0s autopkgtest [18:37:41]: starting date and time: 2025-03-15 18:37:41+0000 0s autopkgtest [18:37:41]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:37:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gyqewf2y/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 autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-20.secgroup --name adt-plucky-s390x-ray-20250315-183741-juju-7f2275-prod-proposed-migration-environment-2-ed245a12-83b1-47e0-bbce-6339c7908022 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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/ 101s autopkgtest [18:39:22]: testbed dpkg architecture: s390x 101s autopkgtest [18:39:22]: testbed apt version: 2.9.33 101s autopkgtest [18:39:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 101s autopkgtest [18:39:22]: testbed release detected to be: None 102s autopkgtest [18:39:23]: updating testbed package index (apt update) 102s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 103s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 103s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 104s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 104s Fetched 1073 kB in 1s (754 kB/s) 104s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s Calculating upgrade... 105s The following packages were automatically installed and are no longer required: 105s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 105s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 105s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 105s linux-tools-6.11.0-8-generic 105s Use 'sudo apt autoremove' to remove them. 105s The following packages will be upgraded: 105s pinentry-curses python3-jinja2 strace 105s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 652 kB of archives. 105s After this operation, 27.6 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 106s Fetched 652 kB in 1s (913 kB/s) 106s (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 ... 81428 files and directories currently installed.) 106s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 106s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 106s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 106s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 106s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 106s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 107s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 107s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 107s Setting up strace (6.13+ds-1ubuntu1) ... 107s Processing triggers for man-db (2.13.0-1) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Solving dependencies... 108s The following packages will be REMOVED: 108s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 108s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 108s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 108s linux-tools-6.11.0-8-generic* 108s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 108s After this operation, 167 MB disk space will be freed. 108s (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 ... 81428 files and directories currently installed.) 108s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 108s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 108s Removing libpython3.12t64:s390x (3.12.9-1) ... 108s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 108s Removing libnsl2:s390x (1.3.0-3build3) ... 108s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 108s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 108s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 109s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 109s Processing triggers for libc-bin (2.41-1ubuntu1) ... 109s (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 ... 56328 files and directories currently installed.) 109s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 109s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 109s autopkgtest [18:39:30]: upgrading testbed (apt dist-upgrade and autopurge) 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 110s Entering ResolveByKeep 110s 110s Calculating upgrade... 110s The following packages will be upgraded: 110s libc-bin libc-dev-bin libc6 libc6-dev locales 110s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 9512 kB of archives. 110s After this operation, 8192 B of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 112s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 115s Preconfiguring packages ... 115s Fetched 9512 kB in 5s (1976 kB/s) 115s (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 ... 56326 files and directories currently installed.) 115s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Setting up libc6:s390x (2.41-1ubuntu2) ... 115s (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 ... 56326 files and directories currently installed.) 115s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 115s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Setting up libc-bin (2.41-1ubuntu2) ... 115s (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 ... 56326 files and directories currently installed.) 115s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 115s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up locales (2.41-1ubuntu2) ... 116s Generating locales (this might take a while)... 117s en_US.UTF-8... done 117s Generation complete. 117s Setting up libc-dev-bin (2.41-1ubuntu2) ... 117s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 117s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for systemd (257.3-1ubuntu3) ... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Starting pkgProblemResolver with broken count: 0 118s Starting 2 pkgProblemResolver with broken count: 0 118s Done 118s Solving dependencies... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [18:39:39]: rebooting testbed after setup commands that affected boot 137s autopkgtest [18:39:58]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 140s autopkgtest [18:40:01]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 143s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (dsc) [2123 B] 143s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (tar) [450 kB] 143s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (diff) [213 kB] 143s gpgv: Signature made Mon Dec 2 16:02:51 2024 UTC 143s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 143s gpgv: issuer "tille@debian.org" 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-9.dsc: no acceptable signature found 143s autopkgtest [18:40:04]: testing package ray version 2.3.1-9 144s autopkgtest [18:40:05]: build not needed 144s autopkgtest [18:40:05]: test run-unit-test: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 145s The following NEW packages will be installed: 145s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 145s libcairo2 libdatrie1 libdeflate0 libevent-pthreads-2.1-7t64 libfabric1 145s libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 145s libharfbuzz0b libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 145s libjpeg8 liblapack3 libmunge2 libopenmpi40 libpango-1.0-0 145s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 145s libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 libsm6 libtcl8.6 145s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 145s libxft2 libxnvctrl0 libxrender1 libxss1 libxt6t64 mpi-default-bin 145s ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core ray ray-doc 145s ray-extra unzip x11-common xdg-utils zip 145s 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 45.0 MB of archives. 145s After this operation, 97.9 MB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 146s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 146s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 147s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 147s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 147s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 147s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 147s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 147s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 147s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 147s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 147s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 147s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 147s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 55.0-1ubuntu1 [73.7 kB] 147s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 148s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 148s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 148s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 148s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 148s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 148s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 148s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 148s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 148s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 148s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 151s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 151s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 151s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 151s Get:31 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 151s Get:32 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 151s Get:33 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 151s Get:34 http://ftpmaster.internal/ubuntu plucky/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 153s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 153s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 153s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 153s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 153s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 153s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 153s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 153s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 153s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 153s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 154s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 154s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 154s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 154s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 154s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 154s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 154s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 154s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-common all 5.0.7-1 [97.9 kB] 154s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-bin s390x 5.0.7-1 [200 kB] 155s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 155s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 155s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 155s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 172s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x mpi-default-bin s390x 1.18 [2510 B] 172s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x ray s390x 2.3.1-9 [771 kB] 172s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x ray-doc all 2.3.1-9 [35.2 kB] 172s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x ray-extra all 2.3.1-9 [12.3 kB] 173s Preconfiguring packages ... 173s Fetched 45.0 MB in 27s (1648 kB/s) 173s Selecting previously unselected package libfreetype6:s390x. 173s (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 ... 56326 files and directories currently installed.) 173s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 173s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 173s Selecting previously unselected package fonts-dejavu-mono. 173s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 173s Unpacking fonts-dejavu-mono (2.37-8) ... 173s Selecting previously unselected package fonts-dejavu-core. 173s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 173s Unpacking fonts-dejavu-core (2.37-8) ... 173s Selecting previously unselected package fontconfig-config. 173s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 173s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 173s Selecting previously unselected package libfontconfig1:s390x. 173s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 173s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 173s Selecting previously unselected package fontconfig. 