429s * [Tue Oct 28 20:27:54 2025] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1429s * [Tue Oct 28 20:27:54 2025] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1429s ---------------------------------------------- 1429s --------------- Inchworm (K=25, asm) --------------------- 1429s -- (Linear contig construction from k-mers) -- 1429s ---------------------------------------------- 1429s 1429s * [Tue Oct 28 20:27:54 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp 1429s Kmer length set to: 25 1429s Min assembly length set to: 25 1429s Monitor turned on, set to: 1 1429s double stranded mode set 1429s min entropy set to: 1 1429s setting number of threads to: 2 1429s -setting parallel iworm mode. 1429s -reading Kmer occurrences... 1429s 1429s done parsing 96295 Kmers, 96295 added, taking 0 seconds. 1429s 1429s TIMING KMER_DB_BUILDING 0 s. 1429s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1429s Pruned 474 kmers from catalog. 1429s Pruning time: 0 seconds = 0 minutes. 1429s 1429s TIMING PRUNING 0 s. 1429s -populating the kmer seed candidate list. 1429s Kcounter hash size: 96295 1429s Processed 95821 non-zero abundance kmers in kcounter. 1429s -Not sorting list of kmers, given parallel mode in effect. 1429s -beginning inchworm contig assembly. 1429s Total kcounter hash size: 96295 vs. sorted list size: 95821 1429s num threads set to: 2 1429s Done opening file. tmp.iworm.fa.pid_90997.thread_0 1429s Done opening file. tmp.iworm.fa.pid_90997.thread_1 1429s 1429s Iworm contig assembly time: 0 seconds = 0 minutes. 1429s 1429s TIMING CONTIG_BUILDING 0 s. 1429s 1429s TIMING PROG_RUNTIME 0 s. 1429s * [Tue Oct 28 20:27:54 2025] Running CMD: mv /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 1429s Tuesday, October 28, 2025: 20:27:54 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished 1429s -------------------------------------------------------- 1429s -------------------- Chrysalis ------------------------- 1429s -- (Contig Clustering & de Bruijn Graph Construction) -- 1429s -------------------------------------------------------- 1429s 1429s inchworm_target: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1429s bowtie_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1429s chrysalis_reads_fa: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1429s * [Tue Oct 28 20:27:54 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1429s * [Tue Oct 28 20:27:54 2025] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1430s * [Tue Oct 28 20:27:55 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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 1437s * [Tue Oct 28 20:28:02 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt 1438s * [Tue Oct 28 20:28:03 2025] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt 1440s * [Tue Oct 28 20:28:05 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted 1440s * [Tue Oct 28 20:28:05 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1440s * [Tue Oct 28 20:28:05 2025] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out 1440s * [Tue Oct 28 20:28:05 2025] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200 1440s * [Tue Oct 28 20:28:05 2025] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.sYnnix/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 1446s * [Tue Oct 28 20:28:11 2025] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort 1446s Tuesday, October 28, 2025: 20:28:11 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0 1446s Tuesday, October 28, 2025: 20:28:11 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok 1446s Tuesday, October 28, 2025: 20:28:11 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.sYnnix/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 1447s Tuesday, October 28, 2025: 20:28:11 CMD: touch recursive_trinity.cmds.ok 1447s Tuesday, October 28, 2025: 20:28:11 CMD: touch recursive_trinity.cmds.ok 1447s 1447s 1447s -------------------------------------------------------------------------------- 1447s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1447s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1447s -------------------------------------------------------------------------------- 1447s 1447s Tuesday, October 28, 2025: 20:28:11 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1447s 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 Tuesday, October 28, 2025: 20:29:15 CMD: find /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp 1510s * [Tue Oct 28 20:29:15 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2 1511s * [Tue Oct 28 20:29:16 2025] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta 1511s Tuesday, October 28, 2025: 20:29:16 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly' 1511s Running example in test_GenomeGuidedTrinity... 1511s make[1]: Entering directory '/tmp/autopkgtest.sYnnix/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 1512s 1512s 1512s 1512s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ] 1512s then 1512s gunzip -c top100k.genome.gz > top100k.genome 1512s fi 1512s 1512s 1512s 1512s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G --output test_GG_use_bam_trinity_outdir 1512s 1512s 1512s ______ ____ ____ ____ ____ ______ __ __ 1512s | || \ | || \ | || || | | 1512s | || D ) | | | _ | | | | || | | 1512s |_| |_|| / | | | | | | | |_| |_|| ~ | 1512s | | | \ | | | | | | | | | |___, | 1512s | | | . \ | | | | | | | | | | | 1512s |__| |__|\_||____||__|__||____| |__| |____/ 1512s 1512s Trinity-v2.15.2 1512s 1512s 1512s 1512s Tuesday, October 28, 2025: 20:29:17 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 Tuesday, October 28, 2025: 20:29:17 CMD: mkdir -p /tmp/autopkgtest.sYnnix/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 Tuesday, October 28, 2025: 20:29:17 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam 1512s Tuesday, October 28, 2025: 20:29:17 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok 1512s Tuesday, October 28, 2025: 20:29:17 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.sYnnix/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.sYnnix/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.sYnnix/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 1514s 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 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads 1517s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads 1517s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok 1517s ## 1517s Done 1517s ## 1517s 1517s Tuesday, October 28, 2025: 20:29:20 CMD: touch partitions.ok 1517s Tuesday, October 28, 2025: 20:29:20 CMD: find Dir_* -name '*reads' > read_files.list 1517s Tuesday, October 28, 2025: 20:29:20 CMD: touch read_files.list.ok 1517s Tuesday, October 28, 2025: 20:29:20 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 1517s Tuesday, October 28, 2025: 20:29:20 CMD: touch trinity_GG.cmds.ok 1517s Tuesday, October 28, 2025: 20:29:20 CMD: touch trinity_GG.cmds.ok 1517s 1517s 1517s -------------------------------------------------------------------------------- 1517s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1517s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1517s -------------------------------------------------------------------------------- 1517s 1517s Tuesday, October 28, 2025: 20:29:20 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1517s Number of Commands: 37 1573s 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. 1573s 1573s All commands completed successfully. :-) 1573s 1573s Tuesday, October 28, 2025: 20:30:18 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp 1573s Tuesday, October 28, 2025: 20:30:18 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map 1573s 1573s 1573s Finished. See /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 1573s 1573s 1573s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta") 1573s ok 1573s if [ $asmsize -le 50000 ]; then 1573s echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete" 1573s exit 1 1573s else 1573s echo "ok" 1573s exit 0 1573s fi 1573s ./run_Schizo_TrinityGG_jaccard_clip.sh 1573s #!/bin/bash -ve 1573s 1573s $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 1573s 1573s 1573s ______ ____ ____ ____ ____ ______ __ __ 1573s | || \ | || \ | || || | | 1573s | || D ) | | | _ | | | | || | | 1573s |_| |_|| / | | | | | | | |_| |_|| ~ | 1573s | | | \ | | | | | | | | | |___, | 1573s | | | . \ | | | | | | | | | | | 1573s |__| |__|\_||____||__|__||____| |__| |____/ 1573s 1573s Trinity-v2.15.2 1573s 1573s 1573s 1573s Tuesday, October 28, 2025: 20:30:18 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam 1573s -appears to be a coordinate sorted bam file. ok. 1573s Tuesday, October 28, 2025: 20:30:18 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir 1573s 1573s 1573s ---------------------------------------------------------------------------------- 1573s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1573s ---------------------------------------------------------------------------------- 1573s 1573s -found paired-end aligned read. Running in paired-end mode. 1573s Tuesday, October 28, 2025: 20:30:18 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam 1573s Tuesday, October 28, 2025: 20:30:18 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok 1573s Tuesday, October 28, 2025: 20:30:18 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.sYnnix/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 1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF 1574s 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 1574s 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 1574s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords 1574s 1574s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords 1574s 1574s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok 1574s 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 1574s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 1574s 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 1574s 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 1575s [1000 lines read] scaff:7000000090838467 lend:6194 rend:6433 [2000 lines read] scaff:7000000090838467 lend:46308 rend:46696 CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok 1575s 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 1575s [3000 lines read] scaff:7000000090838467 lend:59573 rend:59951 [4000 lines read] scaff:7000000090838467 lend:60068 rend:60313 [5000 lines read] scaff:7000000090838467 lend:60602 rend:60807 CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 1575s [6000 lines read] scaff:7000000090838467 lend:65099 rend:65468 [7000 lines read] scaff:7000000090838467 lend:65621 rend:65957 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 1575s [8000 lines read] scaff:7000000090838467 lend:66173 rend:66538 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 1575s [9000 lines read] scaff:7000000090838467 lend:88962 rend:89278 [1000 lines read] scaff:7000000090838467 lend:8022 rend:8237 [2000 lines read] scaff:7000000090838467 lend:8568 rend:8635 CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok 1575s 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 1575s [3000 lines read] scaff:7000000090838467 lend:21591 rend:21888 [4000 lines read] scaff:7000000090838467 lend:29215 rend:29340 [5000 lines read] scaff:7000000090838467 lend:30519 rend:30759 [6000 lines read] scaff:7000000090838467 lend:52660 rend:52989 [7000 lines read] scaff:7000000090838467 lend:56475 rend:56834 CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok 1575s [8000 lines read] scaff:7000000090838467 lend:57224 rend:57489 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 1575s [9000 lines read] scaff:7000000090838467 lend:67627 rend:67818 // parsing paritions. 1575s [73] -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads 1575s [10000 lines read] scaff:7000000090838467 lend:68505 rend:68690 [11000 lines read] scaff:7000000090838467 lend:69245 rend:69544 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads 1575s [12000 lines read] scaff:7000000090838467 lend:82862 rend:83065 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads 1575s [13000 lines read] scaff:7000000090838467 lend:83622 rend:83842 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads 1575s [14000 lines read] scaff:7000000090838467 lend:84137 rend:84436 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads 1575s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok 1575s 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 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads 1575s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok 1575s 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 1575s // parsing paritions. 1575s [57] -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads 1575s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads 1575s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads 1576s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads 1576s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok 1576s ## 1576s Done 1576s ## 1576s 1576s Tuesday, October 28, 2025: 20:30:21 CMD: touch partitions.ok 1576s Tuesday, October 28, 2025: 20:30:21 CMD: find Dir_* -name '*reads' > read_files.list 1576s Tuesday, October 28, 2025: 20:30:21 CMD: touch read_files.list.ok 1576s Tuesday, October 28, 2025: 20:30:21 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 1576s Tuesday, October 28, 2025: 20:30:21 CMD: touch trinity_GG.cmds.ok 1576s Tuesday, October 28, 2025: 20:30:21 CMD: touch trinity_GG.cmds.ok 1576s 1576s 1576s -------------------------------------------------------------------------------- 1576s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1576s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1576s -------------------------------------------------------------------------------- 1576s 1576s Tuesday, October 28, 2025: 20:30:21 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1576s Number of Commands: 53 1576s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s bt2 index files: $VAR1 = []; 1576s Note - bowtie-build indices do not yet exist. Indexing genome now. 1576s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s bt2 index files: $VAR1 = []; 1576s Note - bowtie-build indices do not yet exist. Indexing genome now. 1576s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1576s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1577s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1577s 277 reads; of these: 1577s 277 (100.00%) were unpaired; of these: 1577s 0 (0.00%) aligned 0 times 1577s 277 (100.00%) aligned exactly 1 time 1577s 0 (0.00%) aligned >1 times 1577s 100.00% overall alignment rate 1577s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s 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 1577s 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 1577s 1811 reads; of these: 1577s 1811 (100.00%) were unpaired; of these: 1577s 6 (0.33%) aligned 0 times 1577s 1189 (65.65%) aligned exactly 1 time 1577s 616 (34.01%) aligned >1 times 1577s 99.67% overall alignment rate 1577s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1577s 1577s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1577s 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 1577s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s 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 1577s 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 1577s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1577s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s -processing jaccard pair sensor 1577s 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 1577s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s 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 1577s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s 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 1577s 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 1577s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1577s 1577s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1577s 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 1577s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1577s 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 1577s 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 1577s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1577s -processing jaccard pair sensor 1577s 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 1577s [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 1577s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s succeeded(1) 1.88679% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s bt2 index files: $VAR1 = []; 1580s Note - bowtie-build indices do not yet exist. Indexing genome now. 1580s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s succeeded(2) 3.77358% completed. CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1580s 454 reads; of these: 1580s 454 (100.00%) were unpaired; of these: 1580s 1 (0.22%) aligned 0 times 1580s 368 (81.06%) aligned exactly 1 time 1580s 85 (18.72%) aligned >1 times 1580s 99.78% overall alignment rate 1580s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1580s 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 1580s 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 1581s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1581s -processing jaccard pair sensor 1581s 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 1581s 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 1581s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s bt2 index files: $VAR1 = []; 1581s Note - bowtie-build indices do not yet exist. Indexing genome now. 1581s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1581s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 5953 reads; of these: 1582s 5953 (100.00%) were unpaired; of these: 1582s 11 (0.18%) aligned 0 times 1582s 3807 (63.95%) aligned exactly 1 time 1582s 2135 (35.86%) aligned >1 times 1582s 99.82% overall alignment rate 1582s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s 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 1582s 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 1582s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1582s 1582s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1582s 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 1582s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1582s 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 1582s 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 [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 1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s succeeded(3) 5.66038% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s bt2 index files: $VAR1 = []; 1584s Note - bowtie-build indices do not yet exist. Indexing genome now. 1584s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1584s 115 reads; of these: 1584s 115 (100.00%) were unpaired; of these: 1584s 6 (5.22%) aligned 0 times 1584s 109 (94.78%) aligned exactly 1 time 1584s 0 (0.00%) aligned >1 times 1584s 94.78% overall alignment rate 1584s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s 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 1584s 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 1584s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1584s 1584s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1584s 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 1584s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1584s 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 1584s 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 1584s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1584s -processing jaccard pair sensor 1584s 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s succeeded(4) 7.54717% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 succeeded(5) 9.43396% completed. CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1588s 18 reads; of these: 1588s 18 (100.00%) were unpaired; of these: 1588s 5 (27.78%) aligned 0 times 1588s 13 (72.22%) aligned exactly 1 time 1588s 0 (0.00%) aligned >1 times 1588s 72.22% overall alignment rate 1588s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s 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 1588s 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s bt2 index files: $VAR1 = []; 1588s Note - bowtie-build indices do not yet exist. Indexing genome now. 1588s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1588s 24 reads; of these: 1588s 24 (100.00%) were unpaired; of these: 1588s 1 (4.17%) aligned 0 times 1588s 23 (95.83%) aligned exactly 1 time 1588s 0 (0.00%) aligned >1 times 1588s 95.83% overall alignment rate 1588s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s