0s autopkgtest [16:50:44]: starting date and time: 2025-03-15 16:50:44+0000 0s autopkgtest [16:50:44]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:50:44]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n4no06j8/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.9 lxd-armhf-10.145.243.9:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [16:51:04]: testbed dpkg architecture: armhf 23s autopkgtest [16:51:07]: testbed apt version: 2.9.33 29s autopkgtest [16:51:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [16:51:17]: testbed release detected to be: None 42s autopkgtest [16:51:26]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 45s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 45s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 45s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 46s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 46s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 47s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 47s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 47s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 49s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 73s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 74s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 75s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 75s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 75s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 92s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 94s Fetched 41.0 MB in 49s (832 kB/s) 95s Reading package lists... 101s autopkgtest [16:52:25]: upgrading testbed (apt dist-upgrade and autopurge) 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 104s Entering ResolveByKeep 105s 105s Calculating upgrade... 105s The following packages will be upgraded: 105s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 106s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 8683 kB of archives. 106s After this operation, 23.6 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 115s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 115s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 116s Preconfiguring packages ... 116s Fetched 8683 kB in 10s (890 kB/s) 116s (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 ... 64655 files and directories currently installed.) 116s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 116s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 116s Setting up libc6:armhf (2.41-1ubuntu2) ... 117s (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 ... 64655 files and directories currently installed.) 117s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 117s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 117s Setting up libc-bin (2.41-1ubuntu2) ... 117s (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 ... 64655 files and directories currently installed.) 117s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 117s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 117s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 117s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 117s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 117s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 117s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 117s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 117s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 118s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 118s Setting up sos (4.9.0-5) ... 118s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 118s Setting up locales (2.41-1ubuntu2) ... 119s Generating locales (this might take a while)... 121s en_US.UTF-8... done 121s Generation complete. 121s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 122s Setting up strace (6.13+ds-1ubuntu1) ... 122s Processing triggers for man-db (2.13.0-1) ... 123s Processing triggers for systemd (257.3-1ubuntu3) ... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s Solving dependencies... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [16:52:53]: rebooting testbed after setup commands that affected boot 168s autopkgtest [16:53:32]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 193s autopkgtest [16:53:57]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (dsc) [2123 B] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (tar) [450 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (diff) [213 kB] 211s gpgv: Signature made Mon Dec 2 16:02:51 2024 UTC 211s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 211s gpgv: issuer "tille@debian.org" 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-9.dsc: no acceptable signature found 211s autopkgtest [16:54:15]: testing package ray version 2.3.1-9 213s autopkgtest [16:54:17]: build not needed 216s autopkgtest [16:54:20]: test run-unit-test: preparing testbed 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 219s The following NEW packages will be installed: 219s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hwloc-nox 219s libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 219s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwloc15 libice6 219s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libmpich12 219s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 219s libpaper2 libpixman-1-0 libsharpyuv0 libslurm42t64 libsm6 libtcl8.6 219s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 219s libxft2 libxrender1 libxss1 libxt6t64 mpi-default-bin mpich r-base-core ray 219s ray-doc ray-extra unzip x11-common xdg-utils zip 219s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 219s Need to get 41.4 MB of archives. 219s After this operation, 80.5 MB of additional disk space will be used. 219s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 220s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 222s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 222s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 222s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 222s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 222s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 222s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 222s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 222s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 222s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 223s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 223s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 223s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 223s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 223s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 223s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 225s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf libhwloc15 armhf 2.12.0-1 [147 kB] 225s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 225s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 225s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 225s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 225s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 226s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 227s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 227s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 227s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 227s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 227s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 227s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 227s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 227s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 227s Get:34 http://ftpmaster.internal/ubuntu plucky/universe armhf libslurm42t64 armhf 24.11.1-1 [769 kB] 228s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 228s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 229s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 229s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 230s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 230s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 230s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 230s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 231s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 231s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 231s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 231s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 231s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 263s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf hwloc-nox armhf 2.12.0-1 [213 kB] 264s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpich12 armhf 4.2.1-5 [1574 kB] 265s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf mpich armhf 4.2.1-5 [214 kB] 265s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf mpi-default-bin armhf 1.18 [2504 B] 266s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf ray armhf 2.3.1-9 [856 kB] 266s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf ray-doc all 2.3.1-9 [35.2 kB] 267s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf ray-extra all 2.3.1-9 [12.3 kB] 267s Preconfiguring packages ... 267s Fetched 41.4 MB in 47s (876 kB/s) 267s Selecting previously unselected package libfreetype6:armhf. 268s (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 ... 64655 files and directories currently installed.) 268s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 268s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 268s Selecting previously unselected package fonts-dejavu-mono. 268s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 268s Unpacking fonts-dejavu-mono (2.37-8) ... 268s Selecting previously unselected package fonts-dejavu-core. 268s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 268s Unpacking fonts-dejavu-core (2.37-8) ... 268s Selecting previously unselected package fontconfig-config. 268s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 268s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 268s Selecting previously unselected package libfontconfig1:armhf. 268s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 268s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 268s Selecting previously unselected package fontconfig. 268s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 268s Unpacking fontconfig (2.15.0-2ubuntu1) ... 268s Selecting previously unselected package libblas3:armhf. 268s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 268s Unpacking libblas3:armhf (3.12.1-2) ... 268s Selecting previously unselected package libpixman-1-0:armhf. 268s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 268s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 268s Selecting previously unselected package libxcb-render0:armhf. 268s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 268s Unpacking libxcb-render0:armhf (1.17.0-2) ... 268s Selecting previously unselected package libxcb-shm0:armhf. 268s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 268s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 268s Selecting previously unselected package libxrender1:armhf. 268s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 268s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 268s Selecting previously unselected package libcairo2:armhf. 268s Preparing to unpack .../11-libcairo2_1.18.2-2_armhf.deb ... 268s Unpacking libcairo2:armhf (1.18.2-2) ... 268s Selecting previously unselected package libdatrie1:armhf. 268s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 268s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 268s Selecting previously unselected package libdeflate0:armhf. 268s Preparing to unpack .../13-libdeflate0_1.23-1_armhf.deb ... 268s Unpacking libdeflate0:armhf (1.23-1) ... 268s Selecting previously unselected package libgfortran5:armhf. 268s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 268s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 269s Selecting previously unselected package libgomp1:armhf. 269s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 269s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 269s Selecting previously unselected package libgraphite2-3:armhf. 269s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 269s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 269s Selecting previously unselected package libharfbuzz0b:armhf. 269s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_armhf.deb ... 269s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 269s Selecting previously unselected package libhwloc15:armhf. 269s Preparing to unpack .../18-libhwloc15_2.12.0-1_armhf.deb ... 269s Unpacking libhwloc15:armhf (2.12.0-1) ... 269s Selecting previously unselected package x11-common. 269s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 269s Unpacking x11-common (1:7.7+23ubuntu3) ... 269s Selecting previously unselected package libice6:armhf. 269s Preparing to unpack .../20-libice6_2%3a1.1.1-1_armhf.deb ... 269s Unpacking libice6:armhf (2:1.1.1-1) ... 269s Selecting previously unselected package libjpeg-turbo8:armhf. 269s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 269s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 269s Selecting previously unselected package libjpeg8:armhf. 