0s autopkgtest [16:01:01]: starting date and time: 2024-07-08 16:01:01+0000 0s autopkgtest [16:01:01]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [16:01:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ywbsw2pr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:mpi-defaults --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=mpi-defaults/1.17 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-23.secgroup --name adt-oracular-arm64-ray-20240708-160100-juju-7f2275-prod-proposed-migration-environment-2-8428d008-8138-45d1-bbb7-3e9f2f6022af --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 295s autopkgtest [16:05:56]: testbed dpkg architecture: arm64 295s autopkgtest [16:05:56]: testbed apt version: 2.9.6 295s autopkgtest [16:05:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 295s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 296s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [360 kB] 296s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 296s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 296s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3336 B] 296s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [96.5 kB] 296s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2576 B] 296s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB] 296s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B] 296s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [367 kB] 296s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8844 B] 296s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7596 B] 296s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B] 298s Fetched 1076 kB in 1s (1205 kB/s) 298s Reading package lists... 301s Reading package lists... 302s Building dependency tree... 302s Reading state information... 302s Calculating upgrade... 303s The following packages will be upgraded: 303s libnetplan1 netplan-generator netplan.io python3-netplan 303s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 303s Need to get 269 kB of archives. 303s After this operation, 1024 B of additional disk space will be used. 303s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 netplan-generator arm64 1.0.1-1ubuntu2 [59.2 kB] 303s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-netplan arm64 1.0.1-1ubuntu2 [21.7 kB] 303s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 netplan.io arm64 1.0.1-1ubuntu2 [66.3 kB] 303s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libnetplan1 arm64 1.0.1-1ubuntu2 [122 kB] 304s Fetched 269 kB in 0s (611 kB/s) 305s (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 ... 78372 files and directories currently installed.) 305s Preparing to unpack .../netplan-generator_1.0.1-1ubuntu2_arm64.deb ... 305s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 305s Unpacking netplan-generator (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 309s Preparing to unpack .../python3-netplan_1.0.1-1ubuntu2_arm64.deb ... 309s Unpacking python3-netplan (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 313s Preparing to unpack .../netplan.io_1.0.1-1ubuntu2_arm64.deb ... 313s Unpacking netplan.io (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 316s Preparing to unpack .../libnetplan1_1.0.1-1ubuntu2_arm64.deb ... 316s Unpacking libnetplan1:arm64 (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 316s Setting up libnetplan1:arm64 (1.0.1-1ubuntu2) ... 316s Setting up python3-netplan (1.0.1-1ubuntu2) ... 316s Setting up netplan-generator (1.0.1-1ubuntu2) ... 316s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 316s Setting up netplan.io (1.0.1-1ubuntu2) ... 316s Processing triggers for libc-bin (2.39-0ubuntu9) ... 316s Processing triggers for man-db (2.12.1-2) ... 317s Processing triggers for dbus (1.14.10-4ubuntu4) ... 319s Reading package lists... 319s Building dependency tree... 319s Reading state information... 320s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 323s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 323s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 323s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 323s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 333s Reading package lists... 333s Reading package lists... 334s Building dependency tree... 334s Reading state information... 334s Calculating upgrade... 335s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 335s Reading package lists... 335s Building dependency tree... 335s Reading state information... 