succeeded(6) 11.3208% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1589s bt2 index files: $VAR1 = []; 1589s Note - bowtie-build indices do not yet exist. Indexing genome now. 1589s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1590s 26 reads; of these: 1590s 26 (100.00%) were unpaired; of these: 1590s 0 (0.00%) aligned 0 times 1590s 26 (100.00%) aligned exactly 1 time 1590s 0 (0.00%) aligned >1 times 1590s 100.00% overall alignment rate 1590s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1590s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: /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: /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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s succeeded(7) 13.2075% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s bt2 index files: $VAR1 = []; 1591s Note - bowtie-build indices do not yet exist. Indexing genome now. 1591s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1591s 10 reads; of these: 1591s 10 (100.00%) were unpaired; of these: 1591s 7 (70.00%) aligned 0 times 1591s 3 (30.00%) aligned exactly 1 time 1591s 0 (0.00%) aligned >1 times 1591s 30.00% overall alignment rate 1591s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1591s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s succeeded(8) 15.0943% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s bt2 index files: $VAR1 = []; 1592s Note - bowtie-build indices do not yet exist. Indexing genome now. 1592s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s succeeded(9) 16.9811% completed. CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1592s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1592s 1733 reads; of these: 1592s 1733 (100.00%) were unpaired; of these: 1592s 0 (0.00%) aligned 0 times 1592s 794 (45.82%) aligned exactly 1 time 1592s 939 (54.18%) aligned >1 times 1592s 100.00% overall alignment rate 1593s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s bt2 index files: $VAR1 = []; 1593s Note - bowtie-build indices do not yet exist. Indexing genome now. 1593s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 54 reads; of these: 1593s 54 (100.00%) were unpaired; of these: 1593s 9 (16.67%) aligned 0 times 1593s 45 (83.33%) aligned exactly 1 time 1593s 0 (0.00%) aligned >1 times 1593s 83.33% overall alignment rate 1593s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s -processing jaccard pair sensor 1593s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: /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: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1593s [1000 lines read] scaff:a22;2 lend:1 rend:49 -processing jaccard pair sensor 1593s [2000 lines read] scaff:a3;97 lend:65 rend:131 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 [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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1593s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s succeeded(10) 18.8679% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s bt2 index files: $VAR1 = []; 1595s Note - bowtie-build indices do not yet exist. Indexing genome now. 1595s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1595s 371 reads; of these: 1595s 371 (100.00%) were unpaired; of these: 1595s 2 (0.54%) aligned 0 times 1595s 296 (79.78%) aligned exactly 1 time 1595s 73 (19.68%) aligned >1 times 1595s 99.46% overall alignment rate 1595s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1595s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 1596s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1596s 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 1596s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s 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 1596s 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 1596s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1596s -processing jaccard pair sensor 1596s 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 1596s succeeded(11) 20.7547% completed. 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 1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s bt2 index files: $VAR1 = []; 1596s Note - bowtie-build indices do not yet exist. Indexing genome now. 1596s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1596s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1597s 2128 reads; of these: 1597s 2128 (100.00%) were unpaired; of these: 1597s 6 (0.28%) aligned 0 times 1597s 1722 (80.92%) aligned exactly 1 time 1597s 400 (18.80%) aligned >1 times 1597s 99.72% overall alignment rate 1597s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1597s 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 1597s 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 1597s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1597s 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: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 1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s succeeded(12) 22.6415% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s bt2 index files: $VAR1 = []; 1598s Note - bowtie-build indices do not yet exist. Indexing genome now. 1598s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1598s 26 reads; of these: 1598s 26 (100.00%) were unpaired; of these: 1598s 6 (23.08%) aligned 0 times 1598s 20 (76.92%) aligned exactly 1 time 1598s 0 (0.00%) aligned >1 times 1598s 76.92% overall alignment rate 1598s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1598s 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 1599s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1599s 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 1599s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1599s 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 1599s 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 1599s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1599s -processing jaccard pair sensor 1599s 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 1599s 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 1599s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1601s succeeded(13) 24.5283% completed. succeeded(14) 26.4151% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s bt2 index files: $VAR1 = []; 1602s Note - bowtie-build indices do not yet exist. Indexing genome now. 1602s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s bt2 index files: $VAR1 = []; 1602s Note - bowtie-build indices do not yet exist. Indexing genome now. 1602s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1602s 98 reads; of these: 1602s 98 (100.00%) were unpaired; of these: 1602s 0 (0.00%) aligned 0 times 1602s 98 (100.00%) aligned exactly 1 time 1602s 0 (0.00%) aligned >1 times 1602s 100.00% overall alignment rate 1602s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1602s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s 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 1602s 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 1602s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1602s 1602s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1602s 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 1602s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s 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 1602s 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 1602s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1602s -processing jaccard pair sensor 1602s 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 1602s 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 1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s 4380 reads; of these: 1602s 4380 (100.00%) were unpaired; of these: 1602s 10 (0.23%) aligned 0 times 1602s 2462 (56.21%) aligned exactly 1 time 1602s 1908 (43.56%) aligned >1 times 1602s 99.77% overall alignment rate 1602s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1602s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1603s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1603s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1603s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1603s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 [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 1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1604s succeeded(15) 28.3019% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1604s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1604s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1604s bt2 index files: $VAR1 = []; 1604s Note - bowtie-build indices do not yet exist. Indexing genome now. 1604s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1605s 76 reads; of these: 1605s 76 (100.00%) were unpaired; of these: 1605s 0 (0.00%) aligned 0 times 1605s 76 (100.00%) aligned exactly 1 time 1605s 0 (0.00%) aligned >1 times 1605s 100.00% overall alignment rate 1605s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s 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 1605s 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 1605s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1605s 1605s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1605s 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 1605s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1605s 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 1605s 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 1605s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1605s -processing jaccard pair sensor 1605s 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 1605s 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 1605s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1607s succeeded(16) 30.1887% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1607s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1607s bt2 index files: $VAR1 = []; 1607s Note - bowtie-build indices do not yet exist. Indexing genome now. 1607s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s succeeded(17) 32.0755% completed. CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1608s 18 reads; of these: 1608s 18 (100.00%) were unpaired; of these: 1608s 1 (5.56%) aligned 0 times 1608s 17 (94.44%) aligned exactly 1 time 1608s 0 (0.00%) aligned >1 times 1608s 94.44% overall alignment rate 1608s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s 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 1608s 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 1608s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1608s 1608s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1608s 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 1608s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s 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 1608s 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 1608s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1608s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s -processing jaccard pair sensor 1608s bt2 index files: $VAR1 = []; 1608s Note - bowtie-build indices do not yet exist. Indexing genome now. 1608s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s 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 1608s 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 1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1608s 10 reads; of these: 1608s 10 (100.00%) were unpaired; of these: 1608s 5 (50.00%) aligned 0 times 1608s 5 (50.00%) aligned exactly 1 time 1608s 0 (0.00%) aligned >1 times 1608s 50.00% overall alignment rate 1608s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s 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 1608s 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 1608s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1608s 1608s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1608s 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 1608s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1608s 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 1608s 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 1608s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1608s -processing jaccard pair sensor 1608s 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 1608s 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 1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1609s succeeded(18) 33.9623% completed. succeeded(19) 35.8491% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1609s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1609s bt2 index files: $VAR1 = []; 1609s Note - bowtie-build indices do not yet exist. Indexing genome now. 1609s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s bt2 index files: $VAR1 = []; 1610s Note - bowtie-build indices do not yet exist. Indexing genome now. 1610s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1610s 20 reads; of these: 1610s 20 (100.00%) were unpaired; of these: 1610s 4 (20.00%) aligned 0 times 1610s 16 (80.00%) aligned exactly 1 time 1610s 0 (0.00%) aligned >1 times 1610s 80.00% overall alignment rate 1610s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s 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 1610s 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 1610s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1610s 1610s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1610s 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 1610s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s 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 1610s 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 1610s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1610s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1610s -processing jaccard pair sensor 1610s 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 1610s 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 1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s 997 reads; of these: 1610s 997 (100.00%) were unpaired; of these: 1610s 3 (0.30%) aligned 0 times 1610s 568 (56.97%) aligned exactly 1 time 1610s 426 (42.73%) aligned >1 times 1610s 99.70% overall alignment rate 1610s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s 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 1610s 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 1610s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1610s 1610s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1610s 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 1610s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1610s 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 1610s 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 1610s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1610s -processing jaccard pair sensor 1610s 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 1610s [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 1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1611s succeeded(20) 37.7359% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1611s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 bt2 index files: $VAR1 = []; 1611s Note - bowtie-build indices do not yet exist. Indexing genome now. 1611s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1612s 538 reads; of these: 1612s 538 (100.00%) were unpaired; of these: 1612s 2 (0.37%) aligned 0 times 1612s 530 (98.51%) aligned exactly 1 time 1612s 6 (1.12%) aligned >1 times 1612s 99.63% overall alignment rate 1612s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1612s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s succeeded(21) 39.6226% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s bt2 index files: $VAR1 = []; 1614s Note - bowtie-build indices do not yet exist. Indexing genome now. 1614s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1614s 30 reads; of these: 1614s 30 (100.00%) were unpaired; of these: 1614s 0 (0.00%) aligned 0 times 1614s 18 (60.00%) aligned exactly 1 time 1614s 12 (40.00%) aligned >1 times 1614s 100.00% overall alignment rate 1614s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s 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 1614s 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 1614s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1614s 1614s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1614s 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 1614s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1614s 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 1614s 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s succeeded(22) 41.5094% completed. succeeded(23) 43.3962% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s bt2 index files: $VAR1 = []; 1616s Note - bowtie-build indices do not yet exist. Indexing genome now. 1616s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s bt2 index files: $VAR1 = []; 1616s Note - bowtie-build indices do not yet exist. Indexing genome now. 1616s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1616s 953 reads; of these: 1616s 953 (100.00%) were unpaired; of these: 1616s 4 (0.42%) aligned 0 times 1616s 555 (58.24%) aligned exactly 1 time 1616s 394 (41.34%) aligned >1 times 1616s 99.58% overall alignment rate 1616s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s 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 1616s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1616s 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 1616s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1616s 1616s 213 reads; of these: 1616s 213 (100.00%) were unpaired; of these: 1616s 1 (0.47%) aligned 0 times 1616s 121 (56.81%) aligned exactly 1 time 1616s 91 (42.72%) aligned >1 times 1616s 99.53% overall alignment rate 1616s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1616s 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 1616s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s 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 1616s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s 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 1616s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s 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 1616s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1616s 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 1616s -processing jaccard pair sensor 1616s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1616s 1616s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1616s 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 1616s 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 1616s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s 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 1616s 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 1616s [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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1616s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1616s -processing jaccard pair sensor 1616s 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 1616s 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 1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s succeeded(24) 45.283% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s bt2 index files: $VAR1 = []; 1620s Note - bowtie-build indices do not yet exist. Indexing genome now. 1620s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1620s 77 reads; of these: 1620s 77 (100.00%) were unpaired; of these: 1620s 2 (2.60%) aligned 0 times 1620s 75 (97.40%) aligned exactly 1 time 1620s 0 (0.00%) aligned >1 times 1620s 97.40% overall alignment rate 1620s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1620s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 succeeded(25) 47.1698% completed. -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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s bt2 index files: $VAR1 = []; 1621s Note - bowtie-build indices do not yet exist. Indexing genome now. 1621s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1621s 85 reads; of these: 1621s 85 (100.00%) were unpaired; of these: 1621s 6 (7.06%) aligned 0 times 1621s 79 (92.94%) aligned exactly 1 time 1621s 0 (0.00%) aligned >1 times 1621s 92.94% overall alignment rate 1621s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s 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 1621s 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 1621s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1621s 1621s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1621s 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 1621s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1621s 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 1621s 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 1621s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1621s -processing jaccard pair sensor 1621s 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 1621s 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 1621s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s succeeded(26) 49.0566% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s bt2 index files: $VAR1 = []; 1623s Note - bowtie-build indices do not yet exist. Indexing genome now. 1623s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1623s succeeded(27) 50.9434% completed. 