269s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_armhf.deb ... 269s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 269s Selecting previously unselected package liblapack3:armhf. 269s Preparing to unpack .../23-liblapack3_3.12.1-2_armhf.deb ... 269s Unpacking liblapack3:armhf (3.12.1-2) ... 269s Selecting previously unselected package liblerc4:armhf. 269s Preparing to unpack .../24-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 269s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 269s Selecting previously unselected package libthai-data. 269s Preparing to unpack .../25-libthai-data_0.1.29-2build1_all.deb ... 269s Unpacking libthai-data (0.1.29-2build1) ... 269s Selecting previously unselected package libthai0:armhf. 269s Preparing to unpack .../26-libthai0_0.1.29-2build1_armhf.deb ... 269s Unpacking libthai0:armhf (0.1.29-2build1) ... 269s Selecting previously unselected package libpango-1.0-0:armhf. 269s Preparing to unpack .../27-libpango-1.0-0_1.56.2-1_armhf.deb ... 269s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 269s Selecting previously unselected package libpangoft2-1.0-0:armhf. 269s Preparing to unpack .../28-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 269s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 269s Selecting previously unselected package libpangocairo-1.0-0:armhf. 269s Preparing to unpack .../29-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 269s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 269s Selecting previously unselected package libpaper2:armhf. 269s Preparing to unpack .../30-libpaper2_2.2.5-0.3_armhf.deb ... 269s Unpacking libpaper2:armhf (2.2.5-0.3) ... 269s Selecting previously unselected package libpaper-utils. 269s Preparing to unpack .../31-libpaper-utils_2.2.5-0.3_armhf.deb ... 269s Unpacking libpaper-utils (2.2.5-0.3) ... 269s Selecting previously unselected package libsharpyuv0:armhf. 269s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_armhf.deb ... 269s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 269s Selecting previously unselected package libslurm42t64. 269s Preparing to unpack .../33-libslurm42t64_24.11.1-1_armhf.deb ... 269s Unpacking libslurm42t64 (24.11.1-1) ... 269s Selecting previously unselected package libsm6:armhf. 269s Preparing to unpack .../34-libsm6_2%3a1.2.4-1_armhf.deb ... 269s Unpacking libsm6:armhf (2:1.2.4-1) ... 269s Selecting previously unselected package libtcl8.6:armhf. 270s Preparing to unpack .../35-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 270s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 270s Selecting previously unselected package libjbig0:armhf. 270s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 270s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 270s Selecting previously unselected package libwebp7:armhf. 270s Preparing to unpack .../37-libwebp7_1.5.0-0.1_armhf.deb ... 270s Unpacking libwebp7:armhf (1.5.0-0.1) ... 270s Selecting previously unselected package libtiff6:armhf. 270s Preparing to unpack .../38-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 270s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 270s Selecting previously unselected package libxft2:armhf. 270s Preparing to unpack .../39-libxft2_2.3.6-1build1_armhf.deb ... 270s Unpacking libxft2:armhf (2.3.6-1build1) ... 270s Selecting previously unselected package libxss1:armhf. 270s Preparing to unpack .../40-libxss1_1%3a1.2.3-1build3_armhf.deb ... 270s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 270s Selecting previously unselected package libtk8.6:armhf. 270s Preparing to unpack .../41-libtk8.6_8.6.16-1_armhf.deb ... 270s Unpacking libtk8.6:armhf (8.6.16-1) ... 270s Selecting previously unselected package libxt6t64:armhf. 270s Preparing to unpack .../42-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 270s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 270s Selecting previously unselected package zip. 270s Preparing to unpack .../43-zip_3.0-14ubuntu2_armhf.deb ... 270s Unpacking zip (3.0-14ubuntu2) ... 270s Selecting previously unselected package unzip. 270s Preparing to unpack .../44-unzip_6.0-28ubuntu6_armhf.deb ... 270s Unpacking unzip (6.0-28ubuntu6) ... 270s Selecting previously unselected package xdg-utils. 270s Preparing to unpack .../45-xdg-utils_1.2.1-2ubuntu1_all.deb ... 270s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 270s Selecting previously unselected package r-base-core. 270s Preparing to unpack .../46-r-base-core_4.4.3-1_armhf.deb ... 270s Unpacking r-base-core (4.4.3-1) ... 271s Selecting previously unselected package hwloc-nox. 271s Preparing to unpack .../47-hwloc-nox_2.12.0-1_armhf.deb ... 271s Unpacking hwloc-nox (2.12.0-1) ... 271s Selecting previously unselected package libmpich12:armhf. 271s Preparing to unpack .../48-libmpich12_4.2.1-5_armhf.deb ... 271s Unpacking libmpich12:armhf (4.2.1-5) ... 271s Selecting previously unselected package mpich. 271s Preparing to unpack .../49-mpich_4.2.1-5_armhf.deb ... 271s Unpacking mpich (4.2.1-5) ... 271s Selecting previously unselected package mpi-default-bin. 271s Preparing to unpack .../50-mpi-default-bin_1.18_armhf.deb ... 271s Unpacking mpi-default-bin (1.18) ... 271s Selecting previously unselected package ray. 271s Preparing to unpack .../51-ray_2.3.1-9_armhf.deb ... 271s Unpacking ray (2.3.1-9) ... 271s Selecting previously unselected package ray-doc. 271s Preparing to unpack .../52-ray-doc_2.3.1-9_all.deb ... 271s Unpacking ray-doc (2.3.1-9) ... 271s Selecting previously unselected package ray-extra. 271s Preparing to unpack .../53-ray-extra_2.3.1-9_all.deb ... 271s Unpacking ray-extra (2.3.1-9) ... 271s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 271s Setting up libpixman-1-0:armhf (0.44.0-3) ... 271s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 271s Setting up ray-doc (2.3.1-9) ... 271s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 271s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 271s Setting up libdatrie1:armhf (0.2.13-3build1) ... 271s Setting up libxcb-render0:armhf (1.17.0-2) ... 271s Setting up unzip (6.0-28ubuntu6) ... 271s Setting up x11-common (1:7.7+23ubuntu3) ... 272s Setting up libdeflate0:armhf (1.23-1) ... 272s Setting up libxcb-shm0:armhf (1.17.0-2) ... 272s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 272s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 272s Setting up zip (3.0-14ubuntu2) ... 272s Setting up libblas3:armhf (3.12.1-2) ... 272s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 272s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 272s Setting up libslurm42t64 (24.11.1-1) ... 272s Setting up fonts-dejavu-mono (2.37-8) ... 272s Setting up libhwloc15:armhf (2.12.0-1) ... 272s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 272s Setting up fonts-dejavu-core (2.37-8) ... 272s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 272s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 272s Setting up libwebp7:armhf (1.5.0-0.1) ... 272s Setting up libmpich12:armhf (4.2.1-5) ... 272s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 272s Setting up libthai-data (0.1.29-2build1) ... 272s Setting up libxss1:armhf (1:1.2.3-1build3) ... 272s Setting up libpaper2:armhf (2.2.5-0.3) ... 272s Setting up xdg-utils (1.2.1-2ubuntu1) ... 272s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 272s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 272s Setting up libice6:armhf (2:1.1.1-1) ... 272s Setting up liblapack3:armhf (3.12.1-2) ... 272s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 272s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 272s Setting up hwloc-nox (2.12.0-1) ... 272s Setting up libpaper-utils (2.2.5-0.3) ... 272s Setting up libthai0:armhf (0.1.29-2build1) ... 272s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 272s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 272s Setting up libsm6:armhf (2:1.2.4-1) ... 272s Setting up fontconfig (2.15.0-2ubuntu1) ... 274s Regenerating fonts cache... done. 274s Setting up libxft2:armhf (2.3.6-1build1) ... 274s Setting up mpich (4.2.1-5) ... 274s update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode 274s update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode 274s Setting up libtk8.6:armhf (8.6.16-1) ... 274s Setting up libpango-1.0-0:armhf (1.56.2-1) ... 274s Setting up mpi-default-bin (1.18) ... 274s Setting up libcairo2:armhf (1.18.2-2) ... 274s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 274s Setting up ray (2.3.1-9) ... 274s Setting up libpangoft2-1.0-0:armhf (1.56.2-1) ... 274s Setting up libpangocairo-1.0-0:armhf (1.56.2-1) ... 274s Setting up r-base-core (4.4.3-1) ... 274s Creating config file /etc/R/Renviron with new version 274s Setting up ray-extra (2.3.1-9) ... 274s Processing triggers for libc-bin (2.41-1ubuntu2) ... 274s Processing triggers for man-db (2.13.0-1) ... 275s Processing triggers for install-info (7.1.1-1) ... 287s autopkgtest [16:55:31]: test run-unit-test: [----------------------- 289s 289s ************************************************** 289s This program comes with ABSOLUTELY NO WARRANTY. 289s This is free software, and you are welcome to redistribute it 289s under certain conditions; see "LICENSE.txt" for details. 289s ************************************************** 289s 289s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 289s Centre de recherche en infectiologie de l'Université Laval 289s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 289s http://denovoassembler.sf.net/ 289s 289s References to cite: 289s 289s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 289s Ray Meta: scalable de novo metagenome assembly and profiling. 289s Genome Biology (BioMed Central Ltd). 289s 13:R122, Published: 22 December 2012 289s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 289s 289s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 289s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 289s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 289s November 2010, Volume 17, Issue 11, Pages 1519-1533. 289s http://dx.doi.org/doi:10.1089/cmb.2009.0238 289s 289s Ray version 2.3.1 289s License for Ray: GNU General Public License version 3 289s RayPlatform version: 2.0.1 289s License for RayPlatform: GNU Lesser General Public License version 3 289s 289s MAXKMERLENGTH: 32 289s Maximum coverage depth stored by CoverageDepth: 4294967295 289s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 289s FORCE_PACKING = n 289s ASSERT = n 289s HAVE_LIBZ = y 289s HAVE_LIBBZ2 = y 289s PROFILER_COLLECT = n 289s MINIRANKS = y 289s CLOCK_GETTIME = n 289s __linux__ = y 289s _MSC_VER = n 289s __GNUC__ = y 289s RAY_32_BITS = y 289s RAY_64_BITS = n 289s MPI standard version: MPI 4.1 289s Compiler: GNU gcc/g++ 14.2.0 289s MPI I/O: n 289s 289s 289s -k (to set the k-mer size) 289s Value: 31 289s 289s 289s Paired library # 0 289s -p (paired-end sequences) 289s Left sequences: ecoli_1K_1.fq 289s Right sequences: ecoli_1K_2.fq 289s Average length: automatic detection 289s Standard deviation: automatic detection 289s 289s Ray command: 289s mpiexec -n 1 Ray \ 289s -k \ 289s 31 \ 289s -p \ 289s ecoli_1K_1.fq \ 289s ecoli_1K_2.fq \ 289s -o \ 289s test1 289s 289s Rank 0 wrote test1/RayCommand.txt 289s 289s k-mer length: 31 289s Rank 0: assembler memory usage: 28724 KiB 289s Rank 0: assembler memory usage: 94396 KiB 289s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 1923 289s Rank 0: testing the network, please wait... 289s 289s Rank 0 is testing the network [0/1000] 289s Rank 0 is testing the network [1000/1000] 289s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 289s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 289s 289s Rank 0 wrote test1/NetworkTest.txt 289s 289s 289s *** 289s Step: Network testing 289s Date: Sat Mar 15 16:55:33 2025 289s Elapsed time: 0 seconds 289s Since beginning: 0 seconds 289s *** 289s 289s 289s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 289s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 289s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 289s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 289s Rank 0 wrote test1/NumberOfSequences.txt 289s Rank 0 wrote test1/SequencePartition.txt 289s 289s *** 289s Step: Counting sequences to assemble 289s Date: Sat Mar 15 16:55:33 2025 289s Elapsed time: 0 seconds 289s Since beginning: 0 seconds 289s *** 289s 289s 289s Rank 0 is loading sequence reads 289s Rank 0 : partition is [0;4107], 4108 sequence reads 289s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 289s Rank 0 has 0 sequence reads 289s Rank 0: assembler memory usage: 103920 KiB 289s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 289s Rank 0 has 4108 sequence reads (completed) 289s 289s *** 289s Step: Sequence loading 289s Date: Sat Mar 15 16:55:33 2025 289s Elapsed time: 0 seconds 289s Since beginning: 0 seconds 289s *** 289s 289s 289s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 289s Rank 0 created its Bloom filter 289s Rank 0 is counting k-mers in sequence reads [1/4108] 290s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 290s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 290s 290s 290s *** 290s Step: K-mer counting 290s Date: Sat Mar 15 16:55:34 2025 290s Elapsed time: 1 seconds 290s Since beginning: 1 seconds 290s *** 290s 290s 290s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 290s Rank 0 destroyed its Bloom filter 290s Rank 0 has 1954 k-mers (completed) 290s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 290s Rank 0: assembler memory usage: 103064 KiB 300s 300s 300s Rank 0: the minimum coverage is 3 300s Rank 0: the peak coverage is 3 300s Warning: no peak observed in the k-mer coverage distribution. 