173s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 173s Unpacking fontconfig (2.15.0-2ubuntu1) ... 173s Selecting previously unselected package libblas3:s390x. 173s Preparing to unpack .../06-libblas3_3.12.1-2_s390x.deb ... 173s Unpacking libblas3:s390x (3.12.1-2) ... 173s Selecting previously unselected package libpixman-1-0:s390x. 173s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_s390x.deb ... 173s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 173s Selecting previously unselected package libxcb-render0:s390x. 173s Preparing to unpack .../08-libxcb-render0_1.17.0-2_s390x.deb ... 173s Unpacking libxcb-render0:s390x (1.17.0-2) ... 173s Selecting previously unselected package libxcb-shm0:s390x. 173s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_s390x.deb ... 173s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 173s Selecting previously unselected package libxrender1:s390x. 173s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 173s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 173s Selecting previously unselected package libcairo2:s390x. 173s Preparing to unpack .../11-libcairo2_1.18.2-2_s390x.deb ... 173s Unpacking libcairo2:s390x (1.18.2-2) ... 173s Selecting previously unselected package libdatrie1:s390x. 173s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_s390x.deb ... 173s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 173s Selecting previously unselected package libdeflate0:s390x. 173s Preparing to unpack .../13-libdeflate0_1.23-1_s390x.deb ... 173s Unpacking libdeflate0:s390x (1.23-1) ... 173s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 173s Preparing to unpack .../14-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 173s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 173s Selecting previously unselected package librdmacm1t64:s390x. 173s Preparing to unpack .../15-librdmacm1t64_55.0-1ubuntu1_s390x.deb ... 173s Unpacking librdmacm1t64:s390x (55.0-1ubuntu1) ... 173s Selecting previously unselected package libfabric1:s390x. 173s Preparing to unpack .../16-libfabric1_1.17.0-3.1_s390x.deb ... 173s Unpacking libfabric1:s390x (1.17.0-3.1) ... 173s Selecting previously unselected package libgfortran5:s390x. 173s Preparing to unpack .../17-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 173s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 173s Selecting previously unselected package libgomp1:s390x. 173s Preparing to unpack .../18-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 173s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 173s Selecting previously unselected package libgraphite2-3:s390x. 173s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 173s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 173s Selecting previously unselected package libharfbuzz0b:s390x. 173s Preparing to unpack .../20-libharfbuzz0b_10.2.0-1_s390x.deb ... 173s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 173s Selecting previously unselected package libhwloc15:s390x. 173s Preparing to unpack .../21-libhwloc15_2.12.0-1_s390x.deb ... 173s Unpacking libhwloc15:s390x (2.12.0-1) ... 173s Selecting previously unselected package x11-common. 173s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu3_all.deb ... 173s Unpacking x11-common (1:7.7+23ubuntu3) ... 173s Selecting previously unselected package libice6:s390x. 173s Preparing to unpack .../23-libice6_2%3a1.1.1-1_s390x.deb ... 173s Unpacking libice6:s390x (2:1.1.1-1) ... 173s Selecting previously unselected package libjpeg-turbo8:s390x. 173s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 173s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 173s Selecting previously unselected package libjpeg8:s390x. 173s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_s390x.deb ... 173s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 173s Selecting previously unselected package liblapack3:s390x. 173s Preparing to unpack .../26-liblapack3_3.12.1-2_s390x.deb ... 173s Unpacking liblapack3:s390x (3.12.1-2) ... 173s Selecting previously unselected package libmunge2:s390x. 173s Preparing to unpack .../27-libmunge2_0.5.16-1_s390x.deb ... 173s Unpacking libmunge2:s390x (0.5.16-1) ... 173s Selecting previously unselected package libpciaccess0:s390x. 173s Preparing to unpack .../28-libpciaccess0_0.17-3build1_s390x.deb ... 173s Unpacking libpciaccess0:s390x 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previously unselected package libthai-data. 173s Preparing to unpack .../34-libthai-data_0.1.29-2build1_all.deb ... 173s Unpacking libthai-data (0.1.29-2build1) ... 173s Selecting previously unselected package libthai0:s390x. 173s Preparing to unpack .../35-libthai0_0.1.29-2build1_s390x.deb ... 173s Unpacking libthai0:s390x (0.1.29-2build1) ... 173s Selecting previously unselected package libpango-1.0-0:s390x. 173s Preparing to unpack .../36-libpango-1.0-0_1.56.2-1_s390x.deb ... 173s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 173s Selecting previously unselected package libpangoft2-1.0-0:s390x. 173s Preparing to unpack .../37-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 173s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 173s Selecting previously unselected package libpangocairo-1.0-0:s390x. 173s Preparing to unpack .../38-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 173s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 173s Selecting previously unselected package libpaper2:s390x. 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r-base-core. 174s Preparing to unpack .../56-r-base-core_4.4.3-1_s390x.deb ... 174s Unpacking r-base-core (4.4.3-1) ... 174s Selecting previously unselected package mpi-default-bin. 174s Preparing to unpack .../57-mpi-default-bin_1.18_s390x.deb ... 174s Unpacking mpi-default-bin (1.18) ... 174s Selecting previously unselected package ray. 174s Preparing to unpack .../58-ray_2.3.1-9_s390x.deb ... 174s Unpacking ray (2.3.1-9) ... 174s Selecting previously unselected package ray-doc. 174s Preparing to unpack .../59-ray-doc_2.3.1-9_all.deb ... 174s Unpacking ray-doc (2.3.1-9) ... 174s Selecting previously unselected package ray-extra. 174s Preparing to unpack .../60-ray-extra_2.3.1-9_all.deb ... 174s Unpacking ray-extra (2.3.1-9) ... 174s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 174s Setting up libpixman-1-0:s390x (0.44.0-3) ... 174s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 174s Setting up ray-doc (2.3.1-9) ... 174s Setting up libpciaccess0:s390x (0.17-3build1) ... 174s 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(3.12.1-2) ... 174s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 174s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 174s Setting up libpaper-utils (2.2.5-0.3) ... 174s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 174s Setting up libthai0:s390x (0.1.29-2build1) ... 174s Setting up libpmix2t64:s390x (5.0.6-5) ... 174s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 174s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 174s Setting up libsm6:s390x (2:1.2.4-1) ... 174s Setting up libopenmpi40:s390x (5.0.7-1) ... 174s Setting up fontconfig (2.15.0-2ubuntu1) ... 176s Regenerating fonts cache... done. 176s Setting up libxft2:s390x (2.3.6-1build1) ... 176s Setting up libtk8.6:s390x (8.6.16-1) ... 176s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 176s Setting up libcairo2:s390x (1.18.2-2) ... 176s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 176s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 176s Setting up openmpi-bin (5.0.7-1) ... 176s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 177s 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 177s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 177s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 177s Setting up mpi-default-bin (1.18) ... 177s Setting up r-base-core (4.4.3-1) ... 177s Creating config file /etc/R/Renviron with new version 177s Setting up ray (2.3.1-9) ... 177s Setting up ray-extra (2.3.1-9) ... 177s Processing triggers for libc-bin (2.41-1ubuntu2) ... 177s Processing triggers for man-db (2.13.0-1) ... 177s Processing triggers for install-info (7.1.1-1) ... 178s autopkgtest [18:40:39]: test run-unit-test: [----------------------- 178s 178s ************************************************** 178s This program comes with ABSOLUTELY NO WARRANTY. 178s This is free software, and you are welcome to redistribute it 178s under certain conditions; see "LICENSE.txt" for details. 178s ************************************************** 178s 178s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 178s Centre de recherche en infectiologie de l'Université Laval 178s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 178s http://denovoassembler.sf.net/ 178s 178s References to cite: 178s 178s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 178s Ray Meta: scalable de novo metagenome assembly and profiling. 178s Genome Biology (BioMed Central Ltd). 178s 13:R122, Published: 22 December 2012 178s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 178s 178s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 178s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 178s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 178s November 2010, Volume 17, Issue 11, Pages 1519-1533. 178s http://dx.doi.org/doi:10.1089/cmb.2009.0238 178s 178s Ray version 2.3.1 178s License for Ray: GNU General Public License version 3 178s RayPlatform version: 2.0.1 178s License for RayPlatform: GNU Lesser General Public License version 3 178s 178s MAXKMERLENGTH: 32 178s Maximum coverage depth stored by CoverageDepth: 4294967295 178s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 178s FORCE_PACKING = n 178s ASSERT = n 178s HAVE_LIBZ = y 178s HAVE_LIBBZ2 = y 178s PROFILER_COLLECT = n 178s MINIRANKS = y 178s CLOCK_GETTIME = n 178s __linux__ = y 178s _MSC_VER = n 178s __GNUC__ = y 178s RAY_32_BITS = n 178s RAY_64_BITS = y 178s MPI standard version: MPI 3.1 178s MPI library: Open-MPI 5.0.6 178s Compiler: GNU gcc/g++ 14.2.0 178s MPI I/O: n 178s 178s 178s -k (to set the k-mer size) 178s Value: 31 178s 178s 178s Paired library # 0 178s -p (paired-end sequences) 178s Left sequences: ecoli_1K_1.fq 178s Right sequences: ecoli_1K_2.fq 178s Average length: automatic detection 178s Standard deviation: automatic detection 178s 178s Ray command: 178s mpiexec -n 1 Ray \ 178s -k \ 178s 31 \ 178s -p \ 178s ecoli_1K_1.fq \ 178s ecoli_1K_2.fq \ 178s -o \ 178s test1 178s 178s Rank 0 wrote test1/RayCommand.txt 178s 178s k-mer length: 31 178s Rank 0: assembler memory usage: 33696 KiB 178s Rank 0: assembler memory usage: 99368 KiB 178s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2506 178s Rank 0: testing the network, please wait... 178s 178s Rank 0 is testing the network [0/1000] 178s Rank 0 is testing the network [1000/1000] 178s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 178s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 178s 178s Rank 0 wrote test1/NetworkTest.txt 178s 178s 178s *** 178s Step: Network testing 178s Date: Sat Mar 15 18:40:39 2025 178s Elapsed time: 0 seconds 178s Since beginning: 0 seconds 178s *** 178s 178s 178s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 178s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 178s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 178s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 178s Rank 0 wrote test1/NumberOfSequences.txt 178s Rank 0 wrote test1/SequencePartition.txt 178s 178s *** 178s Step: Counting sequences to assemble 178s Date: Sat Mar 15 18:40:39 2025 178s Elapsed time: 0 seconds 178s Since beginning: 0 seconds 178s *** 178s 178s 178s Rank 0 is loading sequence reads 178s Rank 0 : partition is [0;4107], 4108 sequence reads 178s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 178s Rank 0 has 0 sequence reads 178s Rank 0: assembler memory usage: 112324 KiB 178s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 178s Rank 0 has 4108 sequence reads (completed) 178s 178s *** 178s Step: Sequence loading 178s Date: Sat Mar 15 18:40:39 2025 178s Elapsed time: 0 seconds 178s Since beginning: 0 seconds 178s *** 178s 178s 178s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 178s Rank 0 created its Bloom filter 178s Rank 0 is counting k-mers in sequence reads [1/4108] 178s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 178s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 178s 178s 178s *** 178s Step: K-mer counting 178s Date: Sat Mar 15 18:40:39 2025 178s Elapsed time: 0 seconds 178s Since beginning: 0 seconds 178s *** 178s 178s 178s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 178s Rank 0 destroyed its Bloom filter 178s Rank 0 has 1954 k-mers (completed) 178s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 178s Rank 0: assembler memory usage: 108720 KiB 179s 179s 179s Rank 0: the minimum coverage is 3 179s Rank 0: the peak coverage is 3 179s Warning: no peak observed in the k-mer coverage distribution. 