336s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 340s autopkgtest [16:06:41]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 341s autopkgtest [16:06:42]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 348s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (dsc) [2192 B] 348s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (tar) [450 kB] 348s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (diff) [213 kB] 349s gpgv: Signature made Mon Apr 1 07:35:01 2024 UTC 349s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 349s gpgv: Can't check signature: No public key 349s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8build2.dsc: no acceptable signature found 356s autopkgtest [16:06:57]: testing package ray version 2.3.1-8build2 361s autopkgtest [16:07:02]: build not needed 366s autopkgtest [16:07:07]: test run-unit-test: preparing testbed 370s Reading package lists... 371s Building dependency tree... 371s Reading state information... 371s Starting pkgProblemResolver with broken count: 0 372s Starting 2 pkgProblemResolver with broken count: 0 372s Done 372s The following additional packages will be installed: 372s fontconfig libatomic1 libblas3 libcairo2 libdatrie1 372s libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 libgomp1 libgraphite2-3 372s libharfbuzz0b libhwloc-plugins libhwloc15 libice6 liblapack3 libmunge2 372s libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 372s libpaper-utils libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 372s librdmacm1t64 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 libucx0 372s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6t64 372s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 372s ray ray-doc ray-extra unzip x11-common xdg-utils zip 372s Suggested packages: 372s tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler elpa-ess r-doc-info 372s | r-doc-pdf r-mathlib r-base-html 372s Recommended packages: 372s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 372s libx11-protocol-perl x11-utils x11-xserver-utils 373s The following NEW packages will be installed: 373s autopkgtest-satdep fontconfig libatomic1 libblas3 libcairo2 libdatrie1 373s libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 libgomp1 libgraphite2-3 373s libharfbuzz0b libhwloc-plugins libhwloc15 libice6 liblapack3 libmunge2 373s libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 373s libpaper-utils libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 373s librdmacm1t64 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 libucx0 373s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6t64 373s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 373s ray ray-doc ray-extra unzip x11-common xdg-utils zip 373s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 373s Need to get 41.9 MB/41.9 MB of archives. 373s After this operation, 99.5 MB of additional disk space will be used. 373s Get:1 /tmp/autopkgtest.ltH33k/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 394s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] 394s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libatomic1 arm64 14.1.0-1ubuntu1 [11.4 kB] 394s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 394s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 394s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 394s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 394s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 394s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB] 394s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 394s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 394s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 librdmacm1t64 arm64 52.0-2 [70.8 kB] 394s Get:13 http://ftpmaster.internal/ubuntu oracular/universe arm64 libfabric1 arm64 1.17.0-3build2 [541 kB] 394s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 394s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14.1.0-1ubuntu1 [144 kB] 394s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 394s Get:17 http://ftpmaster.internal/ubuntu oracular/main arm64 libharfbuzz0b arm64 8.3.0-2build2 [463 kB] 394s Get:18 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhwloc15 arm64 2.10.0-1build1 [159 kB] 394s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 394s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB] 394s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 