300s to deal with the sequencing error rate, try to lower the k-mer length (-k) 300s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 300s 300s *** 300s Step: Coverage distribution analysis 300s Date: Sat Mar 15 16:55:44 2025 300s Elapsed time: 10 seconds 300s Since beginning: 11 seconds 300s *** 300s 300s 300s 300s Rank 0 is adding edges [1/4108] 301s Rank 0 is adding edges [4108/4108] (completed) 301s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 301s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 301s 301s *** 301s Step: Graph construction 301s Date: Sat Mar 15 16:55:45 2025 301s Elapsed time: 1 seconds 301s Since beginning: 12 seconds 301s *** 301s 301s 301s Rank 0 has 1954 vertices (completed) 301s Rank 0: assembler memory usage: 103064 KiB 310s Rank 0 is purging edges [1/1954] 310s Rank 0 is purging edges [1954/1954] (completed) 310s Rank 0: assembler memory usage: 103600 KiB 310s VirtualProcessor: completed jobs: 1954 310s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 321s Rank 0 wrote test1/degreeDistribution.txt 321s 321s *** 321s Step: Null edge purging 321s Date: Sat Mar 15 16:56:05 2025 321s Elapsed time: 20 seconds 321s Since beginning: 32 seconds 321s *** 321s 321s 321s Rank 0 is selecting optimal read markers [1/4108] 321s Rank 0: assembler memory usage: 103600 KiB 322s Rank 0 is selecting optimal read markers [4108/4108] (completed) 322s Rank 0: peak number of workers: 599, maximum: 32768 322s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 322s Rank 0: assembler memory usage: 111800 KiB 322s Rank 0: Freeing unused assembler memory: 4096 KiB freed 322s Rank 0: assembler memory usage: 107700 KiB 322s 322s *** 322s Step: Selection of optimal read markers 322s Date: Sat Mar 15 16:56:06 2025 322s Elapsed time: 1 seconds 322s Since beginning: 33 seconds 322s *** 322s 322s 322s Rank 0: memory usage for optimal read markers= 4096 KiB 322s Rank 0 is creating seeds [1/1954] 322s Rank 0: assembler memory usage: 107700 KiB 332s Rank 0 has 1 seeds 332s Rank 0 is creating seeds [1954/1954] (completed) 332s Rank 0: peak number of workers: 746, maximum: 32768 332s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 332s Rank 0 runtime statistics for seeding algorithm: 332s Rank 0 Skipped paths because of dead end for head: 0 332s Rank 0 Skipped paths because of dead end for tail: 0 332s Rank 0 Skipped paths because of two dead ends: 0 332s Rank 0 Skipped paths because of bubble weak component: 0 332s Rank 0 Skipped paths because of short length: 1952 332s Rank 0 Skipped paths because of bad ownership: 1 332s Rank 0 Skipped paths because of low coverage: 0 332s Rank 0 Eligible paths: 1 332s Rank 0: assembler memory usage: 107832 KiB 332s Rank 0 has 1 seeds to register. 332s Rank 0 registered 0/1 332s Rank 0 registered 0/1 332s Rank 0 registered its seeds 332s VirtualProcessor: completed jobs: 0 332s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 341s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 351s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 351s Rank 0 merged its seeds: 1 seeds -> 1 seeds 351s 351s *** 351s Step: Detection of assembly seeds 351s Date: Sat Mar 15 16:56:35 2025 351s Elapsed time: 29 seconds 351s Since beginning: 1 minutes, 2 seconds 351s *** 351s 351s 351s Rank 0 is calculating library lengths [1/1] 351s Rank 0 detected 1737 library lengths 351s Rank 0 is calculating library lengths [1/1] (completed) 351s Rank 0: peak number of workers: 1, maximum: 32768 351s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 351s Rank 0: assembler memory usage: 140604 KiB 351s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 351s 351s Mode= 2 signalAverage= 9 351s CURRENT IS NOISE, 244 351s GOT HIT 212 351s 351s 351s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 351s 351s *** 351s Step: Estimation of outer distances for paired reads 351s Date: Sat Mar 15 16:56:35 2025 351s Elapsed time: 0 seconds 351s Since beginning: 1 minutes, 2 seconds 351s *** 351s 351s 351s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 352s Rank 0 traversed 1000 nucleotide symbols 352s Rank 0: assembler memory usage: 144704 KiB 352s Rank 0 is extending seeds [1/1] (completed) 352s Rank 0 extended 1 seeds out of 1 (100.00%) 352s Rank 0: assembler memory usage: 140604 KiB 352s Rank 0 starting fusions 352s 352s *** 352s Step: Bidirectional extension of seeds 352s Date: Sat Mar 15 16:56:36 2025 352s Elapsed time: 1 seconds 352s Since beginning: 1 minutes, 3 seconds 352s *** 352s 352s 352s Rank 0: starting clear step. cycleNumber= 0 362s Rank 0 adding 0 new fusions 362s Rank 0 cleared, 1 paths 362s Rank 0: starting distribution step 362s Rank 0 is distributing fusions [1/1] 362s Rank 0: assembler memory usage: 140604 KiB 362s Date: Sat Mar 15 16:56:46 2025 362s Rank 0 is distributing fusions [1/1] (completed) 362s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 362s Rank 0: assembler memory usage: 144704 KiB 362s Date: Sat Mar 15 16:56:46 2025 362s Rank 0 tells others to compute fusions. 362s Rank 0 FusionTaskCreator assignNextTask [0/2] 362s Rank 0: assembler memory usage: 144704 KiB 362s Date: Sat Mar 15 16:56:46 2025 362s Rank 0 FusionTaskCreator processWorkerResult [0/2] 362s Rank 0: assembler memory usage: 144704 KiB 362s Date: Sat Mar 15 16:56:46 2025 362s Rank 0 FusionTaskCreator [2/2] 362s Statistics: all paths: 1 eliminated during fusing: 0 362s Rank 0: assembler memory usage: 144704 KiB 362s VirtualProcessor: completed jobs: 2 362s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 362s Rank 0: starting clear step. cycleNumber= 1 372s Rank 0 adding 0 new fusions 372s Rank 0 cleared, 1 paths 372s Rank 0 is distributing fusions [1/1] 372s Rank 0: assembler memory usage: 140604 KiB 372s Date: Sat Mar 15 16:56:56 2025 372s Rank 0 is distributing fusions [1/1] (completed) 372s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 372s Rank 0: assembler memory usage: 144704 KiB 372s Date: Sat Mar 15 16:56:56 2025 372s Rank 0 JoinerTaskCreator assignNextTask [0/2] 372s Rank 0: assembler memory usage: 144704 KiB 372s Date: Sat Mar 15 16:56:56 2025 372s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 372s Rank 0: assembler memory usage: 144704 KiB 372s Date: Sat Mar 15 16:56:56 2025 372s Rank 0 JoinerTaskCreator [2/2] 372s Statistics: all paths: 1 eliminated during joining: 0 372s Rank 0: assembler memory usage: 144704 KiB 372s Date: Sat Mar 15 16:56:56 2025 372s VirtualProcessor: completed jobs: 2 372s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 381s Rank 0 adding 0 new fusions 381s Rank 0 cleared, 1 paths 381s Rank 0: starting distribution step 381s Rank 0 is distributing fusions [1/1] 381s Rank 0: assembler memory usage: 140604 KiB 381s Date: Sat Mar 15 16:57:05 2025 381s Rank 0 is distributing fusions [1/1] (completed) 381s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 381s Rank 0: assembler memory usage: 144704 KiB 381s Date: Sat Mar 15 16:57:05 2025 381s Rank 0 tells others to compute fusions. 381s Rank 0 FusionTaskCreator assignNextTask [0/2] 381s Rank 0: assembler memory usage: 144704 KiB 381s Date: Sat Mar 15 16:57:05 2025 381s Rank 0 FusionTaskCreator processWorkerResult [0/2] 381s Rank 0: assembler memory usage: 144704 KiB 381s Date: Sat Mar 15 16:57:05 2025 381s Rank 0 FusionTaskCreator [2/2] 381s Statistics: all paths: 1 eliminated during fusing: 0 381s Rank 0: assembler memory usage: 144704 KiB 381s VirtualProcessor: completed jobs: 2 381s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 381s Rank 0: starting clear step. cycleNumber= 2 391s Rank 0 adding 0 new fusions 391s Rank 0 cleared, 1 paths 391s Rank 0 is distributing fusions [1/1] 391s Rank 0: assembler memory usage: 140604 KiB 391s Date: Sat Mar 15 16:57:15 2025 391s Rank 0 is distributing fusions [1/1] (completed) 391s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 391s Rank 0: assembler memory usage: 144704 KiB 391s Date: Sat Mar 15 16:57:15 2025 391s Rank 0 JoinerTaskCreator assignNextTask [0/2] 391s Rank 0: assembler memory usage: 144704 KiB 391s Date: Sat Mar 15 16:57:15 2025 391s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 391s Rank 0: assembler memory usage: 144704 KiB 391s Date: Sat Mar 15 16:57:15 2025 391s Rank 0 JoinerTaskCreator [2/2] 391s Statistics: all paths: 1 eliminated during joining: 0 391s Rank 0: assembler memory usage: 144704 KiB 391s Date: Sat Mar 15 16:57:15 2025 391s VirtualProcessor: completed jobs: 2 391s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 401s Rank 0 adding 0 new fusions 401s Rank 0 cleared, 1 paths 401s Rank 0: starting distribution step 401s Rank 0 is distributing fusions [1/1] 401s Rank 0: assembler memory usage: 140604 KiB 401s Date: Sat Mar 15 16:57:25 2025 401s Rank 0 is distributing fusions [1/1] (completed) 401s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 401s Rank 0: assembler memory usage: 144704 KiB 401s Date: Sat Mar 15 16:57:25 2025 401s Rank 0 cycleNumber= 2 401s 401s *** 401s Step: Merging of redundant paths 401s Date: Sat Mar 15 16:57:25 2025 401s Elapsed time: 49 seconds 401s Since beginning: 1 minutes, 52 seconds 401s *** 401s 401s 401s Rank 0 appended 1 elements 401s 401s *** 401s Step: Generation of contigs 401s Date: Sat Mar 15 16:57:25 2025 401s Elapsed time: 0 seconds 401s Since beginning: 1 minutes, 52 seconds 401s *** 401s 401s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 401s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 401s Rank 0 ineligibleObjects: 0/970 (0.00%) 401s Rank 0: assembler memory usage: 144704 KiB 401s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 401s Rank 0 finished gathering scaffold links. 401s Rank 0 will write 1 contig lengths 401s Rank 0 will solve the scaffolding problem. 401s Welcome to GreedySolver v1.0 401s 1 vertices; 0 edges 401s 1 contigs >= 500 401s Edges in solution: 0 401s 401s Conflict statistics: 401s 1 scaffolds, 1 >= 500 401s Total: 1000 nucleotides 401s 401s *** 401s Step: Scaffolding of contigs 401s Date: Sat Mar 15 16:57:25 2025 401s Elapsed time: 0 seconds 401s Since beginning: 1 minutes, 52 seconds 401s *** 401s 401s Rank 0 syncing with master 401s 401s *** 401s Step: Counting sequences to search 401s Date: Sat Mar 15 16:57:25 2025 401s Elapsed time: 0 seconds 401s Since beginning: 1 minutes, 52 seconds 401s *** 401s 401s 401s Rank 0 will add colors, 0 sequences in 0 files to process 401s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 411s 411s *** 411s Step: Graph coloring 411s Date: Sat Mar 15 16:57:35 2025 411s Elapsed time: 10 seconds 411s Since beginning: 2 minutes, 2 seconds 411s *** 411s 411s 411s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 411s Rank 0 shares its counts 411s Rank 0 computing contig abundances [1/1] [1/970] 411s Rank 0 computing contig abundances [1/1] [970/970] 411s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 411s 411s *** 411s Step: Counting contig biological abundances 411s Date: Sat Mar 15 16:57:35 2025 411s Elapsed time: 0 seconds 411s Since beginning: 2 minutes, 2 seconds 411s *** 411s 411s 411s Rank 0 colored the graph with 0 real colors using 1 virtual colors 411s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 411s 411s *** 411s Step: Counting sequence biological abundances 411s Date: Sat Mar 15 16:57:35 2025 411s Elapsed time: 0 seconds 411s Since beginning: 2 minutes, 2 seconds 411s *** 411s 411s 411s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 411s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 421s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 421s 421s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 421s Rank 0 is starting taxon syncing across the compute tribe. 421s 421s *** 421s Step: Loading taxons 421s Date: Sat Mar 15 16:57:45 2025 421s Elapsed time: 10 seconds 421s Since beginning: 2 minutes, 12 seconds 421s *** 421s 421s Rank 0 synced taxons across the grid with 1 poor slaves. 421s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 421s Rank 0 has 0 taxons after syncing with master 431s 431s 431s *** 431s Step: Loading tree 431s Date: Sat Mar 15 16:57:55 2025 431s Elapsed time: 10 seconds 431s Since beginning: 2 minutes, 22 seconds 431s *** 431s 441s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 441s 441s Rank 0: counting ontology terms in the graph... 451s Rank 0: 0 have some biological signal 451s Number of dereferenced alternate handles: 0 451s Number of k-mer observations with gene ontology terms: 0 451s Rank 0: synced ontology term profiles with master 451s Rank 0: synchronization is complete! 