0s autopkgtest [22:44:59]: starting date and time: 2025-03-15 22:44:59+0000 0s autopkgtest [22:44:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:44:59]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4gomyo24/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-26.secgroup --name adt-plucky-amd64-ray-20250315-224459-juju-7f2275-prod-proposed-migration-environment-20-7f7b7129-01c2-4f0f-989f-65b86985ed3a --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [22:45:48]: testbed dpkg architecture: amd64 50s autopkgtest [22:45:48]: testbed apt version: 2.9.31ubuntu1 50s autopkgtest [22:45:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [22:45:49]: testbed release detected to be: None 50s autopkgtest [22:45:49]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 51s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 51s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 51s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 51s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 52s Fetched 1265 kB in 1s (1398 kB/s) 53s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s Calculating upgrade... 54s The following package was automatically installed and is no longer required: 54s libnl-genl-3-200 54s Use 'sudo apt autoremove' to remove it. 54s The following NEW packages will be installed: 54s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 54s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 54s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 54s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 54s The following packages will be upgraded: 54s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 54s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 54s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 54s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 54s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 54s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 54s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 54s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 54s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 54s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 54s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 54s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 54s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 54s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 54s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 54s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 54s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 54s parted pci.ids pciutils pinentry-curses python-apt-common python3 54s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 54s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 54s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 54s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 54s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 54s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 54s xz-utils 54s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 829 MB of archives. 54s After this operation, 325 MB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 55s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 55s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 55s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 55s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 55s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 55s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 55s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 55s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 55s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 55s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 55s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 55s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 55s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 55s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 55s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 56s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 56s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 56s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 56s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 56s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 56s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 56s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 56s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 56s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 56s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 56s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 56s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 56s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 56s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 56s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 56s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 56s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 56s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 56s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 56s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 56s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 56s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 56s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 56s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 56s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 56s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 56s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 56s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 56s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 56s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 56s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 56s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 56s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 56s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 56s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 56s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 56s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 56s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 56s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 56s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 56s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 56s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 56s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 56s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 57s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 57s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 57s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 57s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 57s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 57s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 57s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 57s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 57s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 57s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 57s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 57s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 57s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 57s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 57s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 57s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 57s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 57s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 57s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 57s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 57s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 57s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 57s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 57s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 57s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 57s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 57s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 57s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 57s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 57s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 57s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 57s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 57s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 57s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 57s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 57s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 57s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 58s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 58s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 58s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 58s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 58s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 58s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 58s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 80s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 80s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 80s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 80s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 80s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 80s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 80s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 80s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 82s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 82s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 87s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 87s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 87s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 87s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 87s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 87s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 87s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 87s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 87s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 88s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 88s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 88s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 88s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 88s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 88s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 88s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 88s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 88s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 88s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 88s Preconfiguring packages ... 88s Fetched 829 MB in 34s (24.7 MB/s) 88s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 92s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 92s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 92s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 92s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 92s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 92s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 92s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 92s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 92s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 92s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 92s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 92s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 93s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 93s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 93s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 93s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 93s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ... 93s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ... 93s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 93s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 93s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 93s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 94s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 94s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 94s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 94s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 94s Setting up python3-minimal (3.13.2-2) ... 94s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 94s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 94s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 94s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 94s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 94s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 94s Unpacking media-types (13.0.0) over (12.0.0) ... 94s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 94s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 94s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 94s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 94s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 94s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 94s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 95s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 95s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 95s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 95s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 95s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 95s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 95s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 95s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 95s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 95s Selecting previously unselected package libdebuginfod-common. 95s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 95s Unpacking libdebuginfod-common (0.192-4) ... 95s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 95s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 95s Setting up libsemanage-common (3.7-2.1build1) ... 95s (Reading database ... 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previously unselected package linux-perf. 109s Preparing to unpack .../74-linux-perf_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-perf (6.14.0-10.10) ... 109s Selecting previously unselected package linux-tools-6.14.0-10. 109s Preparing to unpack .../75-linux-tools-6.14.0-10_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-tools-6.14.0-10 (6.14.0-10.10) ... 109s Selecting previously unselected package linux-tools-6.14.0-10-generic. 109s Preparing to unpack .../76-linux-tools-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 109s Preparing to unpack .../77-pinentry-curses_1.3.1-2ubuntu3_amd64.deb ... 109s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 109s Preparing to unpack .../78-python3-lazr.uri_1.0.6-6_all.deb ... 109s Unpacking python3-lazr.uri (1.0.6-6) over (1.0.6-5) ... 109s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 110s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 110s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 110s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 110s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 110s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 110s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 110s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 110s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 110s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 110s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 110s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 110s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 110s Setting up media-types (13.0.0) ... 110s Installing new version of config file /etc/mime.types ... 110s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 110s Setting up ubuntu-kernel-accessories (1.549) ... 110s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 110s Setting up pci.ids (0.0~2025.03.09-1) ... 110s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 110s Setting up apt-utils (2.9.33) ... 110s Setting up libdebuginfod-common (0.192-4) ... 110s Setting up exfatprogs (1.2.8-1) ... 110s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 110s Setting up bpftool (7.6.0+6.14.0-10.10) ... 110s Setting up libestr0:amd64 (0.1.11-2) ... 110s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 110s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 110s Setting up dosfstools (4.2-1.2) ... 