179s to deal with the sequencing error rate, try to lower the k-mer length (-k) 179s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 179s 179s *** 179s Step: Coverage distribution analysis 179s Date: Sat Mar 15 18:40:40 2025 179s Elapsed time: 1 seconds 179s Since beginning: 1 seconds 179s *** 179s 179s 179s 179s Rank 0 is adding edges [1/4108] 179s Rank 0 is adding edges [4108/4108] (completed) 179s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 179s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 179s 179s *** 179s Step: Graph construction 179s Date: Sat Mar 15 18:40:40 2025 179s Elapsed time: 0 seconds 179s Since beginning: 1 seconds 179s *** 179s 179s 179s Rank 0 has 1954 vertices (completed) 179s Rank 0: assembler memory usage: 108720 KiB 180s Rank 0 is purging edges [1/1954] 180s Rank 0 is purging edges [1954/1954] (completed) 180s Rank 0: assembler memory usage: 109248 KiB 180s VirtualProcessor: completed jobs: 1954 180s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 181s Rank 0 wrote test1/degreeDistribution.txt 181s 181s *** 181s Step: Null edge purging 181s Date: Sat Mar 15 18:40:41 2025 181s Elapsed time: 1 seconds 181s Since beginning: 2 seconds 181s *** 181s 181s 181s Rank 0 is selecting optimal read markers [1/4108] 181s Rank 0: assembler memory usage: 109248 KiB 181s Rank 0 is selecting optimal read markers [4108/4108] (completed) 181s Rank 0: peak number of workers: 599, maximum: 32768 181s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 181s Rank 0: assembler memory usage: 117376 KiB 181s Rank 0: Freeing unused assembler memory: 4096 KiB freed 181s Rank 0: assembler memory usage: 117376 KiB 181s 181s *** 181s Step: Selection of optimal read markers 181s Date: Sat Mar 15 18:40:42 2025 181s Elapsed time: 1 seconds 181s Since beginning: 3 seconds 181s *** 181s 181s 181s Rank 0: memory usage for optimal read markers= 4096 KiB 181s Rank 0 is creating seeds [1/1954] 181s Rank 0: assembler memory usage: 117376 KiB 181s Rank 0 has 1 seeds 181s Rank 0 is creating seeds [1954/1954] (completed) 181s Rank 0: peak number of workers: 746, maximum: 32768 181s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 181s Rank 0 runtime statistics for seeding algorithm: 181s Rank 0 Skipped paths because of dead end for head: 0 181s Rank 0 Skipped paths because of dead end for tail: 0 181s Rank 0 Skipped paths because of two dead ends: 0 181s Rank 0 Skipped paths because of bubble weak component: 0 181s Rank 0 Skipped paths because of short length: 1952 181s Rank 0 Skipped paths because of bad ownership: 1 181s Rank 0 Skipped paths because of low coverage: 0 181s Rank 0 Eligible paths: 1 181s Rank 0: assembler memory usage: 117376 KiB 181s Rank 0 has 1 seeds to register. 181s Rank 0 registered 0/1 181s Rank 0 registered 0/1 181s Rank 0 registered its seeds 181s VirtualProcessor: completed jobs: 0 181s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 182s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 192s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 192s Rank 0 merged its seeds: 1 seeds -> 1 seeds 192s 192s *** 192s Step: Detection of assembly seeds 192s Date: Sat Mar 15 18:40:53 2025 192s Elapsed time: 11 seconds 192s Since beginning: 14 seconds 192s *** 192s 192s 192s Rank 0 is calculating library lengths [1/1] 192s Rank 0 detected 1737 library lengths 192s Rank 0 is calculating library lengths [1/1] (completed) 192s Rank 0: peak number of workers: 1, maximum: 32768 192s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 192s Rank 0: assembler memory usage: 154244 KiB 192s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 192s 192s Mode= 2 signalAverage= 9 192s CURRENT IS NOISE, 244 192s GOT HIT 212 192s 192s 192s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 192s 192s *** 192s Step: Estimation of outer distances for paired reads 192s Date: Sat Mar 15 18:40:53 2025 192s Elapsed time: 0 seconds 192s Since beginning: 14 seconds 192s *** 192s 192s 192s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 192s Rank 0 traversed 1000 nucleotide symbols 192s Rank 0: assembler memory usage: 158340 KiB 192s Rank 0 is extending seeds [1/1] (completed) 192s Rank 0 extended 1 seeds out of 1 (100.00%) 192s Rank 0: assembler memory usage: 150148 KiB 192s Rank 0 starting fusions 192s 192s *** 192s Step: Bidirectional extension of seeds 192s Date: Sat Mar 15 18:40:53 2025 192s Elapsed time: 0 seconds 192s Since beginning: 14 seconds 192s *** 192s 192s 192s Rank 0: starting clear step. cycleNumber= 0 193s Rank 0 adding 0 new fusions 193s Rank 0 cleared, 1 paths 193s Rank 0: starting distribution step 193s Rank 0 is distributing fusions [1/1] 193s Rank 0: assembler memory usage: 150148 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 is distributing fusions [1/1] (completed) 193s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 tells others to compute fusions. 193s Rank 0 FusionTaskCreator assignNextTask [0/2] 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 FusionTaskCreator processWorkerResult [0/2] 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 FusionTaskCreator [2/2] 193s Statistics: all paths: 1 eliminated during fusing: 0 193s Rank 0: assembler memory usage: 154244 KiB 193s VirtualProcessor: completed jobs: 2 193s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 193s Rank 0: starting clear step. cycleNumber= 1 193s Rank 0 adding 0 new fusions 193s Rank 0 cleared, 1 paths 193s Rank 0 is distributing fusions [1/1] 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 is distributing fusions [1/1] (completed) 193s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 JoinerTaskCreator assignNextTask [0/2] 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s Rank 0 JoinerTaskCreator [2/2] 193s Statistics: all paths: 1 eliminated during joining: 0 193s Rank 0: assembler memory usage: 154244 KiB 193s Date: Sat Mar 15 18:40:54 2025 193s VirtualProcessor: completed jobs: 2 193s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 194s Rank 0 adding 0 new fusions 194s Rank 0 cleared, 1 paths 194s Rank 0: starting distribution step 194s Rank 0 is distributing fusions [1/1] 194s Rank 0: assembler memory usage: 154244 KiB 194s Date: Sat Mar 15 18:40:55 2025 194s Rank 0 is distributing fusions [1/1] (completed) 194s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 194s Rank 0: assembler memory usage: 154244 KiB 194s Date: Sat Mar 15 18:40:55 2025 194s Rank 0 tells others to compute fusions. 194s Rank 0 FusionTaskCreator assignNextTask [0/2] 194s Rank 0: assembler memory usage: 154244 KiB 194s Date: Sat Mar 15 18:40:55 2025 194s Rank 0 FusionTaskCreator processWorkerResult [0/2] 194s Rank 0: assembler memory usage: 154244 KiB 194s Date: Sat Mar 15 18:40:55 2025 194s Rank 0 FusionTaskCreator [2/2] 194s Statistics: all paths: 1 eliminated during fusing: 0 194s Rank 0: assembler memory usage: 154244 KiB 194s VirtualProcessor: completed jobs: 2 194s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 194s Rank 0: starting clear step. cycleNumber= 2 195s Rank 0 adding 0 new fusions 195s Rank 0 cleared, 1 paths 195s Rank 0 is distributing fusions [1/1] 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:55 2025 195s Rank 0 is distributing fusions [1/1] (completed) 195s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:55 2025 195s Rank 0 JoinerTaskCreator assignNextTask [0/2] 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:55 2025 195s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:55 2025 195s Rank 0 JoinerTaskCreator [2/2] 195s Statistics: all paths: 1 eliminated during joining: 0 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:55 2025 195s VirtualProcessor: completed jobs: 2 195s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 195s Rank 0 adding 0 new fusions 195s Rank 0 cleared, 1 paths 195s Rank 0: starting distribution step 195s Rank 0 is distributing fusions [1/1] 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:56 2025 195s Rank 0 is distributing fusions [1/1] (completed) 195s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 195s Rank 0: assembler memory usage: 154244 KiB 195s Date: Sat Mar 15 18:40:56 2025 195s Rank 0 cycleNumber= 2 195s 195s *** 195s Step: Merging of redundant paths 195s Date: Sat Mar 15 18:40:56 2025 195s Elapsed time: 3 seconds 195s Since beginning: 17 seconds 195s *** 195s 195s 195s Rank 0 appended 1 elements 195s 195s *** 195s Step: Generation of contigs 195s Date: Sat Mar 15 18:40:56 2025 195s Elapsed time: 0 seconds 195s Since beginning: 17 seconds 195s *** 195s 195s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 195s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 195s Rank 0 ineligibleObjects: 0/970 (0.00%) 195s Rank 0: assembler memory usage: 154244 KiB 195s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 195s Rank 0 finished gathering scaffold links. 195s Rank 0 will write 1 contig lengths 195s Rank 0 will solve the scaffolding problem. 195s Welcome to GreedySolver v1.0 195s 1 vertices; 0 edges 195s 1 contigs >= 500 195s Edges in solution: 0 195s 195s Conflict statistics: 195s 1 scaffolds, 1 >= 500 195s Total: 1000 nucleotides 195s 195s *** 195s Step: Scaffolding of contigs 195s Date: Sat Mar 15 18:40:56 2025 195s Elapsed time: 0 seconds 195s Since beginning: 17 seconds 195s *** 195s 195s Rank 0 syncing with master 195s 195s *** 195s Step: Counting sequences to search 195s Date: Sat Mar 15 18:40:56 2025 195s Elapsed time: 0 seconds 195s Since beginning: 17 seconds 195s *** 195s 195s 195s Rank 0 will add colors, 0 sequences in 0 files to process 195s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 196s 196s *** 196s Step: Graph coloring 196s Date: Sat Mar 15 18:40:57 2025 196s Elapsed time: 1 seconds 196s Since beginning: 18 seconds 196s *** 196s 196s 196s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 196s Rank 0 shares its counts 196s Rank 0 computing contig abundances [1/1] [1/970] 196s Rank 0 computing contig abundances [1/1] [970/970] 196s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 196s 196s *** 196s Step: Counting contig biological abundances 196s Date: Sat Mar 15 18:40:57 2025 196s Elapsed time: 0 seconds 196s Since beginning: 18 seconds 196s *** 196s 196s 196s Rank 0 colored the graph with 0 real colors using 1 virtual colors 196s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 196s 196s *** 196s Step: Counting sequence biological abundances 196s Date: Sat Mar 15 18:40:57 2025 196s Elapsed time: 0 seconds 196s Since beginning: 18 seconds 196s *** 196s 196s 196s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 196s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 196s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 196s 196s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 196s Rank 0 is starting taxon syncing across the compute tribe. 196s 196s *** 196s Step: Loading taxons 196s Date: Sat Mar 15 18:40:57 2025 196s Elapsed time: 0 seconds 196s Since beginning: 18 seconds 196s *** 196s 196s Rank 0 synced taxons across the grid with 1 poor slaves. 196s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 196s Rank 0 has 0 taxons after syncing with master 197s 197s 197s *** 197s Step: Loading tree 197s Date: Sat Mar 15 18:40:58 2025 197s Elapsed time: 1 seconds 197s Since beginning: 19 seconds 197s *** 197s 197s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 197s 197s Rank 0: counting ontology terms in the graph... 198s Rank 0: 0 have some biological signal 198s Number of dereferenced alternate handles: 0 198s Number of k-mer observations with gene ontology terms: 0 198s Rank 0: synced ontology term profiles with master 198s Rank 0: synchronization is complete! 198s Rank 0: ontology terms with biological signal: 0 198s Populated recursive values... 