451s Rank 0: ontology terms with biological signal: 0 451s Populated recursive values... 451s Gene ontology terms without depth information: 0 451s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 451s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 451s 451s *** 451s Step: Processing gene ontologies 451s Date: Sat Mar 15 16:58:15 2025 451s Elapsed time: 20 seconds 451s Since beginning: 2 minutes, 42 seconds 451s *** 451s 451s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 451s [GenomeNeighbourhood] in final list: 0 451s 451s *** 451s Step: Computing neighbourhoods 451s Date: Sat Mar 15 16:58:15 2025 451s Elapsed time: 0 seconds 451s Since beginning: 2 minutes, 42 seconds 451s *** 451s 451s Contigs >= 100 nt 451s Number: 1 451s Total length: 1000 451s Average: 1000 451s N50: 1000 451s Median: 1000 451s Largest: 1000 451s Contigs >= 500 nt 451s Number: 1 451s Total length: 1000 451s Average: 1000 451s N50: 1000 451s Median: 1000 451s Largest: 1000 451s Scaffolds >= 100 nt 451s Number: 1 451s Total length: 1000 451s Average: 1000 451s N50: 1000 451s Median: 1000 451s Largest: 1000 451s Scaffolds >= 500 nt 451s Number: 1 451s Total length: 1000 451s Average: 1000 451s N50: 1000 451s Median: 1000 451s Largest: 1000 451s 451s Rank 0 wrote test1/Contigs.fasta 451s Rank 0 wrote test1/Scaffolds.fasta 451s Check for test1/* 451s 451s 451s MPICH: Builtin communicator 44000000 has pending 28 references. 451s 451s ************************************************** 451s This program comes with ABSOLUTELY NO WARRANTY. 451s This is free software, and you are welcome to redistribute it 451s under certain conditions; see "LICENSE.txt" for details. 451s ************************************************** 451s 451s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 451s Centre de recherche en infectiologie de l'Université Laval 451s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 451s http://denovoassembler.sf.net/ 451s 451s References to cite: 451s 451s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 451s Ray Meta: scalable de novo metagenome assembly and profiling. 451s Genome Biology (BioMed Central Ltd). 451s 13:R122, Published: 22 December 2012 451s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 451s 451s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 451s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 451s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 451s November 2010, Volume 17, Issue 11, Pages 1519-1533. 451s http://dx.doi.org/doi:10.1089/cmb.2009.0238 451s 451s Ray version 2.3.1 451s License for Ray: GNU General Public License version 3 451s RayPlatform version: 2.0.1 451s License for RayPlatform: GNU Lesser General Public License version 3 451s 451s MAXKMERLENGTH: 32 451s Maximum coverage depth stored by CoverageDepth: 4294967295 451s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 451s FORCE_PACKING = n 451s ASSERT = n 451s HAVE_LIBZ = y 451s HAVE_LIBBZ2 = y 451s PROFILER_COLLECT = n 451s MINIRANKS = y 451s CLOCK_GETTIME = n 451s __linux__ = y 451s _MSC_VER = n 451s __GNUC__ = y 451s RAY_32_BITS = y 451s RAY_64_BITS = n 451s MPI standard version: MPI 4.1 451s Compiler: GNU gcc/g++ 14.2.0 451s MPI I/O: n 451s 451s 451s -k (to set the k-mer size) 451s Value: 31 451s 451s 451s Paired library # 0 451s -p (paired-end sequences) 451s Left sequences: SampleDirectory/s_6.first1000_1.fastq 451s Right sequences: SampleDirectory/s_6.first1000_2.fastq 451s Average length: automatic detection 451s Standard deviation: automatic detection 451s 451s Ray command: 451s mpiexec -n 1 Ray \ 451s -k \ 451s 31 \ 451s -detect-sequence-files \ 451s SampleDirectory \ 451s -o \ 451s test2 451s 451s Rank 0 wrote test2/RayCommand.txt 451s 451s k-mer length: 31 451s Rank 0: assembler memory usage: 28724 KiB 451s Rank 0: assembler memory usage: 94396 KiB 451s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 1926 451s Rank 0: testing the network, please wait... 451s 451s Rank 0 is testing the network [0/1000] 451s Rank 0 is testing the network [1000/1000] 451s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 451s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 451s 451s Rank 0 wrote test2/NetworkTest.txt 451s 451s 451s *** 451s Step: Network testing 451s Date: Sat Mar 15 16:58:15 2025 451s Elapsed time: 0 seconds 451s Since beginning: 0 seconds 451s *** 451s 451s 451s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 451s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 451s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 451s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 451s Rank 0 wrote test2/NumberOfSequences.txt 451s Rank 0 wrote test2/SequencePartition.txt 451s 451s *** 451s Step: Counting sequences to assemble 451s Date: Sat Mar 15 16:58:15 2025 451s Elapsed time: 0 seconds 451s Since beginning: 0 seconds 451s *** 451s 451s 451s Rank 0 is loading sequence reads 451s Rank 0 : partition is [0;4107], 4108 sequence reads 451s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 451s Rank 0 has 0 sequence reads 451s Rank 0: assembler memory usage: 103920 KiB 451s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 451s Rank 0 has 4108 sequence reads (completed) 451s 451s *** 451s Step: Sequence loading 451s Date: Sat Mar 15 16:58:15 2025 451s Elapsed time: 0 seconds 451s Since beginning: 0 seconds 451s *** 451s 451s 451s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 451s Rank 0 created its Bloom filter 451s Rank 0 is counting k-mers in sequence reads [1/4108] 452s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 452s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 452s 452s 452s *** 452s Step: K-mer counting 452s Date: Sat Mar 15 16:58:16 2025 452s Elapsed time: 1 seconds 452s Since beginning: 1 seconds 452s *** 452s 452s 452s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 452s Rank 0 destroyed its Bloom filter 452s Rank 0 has 1954 k-mers (completed) 452s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 452s Rank 0: assembler memory usage: 103064 KiB 462s 462s 462s Rank 0: the minimum coverage is 3 462s Rank 0: the peak coverage is 3 462s Warning: no peak observed in the k-mer coverage distribution. 462s to deal with the sequencing error rate, try to lower the k-mer length (-k) 462s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 462s 462s *** 462s Step: Coverage distribution analysis 462s Date: Sat Mar 15 16:58:26 2025 462s Elapsed time: 10 seconds 462s Since beginning: 11 seconds 462s *** 462s 462s 462s 462s Rank 0 is adding edges [1/4108] 463s Rank 0 is adding edges [4108/4108] (completed) 463s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 463s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 463s 463s *** 463s Step: Graph construction 463s Date: Sat Mar 15 16:58:27 2025 463s Elapsed time: 1 seconds 463s Since beginning: 12 seconds 463s *** 463s 463s 463s Rank 0 has 1954 vertices (completed) 463s Rank 0: assembler memory usage: 103064 KiB 473s Rank 0 is purging edges [1/1954] 473s Rank 0 is purging edges [1954/1954] (completed) 473s Rank 0: assembler memory usage: 103600 KiB 473s VirtualProcessor: completed jobs: 1954 473s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 482s Rank 0 wrote test2/degreeDistribution.txt 482s 482s *** 482s Step: Null edge purging 482s Date: Sat Mar 15 16:58:46 2025 482s Elapsed time: 19 seconds 482s Since beginning: 31 seconds 482s *** 482s 482s 482s Rank 0 is selecting optimal read markers [1/4108] 482s Rank 0: assembler memory usage: 103600 KiB 483s Rank 0 is selecting optimal read markers [4108/4108] (completed) 483s Rank 0: peak number of workers: 599, maximum: 32768 483s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 483s Rank 0: assembler memory usage: 111800 KiB 483s Rank 0: Freeing unused assembler memory: 4096 KiB freed 483s Rank 0: assembler memory usage: 107700 KiB 483s 483s *** 483s Step: Selection of optimal read markers 483s Date: Sat Mar 15 16:58:47 2025 483s Elapsed time: 1 seconds 483s Since beginning: 32 seconds 483s *** 483s 483s 483s Rank 0: memory usage for optimal read markers= 4096 KiB 483s Rank 0 is creating seeds [1/1954] 483s Rank 0: assembler memory usage: 107700 KiB 493s Rank 0 has 1 seeds 493s Rank 0 is creating seeds [1954/1954] (completed) 493s Rank 0: peak number of workers: 746, maximum: 32768 493s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 493s Rank 0 runtime statistics for seeding algorithm: 493s Rank 0 Skipped paths because of dead end for head: 0 493s Rank 0 Skipped paths because of dead end for tail: 0 493s Rank 0 Skipped paths because of two dead ends: 0 493s Rank 0 Skipped paths because of bubble weak component: 0 493s Rank 0 Skipped paths because of short length: 1952 493s Rank 0 Skipped paths because of bad ownership: 1 493s Rank 0 Skipped paths because of low coverage: 0 493s Rank 0 Eligible paths: 1 493s Rank 0: assembler memory usage: 107832 KiB 493s Rank 0 has 1 seeds to register. 493s Rank 0 registered 0/1 493s Rank 0 registered 0/1 493s Rank 0 registered its seeds 493s VirtualProcessor: completed jobs: 0 493s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 503s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 513s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 513s Rank 0 merged its seeds: 1 seeds -> 1 seeds 513s 513s *** 513s Step: Detection of assembly seeds 513s Date: Sat Mar 15 16:59:17 2025 513s Elapsed time: 30 seconds 513s Since beginning: 1 minutes, 2 seconds 513s *** 513s 513s 513s Rank 0 is calculating library lengths [1/1] 513s Rank 0 detected 1737 library lengths 513s Rank 0 is calculating library lengths [1/1] (completed) 513s Rank 0: peak number of workers: 1, maximum: 32768 513s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 513s Rank 0: assembler memory usage: 140604 KiB 513s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 513s 513s Mode= 2 signalAverage= 9 513s CURRENT IS NOISE, 244 513s GOT HIT 212 513s 513s 513s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 513s 513s *** 513s Step: Estimation of outer distances for paired reads 513s Date: Sat Mar 15 16:59:17 2025 513s Elapsed time: 0 seconds 513s Since beginning: 1 minutes, 2 seconds 513s *** 513s 513s 513s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 514s Rank 0 traversed 1000 nucleotide symbols 514s Rank 0: assembler memory usage: 144704 KiB 514s Rank 0 is extending seeds [1/1] (completed) 514s Rank 0 extended 1 seeds out of 1 (100.00%) 514s Rank 0: assembler memory usage: 140604 KiB 514s Rank 0 starting fusions 514s 514s *** 514s Step: Bidirectional extension of seeds 514s Date: Sat Mar 15 16:59:18 2025 514s Elapsed time: 1 seconds 514s Since beginning: 1 minutes, 3 seconds 514s *** 514s 514s 514s Rank 0: starting clear step. cycleNumber= 0 524s Rank 0 adding 0 new fusions 524s Rank 0 cleared, 1 paths 524s Rank 0: starting distribution step 524s Rank 0 is distributing fusions [1/1] 524s Rank 0: assembler memory usage: 140604 KiB 524s Date: Sat Mar 15 16:59:28 2025 524s Rank 0 is distributing fusions [1/1] (completed) 524s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 524s Rank 0: assembler memory usage: 144704 KiB 524s Date: Sat Mar 15 16:59:28 2025 524s Rank 0 tells others to compute fusions. 524s Rank 0 FusionTaskCreator assignNextTask [0/2] 524s Rank 0: assembler memory usage: 144704 KiB 524s Date: Sat Mar 15 16:59:28 2025 524s Rank 0 FusionTaskCreator processWorkerResult [0/2] 524s Rank 0: assembler memory usage: 144704 KiB 524s Date: Sat Mar 15 16:59:28 2025 524s Rank 0 FusionTaskCreator [2/2] 524s Statistics: all paths: 1 eliminated during fusing: 0 524s Rank 0: assembler memory usage: 144704 KiB 524s VirtualProcessor: completed jobs: 2 524s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 524s Rank 0: starting clear step. cycleNumber= 1 534s Rank 0 adding 0 new fusions 534s Rank 0 cleared, 1 paths 534s Rank 0 is distributing fusions [1/1] 534s Rank 0: assembler memory usage: 140604 KiB 534s Date: Sat Mar 15 16:59:38 2025 534s Rank 0 is distributing fusions [1/1] (completed) 534s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 534s Rank 0: assembler memory usage: 144704 KiB 534s Date: Sat Mar 15 16:59:38 2025 534s Rank 0 JoinerTaskCreator assignNextTask [0/2] 534s Rank 0: assembler memory usage: 144704 KiB 534s Date: Sat Mar 15 16:59:38 2025 534s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 534s Rank 0: assembler memory usage: 144704 KiB 534s Date: Sat Mar 15 16:59:38 2025 534s Rank 0 JoinerTaskCreator [2/2] 534s Statistics: all paths: 1 eliminated during joining: 0 534s Rank 0: assembler memory usage: 144704 KiB 534s Date: Sat Mar 15 16:59:38 2025 534s VirtualProcessor: completed jobs: 2 534s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 543s Rank 0 adding 0 new fusions 543s Rank 0 cleared, 1 paths 543s Rank 0: starting distribution step 543s Rank 0 is distributing fusions [1/1] 543s Rank 0: assembler memory usage: 140604 KiB 543s Date: Sat Mar 15 16:59:47 2025 543s Rank 0 is distributing fusions [1/1] (completed) 543s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 543s Rank 0: assembler memory usage: 144704 KiB 543s Date: Sat Mar 15 16:59:47 2025 543s Rank 0 tells others to compute fusions. 