110s Setting up rsyslog (8.2412.0-2ubuntu2) ... 110s info: The user `syslog' is already a member of `adm'. 111s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 111s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 111s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 111s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 111s Setting up systemd (257.3-1ubuntu3) ... 111s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 111s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 112s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 112s Setting up libparted2t64:amd64 (3.6-5) ... 112s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 112s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 112s Setting up linux-headers-generic (6.14.0-10.10) ... 112s Setting up libjemalloc2:amd64 (5.3.0-3) ... 112s Setting up locales (2.41-1ubuntu1) ... 112s Installing new version of config file /etc/locale.alias ... 113s Generating locales (this might take a while)... 114s en_US.UTF-8... done 114s Generation complete. 114s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 114s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 114s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 114s Installing new version of config file /etc/apparmor.d/fusermount3 ... 114s Installing new version of config file /etc/apparmor.d/lsusb ... 114s Installing new version of config file /etc/apparmor.d/openvpn ... 115s Reloading AppArmor profiles 117s Setting up libftdi1-2:amd64 (1.5-8build1) ... 117s Setting up libglib2.0-data (2.84.0-1) ... 117s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 117s Setting up libncurses6:amd64 (6.5+20250216-2) ... 117s Setting up strace (6.13+ds-1ubuntu1) ... 117s Setting up xz-utils (5.6.4-1) ... 117s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 118s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 118s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 118s Setting up udev (257.3-1ubuntu3) ... 119s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 121s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 121s Setting up libpci3:amd64 (1:3.13.0-2) ... 121s Setting up whiptail (0.52.24-4ubuntu2) ... 121s Setting up python-apt-common (2.9.9build1) ... 121s Setting up pnp.ids (0.393-3) ... 121s Setting up libnl-3-200:amd64 (3.7.0-1) ... 121s Setting up python3.13-minimal (3.13.2-2) ... 121s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 121s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 121s Setting up libc-dev-bin (2.41-1ubuntu1) ... 121s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 121s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 121s Setting up rsync (3.4.1+ds1-3) ... 122s rsync.service is a disabled or a static unit not running, not starting it. 122s Setting up python3.13-gdbm (3.13.2-2) ... 122s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 122s Setting up systemd-resolved (257.3-1ubuntu3) ... 123s Setting up initramfs-tools-bin (0.146ubuntu1) ... 123s Setting up ncurses-term (6.5+20250216-2) ... 123s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 123s Setting up libpython3.13:amd64 (3.13.2-2) ... 123s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 123s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 123s Setting up systemd-sysv (257.3-1ubuntu3) ... 123s Setting up linux-headers-virtual (6.14.0-10.10) ... 123s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 123s Setting up python3.13 (3.13.2-2) ... 124s Setting up htop (3.4.0-2) ... 124s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 126s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 126s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 126s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 126s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 126s Setting up parted (3.6-5) ... 126s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 126s Setting up python3 (3.13.2-2) ... 126s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 126s Setting up python3-markupsafe (2.1.5-1build4) ... 126s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 128s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 128s Setting up hwdata (0.393-3) ... 128s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 128s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 128s No schema files found: doing nothing. 128s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 128s Setting up linux-perf (6.14.0-10.10) ... 128s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 128s Setting up pciutils (1:3.13.0-2) ... 128s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 128s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 128s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 128s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 129s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 129s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 129s Setting up curl (8.12.1-3ubuntu1) ... 129s Setting up linux-image-virtual (6.14.0-10.10) ... 129s Setting up initramfs-tools-core (0.146ubuntu1) ... 129s Setting up linux-tools-common (6.14.0-10.10) ... 129s Setting up python3-systemd (235-1build6) ... 129s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 129s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 129s Setting up linux-image-generic (6.14.0-10.10) ... 129s Setting up python3-dbus (1.3.2-5build5) ... 129s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 129s Setting up initramfs-tools (0.146ubuntu1) ... 129s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 129s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 129s update-initramfs: deferring update (trigger activated) 129s Setting up linux-generic (6.14.0-10.10) ... 129s Setting up ubuntu-minimal (1.549) ... 129s Setting up python3-apt (2.9.9build1) ... 129s Setting up python3-bcrypt (4.2.0-2.1build1) ... 129s Setting up python3-yaml (6.0.2-1build2) ... 129s Setting up libfwupd3:amd64 (2.0.6-4) ... 129s Setting up python3-lazr.uri (1.0.6-6) ... 129s Setting up binutils (2.44-3ubuntu1) ... 129s Setting up ubuntu-standard (1.549) ... 129s Setting up cloud-init-base (25.1-0ubuntu3) ... 131s Setting up linux-virtual (6.14.0-10.10) ... 131s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 131s Setting up python3-gi (3.50.0-4build1) ... 131s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 131s Setting up fwupd (2.0.6-4) ... 131s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 132s Setting up cloud-init (25.1-0ubuntu3) ... 132s Processing triggers for man-db (2.13.0-1) ... 133s Processing triggers for dbus (1.16.2-1ubuntu1) ... 133s Processing triggers for shared-mime-info (2.4-5) ... 133s Warning: program compiled against libxml 212 using older 209 134s Processing triggers for libc-bin (2.41-1ubuntu1) ... 134s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 134s /etc/kernel/postinst.d/initramfs-tools: 134s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 134s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 144s /etc/kernel/postinst.d/zz-update-grub: 144s Sourcing file `/etc/default/grub' 144s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 144s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 144s Generating grub configuration file ... 144s Found linux image: /boot/vmlinuz-6.14.0-10-generic 144s Found initrd image: /boot/initrd.img-6.14.0-10-generic 144s Found linux image: /boot/vmlinuz-6.12.0-16-generic 144s Found initrd image: /boot/initrd.img-6.12.0-16-generic 144s Found linux image: /boot/vmlinuz-6.11.0-8-generic 144s Found initrd image: /boot/initrd.img-6.11.0-8-generic 145s Warning: os-prober will not be executed to detect other bootable partitions. 145s Systems on them will not be added to the GRUB boot configuration. 145s Check GRUB_DISABLE_OS_PROBER documentation entry. 145s Adding boot menu entry for UEFI Firmware Settings ... 145s done 145s Processing triggers for initramfs-tools (0.146ubuntu1) ... 145s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 145s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Solving dependencies... 156s The following packages will be REMOVED: 156s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 156s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 156s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 156s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 156s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 156s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 156s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 156s linux-tools-6.12.0-16-generic* 156s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 156s After this operation, 545 MB disk space will be freed. 156s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 156s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 156s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 156s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 156s Removing libpython3.12t64:amd64 (3.12.9-1) ... 156s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 156s Removing libnsl2:amd64 (1.3.0-3build3) ... 156s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 156s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 157s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 159s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 159s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 161s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 161s /etc/kernel/postrm.d/initramfs-tools: 161s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 162s /etc/kernel/postrm.d/zz-update-grub: 162s Sourcing file `/etc/default/grub' 162s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 162s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 162s Generating grub configuration file ... 162s Found linux image: /boot/vmlinuz-6.14.0-10-generic 162s Found initrd image: /boot/initrd.img-6.14.0-10-generic 162s Found linux image: /boot/vmlinuz-6.12.0-16-generic 162s Found initrd image: /boot/initrd.img-6.12.0-16-generic 162s Warning: os-prober will not be executed to detect other bootable partitions. 162s Systems on them will not be added to the GRUB boot configuration. 162s Check GRUB_DISABLE_OS_PROBER documentation entry. 162s Adding boot menu entry for UEFI Firmware Settings ... 162s done 162s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 162s W: Removing the running kernel 162s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 162s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 162s /etc/kernel/postrm.d/initramfs-tools: 162s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 162s /etc/kernel/postrm.d/zz-update-grub: 162s Sourcing file `/etc/default/grub' 162s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 162s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 162s Generating grub configuration file ... 163s Found linux image: /boot/vmlinuz-6.14.0-10-generic 163s Found initrd image: /boot/initrd.img-6.14.0-10-generic 163s Warning: os-prober will not be executed to detect other bootable partitions. 163s Systems on them will not be added to the GRUB boot configuration. 163s Check GRUB_DISABLE_OS_PROBER documentation entry. 163s Adding boot menu entry for UEFI Firmware Settings ... 163s done 163s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 163s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 165s Processing triggers for libc-bin (2.41-1ubuntu1) ... 165s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76972 files and directories currently installed.) 165s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 165s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 165s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 165s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 165s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 165s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 165s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 165s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 165s autopkgtest [22:47:44]: upgrading testbed (apt dist-upgrade and autopurge) 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 166s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s Entering ResolveByKeep 166s 166s Calculating upgrade... 166s The following packages will be upgraded: 166s libc-bin libc-dev-bin libc6 libc6-dev locales 167s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 10.5 MB of archives. 167s After this operation, 1024 B of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 168s Preconfiguring packages ... 168s Fetched 10.5 MB in 1s (9880 kB/s) 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 168s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Setting up libc6:amd64 (2.41-1ubuntu2) ... 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 169s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc-bin (2.41-1ubuntu2) ... 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 169s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 169s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up locales (2.41-1ubuntu2) ... 170s Generating locales (this might take a while)... 171s en_US.UTF-8... done 171s Generation complete. 171s Setting up libc-dev-bin (2.41-1ubuntu2) ... 171s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 171s Processing triggers for man-db (2.13.0-1) ... 172s Processing triggers for systemd (257.3-1ubuntu3) ... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 173s Solving dependencies... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [22:47:53]: rebooting testbed after setup commands that affected boot 197s autopkgtest [22:48:16]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 200s autopkgtest [22:48:19]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 203s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (dsc) [2123 B] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (tar) [450 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (diff) [213 kB] 203s gpgv: Signature made Mon Dec 2 16:02:51 2024 UTC 203s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 203s gpgv: issuer "tille@debian.org" 203s gpgv: Can't check signature: No public key 203s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-9.dsc: no acceptable signature found 203s autopkgtest [22:48:22]: testing package ray version 2.3.1-9 204s autopkgtest [22:48:23]: build not needed 205s autopkgtest [22:48:24]: test run-unit-test: preparing testbed 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 206s The following NEW packages will be installed: 206s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 206s libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdatrie1 libdeflate0 206s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libgfortran5 libgomp1 206s libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 206s libhwloc15 libibmad5 libibumad3 libice6 libjbig0 libjpeg-turbo8 libjpeg8 206s liblapack3 liblerc4 libllvm17t64 libmunge2 libopenmpi40 libpango-1.0-0 206s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 206s libpixman-1-0 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 206s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 206s libucx0 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 206s libxss1 libxt6t64 mpi-default-bin ocl-icd-libopencl1 openmpi-bin 206s openmpi-common r-base-core ray ray-doc ray-extra unzip x11-common xdg-utils 206s zip 206s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 206s Need to get 99.1 MB of archives. 