2557 reads; of these: 1623s 2557 (100.00%) were unpaired; of these: 1623s 11 (0.43%) aligned 0 times 1623s 1332 (52.09%) aligned exactly 1 time 1623s 1214 (47.48%) aligned >1 times 1623s 99.57% overall alignment rate 1623s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1623s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s bt2 index files: $VAR1 = []; 1624s Note - bowtie-build indices do not yet exist. Indexing genome now. 1624s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 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:a1;81 lend:250 rend:502 [2000 lines read] scaff:a22;2 lend:4 rend:34 46 reads; of these: 1624s 46 (100.00%) were unpaired; of these: 1624s 0 (0.00%) aligned 0 times 1624s 44 (95.65%) aligned exactly 1 time 1624s 2 (4.35%) 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1624s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s succeeded(28) 52.8302% completed. succeeded(29) 54.717% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s bt2 index files: $VAR1 = []; 1627s Note - bowtie-build indices do not yet exist. Indexing genome now. 1627s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1627s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s bt2 index files: $VAR1 = []; 1628s Note - bowtie-build indices do not yet exist. Indexing genome now. 1628s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1628s 1717 reads; of these: 1628s 1717 (100.00%) were unpaired; of these: 1628s 1 (0.06%) aligned 0 times 1628s 1511 (88.00%) aligned exactly 1 time 1628s 205 (11.94%) aligned >1 times 1628s 99.94% overall alignment rate 1628s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1628s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 293 reads; of these: 1628s 293 (100.00%) were unpaired; of these: 1628s 0 (0.00%) aligned 0 times 1628s 293 (100.00%) aligned exactly 1 time 1628s 0 (0.00%) aligned >1 times 1628s 100.00% overall alignment rate 1628s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 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 1628s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 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 1628s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 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 1628s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1628s 1628s 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 1628s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1628s 1628s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1628s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1628s 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 1628s 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 1628s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 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 1628s 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 1628s 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 1628s 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 1628s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1628s -processing jaccard pair sensor 1628s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1628s -processing jaccard pair sensor 1628s 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 1628s 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 1628s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1628s 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 1628s [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 1628s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1631s succeeded(30) 56.6038% completed. succeeded(31) 58.4906% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1631s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s bt2 index files: $VAR1 = []; 1632s Note - bowtie-build indices do not yet exist. Indexing genome now. 1632s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1632s 26 reads; of these: 1632s 26 (100.00%) were unpaired; of these: 1632s 17 (65.38%) aligned 0 times 1632s 9 (34.62%) aligned exactly 1 time 1632s 0 (0.00%) aligned >1 times 1632s 34.62% overall alignment rate 1632s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s 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 1632s 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 1632s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1632s 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s bt2 index files: $VAR1 = []; 1632s Note - bowtie-build indices do not yet exist. Indexing genome now. 1632s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1632s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1633s 5664 reads; of these: 1633s 5664 (100.00%) were unpaired; of these: 1633s 8 (0.14%) aligned 0 times 1633s 3217 (56.80%) aligned exactly 1 time 1633s 2439 (43.06%) aligned >1 times 1633s 99.86% overall alignment rate 1633s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s succeeded(32) 60.3774% completed. CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s 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 1633s 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 1633s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1633s 1633s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1633s 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 1633s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s 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 1633s bt2 index files: $VAR1 = []; 1633s Note - bowtie-build indices do not yet exist. Indexing genome now. 1633s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1633s 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 1634s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1634s -processing jaccard pair sensor 1634s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1634s 818 reads; of these: 1634s 818 (100.00%) were unpaired; of these: 1634s 1 (0.12%) aligned 0 times 1634s 758 (92.67%) aligned exactly 1 time 1634s 59 (7.21%) aligned >1 times 1634s 99.88% overall alignment rate 1634s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s 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 1634s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s 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 1634s [1000 lines read] scaff:a1;95 lend:117 rend:350 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 1634s [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 -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1634s 1634s [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 1634s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1634s 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 1634s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s 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 1634s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1634s 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 1634s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1634s -processing jaccard pair sensor 1634s 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 1634s 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 1634s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s succeeded(33) 62.2641% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s bt2 index files: $VAR1 = []; 1639s Note - bowtie-build indices do not yet exist. Indexing genome now. 1639s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1639s succeeded(34) 64.1509% completed. 70 reads; of these: 1639s 70 (100.00%) were unpaired; of these: 1639s 10 (14.29%) aligned 0 times 1639s 59 (84.29%) aligned exactly 1 time 1639s 1 (1.43%) aligned >1 times 1639s 85.71% overall alignment rate 1639s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 -processing jaccard pair sensor 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 1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1639s bt2 index files: $VAR1 = []; 1639s Note - bowtie-build indices do not yet exist. Indexing genome now. 1639s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1640s 16 reads; of these: 1640s 16 (100.00%) were unpaired; of these: 1640s 0 (0.00%) aligned 0 times 1640s 14 (87.50%) aligned exactly 1 time 1640s 2 (12.50%) aligned >1 times 1640s 100.00% overall alignment rate 1640s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1640s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s succeeded(35) 66.0377% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s bt2 index files: $VAR1 = []; 1641s Note - bowtie-build indices do not yet exist. Indexing genome now. 1641s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1641s 24 reads; of these: 1641s 24 (100.00%) were unpaired; of these: 1641s 3 (12.50%) aligned 0 times 1641s 21 (87.50%) aligned exactly 1 time 1641s 0 (0.00%) aligned >1 times 1641s 87.50% overall alignment rate 1641s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1641s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s succeeded(36) 67.9245% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s bt2 index files: $VAR1 = []; 1642s Note - bowtie-build indices do not yet exist. Indexing genome now. 1642s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1642s 51 reads; of these: 1642s 51 (100.00%) were unpaired; of these: 1642s 4 (7.84%) aligned 0 times 1642s 47 (92.16%) aligned exactly 1 time 1642s 0 (0.00%) aligned >1 times 1642s 92.16% overall alignment rate 1642s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s 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 1642s 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 1642s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1642s 1642s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1642s 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 1642s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1642s 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 1642s 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 1642s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1642s -processing jaccard pair sensor 1642s 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 1642s 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 1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s succeeded(37) 69.8113% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s bt2 index files: $VAR1 = []; 1643s Note - bowtie-build indices do not yet exist. Indexing genome now. 1643s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1643s 27 reads; of these: 1643s 27 (100.00%) were unpaired; of these: 1643s 6 (22.22%) aligned 0 times 1643s 21 (77.78%) aligned exactly 1 time 1643s 0 (0.00%) aligned >1 times 1643s 77.78% overall alignment rate 1643s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1643s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s succeeded(38) 71.6981% completed. succeeded(39) 73.5849% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s bt2 index files: $VAR1 = []; 1644s Note - bowtie-build indices do not yet exist. Indexing genome now. 1644s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1644s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s bt2 index files: $VAR1 = []; 1645s Note - bowtie-build indices do not yet exist. Indexing genome now. 1645s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1645s 907 reads; of these: 1645s 907 (100.00%) were unpaired; of these: 1645s 2 (0.22%) aligned 0 times 1645s 839 (92.50%) aligned exactly 1 time 1645s 66 (7.28%) aligned >1 times 1645s 99.78% overall alignment rate 1645s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1645s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 85 reads; of these: 1645s 85 (100.00%) were unpaired; of these: 1645s 3 (3.53%) aligned 0 times 1645s 82 (96.47%) aligned exactly 1 time 1645s 0 (0.00%) aligned >1 times 1645s 96.47% overall alignment rate 1645s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1645s 1645s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1645s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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/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: /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 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 -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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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/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/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 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: 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/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1647s succeeded(40) 75.4717% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1647s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1647s succeeded(41) 77.3585% completed. CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1647s bt2 index files: $VAR1 = []; 1647s Note - bowtie-build indices do not yet exist. Indexing genome now. 1647s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1648s 42 reads; of these: 1648s 42 (100.00%) were unpaired; of these: 1648s 18 (42.86%) aligned 0 times 1648s 24 (57.14%) aligned exactly 1 time 1648s 0 (0.00%) aligned >1 times 1648s 57.14% overall alignment rate 1648s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s bt2 index files: $VAR1 = []; 1648s Note - bowtie-build indices do not yet exist. Indexing genome now. 1648s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1648s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1649s 3962 reads; of these: 1649s 3962 (100.00%) were unpaired; of these: 1649s 2 (0.05%) aligned 0 times 1649s 2253 (56.87%) aligned exactly 1 time 1649s 1707 (43.08%) aligned >1 times 1649s 99.95% overall alignment rate 1649s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 succeeded(42) 79.2453% completed. -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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s bt2 index files: $VAR1 = []; 1649s Note - bowtie-build indices do not yet exist. Indexing genome now. 1649s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: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 1649s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1649s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1650s 16 reads; of these: 1650s 16 (100.00%) were unpaired; of these: 1650s 10 (62.50%) aligned 0 times 1650s 6 (37.50%) aligned exactly 1 time 1650s 0 (0.00%) aligned >1 times 1650s 37.50% overall alignment rate 1650s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s 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 1650s 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 1650s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1650s 1650s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1650s 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 1650s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1650s 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 1650s 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 1650s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1650s -processing jaccard pair sensor 1650s 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 1650s 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 1650s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s succeeded(43) 81.1321% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s bt2 index files: $VAR1 = []; 1651s Note - bowtie-build indices do not yet exist. Indexing genome now. 1651s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1651s 52 reads; of these: 1651s 52 (100.00%) were unpaired; of these: 1651s 5 (9.62%) aligned 0 times 1651s 47 (90.38%) aligned exactly 1 time 1651s 0 (0.00%) aligned >1 times 1651s 90.38% overall alignment rate 1651s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s 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 1651s 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 1651s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1651s 1651s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1651s 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 1651s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1651s 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 1651s 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 1651s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1651s -processing jaccard pair sensor 1651s 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 1651s 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 1651s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s succeeded(44) 83.0189% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s bt2 index files: $VAR1 = []; 1653s Note - bowtie-build indices do not yet exist. Indexing genome now. 1653s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1653s succeeded(45) 84.9057% completed. 34 reads; of these: 1653s 34 (100.00%) were unpaired; of these: 1653s 1 (2.94%) aligned 0 times 1653s 33 (97.06%) aligned exactly 1 time 1653s 0 (0.00%) aligned >1 times 1653s 97.06% overall alignment rate 1653s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1653s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s bt2 index files: $VAR1 = []; 1654s Note - bowtie-build indices do not yet exist. Indexing genome now. 1654s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1654s 10 reads; of these: 1654s 10 (100.00%) were unpaired; of these: 1654s 2 (20.00%) aligned 0 times 1654s 8 (80.00%) aligned exactly 1 time 1654s 0 (0.00%) aligned >1 times 1654s 80.00% overall alignment rate 1654s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s 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 1654s 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 1654s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1654s 1654s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1654s 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 1654s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1654s 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 1654s 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 1654s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1654s -processing jaccard pair sensor 1654s 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 1654s 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 1654s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s succeeded(46) 86.7924% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s bt2 index files: $VAR1 = []; 1655s Note - bowtie-build indices do not yet exist. Indexing genome now. 1655s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s succeeded(47) 88.6792% completed. CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1655s 20 reads; of these: 1655s 20 (100.00%) were unpaired; of these: 1655s 12 (60.00%) aligned 0 times 1655s 8 (40.00%) aligned exactly 1 time 1655s 0 (0.00%) aligned >1 times 1655s 40.00% overall alignment rate 1655s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 bt2 index files: $VAR1 = []; 1655s Note - bowtie-build indices do not yet exist. Indexing genome now. 1655s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1655s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1656s 30 reads; of these: 1656s 30 (100.00%) were unpaired; of these: 1656s 9 (30.00%) aligned 0 times 1656s 21 (70.00%) aligned exactly 1 time 1656s 0 (0.00%) aligned >1 times 1656s 70.00% overall alignment rate 1656s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s 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 1656s 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 1656s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1656s 1656s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1656s 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 1656s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1656s 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 1656s 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 1656s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1656s -processing jaccard pair sensor 1656s 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 1656s 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 1656s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s succeeded(48) 90.566% completed. succeeded(49) 92.4528% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s bt2 index files: $VAR1 = []; 1657s Note - bowtie-build indices do not yet exist. Indexing genome now. 1657s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s bt2 index files: $VAR1 = []; 1657s Note - bowtie-build indices do not yet exist. Indexing genome now. 1657s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1657s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1657s 10 reads; of these: 1657s 10 (100.00%) were unpaired; of these: 1657s 3 (30.00%) aligned 0 times 1657s 7 (70.00%) aligned exactly 1 time 1657s 0 (0.00%) aligned >1 times 1657s 70.00% overall alignment rate 1657s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1657s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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 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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s 7038 reads; of these: 1658s 7038 (100.00%) were unpaired; of these: 1658s 25 (0.36%) aligned 0 times 1658s 2368 (33.65%) aligned exactly 1 time 1658s 4645 (66.00%) aligned >1 times 1658s 99.64% overall alignment rate 1658s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s succeeded(50) 94.3396% completed. CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 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: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1658s bt2 index files: $VAR1 = []; 1658s Note - bowtie-build indices do not yet exist. Indexing genome now. 1658s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1659s 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 1659s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1659s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s 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 1659s 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 1659s 309 reads; of these: 1659s 309 (100.00%) were unpaired; of these: 1659s 3 (0.97%) aligned 0 times 1659s 201 (65.05%) aligned exactly 1 time 1659s 105 (33.98%) aligned >1 times 1659s 99.03% overall alignment rate 1659s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1659s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s -processing jaccard pair sensor 1659s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s 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 1659s 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 1659s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1659s 1659s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1659s 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 1659s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s 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 1659s 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 1659s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1659s -processing jaccard pair sensor 1659s 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 1659s 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 1659s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1659s 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 1659s [1000 lines read] scaff:a16;2 lend:11 rend:42 [2000 lines read] scaff:a1;131 lend:621 rend:903 [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 1659s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s succeeded(51) 96.2264% completed. CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: samtools faidx /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s bt2 index files: $VAR1 = []; 1662s Note - bowtie-build indices do not yet exist. Indexing genome now. 1662s CMD: bowtie2-build -q /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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" 1662s 145 reads; of these: 1662s 145 (100.00%) were unpaired; of these: 1662s 1 (0.69%) aligned 0 times 1662s 144 (99.31%) aligned exactly 1 time 1662s 0 (0.00%) aligned >1 times 1662s 99.31% overall alignment rate 1662s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: samtools view -bt /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s -cleaning up and removing intermediate file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1662s 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 1662s 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 1663s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1663s 1663s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1663s 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 1663s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1663s 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 1663s 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 1663s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1663s -processing jaccard pair sensor 1663s 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 1663s 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 1663s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/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.sYnnix/autopkgtest_tmp/trinityrnaseq/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 1665s succeeded(52) 98.1132% completed. succeeded(53) 100% completed. 1665s 1665s All commands completed successfully. :-) 1665s 1665s Tuesday, October 28, 2025: 20:31:50 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp 1665s Tuesday, October 28, 2025: 20:31:50 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map 1665s 1665s 1665s Finished. See /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts 1665s 1665s 1665s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta" 1665s asmsize=$(wc -c <"${outfile}") 1665s ok 1665s if [ $asmsize -le 50000 ]; then 1665s echo "Error, ${outfile} potentially incomplete" 1665s exit 1 1665s ./run_small_GG_mutliScaff_test.sh 1665s else 1665s echo "ok" 1665s exit 0 1665s fi 1665s #!/bin/bash -ve 1665s 1665s 1665s $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 1666s 1666s 1666s ______ ____ ____ ____ ____ ______ __ __ 1666s | || \ | || \ | || || | | 1666s | || D ) | | | _ | | | | || | | 1666s |_| |_|| / | | | | | | | |_| |_|| ~ | 1666s | | | \ | | | | | | | | | |___, | 1666s | | | . \ | | | | | | | | | | | 1666s |__| |__|\_||____||__|__||____| |__| |____/ 1666s 1666s Trinity-v2.15.2 1666s 1666s 1666s 1666s Tuesday, October 28, 2025: 20:31:51 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam 1666s -appears to be a coordinate sorted bam file. ok. 1666s Tuesday, October 28, 2025: 20:31:51 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir 1666s 1666s 1666s ---------------------------------------------------------------------------------- 1666s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1666s ---------------------------------------------------------------------------------- 1666s 1666s -found paired-end aligned read. Running in paired-end mode. 1666s Tuesday, October 28, 2025: 20:31:51 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam 1668s Done with chr TRINITY_DN0_c0_g1_i1. 1668s Done with chr TRINITY_DN10_c0_g1_i1. 1668s Done with chr TRINITY_DN12_c0_g1_i1. 1668s Done with chr TRINITY_DN12_c0_g1_i2. 1668s Done with chr TRINITY_DN14_c0_g1_i1. 1668s Done with chr TRINITY_DN14_c0_g2_i1. 1668s Done with chr TRINITY_DN15_c0_g1_i1. 1668s Done with chr TRINITY_DN16_c0_g1_i1. 1668s Done with chr TRINITY_DN16_c0_g2_i1. 1668s Done with chr TRINITY_DN18_c0_g1_i1. 1668s Done with chr TRINITY_DN18_c0_g1_i2. 1668s Done with chr TRINITY_DN19_c0_g1_i1. 1668s Done with chr TRINITY_DN20_c0_g1_i1. 1668s Done with chr TRINITY_DN20_c0_g2_i1. 1668s Done with chr TRINITY_DN20_c0_g1_i2. 1668s Done with chr TRINITY_DN20_c0_g1_i3. 1668s Done with chr TRINITY_DN20_c0_g1_i4. 1668s Done with chr TRINITY_DN20_c0_g1_i5. 1668s Done with chr TRINITY_DN20_c0_g1_i6. 1668s Done with chr TRINITY_DN20_c0_g1_i7. 1668s Done with chr TRINITY_DN21_c0_g1_i1. 1668s Done with chr TRINITY_DN21_c0_g1_i2. 1668s Done with chr TRINITY_DN22_c0_g1_i1. 1668s Done with chr TRINITY_DN22_c0_g2_i1. 1668s Done with chr TRINITY_DN22_c0_g3_i1. 1668s Done with chr TRINITY_DN22_c0_g4_i1. 1668s Done with chr TRINITY_DN22_c0_g3_i2. 1668s Done with chr TRINITY_DN22_c0_g3_i3. 1668s Done with chr TRINITY_DN22_c0_g3_i4. 1668s Done with chr TRINITY_DN22_c0_g5_i1. 1668s Done with chr TRINITY_DN22_c0_g6_i1. 1668s Done with chr TRINITY_DN22_c0_g3_i5. 1668s Done with chr TRINITY_DN22_c0_g7_i1. 1668s Done with chr TRINITY_DN23_c0_g1_i1. 1668s Done with chr TRINITY_DN23_c0_g2_i1. 1668s Done with chr TRINITY_DN23_c0_g1_i2. 1668s Done with chr TRINITY_DN23_c0_g3_i1. 1668s Done with chr TRINITY_DN23_c0_g4_i1. 1668s Done with chr TRINITY_DN23_c0_g5_i1. 1668s Done with chr TRINITY_DN23_c0_g1_i3. 1668s Done with chr TRINITY_DN23_c0_g1_i4. 1668s Done with chr TRINITY_DN24_c0_g1_i1. 1668s Done with chr TRINITY_DN24_c0_g2_i1. 1668s Done with chr TRINITY_DN24_c0_g3_i1. 1668s Done with chr TRINITY_DN24_c0_g3_i2. 1668s Done with chr TRINITY_DN25_c1_g1_i1. 1668s Done with chr TRINITY_DN25_c1_g1_i2. 1668s Done with chr TRINITY_DN25_c1_g1_i3. 1668s Done with chr TRINITY_DN25_c1_g1_i4. 1668s Done with chr TRINITY_DN25_c1_g1_i5. 1668s Done with chr TRINITY_DN26_c0_g1_i1. 1668s Done with chr TRINITY_DN26_c0_g1_i2. 1668s Done with chr TRINITY_DN26_c1_g1_i1. 1668s Done with chr TRINITY_DN26_c1_g1_i2. 1668s Done with chr TRINITY_DN26_c1_g1_i3. 1668s Done with chr TRINITY_DN26_c1_g1_i4. 1668s Done with chr TRINITY_DN26_c1_g1_i5. 1668s Done with chr TRINITY_DN26_c1_g1_i6. 1668s Done with chr TRINITY_DN26_c1_g2_i1. 1668s Done with chr TRINITY_DN26_c1_g1_i7. 1668s Done with chr TRINITY_DN26_c1_g3_i1. 1668s Done with chr TRINITY_DN26_c1_g1_i8. 1668s Done with chr TRINITY_DN26_c1_g1_i9. 1668s Done with chr TRINITY_DN26_c1_g1_i10. 1668s Done with chr TRINITY_DN26_c1_g1_i11. 1668s Done with chr TRINITY_DN26_c1_g3_i2. 1668s Done with chr TRINITY_DN26_c1_g1_i12. 1668s Done with chr TRINITY_DN26_c1_g4_i1. 1668s Done with chr TRINITY_DN26_c1_g1_i13. 1668s Done with chr TRINITY_DN26_c1_g1_i14. 1668s Done with chr TRINITY_DN26_c1_g1_i15. 1668s Done with chr TRINITY_DN26_c1_g1_i16. 1668s Done with chr TRINITY_DN26_c1_g1_i17. 1668s Done with chr TRINITY_DN26_c1_g1_i18. 1668s Done with chr TRINITY_DN26_c1_g3_i3. 1668s Done with chr TRINITY_DN26_c1_g1_i19. 1668s Done with chr TRINITY_DN26_c1_g3_i4. 1668s Done with chr TRINITY_DN26_c1_g5_i1. 1668s Done with chr TRINITY_DN26_c1_g1_i20. 1668s Done with chr TRINITY_DN26_c1_g1_i21. 1668s Done with chr TRINITY_DN26_c1_g3_i5. 1668s Done with chr TRINITY_DN26_c2_g1_i1. 1668s Done with chr TRINITY_DN26_c2_g1_i2. 1668s Done with chr TRINITY_DN26_c2_g2_i1. 1668s Done with chr TRINITY_DN26_c2_g3_i1. 1668s Done with chr TRINITY_DN26_c2_g1_i3. 1668s Done with chr TRINITY_DN26_c2_g1_i4. 1668s Done with chr TRINITY_DN26_c2_g1_i5. 1668s Done with chr TRINITY_DN27_c0_g1_i1. 1668s Done with chr TRINITY_DN4_c0_g1_i1. 1668s Done with chr TRINITY_DN5_c0_g1_i1. 1668s Tuesday, October 28, 2025: 20:31:53 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok 1668s Tuesday, October 28, 2025: 20:31:53 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.sYnnix/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 1668s 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 1668s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords 1668s 1673s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok 1673s 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 1674s CMD: cp /tmp/autopkgtest.sYnnix/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.sYnnix/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 1674s 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 1674s 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 1678s [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 1678s 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 1678s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok 1678s 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 1678s // parsing paritions. 1678s [92] -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads 1678s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads 1679s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads 1680s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads 1681s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads 1682s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads 1683s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads 1684s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads 1684s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok 1684s ## 1684s Done 1684s ## 1684s 1684s Tuesday, October 28, 2025: 20:32:09 CMD: touch partitions.ok 1684s Tuesday, October 28, 2025: 20:32:09 CMD: find Dir_* -name '*reads' > read_files.list 1684s Tuesday, October 28, 2025: 20:32:09 CMD: touch read_files.list.ok 1684s Tuesday, October 28, 2025: 20:32:09 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 --seqType fa --trinity_complete --full_cleanup > trinity_GG.cmds 1684s Tuesday, October 28, 2025: 20:32:09 CMD: touch trinity_GG.cmds.ok 1684s Tuesday, October 28, 2025: 20:32:09 CMD: touch trinity_GG.cmds.ok 1684s 1684s 1684s -------------------------------------------------------------------------------- 1684s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1684s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1684s -------------------------------------------------------------------------------- 1684s 1684s Tuesday, October 28, 2025: 20:32:09 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1684s Number of Commands: 85 1927s 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. 1927s 1927s All commands completed successfully. :-) 1927s 1927s Tuesday, October 28, 2025: 20:36:12 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp 1927s Tuesday, October 28, 2025: 20:36:12 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map 1928s 1928s 1928s Finished. See /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 1928s 1928s 1928s 1928s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta" 1928s asmsize=$(wc -c <"${outfile}") 1928s ok 1928s ./run_chr17_GG_wLongreads.sh 1928s if [ $asmsize -le 650000 ]; then 1928s echo "Error, ${outfile} potentially incomplete" 1928s exit 1 1928s else 1928s echo "ok" 1928s exit 0 1928s fi 1928s #!/bin/bash -ve 1928s 1928s 1928s $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 1928s 1928s 1928s ______ ____ ____ ____ ____ ______ __ __ 1928s | || \ | || \ | || || | | 1928s | || D ) | | | _ | | | | || | | 1928s |_| |_|| / | | | | | | | |_| |_|| ~ | 1928s | | | \ | | | | | | | | | |___, | 1928s | | | . \ | | | | | | | | | | | 1928s |__| |__|\_||____||__|__||____| |__| |____/ 1928s 1928s Trinity-v2.15.2 1928s 1928s 1928s 1928s Tuesday, October 28, 2025: 20:36:13 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam 1928s -appears to be a coordinate sorted bam file. ok. 1928s Tuesday, October 28, 2025: 20:36:13 CMD: mkdir -p /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir 1928s 1928s 1928s ---------------------------------------------------------------------------------- 1928s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1928s ---------------------------------------------------------------------------------- 1928s 1928s -found paired-end aligned read. Running in paired-end mode. 1928s Tuesday, October 28, 2025: 20:36:13 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam 1929s Done with chr chr1. 1929s Tuesday, October 28, 2025: 20:36:14 CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok 1929s * [Tue Oct 28 20:36:14 2025] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam O=/tmp/autopkgtest.sYnnix/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 1930s INFO 2025-10-28 20:36:15 AddOrReplaceReadGroups 1930s 1930s ********** NOTE: Picard's command line syntax is changing. 1930s ********** 1930s ********** For more information, please see: 1930s ********** 1930s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 1930s ********** 1930s ********** The command line looks like this in the new syntax: 1930s ********** 1930s ********** AddOrReplaceReadGroups -I /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.sYnnix/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 1930s ********** 1930s 1930s 1931s 20:36:16.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 1931s 20:36:16.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib 1931s 20:36:16.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 1931s 20:36:16.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 1931s 20:36:16.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib 1931s 20:36:16.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 1931s [Tue Oct 28 20:36:16 UTC 2025] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.sYnnix/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 1931s [Tue Oct 28 20:36:16 UTC 2025] Executing as ubuntu@autopkgtest on Linux 6.17.0-5-generic aarch64; OpenJDK 64-Bit Server VM 21.0.9+10-Ubuntu-1; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.3.0 1931s 20:36:16.041 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 1931s 20:36:16.046 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 1931s INFO 2025-10-28 20:36:16 AddOrReplaceReadGroups Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio 1931s 1931s 20:36:16.097 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater 1931s [Tue Oct 28 20:36:16 UTC 2025] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes. 1931s Runtime.totalMemory()=67108864 1931s * [Tue Oct 28 20:36:16 2025] Running CMD: samtools merge /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam 1932s Tuesday, October 28, 2025: 20:36:17 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.sYnnix/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 1932s 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 1932s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords 1932s 1934s CMD: touch merged_wRGLR.bam.read_coords.ok 1934s 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 1934s CMD: cp /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname 1934s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted 1934s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig 1950s [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 1950s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff 1954s CMD: touch merged_wRGLR.bam.minC1.gff.ok 1954s 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 1954s // parsing paritions. 1954s [100] [116] -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads 1954s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads 1954s -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 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads 1955s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads 1955s -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 Tuesday, October 28, 2025: 20:36:41 CMD: touch partitions.ok 1956s Tuesday, October 28, 2025: 20:36:41 CMD: find Dir_* -name '*reads' > read_files.list 1956s Tuesday, October 28, 2025: 20:36:41 CMD: touch read_files.list.ok 1956s Tuesday, October 28, 2025: 20:36:41 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 Tuesday, October 28, 2025: 20:36:41 CMD: touch trinity_GG.cmds.ok 1956s Tuesday, October 28, 2025: 20:36:41 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 Tuesday, October 28, 2025: 20:36:41 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 1956s Number of Commands: 44 2941s 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. 2941s 2941s All commands completed successfully. :-) 2941s 2941s Tuesday, October 28, 2025: 20:53:06 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.tmp 2941s Tuesday, October 28, 2025: 20:53:06 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.gene_trans_map 2941s 2941s 2941s Finished. See /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 2941s 2941s 2941s find test_chr17_LR_GG_trinity_outdir/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep '>' | grep 'LR\$' > test_chr17_LR_GG_trinity_outdir.LR 2944s 2944s if [[ $(wc -l > left.fa 2944s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa 2944s CMD finished (0 seconds) 2944s CMD finished (0 seconds) 2944s CMD: touch left.fa.ok 2944s CMD finished (0 seconds) 2944s CMD: touch right.fa.ok 2944s CMD finished (0 seconds) 2944s Done converting input files. CMD: cat left.fa right.fa > both.fa 2944s CMD finished (0 seconds) 2944s CMD: touch both.fa.ok 2944s CMD finished (0 seconds) 2944s -kmer counting. 2944s ------------------------------------------- 2944s ----------- Jellyfish -------------------- 2944s -- (building a k-mer catalog from reads) -- 2944s ------------------------------------------- 2944s 2944s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 2945s CMD finished (1 seconds) 2945s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2945s CMD finished (0 seconds) 2945s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2945s CMD finished (0 seconds) 2945s CMD: touch jellyfish.K25.min2.kmers.fa.success 2945s CMD finished (0 seconds) 2945s -generating stats files 2945s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > left.fa.K25.stats 2945s -reading Kmer occurrences... 