543s Rank 0 FusionTaskCreator assignNextTask [0/2] 543s Rank 0: assembler memory usage: 144704 KiB 543s Date: Sat Mar 15 16:59:47 2025 543s Rank 0 FusionTaskCreator processWorkerResult [0/2] 543s Rank 0: assembler memory usage: 144704 KiB 543s Date: Sat Mar 15 16:59:47 2025 543s Rank 0 FusionTaskCreator [2/2] 543s Statistics: all paths: 1 eliminated during fusing: 0 543s Rank 0: assembler memory usage: 144704 KiB 543s VirtualProcessor: completed jobs: 2 543s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 543s Rank 0: starting clear step. cycleNumber= 2 553s Rank 0 adding 0 new fusions 553s Rank 0 cleared, 1 paths 553s Rank 0 is distributing fusions [1/1] 553s Rank 0: assembler memory usage: 140604 KiB 553s Date: Sat Mar 15 16:59:57 2025 553s Rank 0 is distributing fusions [1/1] (completed) 553s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 553s Rank 0: assembler memory usage: 144704 KiB 553s Date: Sat Mar 15 16:59:57 2025 553s Rank 0 JoinerTaskCreator assignNextTask [0/2] 553s Rank 0: assembler memory usage: 144704 KiB 553s Date: Sat Mar 15 16:59:57 2025 553s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 553s Rank 0: assembler memory usage: 144704 KiB 553s Date: Sat Mar 15 16:59:57 2025 553s Rank 0 JoinerTaskCreator [2/2] 553s Statistics: all paths: 1 eliminated during joining: 0 553s Rank 0: assembler memory usage: 144704 KiB 553s Date: Sat Mar 15 16:59:57 2025 553s VirtualProcessor: completed jobs: 2 553s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 563s Rank 0 adding 0 new fusions 563s Rank 0 cleared, 1 paths 563s Rank 0: starting distribution step 563s Rank 0 is distributing fusions [1/1] 563s Rank 0: assembler memory usage: 140604 KiB 563s Date: Sat Mar 15 17:00:07 2025 563s Rank 0 is distributing fusions [1/1] (completed) 563s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 563s Rank 0: assembler memory usage: 144704 KiB 563s Date: Sat Mar 15 17:00:07 2025 563s Rank 0 cycleNumber= 2 563s 563s *** 563s Step: Merging of redundant paths 563s Date: Sat Mar 15 17:00:07 2025 563s Elapsed time: 49 seconds 563s Since beginning: 1 minutes, 52 seconds 563s *** 563s 563s 563s Rank 0 appended 1 elements 563s 563s *** 563s Step: Generation of contigs 563s Date: Sat Mar 15 17:00:07 2025 563s Elapsed time: 0 seconds 563s Since beginning: 1 minutes, 52 seconds 563s *** 563s 563s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 563s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 563s Rank 0 ineligibleObjects: 0/970 (0.00%) 563s Rank 0: assembler memory usage: 144704 KiB 563s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 563s Rank 0 finished gathering scaffold links. 563s Rank 0 will write 1 contig lengths 563s Rank 0 will solve the scaffolding problem. 563s Welcome to GreedySolver v1.0 563s 1 vertices; 0 edges 563s 1 contigs >= 500 563s Edges in solution: 0 563s 563s Conflict statistics: 563s 1 scaffolds, 1 >= 500 563s Total: 1000 nucleotides 563s 563s *** 563s Step: Scaffolding of contigs 563s Date: Sat Mar 15 17:00:07 2025 563s Elapsed time: 0 seconds 563s Since beginning: 1 minutes, 52 seconds 563s *** 563s 563s Rank 0 syncing with master 563s 563s *** 563s Step: Counting sequences to search 563s Date: Sat Mar 15 17:00:07 2025 563s Elapsed time: 0 seconds 563s Since beginning: 1 minutes, 52 seconds 563s *** 563s 563s 563s Rank 0 will add colors, 0 sequences in 0 files to process 563s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 573s 573s *** 573s Step: Graph coloring 573s Date: Sat Mar 15 17:00:17 2025 573s Elapsed time: 10 seconds 573s Since beginning: 2 minutes, 2 seconds 573s *** 573s 573s 573s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 573s Rank 0 shares its counts 573s Rank 0 computing contig abundances [1/1] [1/970] 573s Rank 0 computing contig abundances [1/1] [970/970] 573s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 573s 573s *** 573s Step: Counting contig biological abundances 573s Date: Sat Mar 15 17:00:17 2025 573s Elapsed time: 0 seconds 573s Since beginning: 2 minutes, 2 seconds 573s *** 573s 573s 573s Rank 0 colored the graph with 0 real colors using 1 virtual colors 573s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 573s 573s *** 573s Step: Counting sequence biological abundances 573s Date: Sat Mar 15 17:00:17 2025 573s Elapsed time: 0 seconds 573s Since beginning: 2 minutes, 2 seconds 573s *** 573s 573s 573s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 573s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 583s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 583s 583s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 583s Rank 0 is starting taxon syncing across the compute tribe. 583s 583s *** 583s Step: Loading taxons 583s Date: Sat Mar 15 17:00:27 2025 583s Elapsed time: 10 seconds 583s Since beginning: 2 minutes, 12 seconds 583s *** 583s 583s Rank 0 synced taxons across the grid with 1 poor slaves. 583s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 583s Rank 0 has 0 taxons after syncing with master 594s 594s 594s *** 594s Step: Loading tree 594s Date: Sat Mar 15 17:00:38 2025 594s Elapsed time: 11 seconds 594s Since beginning: 2 minutes, 23 seconds 594s *** 594s 603s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 603s 603s Rank 0: counting ontology terms in the graph... 613s Rank 0: 0 have some biological signal 613s Number of dereferenced alternate handles: 0 613s Number of k-mer observations with gene ontology terms: 0 613s Rank 0: synced ontology term profiles with master 613s Rank 0: synchronization is complete! 613s Rank 0: ontology terms with biological signal: 0 613s Populated recursive values... 613s Gene ontology terms without depth information: 0 613s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 613s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 613s 613s *** 613s Step: Processing gene ontologies 613s Date: Sat Mar 15 17:00:57 2025 613s Elapsed time: 19 seconds 613s Since beginning: 2 minutes, 42 seconds 613s *** 613s 613s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 613s [GenomeNeighbourhood] in final list: 0 613s 613s *** 613s Step: Computing neighbourhoods 613s Date: Sat Mar 15 17:00:57 2025 613s Elapsed time: 0 seconds 613s Since beginning: 2 minutes, 42 seconds 613s *** 613s 613s Contigs >= 100 nt 613s Number: 1 613s Total length: 1000 613s Average: 1000 613s N50: 1000 613s Median: 1000 613s Largest: 1000 613s Contigs >= 500 nt 613s Number: 1 613s Total length: 1000 613s Average: 1000 613s N50: 1000 613s Median: 1000 613s Largest: 1000 613s Scaffolds >= 100 nt 613s Number: 1 613s Total length: 1000 613s Average: 1000 613s N50: 1000 613s Median: 1000 613s Largest: 1000 613s Scaffolds >= 500 nt 613s Number: 1 613s Total length: 1000 613s Average: 1000 613s N50: 1000 613s Median: 1000 613s Largest: 1000 613s 613s Rank 0 wrote test2/Contigs.fasta 613s Rank 0 wrote test2/Scaffolds.fasta 613s Check for test2/* 613s 613s 613s MPICH: Builtin communicator 44000000 has pending 28 references. 613s 613s ************************************************** 613s This program comes with ABSOLUTELY NO WARRANTY. 613s This is free software, and you are welcome to redistribute it 613s under certain conditions; see "LICENSE.txt" for details. 613s ************************************************** 613s 613s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 613s Centre de recherche en infectiologie de l'Université Laval 613s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 613s http://denovoassembler.sf.net/ 613s 613s References to cite: 613s 613s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 613s Ray Meta: scalable de novo metagenome assembly and profiling. 613s Genome Biology (BioMed Central Ltd). 613s 13:R122, Published: 22 December 2012 613s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 613s 613s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 613s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 613s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 613s November 2010, Volume 17, Issue 11, Pages 1519-1533. 613s http://dx.doi.org/doi:10.1089/cmb.2009.0238 613s 613s Ray version 2.3.1 613s License for Ray: GNU General Public License version 3 613s RayPlatform version: 2.0.1 613s License for RayPlatform: GNU Lesser General Public License version 3 613s 613s MAXKMERLENGTH: 32 613s Maximum coverage depth stored by CoverageDepth: 4294967295 613s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 613s FORCE_PACKING = n 613s ASSERT = n 613s HAVE_LIBZ = y 613s HAVE_LIBBZ2 = y 613s PROFILER_COLLECT = n 613s MINIRANKS = y 613s CLOCK_GETTIME = n 613s __linux__ = y 613s _MSC_VER = n 613s __GNUC__ = y 613s RAY_32_BITS = y 613s RAY_64_BITS = n 613s MPI standard version: MPI 4.1 613s Compiler: GNU gcc/g++ 14.2.0 613s MPI I/O: n 613s 613s 613s -k (to set the k-mer size) 613s Value: 29 613s 613s 613s Paired library # 0 613s -p (paired-end sequences) 613s Left sequences: SampleDirectory/s_6.first1000_1.fastq 613s Right sequences: SampleDirectory/s_6.first1000_2.fastq 613s Average length: automatic detection 613s Standard deviation: automatic detection 613s 613s Ray command: 613s mpiexec -n 1 Ray \ 613s -k \ 613s 29 \ 613s -desable-recycling \ 613s -p \ 613s SampleDirectory/s_6.first1000_1.fastq \ 613s SampleDirectory/s_6.first1000_2.fastq 613s 613s Rank 0 wrote RayOutput/RayCommand.txt 613s 613s k-mer length: 29 613s Rank 0: assembler memory usage: 28724 KiB 613s Rank 0: assembler memory usage: 94396 KiB 613s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 1933 613s Rank 0: testing the network, please wait... 613s 613s Rank 0 is testing the network [0/1000] 613s Rank 0 is testing the network [1000/1000] 613s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 613s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 613s 613s Rank 0 wrote RayOutput/NetworkTest.txt 613s 613s 613s *** 613s Step: Network testing 613s Date: Sat Mar 15 17:00:57 2025 613s Elapsed time: 0 seconds 613s Since beginning: 0 seconds 613s *** 613s 613s 613s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 613s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 613s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 613s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 613s Rank 0 wrote RayOutput/NumberOfSequences.txt 613s Rank 0 wrote RayOutput/SequencePartition.txt 613s 613s *** 613s Step: Counting sequences to assemble 613s Date: Sat Mar 15 17:00:57 2025 613s Elapsed time: 0 seconds 613s Since beginning: 0 seconds 613s *** 613s 613s 613s Rank 0 is loading sequence reads 613s Rank 0 : partition is [0;4107], 4108 sequence reads 613s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 613s Rank 0 has 0 sequence reads 613s Rank 0: assembler memory usage: 103920 KiB 613s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 613s Rank 0 has 4108 sequence reads (completed) 613s 613s *** 613s Step: Sequence loading 613s Date: Sat Mar 15 17:00:57 2025 613s Elapsed time: 0 seconds 613s Since beginning: 0 seconds 613s *** 613s 613s 613s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 613s Rank 0 created its Bloom filter 613s Rank 0 is counting k-mers in sequence reads [1/4108] 614s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 614s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 614s 614s 614s *** 614s Step: K-mer counting 614s Date: Sat Mar 15 17:00:58 2025 614s Elapsed time: 1 seconds 614s Since beginning: 1 seconds 614s *** 614s 614s 614s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 614s Rank 0 destroyed its Bloom filter 614s Rank 0 has 1958 k-mers (completed) 614s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 614s Rank 0: assembler memory usage: 103064 KiB 624s 624s 624s Rank 0: the minimum coverage is 3 624s Rank 0: the peak coverage is 3 624s Warning: no peak observed in the k-mer coverage distribution. 