198s Gene ontology terms without depth information: 0 198s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 198s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 198s 198s *** 198s Step: Processing gene ontologies 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 1 seconds 198s Since beginning: 20 seconds 198s *** 198s 198s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 198s [GenomeNeighbourhood] in final list: 0 198s 198s *** 198s Step: Computing neighbourhoods 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 0 seconds 198s Since beginning: 20 seconds 198s *** 198s 198s Contigs >= 100 nt 198s Number: 1 198s Total length: 1000 198s Average: 1000 198s N50: 1000 198s Median: 1000 198s Largest: 1000 198s Contigs >= 500 nt 198s Number: 1 198s Total length: 1000 198s Average: 1000 198s N50: 1000 198s Median: 1000 198s Largest: 1000 198s Scaffolds >= 100 nt 198s Number: 1 198s Total length: 1000 198s Average: 1000 198s N50: 1000 198s Median: 1000 198s Largest: 1000 198s Scaffolds >= 500 nt 198s Number: 1 198s Total length: 1000 198s Average: 1000 198s N50: 1000 198s Median: 1000 198s Largest: 1000 198s 198s Rank 0 wrote test1/Contigs.fasta 198s Rank 0 wrote test1/Scaffolds.fasta 198s Check for test1/* 198s 198s 198s 198s ************************************************** 198s This program comes with ABSOLUTELY NO WARRANTY. 198s This is free software, and you are welcome to redistribute it 198s under certain conditions; see "LICENSE.txt" for details. 198s ************************************************** 198s 198s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 198s Centre de recherche en infectiologie de l'Université Laval 198s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 198s http://denovoassembler.sf.net/ 198s 198s References to cite: 198s 198s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 198s Ray Meta: scalable de novo metagenome assembly and profiling. 198s Genome Biology (BioMed Central Ltd). 198s 13:R122, Published: 22 December 2012 198s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 198s 198s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 198s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 198s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 198s November 2010, Volume 17, Issue 11, Pages 1519-1533. 198s http://dx.doi.org/doi:10.1089/cmb.2009.0238 198s 198s Ray version 2.3.1 198s License for Ray: GNU General Public License version 3 198s RayPlatform version: 2.0.1 198s License for RayPlatform: GNU Lesser General Public License version 3 198s 198s MAXKMERLENGTH: 32 198s Maximum coverage depth stored by CoverageDepth: 4294967295 198s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 198s FORCE_PACKING = n 198s ASSERT = n 198s HAVE_LIBZ = y 198s HAVE_LIBBZ2 = y 198s PROFILER_COLLECT = n 198s MINIRANKS = y 198s CLOCK_GETTIME = n 198s __linux__ = y 198s _MSC_VER = n 198s __GNUC__ = y 198s RAY_32_BITS = n 198s RAY_64_BITS = y 198s MPI standard version: MPI 3.1 198s MPI library: Open-MPI 5.0.6 198s Compiler: GNU gcc/g++ 14.2.0 198s MPI I/O: n 198s 198s 198s -k (to set the k-mer size) 198s Value: 31 198s 198s 198s Paired library # 0 198s -p (paired-end sequences) 198s Left sequences: SampleDirectory/s_6.first1000_1.fastq 198s Right sequences: SampleDirectory/s_6.first1000_2.fastq 198s Average length: automatic detection 198s Standard deviation: automatic detection 198s 198s Ray command: 198s mpiexec -n 1 Ray \ 198s -k \ 198s 31 \ 198s -detect-sequence-files \ 198s SampleDirectory \ 198s -o \ 198s test2 198s 198s Rank 0 wrote test2/RayCommand.txt 198s 198s k-mer length: 31 198s Rank 0: assembler memory usage: 33696 KiB 198s Rank 0: assembler memory usage: 99368 KiB 198s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2508 198s Rank 0: testing the network, please wait... 198s 198s Rank 0 is testing the network [0/1000] 198s Rank 0 is testing the network [1000/1000] 198s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 198s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 198s 198s Rank 0 wrote test2/NetworkTest.txt 198s 198s 198s *** 198s Step: Network testing 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 0 seconds 198s Since beginning: 0 seconds 198s *** 198s 198s 198s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 198s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 198s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 198s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 198s Rank 0 wrote test2/NumberOfSequences.txt 198s Rank 0 wrote test2/SequencePartition.txt 198s 198s *** 198s Step: Counting sequences to assemble 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 0 seconds 198s Since beginning: 0 seconds 198s *** 198s 198s 198s Rank 0 is loading sequence reads 198s Rank 0 : partition is [0;4107], 4108 sequence reads 198s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 198s Rank 0 has 0 sequence reads 198s Rank 0: assembler memory usage: 112320 KiB 198s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 198s Rank 0 has 4108 sequence reads (completed) 198s 198s *** 198s Step: Sequence loading 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 0 seconds 198s Since beginning: 0 seconds 198s *** 198s 198s 198s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 198s Rank 0 created its Bloom filter 198s Rank 0 is counting k-mers in sequence reads [1/4108] 198s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 198s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 198s 198s 198s *** 198s Step: K-mer counting 198s Date: Sat Mar 15 18:40:59 2025 198s Elapsed time: 0 seconds 198s Since beginning: 0 seconds 198s *** 198s 198s 198s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 198s Rank 0 destroyed its Bloom filter 198s Rank 0 has 1954 k-mers (completed) 198s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 198s Rank 0: assembler memory usage: 108712 KiB 199s 199s 199s Rank 0: the minimum coverage is 3 199s Rank 0: the peak coverage is 3 199s Warning: no peak observed in the k-mer coverage distribution. 199s to deal with the sequencing error rate, try to lower the k-mer length (-k) 199s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 199s 199s *** 199s Step: Coverage distribution analysis 199s Date: Sat Mar 15 18:41:00 2025 199s Elapsed time: 1 seconds 199s Since beginning: 1 seconds 199s *** 199s 199s 199s 199s Rank 0 is adding edges [1/4108] 199s Rank 0 is adding edges [4108/4108] (completed) 199s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 199s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 199s 199s *** 199s Step: Graph construction 199s Date: Sat Mar 15 18:41:00 2025 199s Elapsed time: 0 seconds 199s Since beginning: 1 seconds 199s *** 199s 199s 199s Rank 0 has 1954 vertices (completed) 199s Rank 0: assembler memory usage: 108712 KiB 200s Rank 0 is purging edges [1/1954] 200s Rank 0 is purging edges [1954/1954] (completed) 200s Rank 0: assembler memory usage: 109240 KiB 200s VirtualProcessor: completed jobs: 1954 200s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 200s Rank 0 wrote test2/degreeDistribution.txt 200s 200s *** 200s Step: Null edge purging 200s Date: Sat Mar 15 18:41:01 2025 200s Elapsed time: 1 seconds 200s Since beginning: 2 seconds 200s *** 200s 200s 200s Rank 0 is selecting optimal read markers [1/4108] 200s Rank 0: assembler memory usage: 109240 KiB 201s Rank 0 is selecting optimal read markers [4108/4108] (completed) 201s Rank 0: peak number of workers: 599, maximum: 32768 201s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 201s Rank 0: assembler memory usage: 117412 KiB 201s Rank 0: Freeing unused assembler memory: 4096 KiB freed 201s Rank 0: assembler memory usage: 117412 KiB 201s 201s *** 201s Step: Selection of optimal read markers 201s Date: Sat Mar 15 18:41:02 2025 201s Elapsed time: 1 seconds 201s Since beginning: 3 seconds 201s *** 201s 201s 201s Rank 0: memory usage for optimal read markers= 4096 KiB 201s Rank 0 is creating seeds [1/1954] 201s Rank 0: assembler memory usage: 117412 KiB 201s Rank 0 has 1 seeds 201s Rank 0 is creating seeds [1954/1954] (completed) 201s Rank 0: peak number of workers: 746, maximum: 32768 201s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 201s Rank 0 runtime statistics for seeding algorithm: 201s Rank 0 Skipped paths because of dead end for head: 0 201s Rank 0 Skipped paths because of dead end for tail: 0 201s Rank 0 Skipped paths because of two dead ends: 0 201s Rank 0 Skipped paths because of bubble weak component: 0 201s Rank 0 Skipped paths because of short length: 1952 201s Rank 0 Skipped paths because of bad ownership: 1 201s Rank 0 Skipped paths because of low coverage: 0 201s Rank 0 Eligible paths: 1 201s Rank 0: assembler memory usage: 117412 KiB 201s Rank 0 has 1 seeds to register. 201s Rank 0 registered 0/1 201s Rank 0 registered 0/1 201s Rank 0 registered its seeds 201s VirtualProcessor: completed jobs: 0 201s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 202s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 212s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 212s Rank 0 merged its seeds: 1 seeds -> 1 seeds 212s 212s *** 212s Step: Detection of assembly seeds 212s Date: Sat Mar 15 18:41:13 2025 212s Elapsed time: 11 seconds 212s Since beginning: 14 seconds 212s *** 212s 212s 212s Rank 0 is calculating library lengths [1/1] 212s Rank 0 detected 1737 library lengths 212s Rank 0 is calculating library lengths [1/1] (completed) 212s Rank 0: peak number of workers: 1, maximum: 32768 212s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 212s Rank 0: assembler memory usage: 154280 KiB 212s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 212s 212s Mode= 2 signalAverage= 9 212s CURRENT IS NOISE, 244 212s GOT HIT 212 212s 212s 212s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 212s 212s *** 212s Step: Estimation of outer distances for paired reads 212s Date: Sat Mar 15 18:41:13 2025 212s Elapsed time: 0 seconds 212s Since beginning: 14 seconds 212s *** 212s 212s 212s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 212s Rank 0 traversed 1000 nucleotide symbols 212s Rank 0: assembler memory usage: 158376 KiB 212s Rank 0 is extending seeds [1/1] (completed) 212s Rank 0 extended 1 seeds out of 1 (100.00%) 212s Rank 0: assembler memory usage: 150184 KiB 212s Rank 0 starting fusions 212s 212s *** 212s Step: Bidirectional extension of seeds 212s Date: Sat Mar 15 18:41:13 2025 212s Elapsed time: 0 seconds 212s Since beginning: 14 seconds 212s *** 212s 212s 212s Rank 0: starting clear step. cycleNumber= 0 213s Rank 0 adding 0 new fusions 213s Rank 0 cleared, 1 paths 213s Rank 0: starting distribution step 213s Rank 0 is distributing fusions [1/1] 213s Rank 0: assembler memory usage: 150184 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 is distributing fusions [1/1] (completed) 213s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 tells others to compute fusions. 213s Rank 0 FusionTaskCreator assignNextTask [0/2] 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 FusionTaskCreator processWorkerResult [0/2] 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 FusionTaskCreator [2/2] 213s Statistics: all paths: 1 eliminated during fusing: 0 213s Rank 0: assembler memory usage: 154280 KiB 213s VirtualProcessor: completed jobs: 2 213s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 213s Rank 0: starting clear step. cycleNumber= 1 213s Rank 0 adding 0 new fusions 213s Rank 0 cleared, 1 paths 213s Rank 0 is distributing fusions [1/1] 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 is distributing fusions [1/1] (completed) 213s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 JoinerTaskCreator assignNextTask [0/2] 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s Rank 0 JoinerTaskCreator [2/2] 213s Statistics: all paths: 1 eliminated during joining: 0 213s Rank 0: assembler memory usage: 154280 KiB 213s Date: Sat Mar 15 18:41:14 2025 213s VirtualProcessor: completed jobs: 2 213s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 214s Rank 0 adding 0 new fusions 214s Rank 0 cleared, 1 paths 214s Rank 0: starting distribution step 214s Rank 0 is distributing fusions [1/1] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 is distributing fusions [1/1] (completed) 214s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 tells others to compute fusions. 