206s After this operation, 323 MB of additional disk space will be used. 206s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 207s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 208s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 209s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 209s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 209s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 209s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 209s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 209s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 209s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 209s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 209s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 209s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 209s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 209s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 209s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 209s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 209s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 209s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 209s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 209s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 209s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 209s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 209s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 209s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 209s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 209s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 209s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 209s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 210s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 210s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 210s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 210s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 210s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 210s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 210s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 210s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 210s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 210s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 210s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 210s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 210s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 210s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 210s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 210s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 210s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 210s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 210s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 210s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 210s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 210s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 210s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 210s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 210s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 210s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 210s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 210s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 210s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 5.0.7-1 [97.9 kB] 210s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 5.0.7-1 [192 kB] 210s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 210s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 210s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 210s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 212s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 mpi-default-bin amd64 1.18 [2510 B] 212s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 ray amd64 2.3.1-9 [778 kB] 212s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 ray-doc all 2.3.1-9 [35.2 kB] 212s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 ray-extra all 2.3.1-9 [12.3 kB] 212s Preconfiguring packages ... 212s Fetched 99.1 MB in 5s (18.2 MB/s) 212s Selecting previously unselected package fonts-dejavu-mono. 212s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 212s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 212s Unpacking fonts-dejavu-mono (2.37-8) ... 212s Selecting previously unselected package fonts-dejavu-core. 212s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 212s Unpacking fonts-dejavu-core (2.37-8) ... 212s Selecting previously unselected package fontconfig-config. 212s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 212s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 212s Selecting previously unselected package libfontconfig1:amd64. 212s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 212s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 212s Selecting previously unselected package fontconfig. 212s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 212s Unpacking fontconfig (2.15.0-2ubuntu1) ... 212s Selecting previously unselected package libllvm17t64:amd64. 213s Preparing to unpack .../05-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 213s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 213s Selecting previously unselected package libamd-comgr2:amd64. 213s Preparing to unpack .../06-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 213s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 213s Selecting previously unselected package libhsakmt1:amd64. 213s Preparing to unpack .../07-libhsakmt1_5.7.0-1build1_amd64.deb ... 213s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 213s Selecting previously unselected package libhsa-runtime64-1. 213s Preparing to unpack .../08-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 213s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 213s Selecting previously unselected package libamdhip64-5. 213s Preparing to unpack .../09-libamdhip64-5_5.7.1-5_amd64.deb ... 213s Unpacking libamdhip64-5 (5.7.1-5) ... 213s Selecting previously unselected package libblas3:amd64. 213s Preparing to unpack .../10-libblas3_3.12.1-2_amd64.deb ... 213s Unpacking libblas3:amd64 (3.12.1-2) ... 213s Selecting previously unselected package libpixman-1-0:amd64. 213s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_amd64.deb ... 213s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 213s Selecting previously unselected package libxcb-render0:amd64. 213s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 213s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 214s Selecting previously unselected package libxcb-shm0:amd64. 214s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_amd64.deb ... 214s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 214s Selecting previously unselected package libxrender1:amd64. 214s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 214s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 214s Selecting previously unselected package libcairo2:amd64. 214s Preparing to unpack .../15-libcairo2_1.18.2-2_amd64.deb ... 214s Unpacking libcairo2:amd64 (1.18.2-2) ... 214s Selecting previously unselected package libdatrie1:amd64. 214s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_amd64.deb ... 214s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 214s Selecting previously unselected package libdeflate0:amd64. 214s Preparing to unpack .../17-libdeflate0_1.23-1_amd64.deb ... 214s Unpacking libdeflate0:amd64 (1.23-1) ... 214s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 214s Preparing to unpack .../18-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 214s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 214s Selecting previously unselected package libpsm-infinipath1. 214s Preparing to unpack .../19-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 214s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 214s Selecting previously unselected package libpsm2-2. 214s Preparing to unpack .../20-libpsm2-2_11.2.185-2.1_amd64.deb ... 214s Unpacking libpsm2-2 (11.2.185-2.1) ... 214s Selecting previously unselected package librdmacm1t64:amd64. 214s Preparing to unpack .../21-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 214s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 214s Selecting previously unselected package libfabric1:amd64. 214s Preparing to unpack .../22-libfabric1_1.17.0-3.1_amd64.deb ... 214s Unpacking libfabric1:amd64 (1.17.0-3.1) ... 214s Selecting previously unselected package libgfortran5:amd64. 214s Preparing to unpack .../23-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 214s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 214s Selecting previously unselected package libgomp1:amd64. 214s Preparing to unpack .../24-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 214s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 214s Selecting previously unselected package libgraphite2-3:amd64. 214s Preparing to unpack .../25-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 214s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 214s Selecting previously unselected package libharfbuzz0b:amd64. 214s Preparing to unpack .../26-libharfbuzz0b_10.2.0-1_amd64.deb ... 214s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 214s Selecting previously unselected package libhwloc15:amd64. 214s Preparing to unpack .../27-libhwloc15_2.12.0-1_amd64.deb ... 214s Unpacking libhwloc15:amd64 (2.12.0-1) ... 214s Selecting previously unselected package x11-common. 214s Preparing to unpack .../28-x11-common_1%3a7.7+23ubuntu3_all.deb ... 214s Unpacking x11-common (1:7.7+23ubuntu3) ... 214s Selecting previously unselected package libice6:amd64. 214s Preparing to unpack .../29-libice6_2%3a1.1.1-1_amd64.deb ... 214s Unpacking libice6:amd64 (2:1.1.1-1) ... 214s Selecting previously unselected package libjpeg-turbo8:amd64. 214s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 214s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 214s Selecting previously unselected package libjpeg8:amd64. 214s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_amd64.deb ... 214s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 214s Selecting previously unselected package liblapack3:amd64. 214s Preparing to unpack .../32-liblapack3_3.12.1-2_amd64.deb ... 214s Unpacking liblapack3:amd64 (3.12.1-2) ... 214s Selecting previously unselected package liblerc4:amd64. 214s Preparing to unpack .../33-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 214s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 214s Selecting previously unselected package libmunge2:amd64. 214s Preparing to unpack .../34-libmunge2_0.5.16-1_amd64.deb ... 214s Unpacking libmunge2:amd64 (0.5.16-1) ... 214s Selecting previously unselected package libpciaccess0:amd64. 214s Preparing to unpack .../35-libpciaccess0_0.17-3build1_amd64.deb ... 214s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 214s Selecting previously unselected package libxnvctrl0:amd64. 214s Preparing to unpack .../36-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 214s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 214s Selecting previously unselected package ocl-icd-libopencl1:amd64. 214s Preparing to unpack .../37-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 214s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 214s Selecting previously unselected package libhwloc-plugins:amd64. 214s Preparing to unpack .../38-libhwloc-plugins_2.12.0-1_amd64.deb ... 214s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 214s Selecting previously unselected package libpmix2t64:amd64. 214s Preparing to unpack .../39-libpmix2t64_5.0.6-5_amd64.deb ... 214s Unpacking libpmix2t64:amd64 (5.0.6-5) ... 214s Selecting previously unselected package libibumad3:amd64. 214s Preparing to unpack .../40-libibumad3_55.0-1ubuntu1_amd64.deb ... 214s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 214s Selecting previously unselected package libibmad5:amd64. 214s Preparing to unpack .../41-libibmad5_55.0-1ubuntu1_amd64.deb ... 214s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 214s Selecting previously unselected package libucx0:amd64. 214s Preparing to unpack .../42-libucx0_1.18.1+ds-2_amd64.deb ... 214s Unpacking libucx0:amd64 (1.18.1+ds-2) ... 214s Selecting previously unselected package libopenmpi40:amd64. 214s Preparing to unpack .../43-libopenmpi40_5.0.7-1_amd64.deb ... 214s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 214s Selecting previously unselected package libthai-data. 214s Preparing to unpack .../44-libthai-data_0.1.29-2build1_all.deb ... 214s Unpacking libthai-data (0.1.29-2build1) ... 215s Selecting previously unselected package libthai0:amd64. 215s Preparing to unpack .../45-libthai0_0.1.29-2build1_amd64.deb ... 215s Unpacking libthai0:amd64 (0.1.29-2build1) ... 215s Selecting previously unselected package libpango-1.0-0:amd64. 215s Preparing to unpack .../46-libpango-1.0-0_1.56.2-1_amd64.deb ... 215s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 215s Selecting previously unselected package libpangoft2-1.0-0:amd64. 215s Preparing to unpack .../47-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 215s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 215s Selecting previously unselected package libpangocairo-1.0-0:amd64. 215s Preparing to unpack .../48-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 215s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 215s Selecting previously unselected package libpaper2:amd64. 215s Preparing to unpack .../49-libpaper2_2.2.5-0.3_amd64.deb ... 215s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 215s Selecting previously unselected package libpaper-utils. 215s Preparing to unpack .../50-libpaper-utils_2.2.5-0.3_amd64.deb ... 215s Unpacking libpaper-utils (2.2.5-0.3) ... 215s Selecting previously unselected package libsharpyuv0:amd64. 215s Preparing to unpack .../51-libsharpyuv0_1.5.0-0.1_amd64.deb ... 215s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 215s Selecting previously unselected package libsm6:amd64. 215s Preparing to unpack .../52-libsm6_2%3a1.2.4-1_amd64.deb ... 215s Unpacking libsm6:amd64 (2:1.2.4-1) ... 215s Selecting previously unselected package libtcl8.6:amd64. 215s Preparing to unpack .../53-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 215s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 215s Selecting previously unselected package libjbig0:amd64. 215s Preparing to unpack .../54-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 215s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 215s Selecting previously unselected package libwebp7:amd64. 215s Preparing to unpack .../55-libwebp7_1.5.0-0.1_amd64.deb ... 215s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 215s Selecting previously unselected package libtiff6:amd64. 215s Preparing to unpack .../56-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 215s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 215s Selecting previously unselected package libxft2:amd64. 215s Preparing to unpack .../57-libxft2_2.3.6-1build1_amd64.deb ... 215s Unpacking libxft2:amd64 (2.3.6-1build1) ... 215s Selecting previously unselected package libxss1:amd64. 215s Preparing to unpack .../58-libxss1_1%3a1.2.3-1build3_amd64.deb ... 215s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 215s Selecting previously unselected package libtk8.6:amd64. 215s Preparing to unpack .../59-libtk8.6_8.6.16-1_amd64.deb ... 215s Unpacking libtk8.6:amd64 (8.6.16-1) ... 215s Selecting previously unselected package libxt6t64:amd64. 215s Preparing to unpack .../60-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 215s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 215s Selecting previously unselected package openmpi-common. 215s Preparing to unpack .../61-openmpi-common_5.0.7-1_all.deb ... 215s Unpacking openmpi-common (5.0.7-1) ... 215s Selecting previously unselected package openmpi-bin. 215s Preparing to unpack .../62-openmpi-bin_5.0.7-1_amd64.deb ... 215s Unpacking openmpi-bin (5.0.7-1) ... 215s Selecting previously unselected package zip. 215s Preparing to unpack .../63-zip_3.0-14ubuntu2_amd64.deb ... 215s Unpacking zip (3.0-14ubuntu2) ... 215s Selecting previously unselected package unzip. 215s Preparing to unpack .../64-unzip_6.0-28ubuntu6_amd64.deb ... 215s Unpacking unzip (6.0-28ubuntu6) ... 215s Selecting previously unselected package xdg-utils. 215s Preparing to unpack .../65-xdg-utils_1.2.1-2ubuntu1_all.deb ... 215s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 215s Selecting previously unselected package r-base-core. 215s Preparing to unpack .../66-r-base-core_4.4.3-1_amd64.deb ... 215s Unpacking r-base-core (4.4.3-1) ... 216s Selecting previously unselected package mpi-default-bin. 216s Preparing to unpack .../67-mpi-default-bin_1.18_amd64.deb ... 216s Unpacking mpi-default-bin (1.18) ... 216s Selecting previously unselected package ray. 216s Preparing to unpack .../68-ray_2.3.1-9_amd64.deb ... 216s Unpacking ray (2.3.1-9) ... 216s Selecting previously unselected package ray-doc. 216s Preparing to unpack .../69-ray-doc_2.3.1-9_all.deb ... 216s Unpacking ray-doc (2.3.1-9) ... 216s Selecting previously unselected package ray-extra. 