394s Get:22 http://ftpmaster.internal/ubuntu oracular/universe arm64 libmunge2 arm64 0.5.15-4build1 [14.9 kB] 394s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 394s Get:24 http://ftpmaster.internal/ubuntu oracular/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 394s Get:25 http://ftpmaster.internal/ubuntu oracular/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 394s Get:26 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhwloc-plugins arm64 2.10.0-1build1 [15.7 kB] 394s Get:27 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpmix2t64 arm64 5.0.1-4.1build1 [655 kB] 394s Get:28 http://ftpmaster.internal/ubuntu oracular/universe arm64 libucx0 arm64 1.16.0+ds-5ubuntu1 [1074 kB] 394s Get:29 http://ftpmaster.internal/ubuntu oracular/universe arm64 libopenmpi3t64 arm64 4.1.6-7ubuntu2 [2463 kB] 394s Get:30 http://ftpmaster.internal/ubuntu oracular/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 394s Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 394s Get:32 http://ftpmaster.internal/ubuntu oracular/main arm64 libpango-1.0-0 arm64 1.54.0+ds-1 [230 kB] 394s Get:33 http://ftpmaster.internal/ubuntu oracular/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-1 [41.7 kB] 394s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-1 [27.2 kB] 394s Get:35 http://ftpmaster.internal/ubuntu oracular/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] 394s Get:36 http://ftpmaster.internal/ubuntu oracular/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B] 394s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB] 394s Get:38 http://ftpmaster.internal/ubuntu oracular/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] 394s Get:39 http://ftpmaster.internal/ubuntu oracular/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 394s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 394s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] 394s Get:42 http://ftpmaster.internal/ubuntu oracular/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 394s Get:43 http://ftpmaster.internal/ubuntu oracular/universe arm64 openmpi-common all 4.1.6-7ubuntu2 [170 kB] 394s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 openmpi-bin arm64 4.1.6-7ubuntu2 [113 kB] 394s Get:45 http://ftpmaster.internal/ubuntu oracular/main arm64 zip arm64 3.0-13build1 [171 kB] 394s Get:46 http://ftpmaster.internal/ubuntu oracular/main arm64 unzip arm64 6.0-28ubuntu5 [176 kB] 394s Get:47 http://ftpmaster.internal/ubuntu oracular/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 394s Get:48 http://ftpmaster.internal/ubuntu oracular/universe arm64 r-base-core arm64 4.4.1-1 [28.3 MB] 394s Get:49 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 mpi-default-bin arm64 1.17 [2296 B] 394s Get:50 http://ftpmaster.internal/ubuntu oracular/universe arm64 ray arm64 2.3.1-8build2 [729 kB] 394s Get:51 http://ftpmaster.internal/ubuntu oracular/universe arm64 ray-doc all 2.3.1-8build2 [35.1 kB] 394s Get:52 http://ftpmaster.internal/ubuntu oracular/universe arm64 ray-extra all 2.3.1-8build2 [12.1 kB] 394s Preconfiguring packages ... 394s Fetched 41.9 MB in 17s (2424 kB/s) 394s Selecting previously unselected package fontconfig. 395s (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 ... 78372 files and directories currently installed.) 395s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ... 395s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 395s Selecting previously unselected package libatomic1:arm64. 396s Preparing to unpack .../01-libatomic1_14.1.0-1ubuntu1_arm64.deb ... 396s Unpacking libatomic1:arm64 (14.1.0-1ubuntu1) ... 397s Selecting previously unselected package libblas3:arm64. 398s Preparing to unpack .../02-libblas3_3.12.0-3build1_arm64.deb ... 398s Unpacking libblas3:arm64 (3.12.0-3build1) ... 398s Selecting previously unselected package libpixman-1-0:arm64. 398s Preparing to unpack .../03-libpixman-1-0_0.42.2-1build1_arm64.deb ... 398s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 399s Selecting previously unselected package libxcb-render0:arm64. 399s Preparing to unpack .../04-libxcb-render0_1.17.0-2_arm64.deb ... 399s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 399s Selecting previously unselected package libxcb-shm0:arm64. 399s Preparing to unpack .../05-libxcb-shm0_1.17.0-2_arm64.deb ... 399s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 399s Selecting previously unselected package libxrender1:arm64. 