214s Rank 0 FusionTaskCreator assignNextTask [0/2] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 FusionTaskCreator processWorkerResult [0/2] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 FusionTaskCreator [2/2] 214s Statistics: all paths: 1 eliminated during fusing: 0 214s Rank 0: assembler memory usage: 154280 KiB 214s VirtualProcessor: completed jobs: 2 214s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 214s Rank 0: starting clear step. cycleNumber= 2 214s Rank 0 adding 0 new fusions 214s Rank 0 cleared, 1 paths 214s Rank 0 is distributing fusions [1/1] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 is distributing fusions [1/1] (completed) 214s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 JoinerTaskCreator assignNextTask [0/2] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 214s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 214s Rank 0: assembler memory usage: 154280 KiB 214s Date: Sat Mar 15 18:41:15 2025 215s Rank 0 JoinerTaskCreator [2/2] 215s Statistics: all paths: 1 eliminated during joining: 0 215s Rank 0: assembler memory usage: 154280 KiB 215s Date: Sat Mar 15 18:41:15 2025 215s VirtualProcessor: completed jobs: 2 215s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 215s Rank 0 adding 0 new fusions 215s Rank 0 cleared, 1 paths 215s Rank 0: starting distribution step 215s Rank 0 is distributing fusions [1/1] 215s Rank 0: assembler memory usage: 154280 KiB 215s Date: Sat Mar 15 18:41:16 2025 215s Rank 0 is distributing fusions [1/1] (completed) 215s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 215s Rank 0: assembler memory usage: 154280 KiB 215s Date: Sat Mar 15 18:41:16 2025 215s Rank 0 cycleNumber= 2 215s 215s *** 215s Step: Merging of redundant paths 215s Date: Sat Mar 15 18:41:16 2025 215s Elapsed time: 3 seconds 215s Since beginning: 17 seconds 215s *** 215s 215s 215s Rank 0 appended 1 elements 215s 215s *** 215s Step: Generation of contigs 215s Date: Sat Mar 15 18:41:16 2025 215s Elapsed time: 0 seconds 215s Since beginning: 17 seconds 215s *** 215s 215s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 215s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 215s Rank 0 ineligibleObjects: 0/970 (0.00%) 215s Rank 0: assembler memory usage: 154280 KiB 215s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 215s Rank 0 finished gathering scaffold links. 215s Rank 0 will write 1 contig lengths 215s Rank 0 will solve the scaffolding problem. 215s Welcome to GreedySolver v1.0 215s 1 vertices; 0 edges 215s 1 contigs >= 500 215s Edges in solution: 0 215s 215s Conflict statistics: 215s 1 scaffolds, 1 >= 500 215s Total: 1000 nucleotides 215s 215s *** 215s Step: Scaffolding of contigs 215s Date: Sat Mar 15 18:41:16 2025 215s Elapsed time: 0 seconds 215s Since beginning: 17 seconds 215s *** 215s 215s Rank 0 syncing with master 215s 215s *** 215s Step: Counting sequences to search 215s Date: Sat Mar 15 18:41:16 2025 215s Elapsed time: 0 seconds 215s Since beginning: 17 seconds 215s *** 215s 215s 215s Rank 0 will add colors, 0 sequences in 0 files to process 215s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 216s 216s *** 216s Step: Graph coloring 216s Date: Sat Mar 15 18:41:17 2025 216s Elapsed time: 1 seconds 216s Since beginning: 18 seconds 216s *** 216s 216s 216s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 216s Rank 0 shares its counts 216s Rank 0 computing contig abundances [1/1] [1/970] 216s Rank 0 computing contig abundances [1/1] [970/970] 216s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 216s 216s *** 216s Step: Counting contig biological abundances 216s Date: Sat Mar 15 18:41:17 2025 216s Elapsed time: 0 seconds 216s Since beginning: 18 seconds 216s *** 216s 216s 216s Rank 0 colored the graph with 0 real colors using 1 virtual colors 216s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 216s 216s *** 216s Step: Counting sequence biological abundances 216s Date: Sat Mar 15 18:41:17 2025 216s Elapsed time: 0 seconds 216s Since beginning: 18 seconds 216s *** 216s 216s 216s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 216s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 216s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 216s 216s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 216s Rank 0 is starting taxon syncing across the compute tribe. 216s 216s *** 216s Step: Loading taxons 216s Date: Sat Mar 15 18:41:17 2025 216s Elapsed time: 0 seconds 216s Since beginning: 18 seconds 216s *** 216s 216s Rank 0 synced taxons across the grid with 1 poor slaves. 216s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 216s Rank 0 has 0 taxons after syncing with master 217s 217s 217s *** 217s Step: Loading tree 217s Date: Sat Mar 15 18:41:18 2025 217s Elapsed time: 1 seconds 217s Since beginning: 19 seconds 217s *** 217s 217s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 217s 217s Rank 0: counting ontology terms in the graph... 218s Rank 0: 0 have some biological signal 218s Number of dereferenced alternate handles: 0 218s Number of k-mer observations with gene ontology terms: 0 218s Rank 0: synced ontology term profiles with master 218s Rank 0: synchronization is complete! 218s Rank 0: ontology terms with biological signal: 0 218s Populated recursive values... 218s Gene ontology terms without depth information: 0 218s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 218s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 218s 218s *** 218s Step: Processing gene ontologies 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 1 seconds 218s Since beginning: 20 seconds 218s *** 218s 218s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 218s [GenomeNeighbourhood] in final list: 0 218s 218s *** 218s Step: Computing neighbourhoods 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 0 seconds 218s Since beginning: 20 seconds 218s *** 218s 218s Contigs >= 100 nt 218s Number: 1 218s Total length: 1000 218s Average: 1000 218s N50: 1000 218s Median: 1000 218s Largest: 1000 218s Contigs >= 500 nt 218s Number: 1 218s Total length: 1000 218s Average: 1000 218s N50: 1000 218s Median: 1000 218s Largest: 1000 218s Scaffolds >= 100 nt 218s Number: 1 218s Total length: 1000 218s Average: 1000 218s N50: 1000 218s Median: 1000 218s Largest: 1000 218s Scaffolds >= 500 nt 218s Number: 1 218s Total length: 1000 218s Average: 1000 218s N50: 1000 218s Median: 1000 218s Largest: 1000 218s 218s Rank 0 wrote test2/Contigs.fasta 218s Rank 0 wrote test2/Scaffolds.fasta 218s Check for test2/* 218s 218s 218s 218s ************************************************** 218s This program comes with ABSOLUTELY NO WARRANTY. 218s This is free software, and you are welcome to redistribute it 218s under certain conditions; see "LICENSE.txt" for details. 218s ************************************************** 218s 218s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 218s Centre de recherche en infectiologie de l'Université Laval 218s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 218s http://denovoassembler.sf.net/ 218s 218s References to cite: 218s 218s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 218s Ray Meta: scalable de novo metagenome assembly and profiling. 218s Genome Biology (BioMed Central Ltd). 218s 13:R122, Published: 22 December 2012 218s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 218s 218s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 218s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 218s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 218s November 2010, Volume 17, Issue 11, Pages 1519-1533. 218s http://dx.doi.org/doi:10.1089/cmb.2009.0238 218s 218s Ray version 2.3.1 218s License for Ray: GNU General Public License version 3 218s RayPlatform version: 2.0.1 218s License for RayPlatform: GNU Lesser General Public License version 3 218s 218s MAXKMERLENGTH: 32 218s Maximum coverage depth stored by CoverageDepth: 4294967295 218s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 218s FORCE_PACKING = n 218s ASSERT = n 218s HAVE_LIBZ = y 218s HAVE_LIBBZ2 = y 218s PROFILER_COLLECT = n 218s MINIRANKS = y 218s CLOCK_GETTIME = n 218s __linux__ = y 218s _MSC_VER = n 218s __GNUC__ = y 218s RAY_32_BITS = n 218s RAY_64_BITS = y 218s MPI standard version: MPI 3.1 218s MPI library: Open-MPI 5.0.6 218s Compiler: GNU gcc/g++ 14.2.0 218s MPI I/O: n 218s 218s 218s -k (to set the k-mer size) 218s Value: 29 218s 218s 218s Paired library # 0 218s -p (paired-end sequences) 218s Left sequences: SampleDirectory/s_6.first1000_1.fastq 218s Right sequences: SampleDirectory/s_6.first1000_2.fastq 218s Average length: automatic detection 218s Standard deviation: automatic detection 218s 218s Ray command: 218s mpiexec -n 1 Ray \ 218s -k \ 218s 29 \ 218s -desable-recycling \ 218s -p \ 218s SampleDirectory/s_6.first1000_1.fastq \ 218s SampleDirectory/s_6.first1000_2.fastq 218s 218s Rank 0 wrote RayOutput/RayCommand.txt 218s 218s k-mer length: 29 218s Rank 0: assembler memory usage: 33696 KiB 218s Rank 0: assembler memory usage: 99368 KiB 218s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2510 218s Rank 0: testing the network, please wait... 218s 218s Rank 0 is testing the network [0/1000] 218s Rank 0 is testing the network [1000/1000] 218s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 218s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 218s 218s Rank 0 wrote RayOutput/NetworkTest.txt 218s 218s 218s *** 218s Step: Network testing 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 0 seconds 218s Since beginning: 0 seconds 218s *** 218s 218s 218s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 218s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 218s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 218s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 218s Rank 0 wrote RayOutput/NumberOfSequences.txt 218s Rank 0 wrote RayOutput/SequencePartition.txt 218s 218s *** 218s Step: Counting sequences to assemble 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 0 seconds 218s Since beginning: 0 seconds 218s *** 218s 218s 218s Rank 0 is loading sequence reads 218s Rank 0 : partition is [0;4107], 4108 sequence reads 218s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 218s Rank 0 has 0 sequence reads 218s Rank 0: assembler memory usage: 112320 KiB 218s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 218s Rank 0 has 4108 sequence reads (completed) 218s 218s *** 218s Step: Sequence loading 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 0 seconds 218s Since beginning: 0 seconds 218s *** 218s 218s 218s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 218s Rank 0 created its Bloom filter 218s Rank 0 is counting k-mers in sequence reads [1/4108] 218s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 218s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 218s 218s 218s *** 218s Step: K-mer counting 218s Date: Sat Mar 15 18:41:19 2025 218s Elapsed time: 0 seconds 218s Since beginning: 0 seconds 218s *** 218s 218s 218s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 218s Rank 0 destroyed its Bloom filter 218s Rank 0 has 1958 k-mers (completed) 218s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 218s Rank 0: assembler memory usage: 108696 KiB 219s 219s 219s Rank 0: the minimum coverage is 3 219s Rank 0: the peak coverage is 3 219s Warning: no peak observed in the k-mer coverage distribution. 