216s Preparing to unpack .../70-ray-extra_2.3.1-9_all.deb ... 216s Unpacking ray-extra (2.3.1-9) ... 216s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 216s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 216s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 216s Setting up ray-doc (2.3.1-9) ... 216s Setting up libpciaccess0:amd64 (0.17-3build1) ... 216s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 216s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 216s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 216s Setting up libxcb-render0:amd64 (1.17.0-2) ... 216s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 216s Setting up unzip (6.0-28ubuntu6) ... 216s Setting up x11-common (1:7.7+23ubuntu3) ... 216s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 216s Setting up libdeflate0:amd64 (1.23-1) ... 216s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 216s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 216s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 216s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 216s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 216s Setting up zip (3.0-14ubuntu2) ... 216s Setting up libblas3:amd64 (3.12.1-2) ... 216s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 216s Setting up libmunge2:amd64 (0.5.16-1) ... 216s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 216s Setting up fonts-dejavu-mono (2.37-8) ... 216s Setting up libhwloc15:amd64 (2.12.0-1) ... 216s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 216s Setting up fonts-dejavu-core (2.37-8) ... 216s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 216s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 216s Setting up libwebp7:amd64 (1.5.0-0.1) ... 216s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 216s Setting up libpsm2-2 (11.2.185-2.1) ... 216s Setting up openmpi-common (5.0.7-1) ... 216s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 216s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 216s Setting up libthai-data (0.1.29-2build1) ... 216s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 216s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 216s Setting up libpaper2:amd64 (2.2.5-0.3) ... 216s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 216s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 216s Setting up xdg-utils (1.2.1-2ubuntu1) ... 216s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 216s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 216s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 216s Setting up libfabric1:amd64 (1.17.0-3.1) ... 216s Setting up libice6:amd64 (2:1.1.1-1) ... 216s Setting up liblapack3:amd64 (3.12.1-2) ... 216s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 216s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 216s Setting up libpaper-utils (2.2.5-0.3) ... 216s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 216s Setting up libthai0:amd64 (0.1.29-2build1) ... 216s Setting up libpmix2t64:amd64 (5.0.6-5) ... 216s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 216s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 216s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 216s Setting up libsm6:amd64 (2:1.2.4-1) ... 216s Setting up fontconfig (2.15.0-2ubuntu1) ... 218s Regenerating fonts cache... done. 218s Setting up libxft2:amd64 (2.3.6-1build1) ... 218s Setting up libtk8.6:amd64 (8.6.16-1) ... 218s Setting up libpango-1.0-0:amd64 (1.56.2-1) ... 218s Setting up libcairo2:amd64 (1.18.2-2) ... 218s Setting up libamdhip64-5 (5.7.1-5) ... 219s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 219s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 219s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 219s Setting up libucx0:amd64 (1.18.1+ds-2) ... 219s Setting up r-base-core (4.4.3-1) ... 219s Creating config file /etc/R/Renviron with new version 219s Setting up libopenmpi40:amd64 (5.0.7-1) ... 219s Setting up ray-extra (2.3.1-9) ... 219s Setting up openmpi-bin (5.0.7-1) ... 219s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 219s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 219s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 219s Setting up mpi-default-bin (1.18) ... 219s Setting up ray (2.3.1-9) ... 219s Processing triggers for libc-bin (2.41-1ubuntu2) ... 219s Processing triggers for man-db (2.13.0-1) ... 220s Processing triggers for install-info (7.1.1-1) ... 222s autopkgtest [22:48:41]: test run-unit-test: [----------------------- 222s 222s ************************************************** 222s This program comes with ABSOLUTELY NO WARRANTY. 222s This is free software, and you are welcome to redistribute it 222s under certain conditions; see "LICENSE.txt" for details. 222s ************************************************** 222s 222s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 222s Centre de recherche en infectiologie de l'Université Laval 222s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 222s http://denovoassembler.sf.net/ 222s 222s References to cite: 222s 222s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 222s Ray Meta: scalable de novo metagenome assembly and profiling. 222s Genome Biology (BioMed Central Ltd). 222s 13:R122, Published: 22 December 2012 222s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 222s 222s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 222s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 222s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 222s November 2010, Volume 17, Issue 11, Pages 1519-1533. 222s http://dx.doi.org/doi:10.1089/cmb.2009.0238 222s 222s Ray version 2.3.1 222s License for Ray: GNU General Public License version 3 222s RayPlatform version: 2.0.1 222s License for RayPlatform: GNU Lesser General Public License version 3 222s 222s MAXKMERLENGTH: 32 222s Maximum coverage depth stored by CoverageDepth: 4294967295 222s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 222s FORCE_PACKING = n 222s ASSERT = n 222s HAVE_LIBZ = y 222s HAVE_LIBBZ2 = y 222s PROFILER_COLLECT = n 222s MINIRANKS = y 222s CLOCK_GETTIME = n 222s __linux__ = y 222s _MSC_VER = n 222s __GNUC__ = y 222s RAY_32_BITS = n 222s RAY_64_BITS = y 222s MPI standard version: MPI 3.1 222s MPI library: Open-MPI 5.0.6 222s Compiler: GNU gcc/g++ 14.2.0 222s MPI I/O: n 222s 222s 222s -k (to set the k-mer size) 222s Value: 31 222s 222s 222s Paired library # 0 222s -p (paired-end sequences) 222s Left sequences: ecoli_1K_1.fq 222s Right sequences: ecoli_1K_2.fq 222s Average length: automatic detection 222s Standard deviation: automatic detection 222s 222s Ray command: 222s mpiexec -n 1 Ray \ 222s -k \ 222s 31 \ 222s -p \ 222s ecoli_1K_1.fq \ 222s ecoli_1K_2.fq \ 222s -o \ 222s test1 222s 222s Rank 0 wrote test1/RayCommand.txt 222s 222s k-mer length: 31 222s Rank 0: assembler memory usage: 43084 KiB 222s Rank 0: assembler memory usage: 108892 KiB 222s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2571 222s Rank 0: testing the network, please wait... 222s 222s Rank 0 is testing the network [0/1000] 222s Rank 0 is testing the network [1000/1000] 222s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 222s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 222s 222s Rank 0 wrote test1/NetworkTest.txt 222s 222s 222s *** 222s Step: Network testing 222s Date: Sat Mar 15 22:48:41 2025 222s Elapsed time: 0 seconds 222s Since beginning: 0 seconds 222s *** 222s 222s 222s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 222s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 222s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 222s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 222s Rank 0 wrote test1/NumberOfSequences.txt 222s Rank 0 wrote test1/SequencePartition.txt 222s 222s *** 222s Step: Counting sequences to assemble 222s Date: Sat Mar 15 22:48:41 2025 222s Elapsed time: 0 seconds 222s Since beginning: 0 seconds 222s *** 222s 222s 222s Rank 0 is loading sequence reads 222s Rank 0 : partition is [0;4107], 4108 sequence reads 222s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 222s Rank 0 has 0 sequence reads 222s Rank 0: assembler memory usage: 121772 KiB 222s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 222s Rank 0 has 4108 sequence reads (completed) 222s 222s *** 222s Step: Sequence loading 222s Date: Sat Mar 15 22:48:41 2025 222s Elapsed time: 0 seconds 222s Since beginning: 0 seconds 222s *** 222s 222s 222s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 222s Rank 0 created its Bloom filter 222s Rank 0 is counting k-mers in sequence reads [1/4108] 222s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 222s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 222s 222s 222s *** 222s Step: K-mer counting 222s Date: Sat Mar 15 22:48:41 2025 222s Elapsed time: 0 seconds 222s Since beginning: 0 seconds 222s *** 222s 222s 222s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 222s Rank 0 destroyed its Bloom filter 222s Rank 0 has 1954 k-mers (completed) 222s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 222s Rank 0: assembler memory usage: 118168 KiB 223s 223s 223s Rank 0: the minimum coverage is 3 223s Rank 0: the peak coverage is 3 223s Warning: no peak observed in the k-mer coverage distribution. 223s to deal with the sequencing error rate, try to lower the k-mer length (-k) 223s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 223s 223s *** 223s Step: Coverage distribution analysis 223s Date: Sat Mar 15 22:48:42 2025 223s Elapsed time: 1 seconds 223s Since beginning: 1 seconds 223s *** 223s 223s 223s 223s Rank 0 is adding edges [1/4108] 223s Rank 0 is adding edges [4108/4108] (completed) 223s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 223s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 223s 223s *** 223s Step: Graph construction 223s Date: Sat Mar 15 22:48:42 2025 223s Elapsed time: 0 seconds 223s Since beginning: 1 seconds 223s *** 223s 223s 223s Rank 0 has 1954 vertices (completed) 223s Rank 0: assembler memory usage: 118168 KiB 224s Rank 0 is purging edges [1/1954] 224s Rank 0 is purging edges [1954/1954] (completed) 224s Rank 0: assembler memory usage: 118696 KiB 224s VirtualProcessor: completed jobs: 1954 224s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 224s Rank 0 wrote test1/degreeDistribution.txt 224s 224s *** 224s Step: Null edge purging 224s Date: Sat Mar 15 22:48:43 2025 224s Elapsed time: 1 seconds 224s Since beginning: 2 seconds 224s *** 224s 224s 224s Rank 0 is selecting optimal read markers [1/4108] 224s Rank 0: assembler memory usage: 118696 KiB 224s Rank 0 is selecting optimal read markers [4108/4108] (completed) 224s Rank 0: peak number of workers: 599, maximum: 32768 224s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 224s Rank 0: assembler memory usage: 126860 KiB 224s Rank 0: Freeing unused assembler memory: 4096 KiB freed 224s Rank 0: assembler memory usage: 126860 KiB 224s 224s *** 224s Step: Selection of optimal read markers 224s Date: Sat Mar 15 22:48:43 2025 224s Elapsed time: 0 seconds 224s Since beginning: 2 seconds 224s *** 224s 224s 224s Rank 0: memory usage for optimal read markers= 4096 KiB 224s Rank 0 is creating seeds [1/1954] 224s Rank 0: assembler memory usage: 126860 KiB 225s Rank 0 has 1 seeds 225s Rank 0 is creating seeds [1954/1954] (completed) 225s Rank 0: peak number of workers: 746, maximum: 32768 225s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 225s Rank 0 runtime statistics for seeding algorithm: 225s Rank 0 Skipped paths because of dead end for head: 0 225s Rank 0 Skipped paths because of dead end for tail: 0 225s Rank 0 Skipped paths because of two dead ends: 0 225s Rank 0 Skipped paths because of bubble weak component: 0 225s Rank 0 Skipped paths because of short length: 1952 225s Rank 0 Skipped paths because of bad ownership: 1 225s Rank 0 Skipped paths because of low coverage: 0 225s Rank 0 Eligible paths: 1 225s Rank 0: assembler memory usage: 126860 KiB 225s Rank 0 has 1 seeds to register. 225s Rank 0 registered 0/1 225s Rank 0 registered 0/1 225s Rank 0 registered its seeds 225s VirtualProcessor: completed jobs: 0 225s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 226s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 236s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 236s Rank 0 merged its seeds: 1 seeds -> 1 seeds 236s 236s *** 236s Step: Detection of assembly seeds 236s Date: Sat Mar 15 22:48:55 2025 236s Elapsed time: 12 seconds 236s Since beginning: 14 seconds 236s *** 236s 236s 236s Rank 0 is calculating library lengths [1/1] 236s Rank 0 detected 1737 library lengths 236s Rank 0 is calculating library lengths [1/1] (completed) 236s Rank 0: peak number of workers: 1, maximum: 32768 236s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 236s Rank 0: assembler memory usage: 163728 KiB 236s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 236s 236s Mode= 2 signalAverage= 9 236s CURRENT IS NOISE, 244 236s GOT HIT 212 236s 236s 236s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 236s 236s *** 236s Step: Estimation of outer distances for paired reads 236s Date: Sat Mar 15 22:48:55 2025 236s Elapsed time: 0 seconds 236s Since beginning: 14 seconds 236s *** 236s 236s 236s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 236s Rank 0 traversed 1000 nucleotide symbols 236s Rank 0: assembler memory usage: 167824 KiB 236s Rank 0 is extending seeds [1/1] (completed) 236s Rank 0 extended 1 seeds out of 1 (100.00%) 236s Rank 0: assembler memory usage: 159632 KiB 236s Rank 0 starting fusions 236s 236s *** 236s Step: Bidirectional extension of seeds 236s Date: Sat Mar 15 22:48:55 2025 236s Elapsed time: 0 seconds 236s Since beginning: 14 seconds 236s *** 236s 236s 236s Rank 0: starting clear step. cycleNumber= 0 237s Rank 0 adding 0 new fusions 237s Rank 0 cleared, 1 paths 237s Rank 0: starting distribution step 237s Rank 0 is distributing fusions [1/1] 237s Rank 0: assembler memory usage: 159632 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 is distributing fusions [1/1] (completed) 237s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 tells others to compute fusions. 237s Rank 0 FusionTaskCreator assignNextTask [0/2] 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 FusionTaskCreator processWorkerResult [0/2] 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 FusionTaskCreator [2/2] 237s Statistics: all paths: 1 eliminated during fusing: 0 237s Rank 0: assembler memory usage: 163728 KiB 237s VirtualProcessor: completed jobs: 2 237s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 237s Rank 0: starting clear step. cycleNumber= 1 237s Rank 0 adding 0 new fusions 237s Rank 0 cleared, 1 paths 237s Rank 0 is distributing fusions [1/1] 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 is distributing fusions [1/1] (completed) 237s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 JoinerTaskCreator assignNextTask [0/2] 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s Rank 0 JoinerTaskCreator [2/2] 237s Statistics: all paths: 1 eliminated during joining: 0 237s Rank 0: assembler memory usage: 163728 KiB 237s Date: Sat Mar 15 22:48:56 2025 237s VirtualProcessor: completed jobs: 2 237s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 238s Rank 0 adding 0 new fusions 238s Rank 0 cleared, 1 paths 238s Rank 0: starting distribution step 238s Rank 0 is distributing fusions [1/1] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 is distributing fusions [1/1] (completed) 238s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 tells others to compute fusions. 