2945s 2945s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 2946s STATS_GENERATION_TIME: 1 seconds. 2946s CMD finished (1 seconds) 2946s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > right.fa.K25.stats 2946s -reading Kmer occurrences... 2946s 2946s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 2946s STATS_GENERATION_TIME: 0 seconds. 2946s CMD finished (0 seconds) 2946s CMD: touch left.fa.K25.stats.ok 2946s CMD finished (0 seconds) 2946s CMD: touch right.fa.K25.stats.ok 2946s CMD finished (0 seconds) 2946s -sorting each stats file by read name. 2946s 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 2946s CMD finished (0 seconds) 2946s 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 2946s CMD finished (0 seconds) 2946s CMD: touch left.fa.K25.stats.sort.ok 2946s CMD finished (0 seconds) 2946s CMD: touch right.fa.K25.stats.sort.ok 2946s CMD finished (0 seconds) 2946s -defining normalized reads 2946s 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 2946s -opening left.fa.K25.stats.sort 2946s -opening right.fa.K25.stats.sort 2946s -done opening files. 2947s CMD finished (1 seconds) 2947s CMD: touch pairs.K25.stats.ok 2947s CMD finished (0 seconds) 2947s 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 2947s 3826 / 30575 = 12.51% reads selected during normalization. 2947s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2947s 1797 / 30575 = 5.88% reads discarded as below minimum coverage threshold=2 2947s CMD finished (0 seconds) 2947s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok 2947s CMD finished (0 seconds) 2947s -search and capture. 2947s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz ... done prepping, now search and capture. 2947s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz 2947s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz ... done prepping, now search and capture. 2947s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz 2947s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok 2947s CMD finished (0 seconds) 2947s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok 2947s CMD finished (0 seconds) 2947s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq left.norm.fq 2947s CMD finished (0 seconds) 2947s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq right.norm.fq 2947s CMD finished (0 seconds) 2947s 2947s 2947s Normalization complete. See outputs: 2947s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq 2947s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq 2947s 2947s ./test_SE_normalization.sh 2947s 2947s 2947s #!/bin/bash -ve 2947s 2947s if [ ! -e reads.single.fq ]; then 2947s gunzip -c ../test_DATA/reads.left.fq.gz > reads.single.fq 2947s fi 2947s 2947s 2947s # just for testing purposes, use --max_cov 30 or higher for real applications. 2947s $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 2947s -prepping seqs 2947s CMD: seqtk-trinity seq -A -R 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq >> single.fa 2947s CMD finished (0 seconds) 2947s CMD: touch single.fa.ok 2947s CMD finished (0 seconds) 2947s -kmer counting. 2947s ------------------------------------------- 2947s ----------- Jellyfish -------------------- 2947s -- (building a k-mer catalog from reads) -- 2947s ------------------------------------------- 2947s 2947s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical single.fa 2949s CMD finished (2 seconds) 2949s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2949s CMD finished (0 seconds) 2949s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2949s CMD finished (0 seconds) 2949s CMD: touch jellyfish.K25.min2.kmers.fa.success 2949s CMD finished (0 seconds) 2949s -generating stats files 2949s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > single.fa.K25.stats 2949s -reading Kmer occurrences... 2949s 2949s done parsing 70076 Kmers, 70076 added, taking 0 seconds. 2949s STATS_GENERATION_TIME: 0 seconds. 2949s CMD finished (0 seconds) 2949s CMD: touch single.fa.K25.stats.ok 2949s CMD finished (0 seconds) 2949s -sorting each stats file by read name. 2949s 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 2949s CMD finished (0 seconds) 2949s CMD: touch single.fa.K25.stats.sort.ok 2949s CMD finished (0 seconds) 2949s -defining normalized reads 2949s 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 2950s 9127 / 30575 = 29.85% reads selected during normalization. 2950s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2950s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=0 2950s CMD finished (0 seconds) 2950s CMD: touch single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs.ok 2950s CMD finished (0 seconds) 2950s -search and capture. 2950s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq ... done prepping, now search and capture. 2950s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq 2950s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq.ok 2950s CMD finished (0 seconds) 2950s CMD: ln -sf /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq single.norm.fq 2950s CMD finished (0 seconds) 2950s 2950s 2950s Normalization complete. See outputs: 2950s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq 2950s 2950s 2950s 2950s ./test_PE_normalization.mult_read_sets.sh 2950s #!/bin/bash -ve 2950s 2950s CPU=$(nproc || sysctl -n hw.physicalcpu) 2950s 2950s # just for testing purposes, use --max_cov 30 or higher for real applications. 2950s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \ 2950s --left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \ 2950s --right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \ 2950s --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \ 2950s --output test_multi_read_sets_norm_outdir 2950s -prepping seqs 2950s Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa 2950s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa 2950s CMD finished (0 seconds) 2950s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz) >> left.fa 2950s CMD finished (0 seconds) 2950s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz) >> right.fa 2950s CMD finished (0 seconds) 2950s CMD finished (0 seconds) 2950s CMD: touch left.fa.ok 2950s CMD finished (0 seconds) 2950s CMD: touch right.fa.ok 2950s CMD finished (0 seconds) 2950s Done converting input files. CMD: cat left.fa right.fa > both.fa 2950s CMD finished (0 seconds) 2950s CMD: touch both.fa.ok 2950s CMD finished (0 seconds) 2950s -kmer counting. 2950s ------------------------------------------- 2950s ----------- Jellyfish -------------------- 2950s -- (building a k-mer catalog from reads) -- 2950s ------------------------------------------- 2950s 2950s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 2952s CMD finished (2 seconds) 2952s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2952s CMD finished (0 seconds) 2952s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2952s CMD finished (0 seconds) 2952s CMD: touch jellyfish.K25.min2.kmers.fa.success 2952s CMD finished (0 seconds) 2952s -generating stats files 2952s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > left.fa.K25.stats 2952s -reading Kmer occurrences... 2953s 2953s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 2953s STATS_GENERATION_TIME: 0 seconds. 2953s CMD finished (1 seconds) 2953s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > right.fa.K25.stats 2953s -reading Kmer occurrences... 2954s 2954s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 2954s STATS_GENERATION_TIME: 0 seconds. 2955s CMD finished (2 seconds) 2955s CMD: touch left.fa.K25.stats.ok 2955s CMD finished (0 seconds) 2955s CMD: touch right.fa.K25.stats.ok 2955s CMD finished (0 seconds) 2955s -sorting each stats file by read name. 2955s 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 2955s CMD finished (0 seconds) 2955s 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 2955s CMD finished (0 seconds) 2955s CMD: touch left.fa.K25.stats.sort.ok 2955s CMD finished (0 seconds) 2955s CMD: touch right.fa.K25.stats.sort.ok 2955s CMD finished (0 seconds) 2955s -defining normalized reads 2955s 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 2955s -opening left.fa.K25.stats.sort 2955s -opening right.fa.K25.stats.sort 2955s -done opening files. 2956s CMD finished (0 seconds) 2956s CMD: touch pairs.K25.stats.ok 2956s CMD finished (0 seconds) 2956s 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 2956s 7970 / 61150 = 13.03% reads selected during normalization. 2956s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2956s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=0 2956s CMD finished (1 seconds) 2956s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok 2956s CMD finished (0 seconds) 2956s -search and capture. 2956s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz ... done prepping, now search and capture. 2956s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz 2956s -preparing to extract selected reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz ... done prepping, now search and capture. 2956s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz 2956s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz 2956s -capturing normalized reads from: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz 2957s CMD: touch /tmp/autopkgtest.sYnnix/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 2957s CMD finished (0 seconds) 2957s CMD: touch /tmp/autopkgtest.sYnnix/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 2957s CMD finished (0 seconds) 2957s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 2957s CMD finished (0 seconds) 2957s CMD: ln -sf /tmp/autopkgtest.sYnnix/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 2957s CMD finished (0 seconds) 2957s 2957s 2957s Normalization complete. See outputs: 2957s /tmp/autopkgtest.sYnnix/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 2957s /tmp/autopkgtest.sYnnix/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 2957s 2957s 2957s 2957s touch test 2957s make[1]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization' 2957s Running example in test_DE_analysis... 2957s make[1]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis' 2957s Running example in Candida_example... 2957s make[2]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example' 2957s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir 2957s Got 9 samples, and got: 10 data fields. 2957s 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 2957s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 2957s 2957s $VAR1 = { 2957s 'wt_GSNO_1' => 5, 2957s 'wt_37_2' => 1, 2957s 'wt_ph8_1' => 8, 2957s 'wt_37_3' => 2, 2957s 'wt_37_1' => 3, 2957s 'wt_ph8_2' => 9, 2957s 'wt_GSNO_3' => 4, 2957s 'wt_GSNO_2' => 6, 2957s 'wt_ph8_3' => 7 2957s }; 2957s $VAR1 = { 2957s 'wt_GSNO' => [ 2957s 'wt_GSNO_1', 2957s 'wt_GSNO_2', 2957s 'wt_GSNO_3' 2957s ], 2957s 'wt_ph8' => [ 2957s 'wt_ph8_1', 2957s 'wt_ph8_2', 2957s 'wt_ph8_3' 2957s ], 2957s 'wt_37' => [ 2957s 'wt_37_1', 2957s 'wt_37_2', 2957s 'wt_37_3' 2957s ] 2957s }; 2957s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.EdgeR.Rscript 2957s Contrasts to perform are: $VAR1 = [ 2957s [ 2957s 'wt_37', 2957s 'wt_GSNO' 2957s ], 2957s [ 2957s 'wt_37', 2957s 'wt_ph8' 2957s ], 2957s [ 2957s 'wt_GSNO', 2957s 'wt_ph8' 2957s ] 2957s ]; 2957s Loading required package: edgeR 2957s Loading required package: limma 2958s Using classic mode. 2960s null device 2960s 1 2960s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.EdgeR.Rscript 2960s Loading required package: edgeR 2960s Loading required package: limma 2960s Using classic mode. 2962s null device 2962s 1 2962s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.EdgeR.Rscript 2963s Loading required package: edgeR 2963s Loading required package: limma 2963s Using classic mode. 2965s null device 2965s 1 2965s cd edgeR_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 2965s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \ 2965s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 2965s 2965s 2965s ** Found 2060 features as differentially expressed. 2965s 2965s 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 2965s CMD: Rscript diffExpr.P0.001_C2.matrix.R 2965s Loading required package: BiocGenerics 2965s 2965s Attaching package: ‘BiocGenerics’ 2965s 2965s The following objects are masked from ‘package:stats’: 2965s 2965s IQR, mad, sd, var, xtabs 2965s 2965s The following objects are masked from ‘package:base’: 2965s 2965s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2965s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2965s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2965s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2965s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 2965s table, tapply, union, unique, unsplit, which.max, which.min 2965s 2966s Welcome to Bioconductor 2966s 2966s Vignettes contain introductory material; view with 2966s 'browseVignettes()'. To cite Bioconductor, see 2966s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2966s 2967s 2967s Attaching package: ‘fastcluster’ 2967s 2967s The following object is masked from ‘package:stats’: 2967s 2967s hclust 2967s 2967s [1] "Reading matrix file." 2967s for plotting:: min.raw: -0.642808465476069 max.raw: 1 2967s null device 2967s 1 2969s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 2969s null device 2969s 1 2970s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 2970s 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 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 2970s sampleB_mean: File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2970s 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 2970s num discordant: 0 2970s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 2970s 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 2970s 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 92.10033File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2970s 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 2970s num discordant: 0 2970s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 2970s 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 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 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 2970s 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 2970s num discordant: 0 2970s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 2970s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2970s 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 57.61633 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 2970s 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 2970s num discordant: 0 2970s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 2970s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2970s 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 2970s 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 2970s num discordant: 0 2970s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 2970s 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 2970s 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 4004.8 953.5553 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 2970s num discordant: 0 2970s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2970s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2970s touch test_edgeR 2970s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir 2970s Got 9 samples, and got: 10 data fields. 2970s 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 2970s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 2970s 2970s $VAR1 = { 2970s 'wt_GSNO_2' => 6, 2970s 'wt_ph8_3' => 7, 2970s 'wt_37_1' => 3, 2970s 'wt_GSNO_1' => 5, 2970s 'wt_37_3' => 2, 2970s 'wt_ph8_2' => 9, 2970s 'wt_ph8_1' => 8, 2970s 'wt_37_2' => 1, 2970s 'wt_GSNO_3' => 4 2970s }; 2970s $VAR1 = { 2970s 'wt_GSNO' => [ 2970s 'wt_GSNO_1', 2970s 'wt_GSNO_2', 2970s 'wt_GSNO_3' 2970s ], 2970s 'wt_ph8' => [ 2970s 'wt_ph8_1', 2970s 'wt_ph8_2', 2970s 'wt_ph8_3' 2970s ], 2970s 'wt_37' => [ 2970s 'wt_37_1', 2970s 'wt_37_2', 2970s 'wt_37_3' 2970s ] 2970s }; 2970s Contrasts to perform are: $VAR1 = [ 2970s [ 2970s 'wt_37', 2970s 'wt_GSNO' 2970s ], 2970s [ 2970s 'wt_37', 2970s 'wt_ph8' 2970s ], 2970s [ 2970s 'wt_GSNO', 2970s 'wt_ph8' 2970s ] 2970s ]; 2970s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.Rscript 2970s Loading required package: edgeR 2970s Loading required package: limma 2971s Loading required package: DESeq2 2971s Loading required package: S4Vectors 2971s Loading required package: stats4 2971s Loading required package: BiocGenerics 2971s 2971s Attaching package: ‘BiocGenerics’ 2971s 2971s The following object is masked from ‘package:limma’: 2971s 2971s plotMA 2971s 2971s The following objects are masked from ‘package:stats’: 2971s 2971s IQR, mad, sd, var, xtabs 2971s 2971s The following objects are masked from ‘package:base’: 2971s 2971s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2971s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2971s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2971s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2971s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 2971s table, tapply, union, unique, unsplit, which.max, which.min 2971s 2972s 2972s Attaching package: ‘S4Vectors’ 2972s 2972s The following object is masked from ‘package:utils’: 2972s 2972s findMatches 2972s 2972s The following objects are masked from ‘package:base’: 2972s 2972s expand.grid, I, unname 2972s 2972s Loading required package: IRanges 2972s Loading required package: GenomicRanges 2972s Loading required package: GenomeInfoDb 2973s Loading required package: SummarizedExperiment 2973s Loading required package: MatrixGenerics 2973s Loading required package: matrixStats 2973s 2973s Attaching package: ‘MatrixGenerics’ 2973s 2973s The following objects are masked from ‘package:matrixStats’: 2973s 2973s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2973s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2973s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2973s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2973s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2973s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2973s colWeightedMeans, colWeightedMedians, colWeightedSds, 2973s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2973s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2973s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2973s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2973s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2973s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2973s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2973s rowWeightedSds, rowWeightedVars 2973s 2973s Loading required package: Biobase 2974s Welcome to Bioconductor 2974s 2974s Vignettes contain introductory material; view with 2974s 'browseVignettes()'. To cite Bioconductor, see 2974s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2974s 2974s 2974s Attaching package: ‘Biobase’ 2974s 2974s The following object is masked from ‘package:MatrixGenerics’: 2974s 2974s rowMedians 2974s 2974s The following objects are masked from ‘package:matrixStats’: 2974s 2974s anyMissing, rowMedians 2974s 2978s converting counts to integer mode 2979s estimating size factors 2979s estimating dispersions 2979s gene-wise dispersion estimates 2980s mean-dispersion relationship 2980s final dispersion estimates 2980s fitting model and testing 2983s null device 2983s 1 2983s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.Rscript 2983s Loading required package: edgeR 2983s Loading required package: limma 2984s Loading required package: DESeq2 2984s Loading required package: S4Vectors 2984s Loading required package: stats4 2984s Loading required package: BiocGenerics 2984s 2984s Attaching package: ‘BiocGenerics’ 2984s 2984s The following object is masked from ‘package:limma’: 2984s 2984s plotMA 2984s 2984s The following objects are masked from ‘package:stats’: 2984s 2984s IQR, mad, sd, var, xtabs 2984s 2984s The following objects are masked from ‘package:base’: 2984s 2984s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2984s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2984s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2984s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2984s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 2984s table, tapply, union, unique, unsplit, which.max, which.min 2984s 2984s 2984s Attaching package: ‘S4Vectors’ 2984s 2984s The following object is masked from ‘package:utils’: 2984s 