399s Preparing to unpack .../06-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 399s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 399s Selecting previously unselected package libcairo2:arm64. 400s Preparing to unpack .../07-libcairo2_1.18.0-3build1_arm64.deb ... 400s Unpacking libcairo2:arm64 (1.18.0-3build1) ... 400s Selecting previously unselected package libdatrie1:arm64. 400s Preparing to unpack .../08-libdatrie1_0.2.13-3build1_arm64.deb ... 400s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 400s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 400s Preparing to unpack .../09-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 400s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 400s Selecting previously unselected package librdmacm1t64:arm64. 401s Preparing to unpack .../10-librdmacm1t64_52.0-2_arm64.deb ... 401s Unpacking librdmacm1t64:arm64 (52.0-2) ... 401s Selecting previously unselected package libfabric1:arm64. 401s Preparing to unpack .../11-libfabric1_1.17.0-3build2_arm64.deb ... 401s Unpacking libfabric1:arm64 (1.17.0-3build2) ... 401s Selecting previously unselected package libgfortran5:arm64. 401s Preparing to unpack .../12-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 401s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 401s Selecting previously unselected package libgomp1:arm64. 401s Preparing to unpack .../13-libgomp1_14.1.0-1ubuntu1_arm64.deb ... 401s Unpacking libgomp1:arm64 (14.1.0-1ubuntu1) ... 401s Selecting previously unselected package libgraphite2-3:arm64. 401s Preparing to unpack .../14-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 401s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 401s Selecting previously unselected package libharfbuzz0b:arm64. 401s Preparing to unpack .../15-libharfbuzz0b_8.3.0-2build2_arm64.deb ... 401s Unpacking libharfbuzz0b:arm64 (8.3.0-2build2) ... 402s Selecting previously unselected package libhwloc15:arm64. 402s Preparing to unpack .../16-libhwloc15_2.10.0-1build1_arm64.deb ... 402s Unpacking libhwloc15:arm64 (2.10.0-1build1) ... 402s Selecting previously unselected package x11-common. 403s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 403s Unpacking x11-common (1:7.7+23ubuntu3) ... 403s Selecting previously unselected package libice6:arm64. 403s Preparing to unpack .../18-libice6_2%3a1.0.10-1build3_arm64.deb ... 403s Unpacking libice6:arm64 (2:1.0.10-1build3) ... 403s Selecting previously unselected package liblapack3:arm64. 404s Preparing to unpack .../19-liblapack3_3.12.0-3build1_arm64.deb ... 404s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 404s Selecting previously unselected package libmunge2:arm64. 404s Preparing to unpack .../20-libmunge2_0.5.15-4build1_arm64.deb ... 404s Unpacking libmunge2:arm64 (0.5.15-4build1) ... 404s Selecting previously unselected package libpciaccess0:arm64. 405s Preparing to unpack .../21-libpciaccess0_0.17-3build1_arm64.deb ... 405s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 405s Selecting previously unselected package libxnvctrl0:arm64. 405s Preparing to unpack .../22-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 405s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 405s Selecting previously unselected package ocl-icd-libopencl1:arm64. 405s Preparing to unpack .../23-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 405s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 405s Selecting previously unselected package libhwloc-plugins:arm64. 405s Preparing to unpack .../24-libhwloc-plugins_2.10.0-1build1_arm64.deb ... 405s Unpacking libhwloc-plugins:arm64 (2.10.0-1build1) ... 405s Selecting previously unselected package libpmix2t64:arm64. 405s Preparing to unpack .../25-libpmix2t64_5.0.1-4.1build1_arm64.deb ... 405s Unpacking libpmix2t64:arm64 (5.0.1-4.1build1) ... 406s Selecting previously unselected package libucx0:arm64. 407s Preparing to unpack .../26-libucx0_1.16.0+ds-5ubuntu1_arm64.deb ... 407s Unpacking libucx0:arm64 (1.16.0+ds-5ubuntu1) ... 407s Selecting previously unselected package libopenmpi3t64:arm64. 408s Preparing to unpack .../27-libopenmpi3t64_4.1.6-7ubuntu2_arm64.deb ... 408s Unpacking libopenmpi3t64:arm64 (4.1.6-7ubuntu2) ... 408s Selecting previously unselected package libthai-data. 409s Preparing to unpack .../28-libthai-data_0.1.29-2build1_all.deb ... 409s Unpacking libthai-data (0.1.29-2build1) ... 409s Selecting previously unselected package libthai0:arm64. 