238s Rank 0 FusionTaskCreator assignNextTask [0/2] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 FusionTaskCreator processWorkerResult [0/2] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 FusionTaskCreator [2/2] 238s Statistics: all paths: 1 eliminated during fusing: 0 238s Rank 0: assembler memory usage: 163728 KiB 238s VirtualProcessor: completed jobs: 2 238s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 238s Rank 0: starting clear step. cycleNumber= 2 238s Rank 0 adding 0 new fusions 238s Rank 0 cleared, 1 paths 238s Rank 0 is distributing fusions [1/1] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 is distributing fusions [1/1] (completed) 238s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 JoinerTaskCreator assignNextTask [0/2] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s Rank 0 JoinerTaskCreator [2/2] 238s Statistics: all paths: 1 eliminated during joining: 0 238s Rank 0: assembler memory usage: 163728 KiB 238s Date: Sat Mar 15 22:48:57 2025 238s VirtualProcessor: completed jobs: 2 238s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 239s Rank 0 adding 0 new fusions 239s Rank 0 cleared, 1 paths 239s Rank 0: starting distribution step 239s Rank 0 is distributing fusions [1/1] 239s Rank 0: assembler memory usage: 163728 KiB 239s Date: Sat Mar 15 22:48:58 2025 239s Rank 0 is distributing fusions [1/1] (completed) 239s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 239s Rank 0: assembler memory usage: 163728 KiB 239s Date: Sat Mar 15 22:48:58 2025 239s Rank 0 cycleNumber= 2 239s 239s *** 239s Step: Merging of redundant paths 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 3 seconds 239s Since beginning: 17 seconds 239s *** 239s 239s 239s Rank 0 appended 1 elements 239s 239s *** 239s Step: Generation of contigs 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 0 seconds 239s Since beginning: 17 seconds 239s *** 239s 239s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 239s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 239s Rank 0 ineligibleObjects: 0/970 (0.00%) 239s Rank 0: assembler memory usage: 163728 KiB 239s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 239s Rank 0 finished gathering scaffold links. 239s Rank 0 will write 1 contig lengths 239s Rank 0 will solve the scaffolding problem. 239s Welcome to GreedySolver v1.0 239s 1 vertices; 0 edges 239s 1 contigs >= 500 239s Edges in solution: 0 239s 239s Conflict statistics: 239s 1 scaffolds, 1 >= 500 239s Total: 1000 nucleotides 239s 239s *** 239s Step: Scaffolding of contigs 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 0 seconds 239s Since beginning: 17 seconds 239s *** 239s 239s Rank 0 syncing with master 239s 239s *** 239s Step: Counting sequences to search 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 0 seconds 239s Since beginning: 17 seconds 239s *** 239s 239s 239s Rank 0 will add colors, 0 sequences in 0 files to process 239s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 239s 239s *** 239s Step: Graph coloring 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 0 seconds 239s Since beginning: 17 seconds 239s *** 239s 239s 239s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 239s Rank 0 shares its counts 239s Rank 0 computing contig abundances [1/1] [1/970] 239s Rank 0 computing contig abundances [1/1] [970/970] 239s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 239s 239s *** 239s Step: Counting contig biological abundances 239s Date: Sat Mar 15 22:48:58 2025 239s Elapsed time: 0 seconds 239s Since beginning: 17 seconds 240s *** 240s 240s 240s Rank 0 colored the graph with 0 real colors using 1 virtual colors 240s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 240s 240s *** 240s Step: Counting sequence biological abundances 240s Date: Sat Mar 15 22:48:58 2025 240s Elapsed time: 0 seconds 240s Since beginning: 17 seconds 240s *** 240s 240s 240s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 240s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 240s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 240s 240s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 240s Rank 0 is starting taxon syncing across the compute tribe. 240s 240s *** 240s Step: Loading taxons 240s Date: Sat Mar 15 22:48:59 2025 240s Elapsed time: 1 seconds 240s Since beginning: 18 seconds 240s *** 240s 240s Rank 0 synced taxons across the grid with 1 poor slaves. 240s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 240s Rank 0 has 0 taxons after syncing with master 241s 241s 241s *** 241s Step: Loading tree 241s Date: Sat Mar 15 22:49:00 2025 241s Elapsed time: 1 seconds 241s Since beginning: 19 seconds 241s *** 241s 241s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 241s 241s Rank 0: counting ontology terms in the graph... 242s Rank 0: 0 have some biological signal 242s Number of dereferenced alternate handles: 0 242s Number of k-mer observations with gene ontology terms: 0 242s Rank 0: synced ontology term profiles with master 242s Rank 0: synchronization is complete! 242s Rank 0: ontology terms with biological signal: 0 242s Populated recursive values... 242s Gene ontology terms without depth information: 0 242s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 242s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 242s 242s *** 242s Step: Processing gene ontologies 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 1 seconds 242s Since beginning: 20 seconds 242s *** 242s 242s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 242s [GenomeNeighbourhood] in final list: 0 242s 242s *** 242s Step: Computing neighbourhoods 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 0 seconds 242s Since beginning: 20 seconds 242s *** 242s 242s Contigs >= 100 nt 242s Number: 1 242s Total length: 1000 242s Average: 1000 242s N50: 1000 242s Median: 1000 242s Largest: 1000 242s Contigs >= 500 nt 242s Number: 1 242s Total length: 1000 242s Average: 1000 242s N50: 1000 242s Median: 1000 242s Largest: 1000 242s Scaffolds >= 100 nt 242s Number: 1 242s Total length: 1000 242s Average: 1000 242s N50: 1000 242s Median: 1000 242s Largest: 1000 242s Scaffolds >= 500 nt 242s Number: 1 242s Total length: 1000 242s Average: 1000 242s N50: 1000 242s Median: 1000 242s Largest: 1000 242s 242s Rank 0 wrote test1/Contigs.fasta 242s Rank 0 wrote test1/Scaffolds.fasta 242s Check for test1/* 242s 242s 242s 242s ************************************************** 242s This program comes with ABSOLUTELY NO WARRANTY. 242s This is free software, and you are welcome to redistribute it 242s under certain conditions; see "LICENSE.txt" for details. 242s ************************************************** 242s 242s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 242s Centre de recherche en infectiologie de l'Université Laval 242s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 242s http://denovoassembler.sf.net/ 242s 242s References to cite: 242s 242s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 242s Ray Meta: scalable de novo metagenome assembly and profiling. 242s Genome Biology (BioMed Central Ltd). 242s 13:R122, Published: 22 December 2012 242s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 242s 242s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 242s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 242s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 242s November 2010, Volume 17, Issue 11, Pages 1519-1533. 242s http://dx.doi.org/doi:10.1089/cmb.2009.0238 242s 242s Ray version 2.3.1 242s License for Ray: GNU General Public License version 3 242s RayPlatform version: 2.0.1 242s License for RayPlatform: GNU Lesser General Public License version 3 242s 242s MAXKMERLENGTH: 32 242s Maximum coverage depth stored by CoverageDepth: 4294967295 242s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 242s FORCE_PACKING = n 242s ASSERT = n 242s HAVE_LIBZ = y 242s HAVE_LIBBZ2 = y 242s PROFILER_COLLECT = n 242s MINIRANKS = y 242s CLOCK_GETTIME = n 242s __linux__ = y 242s _MSC_VER = n 242s __GNUC__ = y 242s RAY_32_BITS = n 242s RAY_64_BITS = y 242s MPI standard version: MPI 3.1 242s MPI library: Open-MPI 5.0.6 242s Compiler: GNU gcc/g++ 14.2.0 242s MPI I/O: n 242s 242s 242s -k (to set the k-mer size) 242s Value: 31 242s 242s 242s Paired library # 0 242s -p (paired-end sequences) 242s Left sequences: SampleDirectory/s_6.first1000_1.fastq 242s Right sequences: SampleDirectory/s_6.first1000_2.fastq 242s Average length: automatic detection 242s Standard deviation: automatic detection 242s 242s Ray command: 242s mpiexec -n 1 Ray \ 242s -k \ 242s 31 \ 242s -detect-sequence-files \ 242s SampleDirectory \ 242s -o \ 242s test2 242s 242s Rank 0 wrote test2/RayCommand.txt 242s 242s k-mer length: 31 242s Rank 0: assembler memory usage: 43084 KiB 242s Rank 0: assembler memory usage: 108892 KiB 242s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2574 242s Rank 0: testing the network, please wait... 242s 242s Rank 0 is testing the network [0/1000] 242s Rank 0 is testing the network [1000/1000] 242s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 242s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 242s 242s Rank 0 wrote test2/NetworkTest.txt 242s 242s 242s *** 242s Step: Network testing 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 0 seconds 242s Since beginning: 0 seconds 242s *** 242s 242s 242s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 242s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 242s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 242s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 242s Rank 0 wrote test2/NumberOfSequences.txt 242s Rank 0 wrote test2/SequencePartition.txt 242s 242s *** 242s Step: Counting sequences to assemble 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 0 seconds 242s Since beginning: 0 seconds 242s *** 242s 242s 242s Rank 0 is loading sequence reads 242s Rank 0 : partition is [0;4107], 4108 sequence reads 242s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 242s Rank 0 has 0 sequence reads 242s Rank 0: assembler memory usage: 121776 KiB 242s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 242s Rank 0 has 4108 sequence reads (completed) 242s 242s *** 242s Step: Sequence loading 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 0 seconds 242s Since beginning: 0 seconds 242s *** 242s 242s 242s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 242s Rank 0 created its Bloom filter 242s Rank 0 is counting k-mers in sequence reads [1/4108] 242s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 242s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 242s 242s 242s *** 242s Step: K-mer counting 242s Date: Sat Mar 15 22:49:01 2025 242s Elapsed time: 0 seconds 242s Since beginning: 0 seconds 242s *** 242s 242s 242s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 242s Rank 0 destroyed its Bloom filter 242s Rank 0 has 1954 k-mers (completed) 242s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 242s Rank 0: assembler memory usage: 118168 KiB 243s 243s 243s Rank 0: the minimum coverage is 3 243s Rank 0: the peak coverage is 3 243s Warning: no peak observed in the k-mer coverage distribution. 243s to deal with the sequencing error rate, try to lower the k-mer length (-k) 243s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 243s 243s *** 243s Step: Coverage distribution analysis 243s Date: Sat Mar 15 22:49:02 2025 243s Elapsed time: 1 seconds 243s Since beginning: 1 seconds 243s *** 243s 243s 243s 243s Rank 0 is adding edges [1/4108] 243s Rank 0 is adding edges [4108/4108] (completed) 243s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 243s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 243s 243s *** 243s Step: Graph construction 243s Date: Sat Mar 15 22:49:02 2025 243s Elapsed time: 0 seconds 243s Since beginning: 1 seconds 243s *** 243s 243s 243s Rank 0 has 1954 vertices (completed) 243s Rank 0: assembler memory usage: 118168 KiB 244s Rank 0 is purging edges [1/1954] 244s Rank 0 is purging edges [1954/1954] (completed) 244s Rank 0: assembler memory usage: 118696 KiB 244s VirtualProcessor: completed jobs: 1954 244s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 244s Rank 0 wrote test2/degreeDistribution.txt 244s 244s *** 244s Step: Null edge purging 244s Date: Sat Mar 15 22:49:03 2025 244s Elapsed time: 1 seconds 244s Since beginning: 2 seconds 244s *** 244s 244s 244s Rank 0 is selecting optimal read markers [1/4108] 244s Rank 0: assembler memory usage: 118696 KiB 244s Rank 0 is selecting optimal read markers [4108/4108] (completed) 244s Rank 0: peak number of workers: 599, maximum: 32768 244s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 244s Rank 0: assembler memory usage: 126824 KiB 244s Rank 0: Freeing unused assembler memory: 4096 KiB freed 244s Rank 0: assembler memory usage: 126824 KiB 244s 244s *** 244s Step: Selection of optimal read markers 244s Date: Sat Mar 15 22:49:03 2025 244s Elapsed time: 0 seconds 244s Since beginning: 2 seconds 244s *** 244s 244s 244s Rank 0: memory usage for optimal read markers= 4096 KiB 244s Rank 0 is creating seeds [1/1954] 244s Rank 0: assembler memory usage: 126824 KiB 245s Rank 0 has 1 seeds 245s Rank 0 is creating seeds [1954/1954] (completed) 245s Rank 0: peak number of workers: 746, maximum: 32768 245s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 245s Rank 0 runtime statistics for seeding algorithm: 245s Rank 0 Skipped paths because of dead end for head: 0 245s Rank 0 Skipped paths because of dead end for tail: 0 245s Rank 0 Skipped paths because of two dead ends: 0 245s Rank 0 Skipped paths because of bubble weak component: 0 245s Rank 0 Skipped paths because of short length: 1952 245s Rank 0 Skipped paths because of bad ownership: 1 245s Rank 0 Skipped paths because of low coverage: 0 245s Rank 0 Eligible paths: 1 245s Rank 0: assembler memory usage: 126824 KiB 245s Rank 0 has 1 seeds to register. 245s Rank 0 registered 0/1 245s Rank 0 registered 0/1 245s Rank 0 registered its seeds 245s VirtualProcessor: completed jobs: 0 245s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 246s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 256s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 256s Rank 0 merged its seeds: 1 seeds -> 1 seeds 256s 256s *** 256s Step: Detection of assembly seeds 256s Date: Sat Mar 15 22:49:15 2025 256s Elapsed time: 12 seconds 256s Since beginning: 14 seconds 256s *** 256s 256s 256s Rank 0 is calculating library lengths [1/1] 256s Rank 0 detected 1737 library lengths 256s Rank 0 is calculating library lengths [1/1] (completed) 256s Rank 0: peak number of workers: 1, maximum: 32768 256s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 256s Rank 0: assembler memory usage: 163692 KiB 256s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 256s 256s Mode= 2 signalAverage= 9 256s CURRENT IS NOISE, 244 256s GOT HIT 212 256s 256s 256s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 256s 256s *** 256s Step: Estimation of outer distances for paired reads 256s Date: Sat Mar 15 22:49:15 2025 256s Elapsed time: 0 seconds 256s Since beginning: 14 seconds 256s *** 256s 256s 256s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 256s Rank 0 traversed 1000 nucleotide symbols 256s Rank 0: assembler memory usage: 167788 KiB 256s Rank 0 is extending seeds [1/1] (completed) 256s Rank 0 extended 1 seeds out of 1 (100.00%) 256s Rank 0: assembler memory usage: 159596 KiB 256s Rank 0 starting fusions 256s 256s *** 256s Step: Bidirectional extension of seeds 256s Date: Sat Mar 15 22:49:15 2025 256s Elapsed time: 0 seconds 256s Since beginning: 14 seconds 256s *** 256s 256s 256s Rank 0: starting clear step. cycleNumber= 0 257s Rank 0 adding 0 new fusions 257s Rank 0 cleared, 1 paths 257s Rank 0: starting distribution step 257s Rank 0 is distributing fusions [1/1] 257s Rank 0: assembler memory usage: 159596 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 is distributing fusions [1/1] (completed) 257s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 tells others to compute fusions. 257s Rank 0 FusionTaskCreator assignNextTask [0/2] 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 FusionTaskCreator processWorkerResult [0/2] 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 FusionTaskCreator [2/2] 257s Statistics: all paths: 1 eliminated during fusing: 0 257s Rank 0: assembler memory usage: 163692 KiB 257s VirtualProcessor: completed jobs: 2 257s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 257s Rank 0: starting clear step. cycleNumber= 1 257s Rank 0 adding 0 new fusions 257s Rank 0 cleared, 1 paths 257s Rank 0 is distributing fusions [1/1] 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 is distributing fusions [1/1] (completed) 257s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 JoinerTaskCreator assignNextTask [0/2] 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s Rank 0 JoinerTaskCreator [2/2] 257s Statistics: all paths: 1 eliminated during joining: 0 257s Rank 0: assembler memory usage: 163692 KiB 257s Date: Sat Mar 15 22:49:16 2025 257s VirtualProcessor: completed jobs: 2 257s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 258s Rank 0 adding 0 new fusions 258s Rank 0 cleared, 1 paths 258s Rank 0: starting distribution step 258s Rank 0 is distributing fusions [1/1] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 is distributing fusions [1/1] (completed) 258s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 tells others to compute fusions. 