624s to deal with the sequencing error rate, try to lower the k-mer length (-k) 624s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 624s 624s *** 624s Step: Coverage distribution analysis 624s Date: Sat Mar 15 17:01:08 2025 624s Elapsed time: 10 seconds 624s Since beginning: 11 seconds 624s *** 624s 624s 624s 624s Rank 0 is adding edges [1/4108] 625s Rank 0 is adding edges [4108/4108] (completed) 625s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 625s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 625s 625s *** 625s Step: Graph construction 625s Date: Sat Mar 15 17:01:09 2025 625s Elapsed time: 1 seconds 625s Since beginning: 12 seconds 625s *** 625s 625s 625s Rank 0 has 1958 vertices (completed) 625s Rank 0: assembler memory usage: 103064 KiB 635s Rank 0 is purging edges [1/1958] 635s Rank 0 is purging edges [1958/1958] (completed) 635s Rank 0: assembler memory usage: 103600 KiB 635s VirtualProcessor: completed jobs: 1958 635s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 645s Rank 0 wrote RayOutput/degreeDistribution.txt 645s 645s *** 645s Step: Null edge purging 645s Date: Sat Mar 15 17:01:29 2025 645s Elapsed time: 20 seconds 645s Since beginning: 32 seconds 645s *** 645s 645s 645s Rank 0 is selecting optimal read markers [1/4108] 645s Rank 0: assembler memory usage: 103600 KiB 646s Rank 0 is selecting optimal read markers [4108/4108] (completed) 646s Rank 0: peak number of workers: 599, maximum: 32768 646s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 646s Rank 0: assembler memory usage: 111800 KiB 646s Rank 0: Freeing unused assembler memory: 4096 KiB freed 646s Rank 0: assembler memory usage: 107700 KiB 646s 646s *** 646s Step: Selection of optimal read markers 646s Date: Sat Mar 15 17:01:30 2025 646s Elapsed time: 1 seconds 646s Since beginning: 33 seconds 646s *** 646s 646s 646s Rank 0: memory usage for optimal read markers= 4096 KiB 646s Rank 0 is creating seeds [1/1958] 646s Rank 0: assembler memory usage: 107700 KiB 656s Rank 0 has 1 seeds 656s Rank 0 is creating seeds [1958/1958] (completed) 656s Rank 0: peak number of workers: 746, maximum: 32768 656s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 656s Rank 0 runtime statistics for seeding algorithm: 656s Rank 0 Skipped paths because of dead end for head: 0 656s Rank 0 Skipped paths because of dead end for tail: 0 656s Rank 0 Skipped paths because of two dead ends: 0 656s Rank 0 Skipped paths because of bubble weak component: 0 656s Rank 0 Skipped paths because of short length: 1956 656s Rank 0 Skipped paths because of bad ownership: 1 656s Rank 0 Skipped paths because of low coverage: 0 656s Rank 0 Eligible paths: 1 656s Rank 0: assembler memory usage: 107832 KiB 656s Rank 0 has 1 seeds to register. 656s Rank 0 registered 0/1 656s Rank 0 registered 0/1 656s Rank 0 registered its seeds 656s VirtualProcessor: completed jobs: 0 656s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 666s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 676s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 676s Rank 0 merged its seeds: 1 seeds -> 1 seeds 676s 676s *** 676s Step: Detection of assembly seeds 676s Date: Sat Mar 15 17:02:00 2025 676s Elapsed time: 30 seconds 676s Since beginning: 1 minutes, 3 seconds 676s *** 676s 676s 676s Rank 0 is calculating library lengths [1/1] 676s Rank 0 detected 1743 library lengths 676s Rank 0 is calculating library lengths [1/1] (completed) 676s Rank 0: peak number of workers: 1, maximum: 32768 676s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 676s Rank 0: assembler memory usage: 140604 KiB 676s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 676s 676s Mode= 2 signalAverage= 10 676s CURRENT IS NOISE, 244 676s GOT HIT 214 676s 676s 676s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 676s 676s *** 676s Step: Estimation of outer distances for paired reads 676s Date: Sat Mar 15 17:02:00 2025 676s Elapsed time: 0 seconds 676s Since beginning: 1 minutes, 3 seconds 676s *** 676s 676s 676s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 677s Rank 0 traversed 1000 nucleotide symbols 677s Rank 0: assembler memory usage: 144704 KiB 677s Rank 0 is extending seeds [1/1] (completed) 677s Rank 0 extended 1 seeds out of 1 (100.00%) 677s Rank 0: assembler memory usage: 140604 KiB 677s Rank 0 starting fusions 677s 677s *** 677s Step: Bidirectional extension of seeds 677s Date: Sat Mar 15 17:02:01 2025 677s Elapsed time: 1 seconds 677s Since beginning: 1 minutes, 4 seconds 677s *** 677s 677s 677s Rank 0: starting clear step. cycleNumber= 0 687s Rank 0 adding 0 new fusions 687s Rank 0 cleared, 1 paths 687s Rank 0: starting distribution step 687s Rank 0 is distributing fusions [1/1] 687s Rank 0: assembler memory usage: 140604 KiB 687s Date: Sat Mar 15 17:02:11 2025 687s Rank 0 is distributing fusions [1/1] (completed) 687s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 687s Rank 0: assembler memory usage: 144704 KiB 687s Date: Sat Mar 15 17:02:11 2025 687s Rank 0 tells others to compute fusions. 687s Rank 0 FusionTaskCreator assignNextTask [0/2] 687s Rank 0: assembler memory usage: 144704 KiB 687s Date: Sat Mar 15 17:02:11 2025 687s Rank 0 FusionTaskCreator processWorkerResult [0/2] 687s Rank 0: assembler memory usage: 144704 KiB 687s Date: Sat Mar 15 17:02:11 2025 687s Rank 0 FusionTaskCreator [2/2] 687s Statistics: all paths: 1 eliminated during fusing: 0 687s Rank 0: assembler memory usage: 144704 KiB 687s VirtualProcessor: completed jobs: 2 687s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 687s Rank 0: starting clear step. cycleNumber= 1 696s Rank 0 adding 0 new fusions 696s Rank 0 cleared, 1 paths 696s Rank 0 is distributing fusions [1/1] 696s Rank 0: assembler memory usage: 140604 KiB 696s Date: Sat Mar 15 17:02:20 2025 696s Rank 0 is distributing fusions [1/1] (completed) 696s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 696s Rank 0: assembler memory usage: 144704 KiB 696s Date: Sat Mar 15 17:02:20 2025 696s Rank 0 JoinerTaskCreator assignNextTask [0/2] 696s Rank 0: assembler memory usage: 144704 KiB 696s Date: Sat Mar 15 17:02:20 2025 696s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 696s Rank 0: assembler memory usage: 144704 KiB 696s Date: Sat Mar 15 17:02:20 2025 696s Rank 0 JoinerTaskCreator [2/2] 696s Statistics: all paths: 1 eliminated during joining: 0 696s Rank 0: assembler memory usage: 144704 KiB 696s Date: Sat Mar 15 17:02:20 2025 696s VirtualProcessor: completed jobs: 2 696s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 706s Rank 0 adding 0 new fusions 706s Rank 0 cleared, 1 paths 706s Rank 0: starting distribution step 706s Rank 0 is distributing fusions [1/1] 706s Rank 0: assembler memory usage: 140604 KiB 706s Date: Sat Mar 15 17:02:30 2025 706s Rank 0 is distributing fusions [1/1] (completed) 706s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 706s Rank 0: assembler memory usage: 144704 KiB 706s Date: Sat Mar 15 17:02:30 2025 706s Rank 0 tells others to compute fusions. 706s Rank 0 FusionTaskCreator assignNextTask [0/2] 706s Rank 0: assembler memory usage: 144704 KiB 706s Date: Sat Mar 15 17:02:30 2025 706s Rank 0 FusionTaskCreator processWorkerResult [0/2] 706s Rank 0: assembler memory usage: 144704 KiB 706s Date: Sat Mar 15 17:02:30 2025 706s Rank 0 FusionTaskCreator [2/2] 706s Statistics: all paths: 1 eliminated during fusing: 0 706s Rank 0: assembler memory usage: 144704 KiB 706s VirtualProcessor: completed jobs: 2 706s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 706s Rank 0: starting clear step. cycleNumber= 2 716s Rank 0 adding 0 new fusions 716s Rank 0 cleared, 1 paths 716s Rank 0 is distributing fusions [1/1] 716s Rank 0: assembler memory usage: 140604 KiB 716s Date: Sat Mar 15 17:02:40 2025 716s Rank 0 is distributing fusions [1/1] (completed) 716s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 716s Rank 0: assembler memory usage: 144704 KiB 716s Date: Sat Mar 15 17:02:40 2025 716s Rank 0 JoinerTaskCreator assignNextTask [0/2] 716s Rank 0: assembler memory usage: 144704 KiB 716s Date: Sat Mar 15 17:02:40 2025 716s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 716s Rank 0: assembler memory usage: 144704 KiB 716s Date: Sat Mar 15 17:02:40 2025 716s Rank 0 JoinerTaskCreator [2/2] 716s Statistics: all paths: 1 eliminated during joining: 0 716s Rank 0: assembler memory usage: 144704 KiB 716s Date: Sat Mar 15 17:02:40 2025 716s VirtualProcessor: completed jobs: 2 716s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 725s Rank 0 adding 0 new fusions 725s Rank 0 cleared, 1 paths 725s Rank 0: starting distribution step 725s Rank 0 is distributing fusions [1/1] 725s Rank 0: assembler memory usage: 140604 KiB 725s Date: Sat Mar 15 17:02:49 2025 725s Rank 0 is distributing fusions [1/1] (completed) 725s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 725s Rank 0: assembler memory usage: 144704 KiB 725s Date: Sat Mar 15 17:02:49 2025 725s Rank 0 cycleNumber= 2 725s 725s *** 725s Step: Merging of redundant paths 725s Date: Sat Mar 15 17:02:49 2025 725s Elapsed time: 48 seconds 725s Since beginning: 1 minutes, 52 seconds 725s *** 725s 725s 725s Rank 0 appended 1 elements 725s 725s *** 725s Step: Generation of contigs 725s Date: Sat Mar 15 17:02:49 2025 725s Elapsed time: 0 seconds 725s Since beginning: 1 minutes, 52 seconds 725s *** 725s 725s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 726s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 726s Rank 0 ineligibleObjects: 0/972 (0.00%) 726s Rank 0: assembler memory usage: 144704 KiB 726s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 726s Rank 0 finished gathering scaffold links. 726s Rank 0 will write 1 contig lengths 726s Rank 0 will solve the scaffolding problem. 726s Welcome to GreedySolver v1.0 726s 1 vertices; 0 edges 726s 1 contigs >= 500 726s Edges in solution: 0 726s 726s Conflict statistics: 726s 1 scaffolds, 1 >= 500 726s Total: 1000 nucleotides 726s 726s *** 726s Step: Scaffolding of contigs 726s Date: Sat Mar 15 17:02:50 2025 726s Elapsed time: 1 seconds 726s Since beginning: 1 minutes, 53 seconds 726s *** 726s 726s Rank 0 syncing with master 726s 726s *** 726s Step: Counting sequences to search 726s Date: Sat Mar 15 17:02:50 2025 726s Elapsed time: 0 seconds 726s Since beginning: 1 minutes, 53 seconds 726s *** 726s 726s 726s Rank 0 will add colors, 0 sequences in 0 files to process 726s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 736s 736s *** 736s Step: Graph coloring 736s Date: Sat Mar 15 17:02:59 2025 736s Elapsed time: 9 seconds 736s Since beginning: 2 minutes, 2 seconds 736s *** 736s 736s 736s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 736s Rank 0 shares its counts 736s Rank 0 computing contig abundances [1/1] [1/972] 736s Rank 0 computing contig abundances [1/1] [972/972] 736s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 736s 736s *** 736s Step: Counting contig biological abundances 736s Date: Sat Mar 15 17:02:59 2025 736s Elapsed time: 0 seconds 736s Since beginning: 2 minutes, 2 seconds 736s *** 736s 736s 736s Rank 0 colored the graph with 0 real colors using 1 virtual colors 736s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 736s 736s *** 736s Step: Counting sequence biological abundances 736s Date: Sat Mar 15 17:02:59 2025 736s Elapsed time: 0 seconds 736s Since beginning: 2 minutes, 2 seconds 736s *** 736s 736s 736s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 736s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 745s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 745s 745s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 745s Rank 0 is starting taxon syncing across the compute tribe. 745s 745s *** 745s Step: Loading taxons 745s Date: Sat Mar 15 17:03:09 2025 745s Elapsed time: 10 seconds 745s Since beginning: 2 minutes, 12 seconds 745s *** 745s 745s Rank 0 synced taxons across the grid with 1 poor slaves. 745s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 745s Rank 0 has 0 taxons after syncing with master 756s 756s 756s *** 756s Step: Loading tree 756s Date: Sat Mar 15 17:03:20 2025 756s Elapsed time: 11 seconds 756s Since beginning: 2 minutes, 23 seconds 756s *** 756s 765s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 765s 765s Rank 0: counting ontology terms in the graph... 776s Rank 0: 0 have some biological signal 776s Number of dereferenced alternate handles: 0 776s Number of k-mer observations with gene ontology terms: 0 776s Rank 0: synced ontology term profiles with master 776s Rank 0: synchronization is complete! 776s Rank 0: ontology terms with biological signal: 0 776s Populated recursive values... 776s Gene ontology terms without depth information: 0 776s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 776s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 776s 776s *** 776s Step: Processing gene ontologies 776s Date: Sat Mar 15 17:03:40 2025 776s Elapsed time: 20 seconds 776s Since beginning: 2 minutes, 43 seconds 776s *** 776s 776s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 776s [GenomeNeighbourhood] in final list: 0 776s 776s *** 776s Step: Computing neighbourhoods 776s Date: Sat Mar 15 17:03:40 2025 776s Elapsed time: 0 seconds 776s Since beginning: 2 minutes, 43 seconds 776s *** 776s 776s Contigs >= 100 nt 776s Number: 1 776s Total length: 1000 776s Average: 1000 776s N50: 1000 776s Median: 1000 776s Largest: 1000 776s Contigs >= 500 nt 776s Number: 1 776s Total length: 1000 776s Average: 1000 776s N50: 1000 776s Median: 1000 776s Largest: 1000 776s Scaffolds >= 100 nt 776s Number: 1 776s Total length: 1000 776s Average: 1000 776s N50: 1000 776s Median: 1000 776s Largest: 1000 776s Scaffolds >= 500 nt 776s Number: 1 776s Total length: 1000 776s Average: 1000 776s N50: 1000 776s Median: 1000 776s Largest: 1000 776s 776s Rank 0 wrote RayOutput/Contigs.fasta 776s Rank 0 wrote RayOutput/Scaffolds.fasta 776s Check for RayOutput/* 776s 776s 776s MPICH: Builtin communicator 44000000 has pending 22 references. 776s 776s ************************************************** 776s This program comes with ABSOLUTELY NO WARRANTY. 776s This is free software, and you are welcome to redistribute it 776s under certain conditions; see "LICENSE.txt" for details. 