219s to deal with the sequencing error rate, try to lower the k-mer length (-k) 219s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 219s 219s *** 219s Step: Coverage distribution analysis 219s Date: Sat Mar 15 18:41:20 2025 219s Elapsed time: 1 seconds 219s Since beginning: 1 seconds 219s *** 219s 219s 219s 219s Rank 0 is adding edges [1/4108] 219s Rank 0 is adding edges [4108/4108] (completed) 219s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 219s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 219s 219s *** 219s Step: Graph construction 219s Date: Sat Mar 15 18:41:20 2025 219s Elapsed time: 0 seconds 219s Since beginning: 1 seconds 219s *** 219s 219s 219s Rank 0 has 1958 vertices (completed) 219s Rank 0: assembler memory usage: 108696 KiB 220s Rank 0 is purging edges [1/1958] 220s Rank 0 is purging edges [1958/1958] (completed) 220s Rank 0: assembler memory usage: 109228 KiB 220s VirtualProcessor: completed jobs: 1958 220s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 220s Rank 0 wrote RayOutput/degreeDistribution.txt 220s 220s *** 220s Step: Null edge purging 220s Date: Sat Mar 15 18:41:21 2025 220s Elapsed time: 1 seconds 220s Since beginning: 2 seconds 220s *** 220s 220s 220s Rank 0 is selecting optimal read markers [1/4108] 220s Rank 0: assembler memory usage: 109228 KiB 221s Rank 0 is selecting optimal read markers [4108/4108] (completed) 221s Rank 0: peak number of workers: 599, maximum: 32768 221s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 221s Rank 0: assembler memory usage: 117452 KiB 221s Rank 0: Freeing unused assembler memory: 4096 KiB freed 221s Rank 0: assembler memory usage: 117452 KiB 221s 221s *** 221s Step: Selection of optimal read markers 221s Date: Sat Mar 15 18:41:22 2025 221s Elapsed time: 1 seconds 221s Since beginning: 3 seconds 221s *** 221s 221s 221s Rank 0: memory usage for optimal read markers= 4096 KiB 221s Rank 0 is creating seeds [1/1958] 221s Rank 0: assembler memory usage: 117452 KiB 221s Rank 0 has 1 seeds 221s Rank 0 is creating seeds [1958/1958] (completed) 221s Rank 0: peak number of workers: 746, maximum: 32768 221s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 221s Rank 0 runtime statistics for seeding algorithm: 221s Rank 0 Skipped paths because of dead end for head: 0 221s Rank 0 Skipped paths because of dead end for tail: 0 221s Rank 0 Skipped paths because of two dead ends: 0 221s Rank 0 Skipped paths because of bubble weak component: 0 221s Rank 0 Skipped paths because of short length: 1956 221s Rank 0 Skipped paths because of bad ownership: 1 221s Rank 0 Skipped paths because of low coverage: 0 221s Rank 0 Eligible paths: 1 221s Rank 0: assembler memory usage: 117452 KiB 221s Rank 0 has 1 seeds to register. 221s Rank 0 registered 0/1 221s Rank 0 registered 0/1 221s Rank 0 registered its seeds 221s VirtualProcessor: completed jobs: 0 221s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 222s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 232s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 232s Rank 0 merged its seeds: 1 seeds -> 1 seeds 232s 232s *** 232s Step: Detection of assembly seeds 232s Date: Sat Mar 15 18:41:33 2025 232s Elapsed time: 11 seconds 232s Since beginning: 14 seconds 232s *** 232s 232s 232s Rank 0 is calculating library lengths [1/1] 232s Rank 0 detected 1743 library lengths 232s Rank 0 is calculating library lengths [1/1] (completed) 232s Rank 0: peak number of workers: 1, maximum: 32768 232s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 232s Rank 0: assembler memory usage: 154320 KiB 232s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 232s 232s Mode= 2 signalAverage= 10 232s CURRENT IS NOISE, 244 232s GOT HIT 214 232s 232s 232s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 232s 232s *** 232s Step: Estimation of outer distances for paired reads 232s Date: Sat Mar 15 18:41:33 2025 232s Elapsed time: 0 seconds 232s Since beginning: 14 seconds 232s *** 232s 232s 232s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 232s Rank 0 traversed 1000 nucleotide symbols 232s Rank 0: assembler memory usage: 158416 KiB 232s Rank 0 is extending seeds [1/1] (completed) 232s Rank 0 extended 1 seeds out of 1 (100.00%) 232s Rank 0: assembler memory usage: 150224 KiB 232s Rank 0 starting fusions 232s 232s *** 232s Step: Bidirectional extension of seeds 232s Date: Sat Mar 15 18:41:33 2025 232s Elapsed time: 0 seconds 232s Since beginning: 14 seconds 232s *** 232s 232s 232s Rank 0: starting clear step. cycleNumber= 0 233s Rank 0 adding 0 new fusions 233s Rank 0 cleared, 1 paths 233s Rank 0: starting distribution step 233s Rank 0 is distributing fusions [1/1] 233s Rank 0: assembler memory usage: 150224 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 is distributing fusions [1/1] (completed) 233s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 tells others to compute fusions. 233s Rank 0 FusionTaskCreator assignNextTask [0/2] 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 FusionTaskCreator processWorkerResult [0/2] 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 FusionTaskCreator [2/2] 233s Statistics: all paths: 1 eliminated during fusing: 0 233s Rank 0: assembler memory usage: 154320 KiB 233s VirtualProcessor: completed jobs: 2 233s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 233s Rank 0: starting clear step. cycleNumber= 1 233s Rank 0 adding 0 new fusions 233s Rank 0 cleared, 1 paths 233s Rank 0 is distributing fusions [1/1] 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 is distributing fusions [1/1] (completed) 233s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 JoinerTaskCreator assignNextTask [0/2] 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s Rank 0 JoinerTaskCreator [2/2] 233s Statistics: all paths: 1 eliminated during joining: 0 233s Rank 0: assembler memory usage: 154320 KiB 233s Date: Sat Mar 15 18:41:34 2025 233s VirtualProcessor: completed jobs: 2 233s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 234s Rank 0 adding 0 new fusions 234s Rank 0 cleared, 1 paths 234s Rank 0: starting distribution step 234s Rank 0 is distributing fusions [1/1] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 is distributing fusions [1/1] (completed) 234s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 tells others to compute fusions. 234s Rank 0 FusionTaskCreator assignNextTask [0/2] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 FusionTaskCreator processWorkerResult [0/2] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 FusionTaskCreator [2/2] 234s Statistics: all paths: 1 eliminated during fusing: 0 234s Rank 0: assembler memory usage: 154320 KiB 234s VirtualProcessor: completed jobs: 2 234s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 234s Rank 0: starting clear step. cycleNumber= 2 234s Rank 0 adding 0 new fusions 234s Rank 0 cleared, 1 paths 234s Rank 0 is distributing fusions [1/1] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 is distributing fusions [1/1] (completed) 234s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 JoinerTaskCreator assignNextTask [0/2] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 234s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 234s Rank 0: assembler memory usage: 154320 KiB 234s Date: Sat Mar 15 18:41:35 2025 235s Rank 0 JoinerTaskCreator [2/2] 235s Statistics: all paths: 1 eliminated during joining: 0 235s Rank 0: assembler memory usage: 154320 KiB 235s Date: Sat Mar 15 18:41:35 2025 235s VirtualProcessor: completed jobs: 2 235s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 235s Rank 0 adding 0 new fusions 235s Rank 0 cleared, 1 paths 235s Rank 0: starting distribution step 235s Rank 0 is distributing fusions [1/1] 235s Rank 0: assembler memory usage: 154320 KiB 235s Date: Sat Mar 15 18:41:36 2025 235s Rank 0 is distributing fusions [1/1] (completed) 235s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 235s Rank 0: assembler memory usage: 154320 KiB 235s Date: Sat Mar 15 18:41:36 2025 235s Rank 0 cycleNumber= 2 235s 235s *** 235s Step: Merging of redundant paths 235s Date: Sat Mar 15 18:41:36 2025 235s Elapsed time: 3 seconds 235s Since beginning: 17 seconds 235s *** 235s 235s 235s Rank 0 appended 1 elements 235s 235s *** 235s Step: Generation of contigs 235s Date: Sat Mar 15 18:41:36 2025 235s Elapsed time: 0 seconds 235s Since beginning: 17 seconds 235s *** 235s 235s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 235s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 235s Rank 0 ineligibleObjects: 0/972 (0.00%) 235s Rank 0: assembler memory usage: 154320 KiB 235s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 235s Rank 0 finished gathering scaffold links. 235s Rank 0 will write 1 contig lengths 235s Rank 0 will solve the scaffolding problem. 235s Welcome to GreedySolver v1.0 235s 1 vertices; 0 edges 235s 1 contigs >= 500 235s Edges in solution: 0 235s 235s Conflict statistics: 235s 1 scaffolds, 1 >= 500 235s Total: 1000 nucleotides 235s 235s *** 235s Step: Scaffolding of contigs 235s Date: Sat Mar 15 18:41:36 2025 235s Elapsed time: 0 seconds 235s Since beginning: 17 seconds 235s *** 235s 235s Rank 0 syncing with master 235s 235s *** 235s Step: Counting sequences to search 235s Date: Sat Mar 15 18:41:36 2025 235s Elapsed time: 0 seconds 235s Since beginning: 17 seconds 235s *** 235s 235s 235s Rank 0 will add colors, 0 sequences in 0 files to process 235s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 236s 236s *** 236s Step: Graph coloring 236s Date: Sat Mar 15 18:41:37 2025 236s Elapsed time: 1 seconds 236s Since beginning: 18 seconds 236s *** 236s 236s 236s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 236s Rank 0 shares its counts 236s Rank 0 computing contig abundances [1/1] [1/972] 236s Rank 0 computing contig abundances [1/1] [972/972] 236s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 236s 236s *** 236s Step: Counting contig biological abundances 236s Date: Sat Mar 15 18:41:37 2025 236s Elapsed time: 0 seconds 236s Since beginning: 18 seconds 236s *** 236s 236s 236s Rank 0 colored the graph with 0 real colors using 1 virtual colors 236s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 236s 236s *** 236s Step: Counting sequence biological abundances 236s Date: Sat Mar 15 18:41:37 2025 236s Elapsed time: 0 seconds 236s Since beginning: 18 seconds 236s *** 236s 236s 236s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 236s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 236s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 236s 236s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 236s Rank 0 is starting taxon syncing across the compute tribe. 236s 236s *** 236s Step: Loading taxons 236s Date: Sat Mar 15 18:41:37 2025 236s Elapsed time: 0 seconds 236s Since beginning: 18 seconds 236s *** 236s 236s Rank 0 synced taxons across the grid with 1 poor slaves. 236s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 236s Rank 0 has 0 taxons after syncing with master 237s 237s 237s *** 237s Step: Loading tree 237s Date: Sat Mar 15 18:41:38 2025 237s Elapsed time: 1 seconds 237s Since beginning: 19 seconds 237s *** 237s 237s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 237s 237s Rank 0: counting ontology terms in the graph... 238s Rank 0: 0 have some biological signal 238s Number of dereferenced alternate handles: 0 238s Number of k-mer observations with gene ontology terms: 0 238s Rank 0: synced ontology term profiles with master 238s Rank 0: synchronization is complete! 238s Rank 0: ontology terms with biological signal: 0 238s Populated recursive values... 238s Gene ontology terms without depth information: 0 238s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 238s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 238s 238s *** 238s Step: Processing gene ontologies 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 1 seconds 238s Since beginning: 20 seconds 238s *** 238s 238s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 238s [GenomeNeighbourhood] in final list: 0 238s 238s *** 238s Step: Computing neighbourhoods 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 0 seconds 238s Since beginning: 20 seconds 238s *** 238s 238s Contigs >= 100 nt 238s Number: 1 238s Total length: 1000 238s Average: 1000 238s N50: 1000 238s Median: 1000 238s Largest: 1000 238s Contigs >= 500 nt 238s Number: 1 238s Total length: 1000 238s Average: 1000 238s N50: 1000 238s Median: 1000 238s Largest: 1000 238s Scaffolds >= 100 nt 238s Number: 1 238s Total length: 1000 238s Average: 1000 238s N50: 1000 238s Median: 1000 238s Largest: 1000 238s Scaffolds >= 500 nt 238s Number: 1 238s Total length: 1000 238s Average: 1000 238s N50: 1000 238s Median: 1000 238s Largest: 1000 238s 238s Rank 0 wrote RayOutput/Contigs.fasta 238s Rank 0 wrote RayOutput/Scaffolds.fasta 238s Check for RayOutput/* 238s 238s 238s 238s ************************************************** 238s This program comes with ABSOLUTELY NO WARRANTY. 238s This is free software, and you are welcome to redistribute it 238s under certain conditions; see "LICENSE.txt" for details. 238s ************************************************** 238s 238s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 238s Centre de recherche en infectiologie de l'Université Laval 238s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 238s http://denovoassembler.sf.net/ 238s 238s References to cite: 238s 238s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 238s Ray Meta: scalable de novo metagenome assembly and profiling. 238s Genome Biology (BioMed Central Ltd). 