258s Rank 0 FusionTaskCreator assignNextTask [0/2] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 FusionTaskCreator processWorkerResult [0/2] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 FusionTaskCreator [2/2] 258s Statistics: all paths: 1 eliminated during fusing: 0 258s Rank 0: assembler memory usage: 163692 KiB 258s VirtualProcessor: completed jobs: 2 258s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 258s Rank 0: starting clear step. cycleNumber= 2 258s Rank 0 adding 0 new fusions 258s Rank 0 cleared, 1 paths 258s Rank 0 is distributing fusions [1/1] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 is distributing fusions [1/1] (completed) 258s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 JoinerTaskCreator assignNextTask [0/2] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s Rank 0 JoinerTaskCreator [2/2] 258s Statistics: all paths: 1 eliminated during joining: 0 258s Rank 0: assembler memory usage: 163692 KiB 258s Date: Sat Mar 15 22:49:17 2025 258s VirtualProcessor: completed jobs: 2 258s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 259s Rank 0 adding 0 new fusions 259s Rank 0 cleared, 1 paths 259s Rank 0: starting distribution step 259s Rank 0 is distributing fusions [1/1] 259s Rank 0: assembler memory usage: 163692 KiB 259s Date: Sat Mar 15 22:49:18 2025 259s Rank 0 is distributing fusions [1/1] (completed) 259s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 259s Rank 0: assembler memory usage: 163692 KiB 259s Date: Sat Mar 15 22:49:18 2025 259s Rank 0 cycleNumber= 2 259s 259s *** 259s Step: Merging of redundant paths 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 3 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s 259s Rank 0 appended 1 elements 259s 259s *** 259s Step: Generation of contigs 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 0 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 259s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 259s Rank 0 ineligibleObjects: 0/970 (0.00%) 259s Rank 0: assembler memory usage: 163692 KiB 259s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 259s Rank 0 finished gathering scaffold links. 259s Rank 0 will write 1 contig lengths 259s Rank 0 will solve the scaffolding problem. 259s Welcome to GreedySolver v1.0 259s 1 vertices; 0 edges 259s 1 contigs >= 500 259s Edges in solution: 0 259s 259s Conflict statistics: 259s 1 scaffolds, 1 >= 500 259s Total: 1000 nucleotides 259s 259s *** 259s Step: Scaffolding of contigs 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 0 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s Rank 0 syncing with master 259s 259s *** 259s Step: Counting sequences to search 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 0 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s 259s Rank 0 will add colors, 0 sequences in 0 files to process 259s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 259s 259s *** 259s Step: Graph coloring 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 0 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s 259s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 259s Rank 0 shares its counts 259s Rank 0 computing contig abundances [1/1] [1/970] 259s Rank 0 computing contig abundances [1/1] [970/970] 259s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 259s 259s *** 259s Step: Counting contig biological abundances 259s Date: Sat Mar 15 22:49:18 2025 259s Elapsed time: 0 seconds 259s Since beginning: 17 seconds 259s *** 259s 259s 259s Rank 0 colored the graph with 0 real colors using 1 virtual colors 259s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 260s 260s *** 260s Step: Counting sequence biological abundances 260s Date: Sat Mar 15 22:49:18 2025 260s Elapsed time: 0 seconds 260s Since beginning: 17 seconds 260s *** 260s 260s 260s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 260s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 260s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 260s 260s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 260s Rank 0 is starting taxon syncing across the compute tribe. 260s 260s *** 260s Step: Loading taxons 260s Date: Sat Mar 15 22:49:19 2025 260s Elapsed time: 1 seconds 260s Since beginning: 18 seconds 260s *** 260s 260s Rank 0 synced taxons across the grid with 1 poor slaves. 260s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 260s Rank 0 has 0 taxons after syncing with master 261s 261s 261s *** 261s Step: Loading tree 261s Date: Sat Mar 15 22:49:20 2025 261s Elapsed time: 1 seconds 261s Since beginning: 19 seconds 261s *** 261s 261s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 261s 261s Rank 0: counting ontology terms in the graph... 262s Rank 0: 0 have some biological signal 262s Number of dereferenced alternate handles: 0 262s Number of k-mer observations with gene ontology terms: 0 262s Rank 0: synced ontology term profiles with master 262s Rank 0: synchronization is complete! 262s Rank 0: ontology terms with biological signal: 0 262s Populated recursive values... 262s Gene ontology terms without depth information: 0 262s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 262s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 262s 262s *** 262s Step: Processing gene ontologies 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 1 seconds 262s Since beginning: 20 seconds 262s *** 262s 262s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 262s [GenomeNeighbourhood] in final list: 0 262s 262s *** 262s Step: Computing neighbourhoods 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 0 seconds 262s Since beginning: 20 seconds 262s *** 262s 262s Contigs >= 100 nt 262s Number: 1 262s Total length: 1000 262s Average: 1000 262s N50: 1000 262s Median: 1000 262s Largest: 1000 262s Contigs >= 500 nt 262s Number: 1 262s Total length: 1000 262s Average: 1000 262s N50: 1000 262s Median: 1000 262s Largest: 1000 262s Scaffolds >= 100 nt 262s Number: 1 262s Total length: 1000 262s Average: 1000 262s N50: 1000 262s Median: 1000 262s Largest: 1000 262s Scaffolds >= 500 nt 262s Number: 1 262s Total length: 1000 262s Average: 1000 262s N50: 1000 262s Median: 1000 262s Largest: 1000 262s 262s Rank 0 wrote test2/Contigs.fasta 262s Rank 0 wrote test2/Scaffolds.fasta 262s Check for test2/* 262s 262s 262s 262s ************************************************** 262s This program comes with ABSOLUTELY NO WARRANTY. 262s This is free software, and you are welcome to redistribute it 262s under certain conditions; see "LICENSE.txt" for details. 262s ************************************************** 262s 262s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 262s Centre de recherche en infectiologie de l'Université Laval 262s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 262s http://denovoassembler.sf.net/ 262s 262s References to cite: 262s 262s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 262s Ray Meta: scalable de novo metagenome assembly and profiling. 262s Genome Biology (BioMed Central Ltd). 262s 13:R122, Published: 22 December 2012 262s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 262s 262s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 262s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 262s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 262s November 2010, Volume 17, Issue 11, Pages 1519-1533. 262s http://dx.doi.org/doi:10.1089/cmb.2009.0238 262s 262s Ray version 2.3.1 262s License for Ray: GNU General Public License version 3 262s RayPlatform version: 2.0.1 262s License for RayPlatform: GNU Lesser General Public License version 3 262s 262s MAXKMERLENGTH: 32 262s Maximum coverage depth stored by CoverageDepth: 4294967295 262s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 262s FORCE_PACKING = n 262s ASSERT = n 262s HAVE_LIBZ = y 262s HAVE_LIBBZ2 = y 262s PROFILER_COLLECT = n 262s MINIRANKS = y 262s CLOCK_GETTIME = n 262s __linux__ = y 262s _MSC_VER = n 262s __GNUC__ = y 262s RAY_32_BITS = n 262s RAY_64_BITS = y 262s MPI standard version: MPI 3.1 262s MPI library: Open-MPI 5.0.6 262s Compiler: GNU gcc/g++ 14.2.0 262s MPI I/O: n 262s 262s 262s -k (to set the k-mer size) 262s Value: 29 262s 262s 262s Paired library # 0 262s -p (paired-end sequences) 262s Left sequences: SampleDirectory/s_6.first1000_1.fastq 262s Right sequences: SampleDirectory/s_6.first1000_2.fastq 262s Average length: automatic detection 262s Standard deviation: automatic detection 262s 262s Ray command: 262s mpiexec -n 1 Ray \ 262s -k \ 262s 29 \ 262s -desable-recycling \ 262s -p \ 262s SampleDirectory/s_6.first1000_1.fastq \ 262s SampleDirectory/s_6.first1000_2.fastq 262s 262s Rank 0 wrote RayOutput/RayCommand.txt 262s 262s k-mer length: 29 262s Rank 0: assembler memory usage: 43124 KiB 262s Rank 0: assembler memory usage: 108796 KiB 262s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2602 262s Rank 0: testing the network, please wait... 262s 262s Rank 0 is testing the network [0/1000] 262s Rank 0 is testing the network [1000/1000] 262s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 262s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 262s 262s Rank 0 wrote RayOutput/NetworkTest.txt 262s 262s 262s *** 262s Step: Network testing 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 0 seconds 262s Since beginning: 0 seconds 262s *** 262s 262s 262s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 262s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 262s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 262s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 262s Rank 0 wrote RayOutput/NumberOfSequences.txt 262s Rank 0 wrote RayOutput/SequencePartition.txt 262s 262s *** 262s Step: Counting sequences to assemble 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 0 seconds 262s Since beginning: 0 seconds 262s *** 262s 262s 262s Rank 0 is loading sequence reads 262s Rank 0 : partition is [0;4107], 4108 sequence reads 262s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 262s Rank 0 has 0 sequence reads 262s Rank 0: assembler memory usage: 121772 KiB 262s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 262s Rank 0 has 4108 sequence reads (completed) 262s 262s *** 262s Step: Sequence loading 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 0 seconds 262s Since beginning: 0 seconds 262s *** 262s 262s 262s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 262s Rank 0 created its Bloom filter 262s Rank 0 is counting k-mers in sequence reads [1/4108] 262s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 262s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 262s 262s 262s *** 262s Step: K-mer counting 262s Date: Sat Mar 15 22:49:21 2025 262s Elapsed time: 0 seconds 262s Since beginning: 0 seconds 262s *** 262s 262s 262s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 262s Rank 0 destroyed its Bloom filter 262s Rank 0 has 1958 k-mers (completed) 262s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 262s Rank 0: assembler memory usage: 118152 KiB 263s 263s 263s Rank 0: the minimum coverage is 3 263s Rank 0: the peak coverage is 3 263s Warning: no peak observed in the k-mer coverage distribution. 263s to deal with the sequencing error rate, try to lower the k-mer length (-k) 263s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 263s 263s *** 263s Step: Coverage distribution analysis 263s Date: Sat Mar 15 22:49:22 2025 263s Elapsed time: 1 seconds 263s Since beginning: 1 seconds 263s *** 263s 263s 263s 263s Rank 0 is adding edges [1/4108] 263s Rank 0 is adding edges [4108/4108] (completed) 263s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 263s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 263s 263s *** 263s Step: Graph construction 263s Date: Sat Mar 15 22:49:22 2025 263s Elapsed time: 0 seconds 263s Since beginning: 1 seconds 263s *** 263s 263s 263s Rank 0 has 1958 vertices (completed) 263s Rank 0: assembler memory usage: 118152 KiB 264s Rank 0 is purging edges [1/1958] 264s Rank 0 is purging edges [1958/1958] (completed) 264s Rank 0: assembler memory usage: 118684 KiB 264s VirtualProcessor: completed jobs: 1958 264s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 264s Rank 0 wrote RayOutput/degreeDistribution.txt 264s 264s *** 264s Step: Null edge purging 264s Date: Sat Mar 15 22:49:23 2025 264s Elapsed time: 1 seconds 264s Since beginning: 2 seconds 264s *** 264s 264s 264s Rank 0 is selecting optimal read markers [1/4108] 264s Rank 0: assembler memory usage: 118684 KiB 264s Rank 0 is selecting optimal read markers [4108/4108] (completed) 264s Rank 0: peak number of workers: 599, maximum: 32768 264s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 264s Rank 0: assembler memory usage: 126900 KiB 264s Rank 0: Freeing unused assembler memory: 4096 KiB freed 264s Rank 0: assembler memory usage: 126900 KiB 264s 264s *** 264s Step: Selection of optimal read markers 264s Date: Sat Mar 15 22:49:23 2025 264s Elapsed time: 0 seconds 264s Since beginning: 2 seconds 264s *** 264s 264s 264s Rank 0: memory usage for optimal read markers= 4096 KiB 264s Rank 0 is creating seeds [1/1958] 264s Rank 0: assembler memory usage: 126900 KiB 265s Rank 0 has 1 seeds 265s Rank 0 is creating seeds [1958/1958] (completed) 265s Rank 0: peak number of workers: 746, maximum: 32768 265s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 265s Rank 0 runtime statistics for seeding algorithm: 265s Rank 0 Skipped paths because of dead end for head: 0 265s Rank 0 Skipped paths because of dead end for tail: 0 265s Rank 0 Skipped paths because of two dead ends: 0 265s Rank 0 Skipped paths because of bubble weak component: 0 265s Rank 0 Skipped paths because of short length: 1956 265s Rank 0 Skipped paths because of bad ownership: 1 265s Rank 0 Skipped paths because of low coverage: 0 265s Rank 0 Eligible paths: 1 265s Rank 0: assembler memory usage: 126900 KiB 265s Rank 0 has 1 seeds to register. 265s Rank 0 registered 0/1 265s Rank 0 registered 0/1 265s Rank 0 registered its seeds 265s VirtualProcessor: completed jobs: 0 265s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 266s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 276s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 276s Rank 0 merged its seeds: 1 seeds -> 1 seeds 276s 276s *** 276s Step: Detection of assembly seeds 276s Date: Sat Mar 15 22:49:35 2025 276s Elapsed time: 12 seconds 276s Since beginning: 14 seconds 276s *** 276s 276s 276s Rank 0 is calculating library lengths [1/1] 276s Rank 0 detected 1743 library lengths 276s Rank 0 is calculating library lengths [1/1] (completed) 276s Rank 0: peak number of workers: 1, maximum: 32768 276s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 276s Rank 0: assembler memory usage: 163768 KiB 276s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 276s 276s Mode= 2 signalAverage= 10 276s CURRENT IS NOISE, 244 276s GOT HIT 214 276s 276s 276s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 276s 276s *** 276s Step: Estimation of outer distances for paired reads 276s Date: Sat Mar 15 22:49:35 2025 276s Elapsed time: 0 seconds 276s Since beginning: 14 seconds 276s *** 276s 276s 276s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 276s Rank 0 traversed 1000 nucleotide symbols 276s Rank 0: assembler memory usage: 167864 KiB 276s Rank 0 is extending seeds [1/1] (completed) 276s Rank 0 extended 1 seeds out of 1 (100.00%) 276s Rank 0: assembler memory usage: 159672 KiB 276s Rank 0 starting fusions 276s 276s *** 276s Step: Bidirectional extension of seeds 276s Date: Sat Mar 15 22:49:35 2025 276s Elapsed time: 0 seconds 276s Since beginning: 14 seconds 276s *** 276s 276s 276s Rank 0: starting clear step. cycleNumber= 0 277s Rank 0 adding 0 new fusions 277s Rank 0 cleared, 1 paths 277s Rank 0: starting distribution step 277s Rank 0 is distributing fusions [1/1] 277s Rank 0: assembler memory usage: 159672 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 is distributing fusions [1/1] (completed) 277s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 tells others to compute fusions. 