410s Preparing to unpack .../29-libthai0_0.1.29-2build1_arm64.deb ... 410s Unpacking libthai0:arm64 (0.1.29-2build1) ... 410s Selecting previously unselected package libpango-1.0-0:arm64. 410s Preparing to unpack .../30-libpango-1.0-0_1.54.0+ds-1_arm64.deb ... 410s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-1) ... 410s Selecting previously unselected package libpangoft2-1.0-0:arm64. 410s Preparing to unpack .../31-libpangoft2-1.0-0_1.54.0+ds-1_arm64.deb ... 410s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... 410s Selecting previously unselected package libpangocairo-1.0-0:arm64. 410s Preparing to unpack .../32-libpangocairo-1.0-0_1.54.0+ds-1_arm64.deb ... 410s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... 410s Selecting previously unselected package libpaper1:arm64. 410s Preparing to unpack .../33-libpaper1_1.1.29build1_arm64.deb ... 410s Unpacking libpaper1:arm64 (1.1.29build1) ... 410s Selecting previously unselected package libpaper-utils. 410s Preparing to unpack .../34-libpaper-utils_1.1.29build1_arm64.deb ... 410s Unpacking libpaper-utils (1.1.29build1) ... 410s Selecting previously unselected package libsm6:arm64. 410s Preparing to unpack .../35-libsm6_2%3a1.2.3-1build3_arm64.deb ... 410s Unpacking libsm6:arm64 (2:1.2.3-1build3) ... 410s Selecting previously unselected package libtcl8.6:arm64. 410s Preparing to unpack .../36-libtcl8.6_8.6.14+dfsg-1build1_arm64.deb ... 410s Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 410s Selecting previously unselected package libxft2:arm64. 410s Preparing to unpack .../37-libxft2_2.3.6-1build1_arm64.deb ... 410s Unpacking libxft2:arm64 (2.3.6-1build1) ... 410s Selecting previously unselected package libxss1:arm64. 410s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build3_arm64.deb ... 410s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 410s Selecting previously unselected package libtk8.6:arm64. 410s Preparing to unpack .../39-libtk8.6_8.6.14-1build1_arm64.deb ... 410s Unpacking libtk8.6:arm64 (8.6.14-1build1) ... 411s Selecting previously unselected package libxt6t64:arm64. 411s Preparing to unpack .../40-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 411s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 411s Selecting previously unselected package openmpi-common. 411s Preparing to unpack .../41-openmpi-common_4.1.6-7ubuntu2_all.deb ... 411s Unpacking openmpi-common (4.1.6-7ubuntu2) ... 411s Selecting previously unselected package openmpi-bin. 411s Preparing to unpack .../42-openmpi-bin_4.1.6-7ubuntu2_arm64.deb ... 411s Unpacking openmpi-bin (4.1.6-7ubuntu2) ... 411s Selecting previously unselected package zip. 411s Preparing to unpack .../43-zip_3.0-13build1_arm64.deb ... 411s Unpacking zip (3.0-13build1) ... 411s Selecting previously unselected package unzip. 412s Preparing to unpack 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.../50-ray-extra_2.3.1-8build2_all.deb ... 413s Unpacking ray-extra (2.3.1-8build2) ... 413s Selecting previously unselected package autopkgtest-satdep. 413s Preparing to unpack .../51-1-autopkgtest-satdep.deb ... 413s Unpacking autopkgtest-satdep (0) ... 413s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 413s Setting up libpixman-1-0:arm64 (0.42.2-1build1) ... 413s Setting up libpaper1:arm64 (1.1.29build1) ... 414s 414s Creating config file /etc/papersize with new version 414s Setting up ray-doc (2.3.1-8build2) ... 414s Setting up libpciaccess0:arm64 (0.17-3build1) ... 414s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 417s Regenerating fonts cache... done. 417s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 417s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 417s Setting up libxcb-render0:arm64 (1.17.0-2) ... 417s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 417s Setting up unzip (6.0-28ubuntu5) ... 417s Setting up x11-common (1:7.7+23ubuntu3) ... 418s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 418s Setting up libpaper-utils (1.1.29build1) ... 418s Setting up libgomp1:arm64 (14.1.0-1ubuntu1) ... 418s Setting up libcairo2:arm64 (1.18.0-3build1) ... 418s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 418s Setting up zip (3.0-13build1) ... 418s Setting up libblas3:arm64 (3.12.0-3build1) ... 418s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 418s Setting up libmunge2:arm64 (0.5.15-4build1) ... 418s Setting up libhwloc15:arm64 (2.10.0-1build1) ... 418s Setting up libatomic1:arm64 (14.1.0-1ubuntu1) ... 