2984s findMatches 2984s 2984s The following objects are masked from ‘package:base’: 2984s 2984s expand.grid, I, unname 2984s 2984s Loading required package: IRanges 2985s Loading required package: GenomicRanges 2985s Loading required package: GenomeInfoDb 2986s Loading required package: SummarizedExperiment 2986s Loading required package: MatrixGenerics 2986s Loading required package: matrixStats 2986s 2986s Attaching package: ‘MatrixGenerics’ 2986s 2986s The following objects are masked from ‘package:matrixStats’: 2986s 2986s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2986s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2986s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2986s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2986s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2986s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2986s colWeightedMeans, colWeightedMedians, colWeightedSds, 2986s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2986s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2986s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2986s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2986s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2986s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2986s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2986s rowWeightedSds, rowWeightedVars 2986s 2986s Loading required package: Biobase 2986s Welcome to Bioconductor 2986s 2986s Vignettes contain introductory material; view with 2986s 'browseVignettes()'. To cite Bioconductor, see 2986s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2986s 2986s 2986s Attaching package: ‘Biobase’ 2986s 2986s The following object is masked from ‘package:MatrixGenerics’: 2986s 2986s rowMedians 2986s 2986s The following objects are masked from ‘package:matrixStats’: 2986s 2986s anyMissing, rowMedians 2986s 2991s converting counts to integer mode 2991s estimating size factors 2991s estimating dispersions 2992s gene-wise dispersion estimates 2992s mean-dispersion relationship 2992s final dispersion estimates 2993s fitting model and testing 2996s null device 2996s 1 2996s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.Rscript 2996s Loading required package: edgeR 2996s Loading required package: limma 2996s Loading required package: DESeq2 2996s Loading required package: S4Vectors 2996s Loading required package: stats4 2996s Loading required package: BiocGenerics 2997s 2997s Attaching package: ‘BiocGenerics’ 2997s 2997s The following object is masked from ‘package:limma’: 2997s 2997s plotMA 2997s 2997s The following objects are masked from ‘package:stats’: 2997s 2997s IQR, mad, sd, var, xtabs 2997s 2997s The following objects are masked from ‘package:base’: 2997s 2997s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2997s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2997s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2997s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2997s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 2997s table, tapply, union, unique, unsplit, which.max, which.min 2997s 2997s 2997s Attaching package: ‘S4Vectors’ 2997s 2997s The following object is masked from ‘package:utils’: 2997s 2997s findMatches 2997s 2997s The following objects are masked from ‘package:base’: 2997s 2997s expand.grid, I, unname 2997s 2997s Loading required package: IRanges 2998s Loading required package: GenomicRanges 2998s Loading required package: GenomeInfoDb 2999s Loading required package: SummarizedExperiment 2999s Loading required package: MatrixGenerics 2999s Loading required package: matrixStats 2999s 2999s Attaching package: ‘MatrixGenerics’ 2999s 2999s The following objects are masked from ‘package:matrixStats’: 2999s 2999s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2999s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2999s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2999s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2999s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2999s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2999s colWeightedMeans, colWeightedMedians, colWeightedSds, 2999s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2999s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2999s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2999s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2999s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2999s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2999s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2999s rowWeightedSds, rowWeightedVars 2999s 2999s Loading required package: Biobase 2999s Welcome to Bioconductor 2999s 2999s Vignettes contain introductory material; view with 2999s 'browseVignettes()'. To cite Bioconductor, see 2999s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2999s 2999s 2999s Attaching package: ‘Biobase’ 2999s 2999s The following object is masked from ‘package:MatrixGenerics’: 2999s 2999s rowMedians 2999s 2999s The following objects are masked from ‘package:matrixStats’: 2999s 2999s anyMissing, rowMedians 2999s 3004s converting counts to integer mode 3005s estimating size factors 3005s estimating dispersions 3005s gene-wise dispersion estimates 3005s mean-dispersion relationship 3006s final dispersion estimates 3006s fitting model and testing 3009s null device 3009s 1 3009s cd DESeq2_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 3009s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \ 3009s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 3010s 3010s 3010s ** Found 1783 features as differentially expressed. 3010s 3010s 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 3010s CMD: Rscript diffExpr.P0.001_C2.matrix.R 3010s Loading required package: BiocGenerics 3010s 3010s Attaching package: ‘BiocGenerics’ 3010s 3010s The following objects are masked from ‘package:stats’: 3010s 3010s IQR, mad, sd, var, xtabs 3010s 3010s The following objects are masked from ‘package:base’: 3010s 3010s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3010s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3010s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3010s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3010s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3010s table, tapply, union, unique, unsplit, which.max, which.min 3010s 3010s Welcome to Bioconductor 3010s 3010s Vignettes contain introductory material; view with 3010s 'browseVignettes()'. To cite Bioconductor, see 3010s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3010s 3011s 3011s Attaching package: ‘fastcluster’ 3011s 3011s The following object is masked from ‘package:stats’: 3011s 3011s hclust 3011s 3011s [1] "Reading matrix file." 3012s for plotting:: min.raw: -0.674993513119273 max.raw: 1 3012s Warning messages: 3012s 1: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV, : 3012s Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram. 3012s 2: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV, : 3012s Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram. 3012s null device 3012s 1 3013s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 3013s null device 3013s 1 3014s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 3014s sampleA_mean: 4954.434 1326.5 1046.9 1833.283 1037.645 1407.266 1371.045 1262.588 11423.35 1681.385 6030.232 1816.62 335.7477 2191.464 20787.35 1013.064 4776.171 5637.134 982.539 470.179 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 168.4167 15.402 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 3014s sampleB_mean: 175.7007 98.97567 27.41467 63.97333 47.461 33.63533 28.87167 9.133333 534.2237 10.849 173.6673 3.202333 21.376 98.61433 336.3973 18.23967 543.417 68.49367 33.35533 10.76867 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 3014s 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 29.664 0.4626667 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 3014s num discordant: 0 3014s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 3014s 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 37.25567 223.9227 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 66.65833 321.257 497.7577 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 1.851 1001.993 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 21.06767 6.250667 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 21.74467 22.93933 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 3014s 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 3014s sampleB_mean: 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 1237.565 498.566 636.1717 1388.008 188.059 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 2983.166 365.304 1573.052 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 59.07767 6554.638 177.7223 111.3283 71.95633 112.4907 205.2823 272.869 62.202 80.658 92.10033 67.32633 136.3853 92.673 92.91767 114.413 578.1793 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 97.74133 143.2053 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 3014s num discordant: 0 3014s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 3014s sampleA_mean: File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 3014s 4954.434 1326.5 12222.46 2602.336 1751.765 1445.705 1046.9 470.179 5495.505 2002.536 637.4673 4784.861 5797.692 15024.4 36600.33 1833.283 1407.266 1371.045 1262.588 982.539 2635.243 1681.385 6030.232 944.0123 1816.62 335.7477 2191.464 20787.35 4191.816 1013.064 4913.275 887.2083 521.84 3549.085 1265.232 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 3014s sampleB_mean: 175.0553 46.38933 644.6073 28.83167 11.541 39.02467 21.734 14.071 10.731 60.698 9.523667 176.7203 190.2367 126.2827 312.258 18.24467 61.93367 20.785 5.897667 38.35033 149.0183 34.85667 71.58533 40.62 3.02 17.87533 67.15133 1576.856 162.736 20.73967 231.01 11.73133 15.272 54.76233 70.315 143.0547 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 1058.536 263.582 585.796 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 3014s num discordant: 0 3014s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 3014s sampleA_mean: 21.39933 88.57 72.55133 7.685 6.167 15.838 15.04567 224.904 40.988 102.2703 96.61333 103.6867 36.11867 31.261 121.0697 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 3014s sampleB_mean: 1524.761 2830.628 1611.849 339.544 266.1853 2001.57 370.6363 3005.897 1440.661 2786.993 1997.885 1889.849 2415.454 809.747 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 241.776 731.863File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 3014s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 3014s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 3014s 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 3014s num discordant: 0 3014s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 3014s sampleA_mean: 1781.496 876.8277 1636.976 4624.974 512.042 12470.43 440.9727 834.608 871.6373 2550.414 1506.715 1101.219 324.8553 768.306 707.8263 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 173.88 189.5647 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 3014s sampleB_mean: 78.223 59.789 131.954 341.9077 41.31433 312.258 21.142 149.042 107.8423 16.70467 165.372 143.015 42.12067 11.541 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 3014s num discordant: 0 3014s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 3014s sampleA_mean: 825.1763 1020.23 311.829 2661.226 28.62567 53.11833 658.8357 110.7323 773.7893 117.2063 534.2237 112.322 77.55333 407.2907 94.08633 210.276 37.23367 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 3014s sampleB_mean: 3756.434 5398.857 2830.628 13329.63 317.4807 339.544 4216.251 1202.982 3709.705 3506.467 4004.8 2786.993 809.747 2355.907 968.2863 2415.454 461.5343 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 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 3014s num discordant: 0 3014s touch test_DESeq2 3014s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir 3014s Got 9 samples, and got: 10 data fields. 3014s 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 3014s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 3014s 3014s $VAR1 = { 3014s 'wt_GSNO_2' => 6, 3014s 'wt_GSNO_1' => 5, 3014s 'wt_37_3' => 2, 3014s 'wt_GSNO_3' => 4, 3014s 'wt_37_1' => 3, 3014s 'wt_ph8_3' => 7, 3014s 'wt_ph8_1' => 8, 3014s 'wt_37_2' => 1, 3014s 'wt_ph8_2' => 9 3014s }; 3014s $VAR1 = { 3014s 'wt_ph8' => [ 3014s 'wt_ph8_1', 3014s 'wt_ph8_2', 3014s 'wt_ph8_3' 3014s ], 3014s 'wt_37' => [ 3014s 'wt_37_1', 3014s 'wt_37_2', 3014s 'wt_37_3' 3014s ], 3014s 'wt_GSNO' => [ 3014s 'wt_GSNO_1', 3014s 'wt_GSNO_2', 3014s 'wt_GSNO_3' 3014s ] 3014s }; 3014s Contrasts to perform are: $VAR1 = [ 3014s [ 3014s 'wt_37', 3014s 'wt_GSNO' 3014s ], 3014s [ 3014s 'wt_37', 3014s 'wt_ph8' 3014s ], 3014s [ 3014s 'wt_GSNO', 3014s 'wt_ph8' 3014s ] 3014s ]; 3014s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.voom.Rscript 3014s Loading required package: limma 3016s null device 3016s 1 3016s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.voom.Rscript 3016s Loading required package: limma 3018s null device 3018s 1 3018s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.voom.Rscript 3018s Loading required package: limma 3020s null device 3020s 1 3020s cd voom_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 3020s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \ 3020s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 3020s 3020s 3020s ** Found 1817 features as differentially expressed. 3020s 3020s 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 3020s CMD: Rscript diffExpr.P0.001_C2.matrix.R 3020s Loading required package: BiocGenerics 3020s 3020s Attaching package: ‘BiocGenerics’ 3020s 3020s The following objects are masked from ‘package:stats’: 3020s 3020s IQR, mad, sd, var, xtabs 3020s 3020s The following objects are masked from ‘package:base’: 3020s 3020s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3020s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3020s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3020s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3020s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3020s table, tapply, union, unique, unsplit, which.max, which.min 3020s 3020s Welcome to Bioconductor 3020s 3020s Vignettes contain introductory material; view with 3020s 'browseVignettes()'. To cite Bioconductor, see 3020s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3020s 3021s 3021s Attaching package: ‘fastcluster’ 3021s 3021s The following object is masked from ‘package:stats’: 3021s 3021s hclust 3021s 3021s [1] "Reading matrix file." 3022s for plotting:: min.raw: -0.680559894057534 max.raw: 1 3022s null device 3022s 1 3023s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 3023s null device 3023s 1 3024s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset 3024s 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 172.4453File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 3024s 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 3024s 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 3024s num discordant: 0 3024s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 3024s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 3024s 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 3024s 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 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 3024s num discordant: 0 3024s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset 3024s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 3024s 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 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 3024s 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 3024s num discordant: 0 3024s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 3024s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 3024s 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 3024s 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 97.3 162.5713 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 3024s num discordant: 0 3024s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 3024s 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 3024s 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 21.17867 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 47.94933File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 3024s 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 3024s num discordant: 0 3024s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 3024s 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 3024s 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 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 35.44867File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 3024s 19.71067 3024s num discordant: 0 3024s touch test_voom 3024s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save 3024s CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R 3025s Loading required package: BiocGenerics 3025s 3025s Attaching package: ‘BiocGenerics’ 3025s 3025s The following objects are masked from ‘package:stats’: 3025s 3025s IQR, mad, sd, var, xtabs 3025s 3025s The following objects are masked from ‘package:base’: 3025s 3025s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3025s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3025s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3025s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3025s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3025s table, tapply, union, unique, unsplit, which.max, which.min 3025s 3025s Welcome to Bioconductor 3025s 3025s Vignettes contain introductory material; view with 3025s 'browseVignettes()'. To cite Bioconductor, see 3025s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3025s 3026s 3026s Attaching package: ‘fastcluster’ 3026s 3026s The following object is masked from ‘package:stats’: 3026s 3026s hclust 3026s 3026s [1] "Reading matrix file." 3026s for plotting:: min.raw: 0.647032826340685 max.raw: 1 3026s null device 3026s 1 3033s for plotting:: min.raw: 0 max.raw: 15.3986319455363 3033s null device 3033s 1 3043s touch test_PtR_heatmap 3043s ./validate_results.pl 3043s DESeq2_outdir/diffExpr.P0.001_C2.matrix, count: 1784 DE features OK. 3043s edgeR_outdir/diffExpr.P0.001_C2.matrix, count: 2061 DE features OK. 3043s make[2]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example' 3043s voom_outdir/diffExpr.P0.001_C2.matrix, count: 1818 DE features OK. 3043s Running example in Spombe_example... 3043s make[2]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example' 3043s /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 3043s Got 4 samples, and got: 5 data fields. 