776s ************************************************** 776s 776s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 776s Centre de recherche en infectiologie de l'Université Laval 776s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 776s http://denovoassembler.sf.net/ 776s 776s References to cite: 776s 776s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 776s Ray Meta: scalable de novo metagenome assembly and profiling. 776s Genome Biology (BioMed Central Ltd). 776s 13:R122, Published: 22 December 2012 776s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 776s 776s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 776s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 776s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 776s November 2010, Volume 17, Issue 11, Pages 1519-1533. 776s http://dx.doi.org/doi:10.1089/cmb.2009.0238 776s 776s Ray version 2.3.1 776s License for Ray: GNU General Public License version 3 776s RayPlatform version: 2.0.1 776s License for RayPlatform: GNU Lesser General Public License version 3 776s 776s MAXKMERLENGTH: 32 776s Maximum coverage depth stored by CoverageDepth: 4294967295 776s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 776s FORCE_PACKING = n 776s ASSERT = n 776s HAVE_LIBZ = y 776s HAVE_LIBBZ2 = y 776s PROFILER_COLLECT = n 776s MINIRANKS = y 776s CLOCK_GETTIME = n 776s __linux__ = y 776s _MSC_VER = n 776s __GNUC__ = y 776s RAY_32_BITS = y 776s RAY_64_BITS = n 776s MPI standard version: MPI 4.1 776s Compiler: GNU gcc/g++ 14.2.0 776s MPI I/O: n 776s 776s 776s -k (to set the k-mer size) 776s Value: 31 776s 776s 776s Paired library # 0 776s -p (paired-end sequences) 776s Left sequences: ecoli_1K_1.fq 776s Right sequences: ecoli_1K_2.fq 776s Average length: automatic detection 776s Standard deviation: automatic detection 776s 776s Ray command: 776s mpiexec -n 2 Ray \ 776s -k \ 776s 31 \ 776s -p \ 776s ecoli_1K_1.fq \ 776s ecoli_1K_2.fq \ 776s -o \ 776s test3 776s 776s Rank 0 wrote test3/RayCommand.txt 776s 776s k-mer length: 31 776s Rank 1: assembler memory usage: 24604 KiB 776s Rank 0: assembler memory usage: 24604 KiB 776s Rank 1: assembler memory usage: 90420 KiB 776s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 1939 776s Rank 0: assembler memory usage: 90428 KiB 776s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 1938 776s Rank 0: testing the network, please wait... 776s 776s Rank 1 is testing the network [0/1000] 776s Rank 0 is testing the network [0/1000] 776s Rank 0 is testing the network [1000/1000] 776s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 776s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 8 microseconds (10^-6 seconds) 776s Rank 1 is testing the network [1000/1000] 776s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 776s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 8 microseconds (10^-6 seconds) 776s 776s Rank 0 wrote test3/NetworkTest.txt 776s 776s 776s *** 776s Step: Network testing 776s Date: Sat Mar 15 17:03:40 2025 776s Elapsed time: 0 seconds 776s Since beginning: 0 seconds 776s *** 776s 776s 776s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 776s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 776s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 776s Rank 0 wrote test3/NumberOfSequences.txt 776s Rank 0 wrote test3/SequencePartition.txt 776s 776s *** 776s Step: Counting sequences to assemble 776s Date: Sat Mar 15 17:03:40 2025 776s Elapsed time: 0 seconds 776s Since beginning: 0 seconds 776s *** 776s 776s 776s Rank 0 is loading sequence reads 776s Rank 0 : partition is [0;2053], 2054 sequence reads 776s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 776s Rank 1 is loading sequence reads 776s Rank 1 : partition is [2054;4107], 2054 sequence reads 776s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 776s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 776s Rank 1 has 0 sequence reads 776s Rank Rank 1: assembler memory usage: 95720 KiB 776s 0 has 0 sequence reads 776s Rank 0: assembler memory usage: 95728 KiB 776s Rank 1 has 2054 sequence reads (completed) 776s Rank 0 has 2054 sequence reads (completed) 776s 776s *** 776s Step: Sequence loading 776s Date: Sat Mar 15 17:03:40 2025 776s Elapsed time: 0 seconds 776s Since beginning: 0 seconds 776s *** 776s 776s 776s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 776s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 776s Rank 0 created its Bloom filter 776s Rank 1 created its Bloom filter 776s Rank 1 is counting k-mers in sequence reads [1/2054] 776s Rank 0 is counting k-mers in sequence reads [1/2054] 777s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 777s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 777s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 777s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 777s 777s 777s *** 777s Step: K-mer counting 777s Date: Sat Mar 15 17:03:41 2025 777s Elapsed time: 1 seconds 777s Since beginning: 1 seconds 777s *** 777s 777s 777s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 777s Rank 0 destroyed its Bloom filter 777s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (Rank 0 has 1032 k-mers (completed) 777s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 10320.361509%) 777s Rank 1 destroyed its Bloom filter 777s Rank 1 has (100%) 777s 922 k-mers (completed) 777s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 777s Rank 0: assembler memory usage: 95016 KiB 777s Rank 1: assembler memory usage: 94996 KiB 787s 787s 787s Rank 0: the minimum coverage is 3 787s Rank 0: the peak coverage is 3 787s Warning: no peak observed in the k-mer coverage distribution. 787s to deal with the sequencing error rate, try to lower the k-mer length (-k) 787s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 787s 787s *** 787s Step: Coverage distribution analysis 787s Date: Sat Mar 15 17:03:50 2025 787s Elapsed time: 9 seconds 787s Since beginning: 10 seconds 787s *** 787s 787s 787s 787s Rank 0 is adding edges [1/2054] 787s Rank 1 is adding edges [1/2054] 787s Rank 1 is adding edges [2054/2054] (completed) 787s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 787s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 787s Rank 0 is adding edges [2054/2054] (completed) 787s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 787s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 787s 787s *** 787s Step: Graph construction 787s Date: Sat Mar 15 17:03:51 2025 787s Elapsed time: 1 seconds 787s Since beginning: 11 seconds 787s *** 787s 787s 787s Rank 0 has 1032 vertices (completed) 787s Rank 1 has 922 vertices (completed) 787s Rank 0: assembler memory usage: 95016 KiB 787s Rank 1: assembler memory usage: 94996 KiB 797s Rank 1 is purging edges [1/922] 797s Rank 1 is purging edges [922/922] (completed) 797s Rank 1: assembler memory usage: 95128 KiB 797s VirtualProcessor: completed jobs: 922 797s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 797s Rank 0 is purging edges [1/1032] 797s Rank 0 is purging edges [1032/1032] (completed) 797s Rank 0: assembler memory usage: 95148 KiB 797s VirtualProcessor: completed jobs: 1032 797s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 807s Rank 0 wrote test3/degreeDistribution.txt 807s 807s *** 807s Step: Null edge purging 807s Date: Sat Mar 15 17:04:11 2025 807s Elapsed time: 20 seconds 807s Since beginning: 31 seconds 807s *** 807s 807s 807s Rank 0 is selecting optimal read markers [1/2054] 807s Rank 1 is selecting optimal read markers [1/2054] 807s Rank 0: assembler memory usage: 95148 KiB 807s Rank 1: assembler memory usage: 95128 KiB 807s Rank 1 is selecting optimal read markers [2054/2054] (completed) 807s Rank 1: peak number of workers: 1121, maximum: 32768 807s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 807s Rank 1: assembler memory usage: 103328 KiB 807s Rank 1: Freeing unused assembler memory: 4096 KiB freed 807s Rank 1: assembler memory usage: 99228 KiB 807s Rank 0 is selecting optimal read markers [2054/2054] (completed) 807s Rank 0: peak number of workers: 1135, maximum: 32768 807s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 807s Rank 0: assembler memory usage: 103348 KiB 807s Rank 0: Freeing unused assembler memory: 4096 KiB freed 807s Rank 0: assembler memory usage: 99248 KiB 807s 807s *** 807s Step: Selection of optimal read markers 807s Date: Sat Mar 15 17:04:11 2025 807s Elapsed time: 0 seconds 807s Since beginning: 31 seconds 807s *** 807s 807s 807s Rank 0: memory usage for optimal read markers= 4096 KiB 807s Rank 1: memory usage for optimal read markers= 4096 KiB 807s Rank 1 is creating seeds [1/922] 807s Rank 1: assembler memory usage: 99228 KiB 807s Rank 0 is creating seeds [1/1032] 807s Rank 0: assembler memory usage: 99248 KiB 817s Rank 0 has 0 seeds 817s Rank 0 is creating seeds [1032/1032] (completed) 817s Rank 0: peak number of workers: 998, maximum: 32768 817s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 817s Rank 0 runtime statistics for seeding algorithm: 817s Rank 0 Skipped paths because of dead end for head: 0 817s Rank 0 Skipped paths because of dead end for tail: 0 817s Rank 0 Skipped paths because of two dead ends: 0 817s Rank 0 Skipped paths because of bubble weak component: 0 817s Rank 0 Skipped paths because of short length: 1031 817s Rank 0 Skipped paths because of bad ownership: 1 817s Rank 0 Skipped paths because of low coverage: 0 817s Rank 0 Eligible paths: 0 817s Rank 0: assembler memory usage: 99776 KiB 817s Rank 1 has 1 seeds 817s Rank 1 is creating seeds [922/922] (completed) 817s Rank 1: peak number of workers: 916, maximum: 32768 817s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 817s Rank 1 runtime statistics for seeding algorithm: 817s Rank 1 Skipped paths because of dead end for head: 0 817s Rank 1 Skipped paths because of dead end for tail: 0 817s Rank 1 Skipped paths because of two dead ends: 0 817s Rank 1 Skipped paths because of bubble weak component: 0 817s Rank 1 Skipped paths because of short length: 921 817s Rank 1 Skipped paths because of bad ownership: 0 817s Rank 1 Skipped paths because of low coverage: 0 817s Rank 1 Eligible paths: 1 817s Rank 1: assembler memory usage: 99624 KiB 817s Rank 0 registered -1/0 817s Rank 0 registered its seeds 817s Rank 1 has 1 seeds to register. 817s Rank 1 registered 0/1 817s VirtualProcessor: completed jobs: 0 817s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 817s Rank 1 registered 0/1 817s Rank 1 registered its seeds 817s VirtualProcessor: completed jobs: 0 817s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 827s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 827s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 837s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 837s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 837s Rank 0 merged its seeds: 0 seeds -> 0 seeds 837s Rank 1 merged its seeds: 1 seeds -> 1 seeds 837s 837s *** 837s Step: Detection of assembly seeds 837s Date: Sat Mar 15 17:04:41 2025 837s Elapsed time: 30 seconds 837s Since beginning: 1 minutes, 1 seconds 837s *** 837s 837s 837s Rank 0 detected 0 library lengths 837s Rank 0 is calculating library lengths [0/0] (completed) 837s Rank 0: peak number of workers: 0, maximum: 32768 837s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 837s Rank 0: assembler memory usage: 99776 KiB 837s Rank 1 is calculating library lengths [1/1] 837s Rank 1 detected 1737 library lengths 837s Rank 1 is calculating library lengths [1/1] (completed) 837s Rank 1: peak number of workers: 1, maximum: 32768 837s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7985 virtual messages generated 7985 real messages (100%) 837s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 837s 837s Rank 1: assembler memory usage: 132396 KiB 837s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 837s Mode= 2 signalAverage= 9 837s CURRENT IS NOISE, 244 837s GOT HIT 212 837s 837s 837s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 837s 837s *** 837s Step: Estimation of outer distances for paired reads 837s Date: Sat Mar 15 17:04:41 2025 837s Elapsed time: 0 seconds 837s Since beginning: 1 minutes, 1 seconds 837s *** 837s 837s 837s Rank 0 is extending seeds [0/0] (completed) 837s Rank 0 extended 0 seeds out of 0 (0.00%) 837s Rank 0: assembler memory usage: 99776 KiB 837s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 838s Rank 1 traversed 1000 nucleotide symbols 838s Rank 1: assembler memory usage: 136496 KiB 838s Rank 1 is extending seeds [1/1] (completed) 838s Rank 1 extended 1 seeds out of 1 (100.00%) 838s Rank 1: assembler memory usage: 132396 KiB 838s Rank 0 starting fusions 838s 838s *** 838s Step: Bidirectional extension of seeds 838s Date: Sat Mar 15 17:04:42 2025 838s Elapsed time: 1 seconds 838s Since beginning: 1 minutes, 2 seconds 838s *** 838s 838s 838s Rank 0: starting clear step. cycleNumber= 0 848s Rank 1 adding 0 new fusions 848s Rank 1 cleared, 1 paths 848s Rank 0 adding 0 new fusions 848s Rank 0 cleared, 0 paths 848s Rank 0: starting distribution step 848s Rank 0 is distributing fusions [0/0] (completed) 848s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 848s Rank 1 is distributing fusions [1/1] 848s Rank 0: assembler memory usage: 99776 KiB 848s Date: Sat Mar 15 17:04:52 2025 848s Rank 1: assembler memory usage: 132396 KiB 848s Date: Sat Mar 15 17:04:52 2025 848s Rank 1 is distributing fusions [1/1] (completed) 848s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 848s Rank 0 tells others to compute fusions. 