418s Setting up libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 418s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 418s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 418s Setting up openmpi-common (4.1.6-7ubuntu2) ... 418s Setting up librdmacm1t64:arm64 (52.0-2) ... 418s Setting up libharfbuzz0b:arm64 (8.3.0-2build2) ... 418s Setting up libthai-data (0.1.29-2build1) ... 418s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 418s Setting up xdg-utils (1.2.1-0ubuntu1) ... 418s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 418s Setting up libfabric1:arm64 (1.17.0-3build2) ... 418s Setting up libice6:arm64 (2:1.0.10-1build3) ... 418s Setting up libucx0:arm64 (1.16.0+ds-5ubuntu1) ... 418s Setting up liblapack3:arm64 (3.12.0-3build1) ... 418s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 418s Setting up libxft2:arm64 (2.3.6-1build1) ... 418s Setting up libtk8.6:arm64 (8.6.14-1build1) ... 418s Setting up libhwloc-plugins:arm64 (2.10.0-1build1) ... 418s Setting up libthai0:arm64 (0.1.29-2build1) ... 418s Setting up libpmix2t64:arm64 (5.0.1-4.1build1) ... 418s Setting up libopenmpi3t64:arm64 (4.1.6-7ubuntu2) ... 418s Setting up libsm6:arm64 (2:1.2.3-1build3) ... 418s Setting up openmpi-bin (4.1.6-7ubuntu2) ... 418s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 418s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 418s Setting up libpango-1.0-0:arm64 (1.54.0+ds-1) ... 418s Setting up mpi-default-bin (1.17) ... 418s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 418s Setting up ray (2.3.1-8build2) ... 418s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... 418s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... 418s Setting up r-base-core (4.4.1-1) ... 419s 419s Creating config file /etc/R/Renviron with new version 419s Setting up ray-extra (2.3.1-8build2) ... 419s Setting up autopkgtest-satdep (0) ... 419s Processing triggers for man-db (2.12.1-2) ... 420s Processing triggers for install-info (7.1-3build2) ... 421s Processing triggers for libc-bin (2.39-0ubuntu9) ... 427s (Reading database ... 80984 files and directories currently installed.) 427s Removing autopkgtest-satdep (0) ... 427s autopkgtest [16:08:08]: test run-unit-test: [----------------------- 428s 428s ************************************************** 428s This program comes with ABSOLUTELY NO WARRANTY. 428s This is free software, and you are welcome to redistribute it 428s under certain conditions; see "LICENSE.txt" for details. 428s ************************************************** 428s 428s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 428s Centre de recherche en infectiologie de l'Université Laval 428s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 428s http://denovoassembler.sf.net/ 428s 428s References to cite: 428s 428s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 428s Ray Meta: scalable de novo metagenome assembly and profiling. 428s Genome Biology (BioMed Central Ltd). 428s 13:R122, Published: 22 December 2012 428s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 428s 428s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 428s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 428s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 428s November 2010, Volume 17, Issue 11, Pages 1519-1533. 428s http://dx.doi.org/doi:10.1089/cmb.2009.0238 428s 428s Ray version 2.3.1 428s License for Ray: GNU General Public License version 3 428s RayPlatform version: 2.0.1 428s License for RayPlatform: GNU Lesser General Public License version 3 428s 428s MAXKMERLENGTH: 32 428s Maximum coverage depth stored by CoverageDepth: 4294967295 428s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 428s FORCE_PACKING = n 428s ASSERT = n 428s HAVE_LIBZ = y 428s HAVE_LIBBZ2 = y 428s PROFILER_COLLECT = n 428s MINIRANKS = y 428s CLOCK_GETTIME = n 428s __linux__ = y 428s _MSC_VER = n 428s __GNUC__ = y 428s RAY_32_BITS = n 428s RAY_64_BITS = y 428s MPI standard version: MPI 3.1 428s MPI library: Open-MPI 4.1.6 428s Compiler: GNU gcc/g++ 13.2.0 428s MPI I/O: n 428s 428s 428s -k (to set the k-mer size) 428s Value: 31 428s 428s 428s Paired library # 0 428s -p (paired-end sequences) 428s Left sequences: ecoli_1K_1.fq 428s Right sequences: ecoli_1K_2.fq 428s Average length: automatic detection 428s Standard deviation: automatic detection 428s 428s Ray command: 428s mpiexec -n 1 Ray \ 428s -k \ 428s 31 \ 428s -p \ 428s ecoli_1K_1.fq \ 428s