277s Rank 0 FusionTaskCreator assignNextTask [0/2] 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 FusionTaskCreator processWorkerResult [0/2] 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 FusionTaskCreator [2/2] 277s Statistics: all paths: 1 eliminated during fusing: 0 277s Rank 0: assembler memory usage: 163768 KiB 277s VirtualProcessor: completed jobs: 2 277s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 277s Rank 0: starting clear step. cycleNumber= 1 277s Rank 0 adding 0 new fusions 277s Rank 0 cleared, 1 paths 277s Rank 0 is distributing fusions [1/1] 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 is distributing fusions [1/1] (completed) 277s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 JoinerTaskCreator assignNextTask [0/2] 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s Rank 0 JoinerTaskCreator [2/2] 277s Statistics: all paths: 1 eliminated during joining: 0 277s Rank 0: assembler memory usage: 163768 KiB 277s Date: Sat Mar 15 22:49:36 2025 277s VirtualProcessor: completed jobs: 2 277s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 278s Rank 0 adding 0 new fusions 278s Rank 0 cleared, 1 paths 278s Rank 0: starting distribution step 278s Rank 0 is distributing fusions [1/1] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 is distributing fusions [1/1] (completed) 278s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 tells others to compute fusions. 278s Rank 0 FusionTaskCreator assignNextTask [0/2] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 FusionTaskCreator processWorkerResult [0/2] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 FusionTaskCreator [2/2] 278s Statistics: all paths: 1 eliminated during fusing: 0 278s Rank 0: assembler memory usage: 163768 KiB 278s VirtualProcessor: completed jobs: 2 278s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 278s Rank 0: starting clear step. cycleNumber= 2 278s Rank 0 adding 0 new fusions 278s Rank 0 cleared, 1 paths 278s Rank 0 is distributing fusions [1/1] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 is distributing fusions [1/1] (completed) 278s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 JoinerTaskCreator assignNextTask [0/2] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s Rank 0 JoinerTaskCreator [2/2] 278s Statistics: all paths: 1 eliminated during joining: 0 278s Rank 0: assembler memory usage: 163768 KiB 278s Date: Sat Mar 15 22:49:37 2025 278s VirtualProcessor: completed jobs: 2 278s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 279s Rank 0 adding 0 new fusions 279s Rank 0 cleared, 1 paths 279s Rank 0: starting distribution step 279s Rank 0 is distributing fusions [1/1] 279s Rank 0: assembler memory usage: 163768 KiB 279s Date: Sat Mar 15 22:49:38 2025 279s Rank 0 is distributing fusions [1/1] (completed) 279s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 279s Rank 0: assembler memory usage: 163768 KiB 279s Date: Sat Mar 15 22:49:38 2025 279s Rank 0 cycleNumber= 2 279s 279s *** 279s Step: Merging of redundant paths 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 3 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s 279s Rank 0 appended 1 elements 279s 279s *** 279s Step: Generation of contigs 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 279s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 279s Rank 0 ineligibleObjects: 0/972 (0.00%) 279s Rank 0: assembler memory usage: 163768 KiB 279s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 279s Rank 0 finished gathering scaffold links. 279s Rank 0 will write 1 contig lengths 279s Rank 0 will solve the scaffolding problem. 279s Welcome to GreedySolver v1.0 279s 1 vertices; 0 edges 279s 1 contigs >= 500 279s Edges in solution: 0 279s 279s Conflict statistics: 279s 1 scaffolds, 1 >= 500 279s Total: 1000 nucleotides 279s 279s *** 279s Step: Scaffolding of contigs 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s Rank 0 syncing with master 279s 279s *** 279s Step: Counting sequences to search 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s 279s Rank 0 will add colors, 0 sequences in 0 files to process 279s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 279s 279s *** 279s Step: Graph coloring 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s 279s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 279s Rank 0 shares its counts 279s Rank 0 computing contig abundances [1/1] [1/972] 279s Rank 0 computing contig abundances [1/1] [972/972] 279s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 279s 279s *** 279s Step: Counting contig biological abundances 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s 279s Rank 0 colored the graph with 0 real colors using 1 virtual colors 279s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 279s 279s *** 279s Step: Counting sequence biological abundances 279s Date: Sat Mar 15 22:49:38 2025 279s Elapsed time: 0 seconds 279s Since beginning: 17 seconds 279s *** 279s 279s 279s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 279s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 280s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 280s 280s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 280s Rank 0 is starting taxon syncing across the compute tribe. 280s 280s *** 280s Step: Loading taxons 280s Date: Sat Mar 15 22:49:39 2025 280s Elapsed time: 1 seconds 280s Since beginning: 18 seconds 280s *** 280s 280s Rank 0 synced taxons across the grid with 1 poor slaves. 280s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 280s Rank 0 has 0 taxons after syncing with master 281s 281s 281s *** 281s Step: Loading tree 281s Date: Sat Mar 15 22:49:40 2025 281s Elapsed time: 1 seconds 281s Since beginning: 19 seconds 281s *** 281s 281s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 281s 281s Rank 0: counting ontology terms in the graph... 282s Rank 0: 0 have some biological signal 282s Number of dereferenced alternate handles: 0 282s Number of k-mer observations with gene ontology terms: 0 282s Rank 0: synced ontology term profiles with master 282s Rank 0: synchronization is complete! 282s Rank 0: ontology terms with biological signal: 0 282s Populated recursive values... 282s Gene ontology terms without depth information: 0 282s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 282s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 282s 282s *** 282s Step: Processing gene ontologies 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 1 seconds 282s Since beginning: 20 seconds 282s *** 282s 282s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 282s [GenomeNeighbourhood] in final list: 0 282s 282s *** 282s Step: Computing neighbourhoods 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 0 seconds 282s Since beginning: 20 seconds 282s *** 282s 282s Contigs >= 100 nt 282s Number: 1 282s Total length: 1000 282s Average: 1000 282s N50: 1000 282s Median: 1000 282s Largest: 1000 282s Contigs >= 500 nt 282s Number: 1 282s Total length: 1000 282s Average: 1000 282s N50: 1000 282s Median: 1000 282s Largest: 1000 282s Scaffolds >= 100 nt 282s Number: 1 282s Total length: 1000 282s Average: 1000 282s N50: 1000 282s Median: 1000 282s Largest: 1000 282s Scaffolds >= 500 nt 282s Number: 1 282s Total length: 1000 282s Average: 1000 282s N50: 1000 282s Median: 1000 282s Largest: 1000 282s 282s Rank 0 wrote RayOutput/Contigs.fasta 282s Rank 0 wrote RayOutput/Scaffolds.fasta 282s Check for RayOutput/* 282s 282s 282s 282s ************************************************** 282s This program comes with ABSOLUTELY NO WARRANTY. 282s This is free software, and you are welcome to redistribute it 282s under certain conditions; see "LICENSE.txt" for details. 282s ************************************************** 282s 282s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 282s Centre de recherche en infectiologie de l'Université Laval 282s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 282s http://denovoassembler.sf.net/ 282s 282s References to cite: 282s 282s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 282s Ray Meta: scalable de novo metagenome assembly and profiling. 282s Genome Biology (BioMed Central Ltd). 282s 13:R122, Published: 22 December 2012 282s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 282s 282s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 282s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 282s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 282s November 2010, Volume 17, Issue 11, Pages 1519-1533. 282s http://dx.doi.org/doi:10.1089/cmb.2009.0238 282s 282s Ray version 2.3.1 282s License for Ray: GNU General Public License version 3 282s RayPlatform version: 2.0.1 282s License for RayPlatform: GNU Lesser General Public License version 3 282s 282s MAXKMERLENGTH: 32 282s Maximum coverage depth stored by CoverageDepth: 4294967295 282s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 282s FORCE_PACKING = n 282s ASSERT = n 282s HAVE_LIBZ = y 282s HAVE_LIBBZ2 = y 282s PROFILER_COLLECT = n 282s MINIRANKS = y 282s CLOCK_GETTIME = n 282s __linux__ = y 282s _MSC_VER = n 282s __GNUC__ = y 282s RAY_32_BITS = n 282s RAY_64_BITS = y 282s MPI standard version: MPI 3.1 282s MPI library: Open-MPI 5.0.6 282s Compiler: GNU gcc/g++ 14.2.0 282s MPI I/O: n 282s 282s 282s -k (to set the k-mer size) 282s Value: 31 282s 282s 282s Paired library # 0 282s -p (paired-end sequences) 282s Left sequences: ecoli_1K_1.fq 282s Right sequences: ecoli_1K_2.fq 282s Average length: automatic detection 282s Standard deviation: automatic detection 282s 282s Ray command: 282s mpiexec -n 2 Ray \ 282s -k \ 282s 31 \ 282s -p \ 282s ecoli_1K_1.fq \ 282s ecoli_1K_2.fq \ 282s -o \ 282s test3 282s 282s Rank 0 wrote test3/RayCommand.txt 282s 282s k-mer length: 31 282s Rank 0: assembler memory usage: 42372 KiB 282s Rank 1: assembler memory usage: 42376 KiB 282s Rank 0: assembler memory usage: 108064 KiB 282s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 2618 282s Rank 0: testing the network, please wait... 282s 282s Rank 1: assembler memory usage: 108056 KiB 282s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 2619 282s Rank 1 is testing the network [0/1000] 282s Rank 0 is testing the network [0/1000] 282s Rank 0 is testing the network [1000/1000] 282s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 282s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 282s Rank 1 is testing the network [1000/1000] 282s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 282s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 282s 282s Rank 0 wrote test3/NetworkTest.txt 282s 282s 282s *** 282s Step: Network testing 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 0 seconds 282s Since beginning: 0 seconds 282s *** 282s 282s 282s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 282s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 282s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 282s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 282s Rank 0 wrote test3/NumberOfSequences.txt 282s Rank 0 wrote test3/SequencePartition.txt 282s 282s *** 282s Step: Counting sequences to assemble 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 0 seconds 282s Since beginning: 0 seconds 282s *** 282s 282s 282s Rank 0 is loading sequence reads 282s Rank 1 is loading sequence reads 282s Rank 1 : partition is [2054;4107], 2054 sequence reads 282s Rank 0 : partition is [0;2053], 2054 sequence reads 282s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 282s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 282s Rank 1 has 0 sequence reads 282s Rank 1: assembler memory usage: 116896 KiB 282s Rank 0 has 0 sequence reads 282s Rank 0: assembler memory usage: 116912 KiB 282s Rank 1 has 2054 sequence reads (completed) 282s Rank 0 has 2054 sequence reads (completed) 282s 282s *** 282s Step: Sequence loading 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 0 seconds 282s Since beginning: 0 seconds 282s *** 282s 282s 282s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 282s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 282s Rank 0 created its Bloom filter 282s Rank 0 is counting k-mers in sequence reads [1/2054] 282s Rank 1 created its Bloom filter 282s Rank 1 is counting k-mers in sequence reads [1/2054] 282s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 282s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 282s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 282s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 282s 282s 282s *** 282s Step: K-mer counting 282s Date: Sat Mar 15 22:49:41 2025 282s Elapsed time: 0 seconds 282s Since beginning: 0 seconds 282s *** 282s 282s 282s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 282s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 282s Rank 1 destroyed its Bloom filter 282s Rank 1 has 922 k-mers (completed) 282s Rank 0 destroyed its Bloom filter 282s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 282s Rank 0 has 1032 k-mers (completed) 282s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 282s Rank 1: assembler memory usage: 116896 KiB 282s Rank 0: assembler memory usage: 113180 KiB 283s 283s 283s Rank 0: the minimum coverage is 3 283s Rank 0: the peak coverage is 3 283s Warning: no peak observed in the k-mer coverage distribution. 283s to deal with the sequencing error rate, try to lower the k-mer length (-k) 283s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 283s 283s *** 283s Step: Coverage distribution analysis 283s Date: Sat Mar 15 22:49:42 2025 283s Elapsed time: 1 seconds 283s Since beginning: 1 seconds 283s *** 283s 283s 283s 283s Rank 0 is adding edges [1/2054] 283s Rank 1 is adding edges [1/2054] 283s Rank 1 is adding edges [2054/2054] (completed) 283s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 283s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 283s Rank 0 is adding edges [2054/2054] (completed) 283s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 283s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 283s 283s *** 283s Step: Graph construction 283s Date: Sat Mar 15 22:49:42 2025 283s Elapsed time: 0 seconds 283s Since beginning: 1 seconds 283s *** 283s 283s 283s Rank 1 has 922 vertices (completed) 283s Rank 0 has 1032 vertices (completed) 283s Rank 1: assembler memory usage: 116896 KiB 283s Rank 0: assembler memory usage: 113180 KiB 283s Rank 1 is purging edges [1/922] 283s Rank 0 is purging edges [1/1032] 283s Rank 1 is purging edges [922/922] (completed) 283s Rank 1: assembler memory usage: 116896 KiB 283s VirtualProcessor: completed jobs: 922 283s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 283s Rank 0 is purging edges [1032/1032] (completed) 283s Rank 0: assembler memory usage: 113444 KiB 283s VirtualProcessor: completed jobs: 1032 283s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 284s Rank 0 wrote test3/degreeDistribution.txt 284s 284s *** 284s Step: Null edge purging 284s Date: Sat Mar 15 22:49:43 2025 284s Elapsed time: 1 seconds 284s Since beginning: 2 seconds 284s *** 284s 284s 284s Rank 0 is selecting optimal read markers [1/2054] 284s Rank 0: assembler memory usage: 113444 KiB 284s Rank 1 is selecting optimal read markers [1/2054] 284s Rank 1: assembler memory usage: 116896 KiB 284s Rank 1 is selecting optimal read markers [2054/2054] (completed) 284s Rank 1: peak number of workers: 1121, maximum: 32768 284s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 284s Rank 1: assembler memory usage: 124576 KiB 284s Rank 1: Freeing unused assembler memory: 4096 KiB freed 284s Rank 1: assembler memory usage: 124576 KiB 284s Rank 0 is selecting optimal read markers [2054/2054] (completed) 284s Rank 0: peak number of workers: 1135, maximum: 32768 284s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 284s Rank 0: assembler memory usage: 121688 KiB 284s Rank 0: Freeing unused assembler memory: 4096 KiB freed 284s Rank 0: assembler memory usage: 121688 KiB 284s 284s *** 284s Step: Selection of optimal read markers 284s Date: Sat Mar 15 22:49:43 2025 284s Elapsed time: 0 seconds 284s Since beginning: 2 seconds 284s *** 284s 284s 284s Rank 0: memory usage for optimal read markers= 4096 KiB 284s Rank 1: memory usage for optimal read markers= 4096 KiB 284s Rank 1 is creating seeds [1/922] 284s Rank 1: assembler memory usage: 124576 KiB 284s Rank 0 is creating seeds [1/1032] 284s Rank 0: assembler memory usage: 121688 KiB 285s Rank 0 has 0 seeds 285s Rank 0 is creating seeds [1032/1032] (completed) 285s Rank 0: peak number of workers: 998, maximum: 32768 285s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 285s Rank 0 runtime statistics for seeding algorithm: 285s Rank 0 Skipped paths because of dead end for head: 0 285s Rank 0 Skipped paths because of dead end for tail: 0 285s Rank 0 Skipped paths because of two dead ends: 0 285s Rank 0 Skipped paths because of bubble weak component: 0 285s Rank 0 Skipped paths because of short length: 1031 285s Rank 0 Skipped paths because of bad ownership: 1 285s Rank 0 Skipped paths because of low coverage: 0 285s Rank 0 Eligible paths: 0 285s Rank 0: assembler memory usage: 121688 KiB 285s Rank 1 has 1 seeds 285s Rank 1 is creating seeds [922/922] (completed) 285s Rank 1: peak number of workers: 916, maximum: 32768 285s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 285s Rank 1 runtime statistics for seeding algorithm: 285s Rank 1 Skipped paths because of dead end for head: 0 285s Rank 1 Skipped paths because of dead end for tail: 0 285s Rank 1 Skipped paths because of two dead ends: 0 285s Rank 1 Skipped paths because of bubble weak component: 0 285s Rank 1 Skipped paths because of short length: 921 285s Rank 1 Skipped paths because of bad ownership: 0 285s Rank 1 Skipped paths because of low coverage: 0 285s Rank 1 Eligible paths: 1 285s Rank 1: assembler memory usage: 124576 KiB 285s Rank 1 has 1 seeds to register. 