848s Rank 0 FusionTaskCreator [0/0] 848s Statistics: all paths: 0 eliminated during fusing: 0 848s Rank 0: assembler memory usage: 103876 KiB 848s VirtualProcessor: completed jobs: 0 848s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 848s Rank 1: assembler memory usage: 136496 KiB 848s Date: Sat Mar 15 17:04:52 2025 848s Rank 1 FusionTaskCreator assignNextTask [0/2] 848s Rank 1: assembler memory usage: 136496 KiB 848s Date: Sat Mar 15 17:04:52 2025 848s Rank 1 FusionTaskCreator processWorkerResult [0/2] 848s Rank 1: assembler memory usage: 136496 KiB 848s Date: Sat Mar 15 17:04:52 2025 848s Rank 1 FusionTaskCreator [2/2] 848s Statistics: all paths: 1 eliminated during fusing: 0 848s Rank 1: assembler memory usage: 136496 KiB 848s VirtualProcessor: completed jobs: 2 848s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10895 virtual messages generated 10895 real messages (100%) 848s Rank 0: starting clear step. cycleNumber= 1 857s Rank 1 adding 0 new fusions 857s Rank 1 cleared, 1 paths 857s Rank 0 adding 0 new fusions 857s Rank 0 cleared, 0 paths 857s Rank 0 is distributing fusions [0/0] (completed) 857s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 857s Rank 1 is distributing fusions [1/1] 857s Rank 0: assembler memory usage: 99776 KiB 857s Date: Sat Mar 15 17:05:01 2025 857s Rank 1: assembler memory usage: 132396 KiB 857s Date: Sat Mar 15 17:05:01 2025 857s Rank 1 is distributing fusions [1/1] (completed) 857s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 857s Rank 1: assembler memory usage: 136496 KiB 857s Rank 0 JoinerTaskCreator [0/0] 857s Statistics: all paths: 0 eliminated during joining: 0 857s Rank 0: assembler memory usage: 103876 KiB 857s Date: Sat Mar 15 17:05:01 2025 857s VirtualProcessor: completed jobs: 0 857s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 857s Date: Sat Mar 15 17:05:01 2025 857s Rank 1 JoinerTaskCreator assignNextTask [0/2] 857s Rank 1: assembler memory usage: 136496 KiB 857s Date: Sat Mar 15 17:05:01 2025 857s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 857s Rank 1: assembler memory usage: 136496 KiB 857s Date: Sat Mar 15 17:05:01 2025 857s Rank 1 JoinerTaskCreator [2/2] 857s Statistics: all paths: 1 eliminated during joining: 0 857s Rank 1: assembler memory usage: 136496 KiB 858s Date: Sat Mar 15 17:05:01 2025 858s VirtualProcessor: completed jobs: 2 858s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13805 virtual messages generated 13805 real messages (100%) 867s Rank 1 adding 0 new fusions 867s Rank 1 cleared, 1 paths 867s Rank 0 adding 0 new fusions 867s Rank 0 cleared, 0 paths 867s Rank 0: starting distribution step 867s Rank 0 is distributing fusions [0/0] (completed) 867s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 867s Rank 0: assembler memory usage: 99776 KiB 867s Date: Sat Mar 15 17:05:11 2025 867s Rank 1 is distributing fusions [1/1] 867s Rank 1: assembler memory usage: 132396 KiB 867s Date: Sat Mar 15 17:05:11 2025 867s Rank 1 is distributing fusions [1/1] (completed) 867s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 867s Rank 0 tells others to compute fusions. 867s Rank 0 FusionTaskCreator [0/0] 867s Statistics: all paths: 0 eliminated during fusing: 0 867s Rank 0Rank 1: assembler memory usage: 136496 KiB 867s Date: Sat Mar 15 17:05:11 2025 867s Rank 1 FusionTaskCreator assignNextTask [0/2] 867s Rank 1: assembler memory usage: 136496 KiB 867s Date: Sat Mar 15 17:05:11 2025 867s : assembler memory usage: 103876 KiB 867s VirtualProcessor: completed jobs: 0 867s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 867s Rank 1 FusionTaskCreator processWorkerResult [0/2] 867s Rank 1: assembler memory usage: 136496 KiB 867s Date: Sat Mar 15 17:05:11 2025 867s Rank 1 FusionTaskCreator [2/2] 867s Statistics: all paths: 1 eliminated during fusing: 0 867s Rank 1: assembler memory usage: 136496 KiB 867s VirtualProcessor: completed jobs: 2 867s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16715 virtual messages generated 16715 real messages (100%) 867s Rank 0: starting clear step. cycleNumber= 2 877s Rank 1 adding 0 new fusions 877s Rank 1 cleared, 1 paths 877s Rank 0 adding 0 new fusions 877s Rank 0 cleared, 0 paths 877s Rank 0 is distributing fusions [0/0] (completed) 877s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 877s Rank 1 is distributing fusions [1/1] 877s Rank 0: assembler memory usage: 99776 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s Rank 1: assembler memory usage: 132396 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s Rank 1 is distributing fusions [1/1] (completed) 877s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 877s Rank 1: assembler memory usage: 136496 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s Rank 1 JoinerTaskCreator assignNextTask [0/2] 877s Rank 0 JoinerTaskCreator [0/0] 877s Statistics: all paths: 0 eliminated during joining: 0 877s Rank 1: assembler memory usage: 136496 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s Rank 0: assembler memory usage: 103876 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s VirtualProcessor: completed jobs: 0 877s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 877s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 877s Rank 1: assembler memory usage: 136496 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s Rank 1 JoinerTaskCreator [2/2] 877s Statistics: all paths: 1 eliminated during joining: 0 877s Rank 1: assembler memory usage: 136496 KiB 877s Date: Sat Mar 15 17:05:21 2025 877s VirtualProcessor: completed jobs: 2 877s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19625 virtual messages generated 19625 real messages (100%) 886s Rank 1 adding 0 new fusions 886s Rank 1 cleared, 1 paths 887s Rank 0 adding 0 new fusions 887s Rank 0 cleared, 0 paths 887s Rank 0: starting distribution step 887s Rank 0 is distributing fusions [0/0] (completed) 887s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 887s Rank 0: assembler memory usage: 99776 KiB 887s Date: Sat Mar 15 17:05:31 2025 887s Rank 1 is distributing fusions [1/1] 887s Rank 1: assembler memory usage: 132396 KiB 887s Date: Sat Mar 15 17:05:31 2025 887s Rank 1 is distributing fusions [1/1] (completed) 887s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 887s Rank 0 cycleNumber= 2 887s Rank 1: assembler memory usage: 136496 KiB 887s Date: Sat Mar 15 17:05:31 2025 887s 887s *** 887s Step: Merging of redundant paths 887s Date: Sat Mar 15 17:05:31 2025 887s Elapsed time: 49 seconds 887s Since beginning: 1 minutes, 51 seconds 887s *** 887s 887s 887s Rank 0 appended 0 elements 887s Rank 1 appended 1 elements 887s 887s *** 887s Step: Generation of contigs 887s Date: Sat Mar 15 17:05:31 2025 887s Elapsed time: 0 seconds 887s Since beginning: 1 minutes, 51 seconds 887s *** 887s 887s Rank 0 finished gathering scaffold links. 887s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 887s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 887s Rank 0 ineligibleObjects: 0/970 (0.00%) 887s Rank 1: assembler memory usage: 136496 KiB 887s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 887s Rank 1 finished gathering scaffold links. 887s Rank 0 will write 1 contig lengths 887s Rank 0 will solve the scaffolding problem. 887s Welcome to GreedySolver v1.0 887s 1 vertices; 0 edges 887s 1 contigs >= 500 887s Edges in solution: 0 887s 887s Conflict statistics: 887s 1 scaffolds, 1 >= 500 887s Total: 1000 nucleotides 887s 887s *** 887s Step: Scaffolding of contigs 887s Date: Sat Mar 15 17:05:31 2025 887s Elapsed time: 0 seconds 887s Since beginning: 1 minutes, 51 seconds 887s *** 887s 887s Rank 0Rank 1 syncing with master 887s syncing with master 887s 887s *** 887s Step: Counting sequences to search 887s Date: Sat Mar 15 17:05:31 2025 887s Elapsed time: 0 seconds 887s Since beginning: 1 minutes, 51 seconds 887s *** 887s 887s 887s Rank 0 will add colors, 0 sequences in 0 files to process 887s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 887s Rank 1 will add colors, 0 sequences in 0 files to process 887s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 897s 897s *** 897s Step: Graph coloring 897s Date: Sat Mar 15 17:05:41 2025 897s Elapsed time: 10 seconds 897s Since beginning: 2 minutes, 1 seconds 897s *** 897s 897s 897s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 897s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 897s Rank 0 shares its counts 897s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 897s Rank 1 computing contig abundances [1/1] [1/970] 897s Rank 1 computing contig abundances [1/1] [970/970] 897s [IO] Input/output operations for coverage XML objects: 897s *** 897s Step: Counting contig biological abundances 897s Date: Sat Mar 15 17:05:41 2025 897s Elapsed time: 0 seconds 897s Since beginning: 2 minutes, 1 seconds 897s *** 897s 897s 897s Rank 0 colored the graph with 0 real colors using 1 virtual colors 897s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 897s 897s *** 897s Step: Counting sequence biological abundances 897s Date: Sat Mar 15 17:05:41 2025 897s Elapsed time: 0 seconds 897s Since beginning: 2 minutes, 1 seconds 897s *** 897s 897s 897s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 897s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 897s 1 / bufferSize: 16777216 bytes 897s Rank 1 colored the graph with 0 real colors using 1 virtual colors 897s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 897s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 897s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 907s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 907s 907s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 907s 907s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 907s Rank 0 is starting taxon syncing across the compute tribe. 907s 907s *** 907s Step: Loading taxons 907s Date: Sat Mar 15 17:05:51 2025 907s Elapsed time: 10 seconds 907s Since beginning: 2 minutes, 11 seconds 907s *** 907s 907s Rank 0 synced taxons across the grid with 2 poor slaves. 907s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 907s Rank 0 has 0 taxons after syncing with master 907s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 907s Rank 1 has 0 taxons after syncing with master 917s 918s 918s 918s *** 918s Step: Loading tree 918s Date: Sat Mar 15 17:06:02 2025 918s Elapsed time: 11 seconds 918s Since beginning: 2 minutes, 22 seconds 918s *** 918s 927s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 927s 927s Rank 0: counting ontology terms in the graph... 927s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 927s 927s Rank 1: counting ontology terms in the graph... 937s Rank 1: 0 have some biological signal 937s Number of dereferenced alternate handles: 0 937s Number of k-mer observations with gene ontology terms: 0 938s Rank 0: 0 have some biological signal 938s Number of dereferenced alternate handles: 0 938s Number of k-mer observations with gene ontology terms: 0 938s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 938s Rank 0: synced ontology term profiles with master 938s Rank 0: synchronization is complete! 938s Rank 0: ontology terms with biological signal: 0 938s Populated recursive values... 938s Gene ontology terms without depth information: 0 938s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 938s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 938s 938s *** 938s Step: Processing gene ontologies 938s Date: Sat Mar 15 17:06:22 2025 938s Elapsed time: 20 seconds 938s Since beginning: 2 minutes, 42 seconds 938s *** 938s 938s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 938s [GenomeNeighbourhood] in final list: 0 938s 938s *** 938s Step: Computing neighbourhoods 938s Date: Sat Mar 15 17:06:22 2025 938s Elapsed time: 0 seconds 938s Since beginning: 2 minutes, 42 seconds 938s *** 938s 938s Contigs >= 100 nt 938s Number: 1 938s Total length: 1000 938s Average: 1000 938s N50: 1000 938s Median: 1000 938s Largest: 1000 938s Contigs >= 500 nt 938s Number: 1 938s Total length: 1000 938s Average: 1000 938s N50: 1000 938s Median: 1000 938s Largest: 1000 938s Scaffolds >= 100 nt 938s Number: 1 938s Total length: 1000 938s Average: 1000 938s N50: 1000 938s Median: 1000 938s Largest: 1000 938s Scaffolds >= 500 nt 938s Number: 1 938s Total length: 1000 938s Average: 1000 938s N50: 1000 938s Median: 1000 938s Largest: 1000 938s Rank 1: synced ontology term profiles with master 938s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 938s 938s Rank 0 wrote test3/Contigs.fasta 938s Rank 0 wrote test3/Scaffolds.fasta 938s Check for test3/* 938s 938s 938s MPICH: Builtin communicator 44000000 has pending 7 references. 938s MPICH: Builtin communicator 44000000 has pending 32 references. 938s autopkgtest [17:06:22]: test run-unit-test: -----------------------] 943s autopkgtest [17:06:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 943s run-unit-test PASS 946s autopkgtest [17:06:30]: @@@@@@@@@@@@@@@@@@@@ summary 946s run-unit-test PASS