3043s Header: ds_rep1 hs_rep1 log_rep1 plat_rep1 3043s Next: TRINITY_DN5555_c0_g1 0.00 0.00 0.00 0.00 3043s 3043s $VAR1 = { 3043s 'log_rep1' => 3, 3043s 'plat_rep1' => 4, 3043s 'hs_rep1' => 2, 3043s 'ds_rep1' => 1 3043s }; 3043s $VAR1 = { 3043s 'heatshock' => [ 3043s 'hs_rep1' 3043s ], 3043s 'diauxic_shift' => [ 3043s 'ds_rep1' 3043s ], 3043s 'plateau' => [ 3043s 'plat_rep1' 3043s ], 3043s 'log_growth' => [ 3043s 'log_rep1' 3043s ] 3043s }; 3043s Contrasts to perform are: $VAR1 = [ 3043s [ 3043s 'diauxic_shift', 3043s 'heatshock' 3043s ], 3043s [ 3043s 'diauxic_shift', 3043s 'log_growth' 3043s ], 3043s [ 3043s 'diauxic_shift', 3043s 'plateau' 3043s ], 3043s [ 3043s 'heatshock', 3043s 'log_growth' 3043s ], 3043s [ 3043s 'heatshock', 3043s 'plateau' 3043s ], 3043s [ 3043s 'log_growth', 3043s 'plateau' 3043s ] 3043s ]; 3043s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.diauxic_shift.vs.heatshock.EdgeR.Rscript 3043s Loading required package: edgeR 3043s Loading required package: limma 3043s null device 3043s 1 3043s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.diauxic_shift.vs.log_growth.EdgeR.Rscript 3043s Loading required package: edgeR 3043s Loading required package: limma 3044s null device 3044s 1 3044s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.diauxic_shift.vs.plateau.EdgeR.Rscript 3044s Loading required package: edgeR 3044s Loading required package: limma 3044s null device 3044s 1 3044s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_log_growth.heatshock.vs.log_growth.EdgeR.Rscript 3045s Loading required package: edgeR 3045s Loading required package: limma 3045s null device 3045s 1 3045s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_plateau.heatshock.vs.plateau.EdgeR.Rscript 3045s Loading required package: edgeR 3045s Loading required package: limma 3046s null device 3046s 1 3046s CMD: Rscript Trinity_genes.counts.matrix.log_growth_vs_plateau.log_growth.vs.plateau.EdgeR.Rscript 3046s Loading required package: edgeR 3046s Loading required package: limma 3046s null device 3046s 1 3046s cd edgeR_genes && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl -m ../Trinity_genes.TMM.EXPR.matrix \ 3046s -s ../samples.txt --examine_GO_enrichment --GO_annots ../Trinotate_report.xls.gene_ontology --gene_lengths ../Trinity_genes.lengths && \ 3046s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 3046s 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 3047s Loading required package: BiasedUrn 3047s Loading required package: geneLenDataBase 3058s Warning: program compiled against libxml 215 using older 214 3058s 3059s Loading required package: AnnotationDbi 3059s Loading required package: stats4 3059s Loading required package: BiocGenerics 3059s 3059s Attaching package: ‘BiocGenerics’ 3059s 3059s The following objects are masked from ‘package:stats’: 3059s 3059s IQR, mad, sd, var, xtabs 3059s 3059s The following objects are masked from ‘package:base’: 3059s 3059s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3059s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3059s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3059s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3059s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3059s table, tapply, union, unique, unsplit, which.max, which.min 3059s 3059s Loading required package: Biobase 3059s Welcome to Bioconductor 3059s 3059s Vignettes contain introductory material; view with 3059s 'browseVignettes()'. To cite Bioconductor, see 3059s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3059s 3059s Loading required package: IRanges 3059s Loading required package: S4Vectors 3059s 3059s Attaching package: ‘S4Vectors’ 3059s 3059s The following object is masked from ‘package:geneLenDataBase’: 3059s 3059s unfactor 3059s 3059s The following object is masked from ‘package:utils’: 3059s 3059s findMatches 3059s 3059s The following objects are masked from ‘package:base’: 3059s 3059s expand.grid, I, unname 3059s 3061s Processing category: custom_list 3061s Using manually entered categories. 3061s Calculating the p-values... 3062s 'select()' returned 1:1 mapping between keys and columns 3062s 3062s 3062s Done. 3062s 3062s 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 3062s Loading required package: BiasedUrn 3062s Loading required package: geneLenDataBase 3074s Warning: program compiled against libxml 215 using older 214 3074s 3074s Loading required package: AnnotationDbi 3074s Loading required package: stats4 3074s Loading required package: BiocGenerics 3074s 3074s Attaching package: ‘BiocGenerics’ 3074s 3074s The following objects are masked from ‘package:stats’: 3074s 3074s IQR, mad, sd, var, xtabs 3074s 3074s The following objects are masked from ‘package:base’: 3074s 3074s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3074s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3074s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3074s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3074s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3074s table, tapply, union, unique, unsplit, which.max, which.min 3074s 3074s Loading required package: Biobase 3074s Welcome to Bioconductor 3074s 3074s Vignettes contain introductory material; view with 3074s 'browseVignettes()'. To cite Bioconductor, see 3074s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3074s 3074s Loading required package: IRanges 3074s Loading required package: S4Vectors 3074s 3074s Attaching package: ‘S4Vectors’ 3074s 3074s The following object is masked from ‘package:geneLenDataBase’: 3074s 3074s unfactor 3074s 3074s The following object is masked from ‘package:utils’: 3074s 3074s findMatches 3074s 3074s The following objects are masked from ‘package:base’: 3074s 3074s expand.grid, I, unname 3074s 3075s Processing category: custom_list 3075s Using manually entered categories. 3075s Calculating the p-values... 3076s 'select()' returned 1:1 mapping between keys and columns 3076s 3076s 3076s Done. 3076s 3076s 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 3076s Loading required package: BiasedUrn 3076s Loading required package: geneLenDataBase 3087s Warning: program compiled against libxml 215 using older 214 3088s 3088s Loading required package: AnnotationDbi 3088s Loading required package: stats4 3088s Loading required package: BiocGenerics 3088s 3088s Attaching package: ‘BiocGenerics’ 3088s 3088s The following objects are masked from ‘package:stats’: 3088s 3088s IQR, mad, sd, var, xtabs 3088s 3088s The following objects are masked from ‘package:base’: 3088s 3088s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3088s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3088s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3088s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3088s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3088s table, tapply, union, unique, unsplit, which.max, which.min 3088s 3088s Loading required package: Biobase 3088s Welcome to Bioconductor 3088s 3088s Vignettes contain introductory material; view with 3088s 'browseVignettes()'. To cite Bioconductor, see 3088s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3088s 3088s Loading required package: IRanges 3088s Loading required package: S4Vectors 3088s 3088s Attaching package: ‘S4Vectors’ 3088s 3088s The following object is masked from ‘package:geneLenDataBase’: 3088s 3088s unfactor 3088s 3088s The following object is masked from ‘package:utils’: 3088s 3088s findMatches 3088s 3088s The following objects are masked from ‘package:base’: 3088s 3088s expand.grid, I, unname 3088s 3090s Processing category: custom_list 3090s Using manually entered categories. 3090s Calculating the p-values... 3090s 'select()' returned 1:1 mapping between keys and columns 3090s 3090s 3090s Done. 3090s 3090s 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 3090s Loading required package: BiasedUrn 3090s Loading required package: geneLenDataBase 3102s Warning: program compiled against libxml 215 using older 214 3102s 3102s Loading required package: AnnotationDbi 3102s Loading required package: stats4 3102s Loading required package: BiocGenerics 3102s 3102s Attaching package: ‘BiocGenerics’ 3102s 3102s The following objects are masked from ‘package:stats’: 3102s 3102s IQR, mad, sd, var, xtabs 3102s 3102s The following objects are masked from ‘package:base’: 3102s 3102s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3102s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3102s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3102s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3102s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3102s table, tapply, union, unique, unsplit, which.max, which.min 3102s 3102s Loading required package: Biobase 3102s Welcome to Bioconductor 3102s 3102s Vignettes contain introductory material; view with 3102s 'browseVignettes()'. To cite Bioconductor, see 3102s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3102s 3102s Loading required package: IRanges 3102s Loading required package: S4Vectors 3102s 3102s Attaching package: ‘S4Vectors’ 3102s 3102s The following object is masked from ‘package:geneLenDataBase’: 3102s 3102s unfactor 3102s 3102s The following object is masked from ‘package:utils’: 3102s 3102s findMatches 3102s 3102s The following objects are masked from ‘package:base’: 3102s 3102s expand.grid, I, unname 3102s 3104s Processing category: custom_list 3104s Using manually entered categories. 3104s Calculating the p-values... 3104s 'select()' returned 1:1 mapping between keys and columns 3104s 3104s 3104s Done. 3104s 3104s 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 3105s Loading required package: BiasedUrn 3105s Loading required package: geneLenDataBase 3116s Warning: program compiled against libxml 215 using older 214 3116s 3116s Loading required package: AnnotationDbi 3116s Loading required package: stats4 3116s Loading required package: BiocGenerics 3116s 3116s Attaching package: ‘BiocGenerics’ 3116s 3116s The following objects are masked from ‘package:stats’: 3116s 3116s IQR, mad, sd, var, xtabs 3116s 3116s The following objects are masked from ‘package:base’: 3116s 3116s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3116s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3116s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3116s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3116s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3116s table, tapply, union, unique, unsplit, which.max, which.min 3116s 3116s Loading required package: Biobase 3116s Welcome to Bioconductor 3116s 3116s Vignettes contain introductory material; view with 3116s 'browseVignettes()'. To cite Bioconductor, see 3116s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3116s 3116s Loading required package: IRanges 3116s Loading required package: S4Vectors 3116s 3116s Attaching package: ‘S4Vectors’ 3116s 3116s The following object is masked from ‘package:geneLenDataBase’: 3116s 3116s unfactor 3116s 3116s The following object is masked from ‘package:utils’: 3116s 3116s findMatches 3116s 3116s The following objects are masked from ‘package:base’: 3116s 3116s expand.grid, I, unname 3116s 3121s Warning message: 3121s In pcls(G) : initial point very close to some inequality constraints 3121s Processing category: custom_list 3121s Using manually entered categories. 3121s Calculating the p-values... 3122s 'select()' returned 1:1 mapping between keys and columns 3123s 3123s 3123s Done. 3123s 3123s 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 3124s Loading required package: BiasedUrn 3124s Loading required package: geneLenDataBase 3135s Warning: program compiled against libxml 215 using older 214 3135s 3135s Loading required package: AnnotationDbi 3135s Loading required package: stats4 3135s Loading required package: BiocGenerics 3135s 3135s Attaching package: ‘BiocGenerics’ 3135s 3135s The following objects are masked from ‘package:stats’: 3135s 3135s IQR, mad, sd, var, xtabs 3135s 3135s The following objects are masked from ‘package:base’: 3135s 3135s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3135s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3135s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3135s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3135s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3135s table, tapply, union, unique, unsplit, which.max, which.min 3135s 3135s Loading required package: Biobase 3135s Welcome to Bioconductor 3135s 3135s Vignettes contain introductory material; view with 3135s 'browseVignettes()'. To cite Bioconductor, see 3135s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3135s 3135s Loading required package: IRanges 3135s Loading required package: S4Vectors 3135s 3135s Attaching package: ‘S4Vectors’ 3135s 3135s The following object is masked from ‘package:geneLenDataBase’: 3135s 3135s unfactor 3135s 3135s The following object is masked from ‘package:utils’: 3135s 3135s findMatches 3135s 3135s The following objects are masked from ‘package:base’: 3135s 3135s expand.grid, I, unname 3135s 3140s Processing category: custom_list 3140s Using manually entered categories. 3140s Calculating the p-values... 3141s 'select()' returned 1:1 mapping between keys and columns 3142s 3142s 3142s Done. 3142s 3142s 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 3142s Loading required package: BiasedUrn 3142s Loading required package: geneLenDataBase 3153s Warning: program compiled against libxml 215 using older 214 3153s 3153s Loading required package: AnnotationDbi 3153s Loading required package: stats4 3153s Loading required package: BiocGenerics 3153s 3153s Attaching package: ‘BiocGenerics’ 3153s 3153s The following objects are masked from ‘package:stats’: 3153s 3153s IQR, mad, sd, var, xtabs 3153s 3153s The following objects are masked from ‘package:base’: 3153s 3153s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3153s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3153s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3153s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3153s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3153s table, tapply, union, unique, unsplit, which.max, which.min 3153s 3153s Loading required package: Biobase 3153s Welcome to Bioconductor 3153s 3153s Vignettes contain introductory material; view with 3153s 'browseVignettes()'. To cite Bioconductor, see 3153s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3153s 3153s Loading required package: IRanges 3153s Loading required package: S4Vectors 3153s 3153s Attaching package: ‘S4Vectors’ 3153s 3153s The following object is masked from ‘package:geneLenDataBase’: 3153s 3153s unfactor 3153s 3153s The following object is masked from ‘package:utils’: 3153s 3153s findMatches 3153s 3153s The following objects are masked from ‘package:base’: 3153s 3153s expand.grid, I, unname 3153s 3157s Warning message: 3157s In pcls(G) : initial point very close to some inequality constraints 3158s Processing category: custom_list 3158s Using manually entered categories. 3158s Calculating the p-values... 3159s 'select()' returned 1:1 mapping between keys and columns 3160s 3160s 3160s Done. 3160s 3160s 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 3160s Loading required package: BiasedUrn 3160s Loading required package: geneLenDataBase 3171s Warning: program compiled against libxml 215 using older 214 3172s 3172s Loading required package: AnnotationDbi 3172s Loading required package: stats4 3172s Loading required package: BiocGenerics 3172s 3172s Attaching package: ‘BiocGenerics’ 3172s 3172s The following objects are masked from ‘package:stats’: 3172s 3172s IQR, mad, sd, var, xtabs 3172s 3172s The following objects are masked from ‘package:base’: 3172s 3172s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3172s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3172s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3172s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3172s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3172s table, tapply, union, unique, unsplit, which.max, which.min 3172s 3172s Loading required package: Biobase 3172s Welcome to Bioconductor 3172s 3172s Vignettes contain introductory material; view with 3172s 'browseVignettes()'. To cite Bioconductor, see 3172s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3172s 3172s Loading required package: IRanges 3172s Loading required package: S4Vectors 3172s 3172s Attaching package: ‘S4Vectors’ 3172s 3172s The following object is masked from ‘package:geneLenDataBase’: 3172s 3172s unfactor 3172s 3172s The following object is masked from ‘package:utils’: 3172s 3172s findMatches 3172s 3172s The following objects are masked from ‘package:base’: 3172s 3172s expand.grid, I, unname 3172s 3174s Warning message: 3174s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : 3174s Iteration limit reached without full convergence - check carefully 3174s Processing category: custom_list 3174s Using manually entered categories. 3174s Calculating the p-values... 3174s 'select()' returned 1:1 mapping between keys and columns 3174s 3174s 3174s Done. 3174s 3174s 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 3175s Loading required package: BiasedUrn 3175s Loading required package: geneLenDataBase 3186s Warning: program compiled against libxml 215 using older 214 3186s 3186s Loading required package: AnnotationDbi 3186s Loading required package: stats4 3186s Loading required package: BiocGenerics 3186s 3186s Attaching package: ‘BiocGenerics’ 3186s 3186s The following objects are masked from ‘package:stats’: 3186s 3186s IQR, mad, sd, var, xtabs 3186s 3186s The following objects are masked from ‘package:base’: 3186s 3186s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3186s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3186s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3186s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3186s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3186s table, tapply, union, unique, unsplit, which.max, which.min 3186s 3186s Loading required package: Biobase 3186s Welcome to Bioconductor 3186s 3186s Vignettes contain introductory material; view with 3186s 'browseVignettes()'. To cite Bioconductor, see 3186s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3186s 3186s Loading required package: IRanges 3186s Loading required package: S4Vectors 3186s 3186s Attaching package: ‘S4Vectors’ 3186s 3186s The following object is masked from ‘package:geneLenDataBase’: 3186s 3186s unfactor 3186s 3186s The following object is masked from ‘package:utils’: 3186s 3186s findMatches 3186s 3186s The following objects are masked from ‘package:base’: 3186s 3186s expand.grid, I, unname 3186s 3189s Warning message: 3189s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : 3189s Iteration limit reached without full convergence - check carefully 3189s Processing category: custom_list 3189s Using manually entered categories. 3189s Calculating the p-values... 3189s 'select()' returned 1:1 mapping between keys and columns 3189s 3189s 3189s Done. 3189s 3189s 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 3189s Loading required package: BiasedUrn 3189s Loading required package: geneLenDataBase 3200s Warning: program compiled against libxml 215 using older 214 3200s 3200s Loading required package: AnnotationDbi 3200s Loading required package: stats4 3200s Loading required package: BiocGenerics 3200s 3200s Attaching package: ‘BiocGenerics’ 3200s 3200s The following objects are masked from ‘package:stats’: 3200s 3200s IQR, mad, sd, var, xtabs 3200s 3200s The following objects are masked from ‘package:base’: 3200s 3200s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3200s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3200s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3200s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3200s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3200s table, tapply, union, unique, unsplit, which.max, which.min 3200s 3200s Loading required package: Biobase 3200s Welcome to Bioconductor 3200s 3200s Vignettes contain introductory material; view with 3200s 'browseVignettes()'. To cite Bioconductor, see 3200s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3200s 3200s Loading required package: IRanges 3200s Loading required package: S4Vectors 3200s 3200s Attaching package: ‘S4Vectors’ 3200s 3200s The following object is masked from ‘package:geneLenDataBase’: 3200s 3200s unfactor 3200s 3200s The following object is masked from ‘package:utils’: 3200s 3200s findMatches 3200s 3200s The following objects are masked from ‘package:base’: 3200s 3200s expand.grid, I, unname 3200s 3202s Processing category: custom_list 3202s Using manually entered categories. 3202s Calculating the p-values... 3202s 'select()' returned 1:1 mapping between keys and columns 3202s 3202s 3202s Done. 3202s 3202s 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 3203s Loading required package: BiasedUrn 3203s Loading required package: geneLenDataBase 3213s Warning: program compiled against libxml 215 using older 214 3214s 3214s Loading required package: AnnotationDbi 3214s Loading required package: stats4 3214s Loading required package: BiocGenerics 3214s 3214s Attaching package: ‘BiocGenerics’ 3214s 3214s The following objects are masked from ‘package:stats’: 3214s 3214s IQR, mad, sd, var, xtabs 3214s 3214s The following objects are masked from ‘package:base’: 3214s 3214s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3214s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3214s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3214s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3214s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3214s table, tapply, union, unique, unsplit, which.max, which.min 3214s 3214s Loading required package: Biobase 3214s Welcome to Bioconductor 3214s 3214s Vignettes contain introductory material; view with 3214s 'browseVignettes()'. To cite Bioconductor, see 3214s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3214s 3214s Loading required package: IRanges 3214s Loading required package: S4Vectors 3214s 3214s Attaching package: ‘S4Vectors’ 3214s 3214s The following object is masked from ‘package:geneLenDataBase’: 3214s 3214s unfactor 3214s 3214s The following object is masked from ‘package:utils’: 3214s 3214s findMatches 3214s 3214s The following objects are masked from ‘package:base’: 3214s 3214s expand.grid, I, unname 3214s 3216s Processing category: custom_list 3216s Using manually entered categories. 3216s Calculating the p-values... 