285s Rank 0 registered -1/0 285s Rank 0 registered its seeds 285s Rank 1 registered 0/1 285s Rank 1 registered 0/1 285s Rank 1 registered its seeds 285s VirtualProcessor: completed jobs: 0 285s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 285s VirtualProcessor: completed jobs: 0 285s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 285s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 285s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 295s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 295s Rank 0 merged its seeds: 0 seeds -> 0 seeds 295s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 295s Rank 1 merged its seeds: 1 seeds -> 1 seeds 295s 295s *** 295s Step: Detection of assembly seeds 295s Date: Sat Mar 15 22:49:54 2025 295s Elapsed time: 11 seconds 295s Since beginning: 13 seconds 295s *** 295s 295s 295s Rank 0 detected 0 library lengths 295s Rank 0 is calculating library lengths [0/0] (completed) 295s Rank 0: peak number of workers: 0, maximum: 32768 295s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 295s Rank 0: assembler memory usage: 125784 KiB 295s Rank 1 is calculating library lengths [1/1] 295s Rank 1 detected 1737 library lengths 295s Rank 1 is calculating library lengths [1/1] (completed) 295s Rank 1: peak number of workers: 1, maximum: 32768 295s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7990 virtual messages generated 7990 real messages (100%) 295s Rank 1: assembler memory usage: 157348 KiB 295s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 295s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 295s 295s Mode= 2 signalAverage= 9 295s CURRENT IS NOISE, 244 295s GOT HIT 212 295s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 295s 295s 295s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 295s 295s *** 295s Step: Estimation of outer distances for paired reads 295s Date: Sat Mar 15 22:49:54 2025 295s Elapsed time: 0 seconds 295s Since beginning: 13 seconds 295s *** 295s 295s 295s Rank 0 is extending seeds [0/0] (completed) 295s Rank 0 extended 0 seeds out of 0 (0.00%) 295s Rank 0: assembler memory usage: 125784 KiB 295s Rank 1 traversed 1000 nucleotide symbols 295s Rank 1: assembler memory usage: 161444 KiB 295s Rank 1 is extending seeds [1/1] (completed) 295s Rank 1 extended 1 seeds out of 1 (100.00%) 295s Rank 1: assembler memory usage: 161444 KiB 295s Rank 0 starting fusions 295s 295s *** 295s Step: Bidirectional extension of seeds 295s Date: Sat Mar 15 22:49:54 2025 295s Elapsed time: 0 seconds 295s Since beginning: 13 seconds 295s *** 295s 295s 295s Rank 0: starting clear step. cycleNumber= 0 296s Rank 1 adding 0 new fusions 296s Rank 1 cleared, 1 paths 296s Rank 0 adding 0 new fusions 296s Rank 0 cleared, 0 paths 296s Rank 0: starting distribution step 296s Rank 0 is distributing fusions [0/0] (completed) 296s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 296s Rank 1 is distributing fusions [1/1] 296s Rank 0: assembler memory usage: 125784 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 is distributing fusions [1/1] (completed) 296s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 0 tells others to compute fusions. 296s Rank 0 FusionTaskCreator [0/0] 296s Statistics: all paths: 0 eliminated during fusing: 0 296s Rank 0: assembler memory usage: 125784 KiB 296s VirtualProcessor: completed jobs: 0 296s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 296s Rank 1 FusionTaskCreator assignNextTask [0/2] 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 FusionTaskCreator processWorkerResult [0/2] 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 FusionTaskCreator [2/2] 296s Statistics: all paths: 1 eliminated during fusing: 0 296s Rank 1: assembler memory usage: 161444 KiB 296s VirtualProcessor: completed jobs: 2 296s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10900 virtual messages generated 10900 real messages (100%) 296s Rank 0: starting clear step. cycleNumber= 1 296s Rank 0 adding 0 new fusions 296s Rank 0 cleared, 0 paths 296s Rank 1 adding 0 new fusions 296s Rank 1 cleared, 1 paths 296s Rank 0 is distributing fusions [0/0] (completed) 296s Rank 1 is distributing fusions [1/1] 296s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 0: assembler memory usage: 125784 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 is distributing fusions [1/1] (completed) 296s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 JoinerTaskCreator assignNextTask [0/2] 296s Rank 0 JoinerTaskCreator [0/0] 296s Statistics: all paths: 0 eliminated during joining: 0 296s Rank 0: assembler memory usage: 125784 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s VirtualProcessor: completed jobs: 0 296s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s Rank 1 JoinerTaskCreator [2/2] 296s Statistics: all paths: 1 eliminated during joining: 0 296s Rank 1: assembler memory usage: 161444 KiB 296s Date: Sat Mar 15 22:49:55 2025 296s VirtualProcessor: completed jobs: 2 296s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13810 virtual messages generated 13810 real messages (100%) 297s Rank 1 adding 0 new fusions 297s Rank 1 cleared, 1 paths 297s Rank 0 adding 0 new fusions 297s Rank 0 cleared, 0 paths 297s Rank 1 is distributing fusions [1/1] 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 0: starting distribution step 297s Rank 0 is distributing fusions [0/0] (completed) 297s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 297s Rank 0: assembler memory usage: 125784 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 is distributing fusions [1/1] (completed) 297s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 0 tells others to compute fusions. 297s Rank 1 FusionTaskCreator assignNextTask [0/2] 297s Rank 0 FusionTaskCreator [0/0] 297s Statistics: all paths: 0 eliminated during fusing: 0 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 0: assembler memory usage: 125784 KiB 297s VirtualProcessor: completed jobs: 0 297s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 297s Rank 1 FusionTaskCreator processWorkerResult [0/2] 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 FusionTaskCreator [2/2] 297s Statistics: all paths: 1 eliminated during fusing: 0 297s Rank 1: assembler memory usage: 161444 KiB 297s VirtualProcessor: completed jobs: 2 297s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16720 virtual messages generated 16720 real messages (100%) 297s Rank 0: starting clear step. cycleNumber= 2 297s Rank 1 adding 0 new fusions 297s Rank 1 cleared, 1 paths 297s Rank 0 adding 0 new fusions 297s Rank 0 cleared, 0 paths 297s Rank 1 is distributing fusions [1/1] 297s Rank 1: assembler memory usage: 161444 KiB 297s Rank 0 is distributing fusions [0/0] (completed) 297s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 0: assembler memory usage: 125784 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 is distributing fusions [1/1] (completed) 297s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 JoinerTaskCreator assignNextTask [0/2] 297s Rank 0 JoinerTaskCreator [0/0] 297s Rank 1: assembler memory usage: 161444 KiB 297s Statistics: all paths: 0 eliminated during joining: 0 297s Rank 0: assembler memory usage: 125784 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s VirtualProcessor: completed jobs: 0 297s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s Rank 1 JoinerTaskCreator [2/2] 297s Statistics: all paths: 1 eliminated during joining: 0 297s Rank 1: assembler memory usage: 161444 KiB 297s Date: Sat Mar 15 22:49:56 2025 297s VirtualProcessor: completed jobs: 2 297s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19630 virtual messages generated 19630 real messages (100%) 298s Rank 1 adding 0 new fusions 298s Rank 1 cleared, 1 paths 298s Rank 0 adding 0 new fusions 298s Rank 0 cleared, 0 paths 298s Rank 0: starting distribution step 298s Rank 0 is distributing fusions [0/0] (completed) 298s Rank 1 is distributing fusions [1/1] 298s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 298s Rank 0: assembler memory usage: 125784 KiB 298s Rank 1: assembler memory usage: 161444 KiB 298s Date: Sat Mar 15 22:49:57 2025 298s Date: Sat Mar 15 22:49:57 2025 298s Rank 1 is distributing fusions [1/1] (completed) 298s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 298s Rank 1: assembler memory usage: 161444 KiB 298s Date: Sat Mar 15 22:49:57 2025 298s Rank 0 cycleNumber= 2 298s 298s *** 298s Step: Merging of redundant paths 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 3 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s 298s Rank 0 appended 0 elements 298s Rank 1 appended 1 elements 298s 298s *** 298s Step: Generation of contigs 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 0 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s Rank 0 finished gathering scaffold links. 298s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 298s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 298s Rank 0 ineligibleObjects: 0/970 (0.00%) 298s Rank 1: assembler memory usage: 161444 KiB 298s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 298s Rank 1 finished gathering scaffold links. 298s Rank 0 will write 1 contig lengths 298s Rank 0 will solve the scaffolding problem. 298s Welcome to GreedySolver v1.0 298s 1 vertices; 0 edges 298s 1 contigs >= 500 298s Edges in solution: 0 298s 298s Conflict statistics: 298s 1 scaffolds, 1 >= 500 298s Total: 1000 nucleotides 298s 298s *** 298s Step: Scaffolding of contigs 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 0 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s Rank 0 syncing with master 298s Rank 1 syncing with master 298s 298s *** 298s Step: Counting sequences to search 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 0 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s 298s Rank 1 will add colors, 0 sequences in 0 files to process 298s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 298s Rank 0 will add colors, 0 sequences in 0 files to process 298s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 298s 298s *** 298s Step: Graph coloring 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 0 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s 298s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 298s Rank 0 shares its counts 298s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 298s Rank 1 computing contig abundances [1/1] [1/970] 298s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 298s Rank 1 computing contig abundances [1/1] [970/970] 298s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 298s 298s *** 298s Step: Counting contig biological abundances 298s Date: Sat Mar 15 22:49:57 2025 298s Elapsed time: 0 seconds 298s Since beginning: 16 seconds 298s *** 298s 298s 298s Rank 1 colored the graph with 0 real colors using 1 virtual colors 298s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 298s Rank 0 colored the graph with 0 real colors using 1 virtual colors 298s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 298s 298s *** 298s Step: Counting sequence biological abundances 298s Date: Sat Mar 15 22:49:57 2025 299s Elapsed time: 0 seconds 299s Since beginning: 16 seconds 299s *** 299s 299s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 299s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 299s 299s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 299s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 299s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 299s 299s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 299s 299s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 299s Rank 0 is starting taxon syncing across the compute tribe. 299s 299s *** 299s Step: Loading taxons 299s Date: Sat Mar 15 22:49:58 2025 299s Elapsed time: 1 seconds 299s Since beginning: 17 seconds 299s *** 299s 299s Rank 0 synced taxons across the grid with 2 poor slaves. 299s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 299s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 299s Rank 1 has 0 taxons after syncing with master 299s Rank 0 has 0 taxons after syncing with master 300s 300s 300s 300s *** 300s Step: Loading tree 300s Date: Sat Mar 15 22:49:59 2025 300s Elapsed time: 1 seconds 300s Since beginning: 18 seconds 300s *** 300s 300s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 300s 300s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 300s 300s Rank 0: counting ontology terms in the graph... 300s Rank 1: counting ontology terms in the graph... 301s Rank 0: 0 have some biological signal 301s Number of dereferenced alternate handles: 0 301s Number of k-mer observations with gene ontology terms: 0 301s Rank 0: synced ontology term profiles with master 301s Rank 1: 0 have some biological signal 301s Number of dereferenced alternate handles: 0 301s Number of k-mer observations with gene ontology terms: 0 301s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 301s Rank 1: synced ontology term profiles with master 301s Rank 0: synchronization is complete! 301s Rank 0: ontology terms with biological signal: 0 301s Populated recursive values... 301s Gene ontology terms without depth information: 0 301s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 301s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 301s 301s *** 301s Step: Processing gene ontologies 301s Date: Sat Mar 15 22:50:00 2025 301s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 301s Elapsed time: 1 seconds 301s Since beginning: 19 seconds 301s *** 301s 301s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 301s [GenomeNeighbourhood] in final list: 0 301s 301s *** 301s Step: Computing neighbourhoods 301s Date: Sat Mar 15 22:50:00 2025 301s Elapsed time: 0 seconds 301s Since beginning: 19 seconds 301s *** 301s 301s Contigs >= 100 nt 301s Number: 1 301s Total length: 1000 301s Average: 1000 301s N50: 1000 301s Median: 1000 301s Largest: 1000 301s Contigs >= 500 nt 301s Number: 1 301s Total length: 1000 301s Average: 1000 301s N50: 1000 301s Median: 1000 301s Largest: 1000 301s Scaffolds >= 100 nt 301s Number: 1 301s Total length: 1000 301s Average: 1000 301s N50: 1000 301s Median: 1000 301s Largest: 1000 301s Scaffolds >= 500 nt 301s Number: 1 301s Total length: 1000 301s Average: 1000 301s N50: 1000 301s Median: 1000 301s Largest: 1000 301s 301s Rank 0 wrote test3/Contigs.fasta 301s Rank 0 wrote test3/Scaffolds.fasta 301s Check for test3/* 301s 301s 301s autopkgtest [22:50:00]: test run-unit-test: -----------------------] 302s autopkgtest [22:50:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 302s run-unit-test PASS 302s autopkgtest [22:50:01]: @@@@@@@@@@@@@@@@@@@@ summary 302s run-unit-test PASS 319s nova [W] Skipping flock for amd64 319s Creating nova instance adt-plucky-amd64-ray-20250315-224459-juju-7f2275-prod-proposed-migration-environment-20-7f7b7129-01c2-4f0f-989f-65b86985ed3a from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 319s nova [W] Timed out waiting for 0546c054-7faf-4f3e-a841-d6168c6b2500 to get deleted.