238s 13:R122, Published: 22 December 2012 238s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 238s 238s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 238s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 238s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 238s November 2010, Volume 17, Issue 11, Pages 1519-1533. 238s http://dx.doi.org/doi:10.1089/cmb.2009.0238 238s 238s Ray version 2.3.1 238s License for Ray: GNU General Public License version 3 238s RayPlatform version: 2.0.1 238s License for RayPlatform: GNU Lesser General Public License version 3 238s 238s MAXKMERLENGTH: 32 238s Maximum coverage depth stored by CoverageDepth: 4294967295 238s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 238s FORCE_PACKING = n 238s ASSERT = n 238s HAVE_LIBZ = y 238s HAVE_LIBBZ2 = y 238s PROFILER_COLLECT = n 238s MINIRANKS = y 238s CLOCK_GETTIME = n 238s __linux__ = y 238s _MSC_VER = n 238s __GNUC__ = y 238s RAY_32_BITS = n 238s RAY_64_BITS = y 238s MPI standard version: MPI 3.1 238s MPI library: Open-MPI 5.0.6 238s Compiler: GNU gcc/g++ 14.2.0 238s MPI I/O: n 238s 238s 238s -k (to set the k-mer size) 238s Value: 31 238s 238s 238s Paired library # 0 238s -p (paired-end sequences) 238s Left sequences: ecoli_1K_1.fq 238s Right sequences: ecoli_1K_2.fq 238s Average length: automatic detection 238s Standard deviation: automatic detection 238s 238s Ray command: 238s mpiexec -n 2 Ray \ 238s -k \ 238s 31 \ 238s -p \ 238s ecoli_1K_1.fq \ 238s ecoli_1K_2.fq \ 238s -o \ 238s test3 238s 238s Rank 0 wrote test3/RayCommand.txt 238s 238s k-mer length: 31 238s Rank 1: assembler memory usage: 33740 KiB 238s Rank 0: assembler memory usage: 33744 KiB 238s Rank 1: assembler memory usage: 99424 KiB 238s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 2516 238s Rank 0: assembler memory usage: 99436 KiB 238s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 2515 238s Rank 0: testing the network, please wait... 238s 238s Rank 1 is testing the network [0/1000] 238s Rank 0 is testing the network [0/1000] 238s Rank 1 is testing the network [1000/1000] 238s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 238s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 238s Rank 0 is testing the network [1000/1000] 238s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 238s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 238s 238s Rank 0 wrote test3/NetworkTest.txt 238s 238s 238s *** 238s Step: Network testing 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 0 seconds 238s Since beginning: 0 seconds 238s *** 238s 238s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 238s 238s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 238s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 238s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 238s Rank 0 wrote test3/NumberOfSequences.txt 238s Rank 0 wrote test3/SequencePartition.txt 238s 238s *** 238s Step: Counting sequences to assemble 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 0 seconds 238s Since beginning: 0 seconds 238s *** 238s 238s 238s Rank 1 is loading sequence reads 238s Rank 0 is loading sequence reads 238s Rank 0 : partition is [0;2053], 2054 sequence reads 238s Rank 1 : partition is [2054;4107], 2054 sequence reads 238s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 238s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 238s Rank 1 has 0 sequence reads 238s Rank 1: assembler memory usage: 108268 KiB 238s Rank 1 has 2054 sequence reads (completed) 238s Rank 0 has 0 sequence reads 238s Rank 0: assembler memory usage: 108288 KiB 238s Rank 0 has 2054 sequence reads (completed) 238s 238s *** 238s Step: Sequence loading 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 0 seconds 238s Since beginning: 0 seconds 238s *** 238s 238s 238s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 238s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 238s Rank 1 created its Bloom filter 238s Rank 1 is counting k-mers in sequence reads [1/2054] 238s Rank 0 created its Bloom filter 238s Rank 0 is counting k-mers in sequence reads [1/2054] 238s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 238s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 238s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 238s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 238s 238s 238s *** 238s Step: K-mer counting 238s Date: Sat Mar 15 18:41:39 2025 238s Elapsed time: 0 seconds 238s Since beginning: 0 seconds 238s *** 238s 238s 238s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 238s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 238s Rank 1 destroyed its Bloom filter 238s Rank 1 has 922 k-mers (completed) 238s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 238s Rank 0 destroyed its Bloom filter 238s Rank 0 has 1032 k-mers (completed) 238s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 238s Rank 1: assembler memory usage: 108268 KiB 238s Rank 0: assembler memory usage: 104556 KiB 239s 239s 239s Rank 0: the minimum coverage is 3 239s Rank 0: the peak coverage is 3 239s Warning: no peak observed in the k-mer coverage distribution. 239s to deal with the sequencing error rate, try to lower the k-mer length (-k) 239s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 239s 239s *** 239s Step: Coverage distribution analysis 239s Date: Sat Mar 15 18:41:40 2025 239s Elapsed time: 1 seconds 239s Since beginning: 1 seconds 239s *** 239s 239s 239s 239s Rank 0 is adding edges [1/2054] 239s Rank 1 is adding edges [1/2054] 239s Rank 1 is adding edges [2054/2054] (completed) 239s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 239s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 239s Rank 0 is adding edges [2054/2054] (completed) 239s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 239s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 239s 239s *** 239s Step: Graph construction 239s Date: Sat Mar 15 18:41:40 2025 239s Elapsed time: 0 seconds 239s Since beginning: 1 seconds 239s *** 239s 239s 239s Rank 0 has 1032 vertices (completed) 239s Rank 1 has 922 vertices (completed) 239s Rank 0: assembler memory usage: 104556 KiB 239s Rank 1: assembler memory usage: 108268 KiB 240s Rank 1 is purging edges [1/922] 240s Rank 0 is purging edges [1/1032] 240s Rank 1 is purging edges [922/922] (completed) 240s Rank 1: assembler memory usage: 108268 KiB 240s VirtualProcessor: completed jobs: 922 240s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 240s Rank 0 is purging edges [1032/1032] (completed) 240s Rank 0: assembler memory usage: 104828 KiB 240s VirtualProcessor: completed jobs: 1032 240s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 240s Rank 0 wrote test3/degreeDistribution.txt 240s 240s *** 240s Step: Null edge purging 240s Date: Sat Mar 15 18:41:41 2025 240s Elapsed time: 1 seconds 240s Since beginning: 2 seconds 240s *** 240s 240s 240s Rank 1 is selecting optimal read markers [1/2054] 240s Rank 1: assembler memory usage: 108268 KiB 240s Rank 0 is selecting optimal read markers [1/2054] 240s Rank 0: assembler memory usage: 104828 KiB 240s Rank 1 is selecting optimal read markers [2054/2054] (completed) 240s Rank 1: peak number of workers: 1121, maximum: 32768 240s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 240s Rank 1: assembler memory usage: 115948 KiB 240s Rank 1: Freeing unused assembler memory: 4096 KiB freed 240s Rank 1: assembler memory usage: 115948 KiB 240s Rank 0 is selecting optimal read markers [2054/2054] (completed) 240s Rank 0: peak number of workers: 1135, maximum: 32768 240s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 240s Rank 0: assembler memory usage: 113032 KiB 240s Rank 0: Freeing unused assembler memory: 4096 KiB freed 240s Rank 0: assembler memory usage: 113032 KiB 240s 240s *** 240s Step: Selection of optimal read markers 240s Date: Sat Mar 15 18:41:41 2025 240s Elapsed time: 0 seconds 240s Since beginning: 2 seconds 240s *** 240s 240s 240s Rank 1: memory usage for optimal read markers= 4096 KiB 240s Rank 0: memory usage for optimal read markers= 4096 KiB 240s Rank 1 is creating seeds [1/922] 240s Rank 1: assembler memory usage: 115948 KiB 240s Rank 0 is creating seeds [1/1032] 240s Rank 0: assembler memory usage: 113032 KiB 241s Rank 1 has 1 seeds 241s Rank 1 is creating seeds [922/922] (completed) 241s Rank 1: peak number of workers: 916, maximum: 32768 241s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 241s Rank 1 runtime statistics for seeding algorithm: 241s Rank 1 Skipped paths because of dead end for head: 0 241s Rank 1 Skipped paths because of dead end for tail: 0 241s Rank 1 Skipped paths because of two dead ends: 0 241s Rank 1 Skipped paths because of bubble weak component: 0 241s Rank 1 Skipped paths because of short length: 921 241s Rank 1 Skipped paths because of bad ownership: 0 241s Rank 1 Skipped paths because of low coverage: 0 241s Rank 1 Eligible paths: 1 241s Rank 1: assembler memory usage: 115948 KiB 241s Rank 0 has 0 seeds 241s Rank 0 is creating seeds [1032/1032] (completed) 241s Rank 0: peak number of workers: 998, maximum: 32768 241s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 241s Rank 0 runtime statistics for seeding algorithm: 241s Rank 0 Skipped paths because of dead end for head: 0 241s Rank 0 Skipped paths because of dead end for tail: 0 241s Rank 0 Skipped paths because of two dead ends: 0 241s Rank 0 Skipped paths because of bubble weak component: 0 241s Rank 0 Skipped paths because of short length: 1031 241s Rank 0 Skipped paths because of bad ownership: 1 241s Rank 0 Skipped paths because of low coverage: 0 241s Rank 0 Eligible paths: 0 241s Rank 0: assembler memory usage: 113032 KiB 241s Rank 0 registered -1/0 241s Rank 1 has 1 seeds to register. 241s Rank 0 registered its seeds 241s Rank 1 registered 0/1 241s Rank 1 registered 0/1 241s Rank 1 registered its seeds 241s VirtualProcessor: completed jobs: 0 241s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 241s VirtualProcessor: completed jobs: 0 241s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 242s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 242s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 251s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 251s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 251s Rank 0 merged its seeds: 0 seeds -> 0 seeds 251s Rank 1 merged its seeds: 1 seeds -> 1 seeds 251s 251s *** 251s Step: Detection of assembly seeds 251s Date: Sat Mar 15 18:41:52 2025 251s Elapsed time: 11 seconds 251s Since beginning: 13 seconds 251s *** 251s 251s 251s Rank 0 detected 0 library lengths 251s Rank 0 is calculating library lengths [0/0] (completed) 251s Rank 0: peak number of workers: 0, maximum: 32768 251s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 251s Rank 0: assembler memory usage: 117128 KiB 251s Rank 1 is calculating library lengths [1/1] 251s Rank 1 detected 1737 library lengths 251s Rank 1 is calculating library lengths [1/1] (completed) 251s Rank 1: peak number of workers: 1, maximum: 32768 251s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7987 virtual messages generated 7987 real messages (100%) 251s Rank 1: assembler memory usage: 148720 KiB 251s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 251s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 251s 251s Mode= 2 signalAverage= 9 251s CURRENT IS NOISE, 244 251s GOT HIT 212 251s 251s 251s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 251s 251s *** 251s Step: Estimation of outer distances for paired reads 251s Date: Sat Mar 15 18:41:52 2025 251s Elapsed time: 0 seconds 251s Since beginning: 13 seconds 251s *** 251s 251s 251s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 251s Rank 0 is extending seeds [0/0] (completed) 251s Rank 0 extended 0 seeds out of 0 (0.00%) 251s Rank 0: assembler memory usage: 117128 KiB 251s Rank 1 traversed 1000 nucleotide symbols 251s Rank 1: assembler memory usage: 152816 KiB 251s Rank 1 is extending seeds [1/1] (completed) 251s Rank 1 extended 1 seeds out of 1 (100.00%) 251s Rank 1: assembler memory usage: 152816 KiB 251s Rank 0 starting fusions 251s 251s *** 251s Step: Bidirectional extension of seeds 251s Date: Sat Mar 15 18:41:52 2025 251s Elapsed time: 0 seconds 251s Since beginning: 13 seconds 251s *** 251s 251s 251s Rank 0: starting clear step. cycleNumber= 0 252s Rank 0 adding 0 new fusions 252s Rank 0 cleared, 0 paths 252s Rank 1 adding 0 new fusions 252s Rank 1 cleared, 1 paths 252s Rank 0: starting distribution step 252s Rank 0 is distributing fusions [0/0] (completed) 252s Rank 1 is distributing fusions [1/1] 252s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 252s Rank 1: assembler memory usage: 152816 KiB 252s Rank 0: assembler memory usage: 117128 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 is distributing fusions [1/1] (completed) 252s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 0 tells others to compute fusions. 