3216s 'select()' returned 1:1 mapping between keys and columns 3216s 3216s 3216s Done. 3216s 3216s 3216s 3216s ** Found 25 features as differentially expressed. 3216s 3216s 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 3216s CMD: Rscript diffExpr.P0.001_C2.matrix.R 3216s Loading required package: BiocGenerics 3216s 3216s Attaching package: ‘BiocGenerics’ 3216s 3216s The following objects are masked from ‘package:stats’: 3216s 3216s IQR, mad, sd, var, xtabs 3216s 3216s The following objects are masked from ‘package:base’: 3216s 3216s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3216s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3216s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3216s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3216s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 3216s table, tapply, union, unique, unsplit, which.max, which.min 3216s 3217s Welcome to Bioconductor 3217s 3217s Vignettes contain introductory material; view with 3217s 'browseVignettes()'. To cite Bioconductor, see 3217s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3217s 3217s 3217s Attaching package: ‘fastcluster’ 3217s 3217s The following object is masked from ‘package:stats’: 3217s 3217s hclust 3217s 3217s [1] "Reading matrix file." 3218s for plotting:: min.raw: -0.790731955608766 max.raw: 1 3218s null device 3218s 1 3218s for plotting:: min.raw: -9.76652141391246 max.raw: 9.76652141391246 3218s null device 3218s 1 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3218s sampleA_mean: 351.239 3218s sampleB_mean: 10243.92 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3218s sampleA_mean: 24474.99 3218s sampleB_mean: 655.981 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3218s validating: Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3218s 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 3218s 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 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3218s sampleA_mean: 2036.649 135.207 3218s sampleB_mean: 11080.21 1620.935 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3218s sampleA_mean: 7754.294 3218s sampleB_mean: 252.38 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3218s validating: File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3218s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3218s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3218s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3218s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3218s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3218s no DE entries reported here. 3218s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3218s Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3218s sampleA_mean: 9466.084 3218s sampleB_mean: 470.915 3218s num discordant: 0 3218s validating: Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3218s edgeR_genes/diffExpr.P0.001_C2.matrix, count: 26 DE features OK. 3218s 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. 3218s 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. 3218s ./validate_results.pl 3218s touch test 3218s make[2]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example' 3218s make[1]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis' 3218s Running example in test_align_and_estimate_abundance... 3218s make[1]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance' 3218s Running example in PAIRED_END_ABUNDANCE_ESTIMATION... 3218s make[2]: Entering directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION' 3218s ../align_and_estimate_tester.pl RSEM "samples.txt" "../../test_DATA/Trinity.fasta" 3218s CMD: ln -sf ../../test_DATA/Trinity.fasta . 3219s CMD: /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference --left /tmp/autopkgtest.sYnnix/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.sYnnix/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 3219s CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta > /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map 3219s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.started 3219s CMD: bowtie2-build /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 3219s Settings: 3219s Output files: "/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.*.bt2" 3219s Building a SMALL index 3219s Line rate: 6 (line is 64 bytes) 3219s Lines per side: 1 (side is 64 bytes) 3219s Offset rate: 4 (one in 16) 3219s FTable chars: 10 3219s Strings: unpacked 3219s Max bucket size: default 3219s Max bucket size, sqrt multiplier: default 3219s Max bucket size, len divisor: 4 3219s Difference-cover sample period: 1024 3219s Endianness: little 3219s Actual local endianness: little 3219s Sanity checking: disabled 3219s Assertions: disabled 3219s Random seed: 0 3219s Sizeofs: void*:8, int:4, long:8, size_t:8 3219s Input files DNA, FASTA: 3219s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta 3219s Reading reference sizes 3219s Time reading reference sizes: 00:00:00 3219s Calculating joined length 3219s Writing header 3219s Reserving space for joined string 3219s Joining reference sequences 3219s Time to join reference sequences: 00:00:00 3219s bmax according to bmaxDivN setting: 54360 3219s Using parameters --bmax 40770 --dcv 1024 3219s Doing ahead-of-time memory usage test 3219s Passed! Constructing with these parameters: --bmax 40770 --dcv 1024 3219s Constructing suffix-array element generator 3219s Building DifferenceCoverSample 3219s Building sPrime 3219s Building sPrimeOrder 3219s V-Sorting samples 3219s V-Sorting samples time: 00:00:00 3219s Allocating rank array 3219s Ranking v-sort output 3219s Ranking v-sort output time: 00:00:00 3219s Invoking Larsson-Sadakane on ranks 3219s Invoking Larsson-Sadakane on ranks time: 00:00:00 3219s Sanity-checking and returning 3219s Building samples 3219s Reserving space for 12 sample suffixes 3219s Generating random suffixes 3219s QSorting 12 sample offsets, eliminating duplicates 3219s QSorting sample offsets, eliminating duplicates time: 00:00:00 3219s Multikey QSorting 12 samples 3219s (Using difference cover) 3219s Multikey QSorting samples time: 00:00:00 3219s Calculating bucket sizes 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Split 2, merged 6; iterating... 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Split 1, merged 2; iterating... 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Split 1, merged 0; iterating... 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Avg bucket size: 27179.5 (target: 40769) 3219s Converting suffix-array elements to index image 3219s Allocating ftab, absorbFtab 3219s Entering Ebwt loop 3219s Getting block 1 of 8 3219s Reserving size (40770) for bucket 1 3219s Calculating Z arrays for bucket 1 3219s Entering block accumulator loop for bucket 1: 3219s bucket 1: 10% 3219s bucket 1: 20% 3219s bucket 1: 30% 3219s bucket 1: 40% 3219s bucket 1: 50% 3219s bucket 1: 60% 3219s bucket 1: 70% 3219s bucket 1: 80% 3219s bucket 1: 90% 3219s bucket 1: 100% 3219s Sorting block of length 34231 for bucket 1 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 34232 for bucket 1 3219s Getting block 2 of 8 3219s Reserving size (40770) for bucket 2 3219s Calculating Z arrays for bucket 2 3219s Entering block accumulator loop for bucket 2: 3219s bucket 2: 10% 3219s bucket 2: 20% 3219s bucket 2: 30% 3219s bucket 2: 40% 3219s bucket 2: 50% 3219s bucket 2: 60% 3219s bucket 2: 70% 3219s bucket 2: 80% 3219s bucket 2: 90% 3219s bucket 2: 100% 3219s Sorting block of length 39793 for bucket 2 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 39794 for bucket 2 3219s Getting block 3 of 8 3219s Reserving size (40770) for bucket 3 3219s Calculating Z arrays for bucket 3 3219s Entering block accumulator loop for bucket 3: 3219s bucket 3: 10% 3219s bucket 3: 20% 3219s bucket 3: 30% 3219s bucket 3: 40% 3219s bucket 3: 50% 3219s bucket 3: 60% 3219s bucket 3: 70% 3219s bucket 3: 80% 3219s bucket 3: 90% 3219s bucket 3: 100% 3219s Sorting block of length 9793 for bucket 3 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 9794 for bucket 3 3219s Getting block 4 of 8 3219s Reserving size (40770) for bucket 4 3219s Calculating Z arrays for bucket 4 3219s Entering block accumulator loop for bucket 4: 3219s bucket 4: 10% 3219s bucket 4: 20% 3219s bucket 4: 30% 3219s bucket 4: 40% 3219s bucket 4: 50% 3219s bucket 4: 60% 3219s bucket 4: 70% 3219s bucket 4: 80% 3219s bucket 4: 90% 3219s bucket 4: 100% 3219s Sorting block of length 31901 for bucket 4 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 31902 for bucket 4 3219s Getting block 5 of 8 3219s Reserving size (40770) for bucket 5 3219s Calculating Z arrays for bucket 5 3219s Entering block accumulator loop for bucket 5: 3219s bucket 5: 10% 3219s bucket 5: 20% 3219s bucket 5: 30% 3219s bucket 5: 40% 3219s bucket 5: 50% 3219s bucket 5: 60% 3219s bucket 5: 70% 3219s bucket 5: 80% 3219s bucket 5: 90% 3219s bucket 5: 100% 3219s Sorting block of length 10600 for bucket 5 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 10601 for bucket 5 3219s Getting block 6 of 8 3219s Reserving size (40770) for bucket 6 3219s Calculating Z arrays for bucket 6 3219s Entering block accumulator loop for bucket 6: 3219s bucket 6: 10% 3219s bucket 6: 20% 3219s bucket 6: 30% 3219s bucket 6: 40% 3219s bucket 6: 50% 3219s bucket 6: 60% 3219s bucket 6: 70% 3219s bucket 6: 80% 3219s bucket 6: 90% 3219s bucket 6: 100% 3219s Sorting block of length 40652 for bucket 6 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 40653 for bucket 6 3219s Getting block 7 of 8 3219s Reserving size (40770) for bucket 7 3219s Calculating Z arrays for bucket 7 3219s Entering block accumulator loop for bucket 7: 3219s bucket 7: 10% 3219s bucket 7: 20% 3219s bucket 7: 30% 3219s bucket 7: 40% 3219s bucket 7: 50% 3219s bucket 7: 60% 3219s bucket 7: 70% 3219s bucket 7: 80% 3219s bucket 7: 90% 3219s bucket 7: 100% 3219s Sorting block of length 18337 for bucket 7 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 18338 for bucket 7 3219s Getting block 8 of 8 3219s Reserving size (40770) for bucket 8 3219s Calculating Z arrays for bucket 8 3219s Entering block accumulator loop for bucket 8: 3219s bucket 8: 10% 3219s bucket 8: 20% 3219s bucket 8: 30% 3219s bucket 8: 40% 3219s bucket 8: 50% 3219s bucket 8: 60% 3219s bucket 8: 70% 3219s bucket 8: 80% 3219s bucket 8: 90% 3219s bucket 8: 100% 3219s Sorting block of length 32129 for bucket 8 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 32130 for bucket 8 3219s Exited Ebwt loop 3219s fchr[A]: 0 3219s fchr[C]: 59864 3219s fchr[G]: 108205 3219s fchr[T]: 157829 3219s fchr[$]: 217443 3219s Exiting Ebwt::buildToDisk() 3219s Returning from initFromVector 3219s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp 3219s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp 3219s Re-opening _in1 and _in2 as input streams 3219s Returning from Ebwt constructor 3219s Headers: 3219s len: 217443 3219s bwtLen: 217444 3219s sz: 54361 3219s bwtSz: 54361 3219s lineRate: 6 3219s offRate: 4 3219s offMask: 0xfffffff0 3219s ftabChars: 10 3219s eftabLen: 20 3219s eftabSz: 80 3219s ftabLen: 1048577 3219s ftabSz: 4194308 3219s offsLen: 13591 3219s offsSz: 54364 3219s lineSz: 64 3219s sideSz: 64 3219s sideBwtSz: 48 3219s sideBwtLen: 192 3219s numSides: 1133 3219s numLines: 1133 3219s ebwtTotLen: 72512 3219s ebwtTotSz: 72512 3219s color: 0 3219s reverse: 0 3219s Total time for call to driver() for forward index: 00:00:00 3219s Reading reference sizes 3219s Time reading reference sizes: 00:00:00 3219s Calculating joined length 3219s Writing header 3219s Reserving space for joined string 3219s Joining reference sequences 3219s Time to join reference sequences: 00:00:00 3219s Time to reverse reference sequence: 00:00:00 3219s bmax according to bmaxDivN setting: 54360 3219s Using parameters --bmax 40770 --dcv 1024 3219s Doing ahead-of-time memory usage test 3219s Passed! Constructing with these parameters: --bmax 40770 --dcv 1024 3219s Constructing suffix-array element generator 3219s Building DifferenceCoverSample 3219s Building sPrime 3219s Building sPrimeOrder 3219s V-Sorting samples 3219s V-Sorting samples time: 00:00:00 3219s Allocating rank array 3219s Ranking v-sort output 3219s Ranking v-sort output time: 00:00:00 3219s Invoking Larsson-Sadakane on ranks 3219s Invoking Larsson-Sadakane on ranks time: 00:00:00 3219s Sanity-checking and returning 3219s Building samples 3219s Reserving space for 12 sample suffixes 3219s Generating random suffixes 3219s QSorting 12 sample offsets, eliminating duplicates 3219s QSorting sample offsets, eliminating duplicates time: 00:00:00 3219s Multikey QSorting 12 samples 3219s (Using difference cover) 3219s Multikey QSorting samples time: 00:00:00 3219s Calculating bucket sizes 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Split 1, merged 6; iterating... 3219s Splitting and merging 3219s Splitting and merging time: 00:00:00 3219s Avg bucket size: 31062.4 (target: 40769) 3219s Converting suffix-array elements to index image 3219s Allocating ftab, absorbFtab 3219s Entering Ebwt loop 3219s Getting block 1 of 7 3219s Reserving size (40770) for bucket 1 3219s Calculating Z arrays for bucket 1 3219s Entering block accumulator loop for bucket 1: 3219s bucket 1: 10% 3219s bucket 1: 20% 3219s bucket 1: 30% 3219s bucket 1: 40% 3219s bucket 1: 50% 3219s bucket 1: 60% 3219s bucket 1: 70% 3219s bucket 1: 80% 3219s bucket 1: 90% 3219s bucket 1: 100% 3219s Sorting block of length 37058 for bucket 1 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 37059 for bucket 1 3219s Getting block 2 of 7 3219s Reserving size (40770) for bucket 2 3219s Calculating Z arrays for bucket 2 3219s Entering block accumulator loop for bucket 2: 3219s bucket 2: 10% 3219s bucket 2: 20% 3219s bucket 2: 30% 3219s bucket 2: 40% 3219s bucket 2: 50% 3219s bucket 2: 60% 3219s bucket 2: 70% 3219s bucket 2: 80% 3219s bucket 2: 90% 3219s bucket 2: 100% 3219s Sorting block of length 17846 for bucket 2 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 17847 for bucket 2 3219s Getting block 3 of 7 3219s Reserving size (40770) for bucket 3 3219s Calculating Z arrays for bucket 3 3219s Entering block accumulator loop for bucket 3: 3219s bucket 3: 10% 3219s bucket 3: 20% 3219s bucket 3: 30% 3219s bucket 3: 40% 3219s bucket 3: 50% 3219s bucket 3: 60% 3219s bucket 3: 70% 3219s bucket 3: 80% 3219s bucket 3: 90% 3219s bucket 3: 100% 3219s Sorting block of length 39327 for bucket 3 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 39328 for bucket 3 3219s Getting block 4 of 7 3219s Reserving size (40770) for bucket 4 3219s Calculating Z arrays for bucket 4 3219s Entering block accumulator loop for bucket 4: 3219s bucket 4: 10% 3219s bucket 4: 20% 3219s bucket 4: 30% 3219s bucket 4: 40% 3219s bucket 4: 50% 3219s bucket 4: 60% 3219s bucket 4: 70% 3219s bucket 4: 80% 3219s bucket 4: 90% 3219s bucket 4: 100% 3219s Sorting block of length 34139 for bucket 4 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 34140 for bucket 4 3219s Getting block 5 of 7 3219s Reserving size (40770) for bucket 5 3219s Calculating Z arrays for bucket 5 3219s Entering block accumulator loop for bucket 5: 3219s bucket 5: 10% 3219s bucket 5: 20% 3219s bucket 5: 30% 3219s bucket 5: 40% 3219s bucket 5: 50% 3219s bucket 5: 60% 3219s bucket 5: 70% 3219s bucket 5: 80% 3219s bucket 5: 90% 3219s bucket 5: 100% 3219s Sorting block of length 31038 for bucket 5 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 31039 for bucket 5 3219s Getting block 6 of 7 3219s Reserving size (40770) for bucket 6 3219s Calculating Z arrays for bucket 6 3219s Entering block accumulator loop for bucket 6: 3219s bucket 6: 10% 3219s bucket 6: 20% 3219s bucket 6: 30% 3219s bucket 6: 40% 3219s bucket 6: 50% 3219s bucket 6: 60% 3219s bucket 6: 70% 3219s bucket 6: 80% 3219s bucket 6: 90% 3219s bucket 6: 100% 3219s Sorting block of length 21215 for bucket 6 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 21216 for bucket 6 3219s Getting block 7 of 7 3219s Reserving size (40770) for bucket 7 3219s Calculating Z arrays for bucket 7 3219s Entering block accumulator loop for bucket 7: 3219s bucket 7: 10% 3219s bucket 7: 20% 3219s bucket 7: 30% 3219s bucket 7: 40% 3219s bucket 7: 50% 3219s bucket 7: 60% 3219s bucket 7: 70% 3219s bucket 7: 80% 3219s bucket 7: 90% 3219s bucket 7: 100% 3219s Sorting block of length 36814 for bucket 7 3219s (Using difference cover) 3219s Sorting block time: 00:00:00 3219s Returning block of 36815 for bucket 7 3219s Exited Ebwt loop 3219s fchr[A]: 0 3219s fchr[C]: 59864 3219s fchr[G]: 108205 3219s fchr[T]: 157829 3219s fchr[$]: 217443 3219s Exiting Ebwt::buildToDisk() 3219s Returning from initFromVector 3219s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp 3219s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp 3219s Re-opening _in1 and _in2 as input streams 3219s Returning from Ebwt constructor 3219s Headers: 3219s len: 217443 3219s bwtLen: 217444 3219s sz: 54361 3219s bwtSz: 54361 3219s lineRate: 6 3219s offRate: 4 3219s offMask: 0xfffffff0 3219s ftabChars: 10 3219s eftabLen: 20 3219s eftabSz: 80 3219s ftabLen: 1048577 3219s ftabSz: 4194308 3219s offsLen: 13591 3219s offsSz: 54364 3219s lineSz: 64 3219s sideSz: 64 3219s sideBwtSz: 48 3219s sideBwtLen: 192 3219s numSides: 1133 3219s numLines: 1133 3219s ebwtTotLen: 72512 3219s ebwtTotSz: 72512 3219s color: 0 3219s reverse: 1 3219s Total time for backward call to driver() for mirror index: 00:00:00 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2 3219s Renaming /tmp/autopkgtest.sYnnix/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.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2 3219s CMD: touch /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.rsem.prepped.started 3219s CMD: rsem-prepare-reference --transcript-to-gene-map /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 3219s rsem-synthesis-reference-transcripts /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 0 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta 3219s Transcript Information File is generated! 3219s Group File is generated! 3219s Extracted Sequences File is generated! 3219s 3219s rsem-preref /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.transcripts.fa 1 /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 3219s Refs.makeRefs finished! 3219s Refs.saveRefs finished! 3219s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.idx.fa is generated! 3219s /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.n2g.idx.fa is generated! 3219s 3219s $VAR1 = [ 3219s { 3219s 'output_dir' => 'RSEM-heatshock', 3219s 'left' => '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz', 3219s 'right' => '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz' 3219s } 3219s ]; 3219s CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200 -q -X 800 -x /tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 -1 /tmp/autopkgtest.sYnnix/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.sYnnix/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 3221s 10000 reads; of these: 3221s 10000 (100.00%) were paired; of these: 3221s 7088 (70.88%) aligned concordantly 0 times 3221s 1764 (17.64%) aligned concordantly exactly 1 time 3221s 1148 (11.48%) aligned concordantly >1 times 3221s 29.12% overall alignment rate 3221s [bam_sort_core] merging from 0 files and 4 in-memory blocks... 3221s CMD: touch bowtie2.bam.ok 3221s CMD: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem 3221s samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam 3221s samtools sort: couldn't allocate memory for bam_mem 3221s "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! 3221s 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. 3221s Error, cmd: 3221s /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference --left /tmp/autopkgtest.sYnnix/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.sYnnix/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 3221s died with ret (512) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19. 3221s Process_cmd::process_cmd("/usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl -"...) called at ../align_and_estimate_tester.pl line 98 3221s make[2]: *** [Makefile:25: test_RSEM] Error 2 3221s make[1]: *** [Makefile:8: test] Error 2 3221s make: *** [Makefile:18: test] Error 2 3221s make[2]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION' 3221s make[1]: Leaving directory '/tmp/autopkgtest.sYnnix/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance' 3221s autopkgtest [20:57:46]: test run-tests: -----------------------] 3222s autopkgtest [20:57:47]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 3222s run-tests FAIL non-zero exit status 2 3223s autopkgtest [20:57:48]: @@@@@@@@@@@@@@@@@@@@ summary 3223s run-tests FAIL non-zero exit status 2