252s Rank 0 FusionTaskCreator [0/0] 252s Rank 1 FusionTaskCreator assignNextTask [0/2] 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Statistics: all paths: 0 eliminated during fusing: 0 252s Rank 0: assembler memory usage: 117128 KiB 252s VirtualProcessor: completed jobs: 0 252s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 252s Rank 1 FusionTaskCreator processWorkerResult [0/2] 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 FusionTaskCreator [2/2] 252s Statistics: all paths: 1 eliminated during fusing: 0 252s Rank 1: assembler memory usage: 152816 KiB 252s VirtualProcessor: completed jobs: 2 252s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10897 virtual messages generated 10897 real messages (100%) 252s Rank 0: starting clear step. cycleNumber= 1 252s Rank 0 adding 0 new fusions 252s Rank 0 cleared, 0 paths 252s Rank 1 adding 0 new fusions 252s Rank 1 cleared, 1 paths 252s Rank 0 is distributing fusions [0/0] (completed) 252s Rank 1 is distributing fusions [1/1] 252s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 252s Rank 0: assembler memory usage: 117128 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 is distributing fusions [1/1] (completed) 252s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 JoinerTaskCreator assignNextTask [0/2] 252s Rank 0 JoinerTaskCreator [0/0] 252s Statistics: all paths: 0 eliminated during joining: 0 252s Rank 0: assembler memory usage: 117128 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s VirtualProcessor: completed jobs: 0 252s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s Rank 1 JoinerTaskCreator [2/2] 252s Statistics: all paths: 1 eliminated during joining: 0 252s Rank 1: assembler memory usage: 152816 KiB 252s Date: Sat Mar 15 18:41:53 2025 252s VirtualProcessor: completed jobs: 2 252s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13807 virtual messages generated 13807 real messages (100%) 253s Rank 1 adding 0 new fusions 253s Rank 0 adding 0 new fusions 253s Rank 1 cleared, 1 paths 253s Rank 0 cleared, 0 paths 253s Rank 0: starting distribution step 253s Rank 0 is distributing fusions [0/0] (completed) 253s Rank 1 is distributing fusions [1/1] 253s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 0: assembler memory usage: 117128 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 1 is distributing fusions [1/1] (completed) 253s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 0 tells others to compute fusions. 253s Rank 0 FusionTaskCreator [0/0] 253s Rank 1 FusionTaskCreator assignNextTask [0/2] 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Statistics: all paths: 0 eliminated during fusing: 0 253s Rank 0: assembler memory usage: 117128 KiB 253s VirtualProcessor: completed jobs: 0 253s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 253s Rank 1 FusionTaskCreator processWorkerResult [0/2] 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 1 FusionTaskCreator [2/2] 253s Statistics: all paths: 1 eliminated during fusing: 0 253s Rank 1: assembler memory usage: 152816 KiB 253s VirtualProcessor: completed jobs: 2 253s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16717 virtual messages generated 16717 real messages (100%) 253s Rank 0: starting clear step. cycleNumber= 2 253s Rank 1 adding 0 new fusions 253s Rank 0 adding 0 new fusions 253s Rank 0 cleared, 0 paths 253s Rank 0 is distributing fusions [0/0] (completed) 253s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 253s Rank 1 cleared, 1 paths 253s Rank 1 is distributing fusions [1/1] 253s Rank 1: assembler memory usage: 152816 KiB 253s Rank 0: assembler memory usage: 117128 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 1 is distributing fusions [1/1] (completed) 253s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Rank 1 JoinerTaskCreator assignNextTask [0/2] 253s Rank 0 JoinerTaskCreator [0/0] 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s Statistics: all paths: 0 eliminated during joining: 0 253s Rank 0: assembler memory usage: 117128 KiB 253s Date: Sat Mar 15 18:41:54 2025 253s VirtualProcessor: completed jobs: 0 253s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 253s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 253s Rank 1: assembler memory usage: 152816 KiB 253s Date: Sat Mar 15 18:41:54 2025 254s Rank 1 JoinerTaskCreator [2/2] 254s Statistics: all paths: 1 eliminated during joining: 0 254s Rank 1: assembler memory usage: 152816 KiB 254s Date: Sat Mar 15 18:41:54 2025 254s VirtualProcessor: completed jobs: 2 254s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19627 virtual messages generated 19627 real messages (100%) 254s Rank 0 adding 0 new fusions 254s Rank 0 cleared, 0 paths 254s Rank 1 adding 0 new fusions 254s Rank 1 cleared, 1 paths 254s Rank 0: starting distribution step 254s Rank 0 is distributing fusions [0/0] (completed) 254s Rank 1 is distributing fusions [1/1] 254s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 254s Rank 1: assembler memory usage: 152816 KiB 254s Date: Sat Mar 15 18:41:55 2025 254s Rank 0: assembler memory usage: 117128 KiB 254s Date: Sat Mar 15 18:41:55 2025 254s Rank 1 is distributing fusions [1/1] (completed) 254s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 254s Rank 1: assembler memory usage: 152816 KiB 254s Date: Sat Mar 15 18:41:55 2025 254s Rank 0 cycleNumber= 2 254s 254s *** 254s Step: Merging of redundant paths 254s Date: Sat Mar 15 18:41:55 2025 254s Elapsed time: 3 seconds 254s Since beginning: 16 seconds 254s *** 254s 254s 254s Rank 0 appended 0 elements 254s Rank 1 appended 1 elements 254s 254s *** 254s Step: Generation of contigs 254s Date: Sat Mar 15 18:41:55 2025 254s Elapsed time: 0 seconds 254s Since beginning: 16 seconds 254s *** 254s 254s Rank 0 finished gathering scaffold links. 254s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 254s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 254s Rank 0 ineligibleObjects: 0/970 (0.00%) 254s Rank 1: assembler memory usage: 152816 KiB 254s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 254s Rank 1 finished gathering scaffold links. 254s Rank 0 will write 1 contig lengths 254s Rank 0 will solve the scaffolding problem. 254s Welcome to GreedySolver v1.0 254s 1 vertices; 0 edges 254s 1 contigs >= 500 254s Edges in solution: 0 254s 254s Conflict statistics: 254s 1 scaffolds, 1 >= 500 254s Total: 1000 nucleotides 254s 254s *** 254s Step: Scaffolding of contigs 254s Date: Sat Mar 15 18:41:55 2025 254s Elapsed time: 0 seconds 254s Since beginning: 16 seconds 254s *** 254s Rank 1 syncing with master 254s 254s Rank 0 syncing with master 254s 254s *** 254s Step: Counting sequences to search 254s Date: Sat Mar 15 18:41:55 2025 254s Elapsed time: 0 seconds 254s Since beginning: 16 seconds 254s *** 254s 254s 254s Rank 1 will add colors, 0 sequences in 0 files to process 254s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 254s Rank 0 will add colors, 0 sequences in 0 files to process 254s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 255s 255s *** 255s Step: Graph coloring 255s Date: Sat Mar 15 18:41:56 2025 255s Elapsed time: 1 seconds 255s Since beginning: 17 seconds 255s *** 255s 255s 255s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 255s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 255s Rank 1 computing contig abundances [1/1] [1/970] 255s Rank 0 shares its counts 255s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 255s Rank 1 computing contig abundances [1/1] [970/970] 255s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 255s 255s *** 255s Step: Counting contig biological abundances 255s Date: Sat Mar 15 18:41:56 2025 255s Elapsed time: 0 seconds 255s Since beginning: 17 seconds 255s *** 255s 255s 255s Rank 0 colored the graph with 0 real colors using 1 virtual colors 255s Rank 1 colored the graph with 0 real colors using 1 virtual colors 255s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 255s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 255s 255s *** 255s Step: Counting sequence biological abundances 255s Date: Sat Mar 15 18:41:56 2025 255s Elapsed time: 0 seconds 255s Since beginning: 17 seconds 255s *** 255s 255s 255s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 255s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 255s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 255s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 255s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 255s 255s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 255s 255s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 255s Rank 0 is starting taxon syncing across the compute tribe. 255s 255s *** 255s Step: Loading taxons 255s Date: Sat Mar 15 18:41:56 2025 255s Elapsed time: 0 seconds 255s Since beginning: 17 seconds 255s *** 255s 255s Rank 0 synced taxons across the grid with 2 poor slaves. 255s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 255s Rank 0 has 0 taxons after syncing with master 255s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 255s Rank 1 has 0 taxons after syncing with master 256s 256s 256s 256s *** 256s Step: Loading tree 256s Date: Sat Mar 15 18:41:57 2025 256s Elapsed time: 1 seconds 256s Since beginning: 18 seconds 256s *** 256s 256s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 256s 256s Rank 0: counting ontology terms in the graph... 256s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 256s 256s Rank 1: counting ontology terms in the graph... 257s Rank 0: 0 have some biological signal 257s Number of dereferenced alternate handles: 0 257s Number of k-mer observations with gene ontology terms: 0 257s Rank 0: synced ontology term profiles with master 257s Rank 1: 0 have some biological signal 257s Number of dereferenced alternate handles: 0 257s Number of k-mer observations with gene ontology terms: 0 257s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 257s Rank 1: synced ontology term profiles with master 257s Rank 0: synchronization is complete! 257s Rank 0: ontology terms with biological signal: 0 257s Populated recursive values... 257s Gene ontology terms without depth information: 0 257s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 257s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 257s 257s *** 257s Step: Processing gene ontologies 257s Date: Sat Mar 15 18:41:58 2025 257s Elapsed time: 1 seconds 257s Since beginning: 19 seconds 257s *** 257s 257s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 257s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 257s [GenomeNeighbourhood] in final list: 0 257s 257s *** 257s Step: Computing neighbourhoods 257s Date: Sat Mar 15 18:41:58 2025 257s Elapsed time: 0 seconds 257s Since beginning: 19 seconds 257s *** 257s 257s Contigs >= 100 nt 257s Number: 1 257s Total length: 1000 257s Average: 1000 257s N50: 1000 257s Median: 1000 257s Largest: 1000 257s Contigs >= 500 nt 257s Number: 1 257s Total length: 1000 257s Average: 1000 257s N50: 1000 257s Median: 1000 257s Largest: 1000 257s Scaffolds >= 100 nt 257s Number: 1 257s Total length: 1000 257s Average: 1000 257s N50: 1000 257s Median: 1000 257s Largest: 1000 257s Scaffolds >= 500 nt 257s Number: 1 257s Total length: 1000 257s Average: 1000 257s N50: 1000 257s Median: 1000 257s Largest: 1000 257s 257s Rank 0 wrote test3/Contigs.fasta 257s Rank 0 wrote test3/Scaffolds.fasta 257s Check for test3/* 257s 257s 257s autopkgtest [18:41:58]: test run-unit-test: -----------------------] 258s autopkgtest [18:41:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 258s run-unit-test PASS 258s autopkgtest [18:41:59]: @@@@@@@@@@@@@@@@@@@@ summary 258s run-unit-test PASS 276s nova [W] Using flock in prodstack6-s390x 276s Creating nova instance adt-plucky-s390x-ray-20250315-183741-juju-7f2275-prod-proposed-migration-environment-2-ed245a12-83b1-47e0-bbce-6339c7908022 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 276s nova [W] Timed out waiting for 4c9d42db-7fc3-4e93-a3da-70efc16ef3bf to get deleted.