ecoli_1K_2.fq \ 428s -o \ 428s test1 428s 428s Rank 0 wrote test1/RayCommand.txt 428s 428s k-mer length: 31 428s Rank 0: assembler memory usage: 41928 KiB 428s Rank 0: assembler memory usage: 107764 KiB 428s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3146 428s Rank 0: testing the network, please wait... 428s 428s Rank 0 is testing the network [0/1000] 428s Rank 0 is testing the network [1000/1000] 428s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 428s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 428s 428s Rank 0 wrote test1/NetworkTest.txt 428s 428s 428s *** 428s Step: Network testing 428s Date: Mon Jul 8 16:08:09 2024 428s Elapsed time: 0 seconds 428s Since beginning: 0 seconds 428s *** 428s 428s 428s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 428s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 428s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 428s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 428s Rank 0 wrote test1/NumberOfSequences.txt 428s Rank 0 wrote test1/SequencePartition.txt 428s 428s *** 428s Step: Counting sequences to assemble 428s Date: Mon Jul 8 16:08:09 2024 428s Elapsed time: 0 seconds 428s Since beginning: 0 seconds 428s *** 428s 428s 428s Rank 0 is loading sequence reads 428s Rank 0 : partition is [0;4107], 4108 sequence reads 428s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 428s Rank 0 has 0 sequence reads 428s Rank 0: assembler memory usage: 120644 KiB 428s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 428s Rank 0 has 4108 sequence reads (completed) 428s 428s *** 428s Step: Sequence loading 428s Date: Mon Jul 8 16:08:09 2024 428s Elapsed time: 0 seconds 428s Since beginning: 0 seconds 428s *** 428s 428s 428s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 428s Rank 0 created its Bloom filter 428s Rank 0 is counting k-mers in sequence reads [1/4108] 428s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 428s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 428s 428s 428s *** 428s Step: K-mer counting 428s Date: Mon Jul 8 16:08:09 2024 428s Elapsed time: 0 seconds 428s Since beginning: 0 seconds 428s *** 428s 428s 428s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 428s Rank 0 destroyed its Bloom filter 428s Rank 0 has 1954 k-mers (completed) 428s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 428s Rank 0: assembler memory usage: 117036 KiB 429s 429s 429s Rank 0: the minimum coverage is 3 429s Rank 0: the peak coverage is 3 429s Warning: no peak observed in the k-mer coverage distribution. 429s to deal with the sequencing error rate, try to lower the k-mer length (-k) 429s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 429s 429s *** 429s Step: Coverage distribution analysis 429s Date: Mon Jul 8 16:08:10 2024 429s Elapsed time: 1 seconds 429s Since beginning: 1 seconds 429s *** 429s 429s 429s 430s Rank 0 is adding edges [1/4108] 430s Rank 0 is adding edges [4108/4108] (completed) 430s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 430s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 430s 430s *** 430s Step: Graph construction 430s Date: Mon Jul 8 16:08:11 2024 430s Elapsed time: 1 seconds 430s Since beginning: 2 seconds 430s *** 430s 430s 430s Rank 0 has 1954 vertices (completed) 430s Rank 0: assembler memory usage: 117036 KiB 430s Rank 0 is purging edges [1/1954] 430s Rank 0 is purging edges [1954/1954] (completed) 430s Rank 0: assembler memory usage: 117564 KiB 430s VirtualProcessor: completed jobs: 1954 430s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 431s Rank 0 wrote test1/degreeDistribution.txt 431s 431s *** 431s Step: Null edge purging 431s Date: Mon Jul 8 16:08:12 2024 431s Elapsed time: 1 seconds 431s Since beginning: 3 seconds 431s *** 431s 431s 431s Rank 0 is selecting optimal read markers [1/4108] 431s Rank 0: assembler memory usage: 117564 KiB 431s Rank 0 is selecting optimal read markers [4108/4108] (completed) 431s Rank 0: peak number of workers: 599, maximum: 32768 431s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 431s Rank 0: assembler memory usage: 125732 KiB 431s Rank 0: Freeing unused assembler memory: 4096 KiB freed 431s Rank 0: assembler memory usage: 125732 KiB 431s 431s *** 431s Step: Selection of optimal read markers 431s Date: Mon Jul 8 16:08:12 2024 431s Elapsed time: 0 seconds 431s Since beginning: 3 seconds 431s *** 431s 431s 431s Rank 0: memory usage for optimal read markers= 4096 KiB 431s Rank 0 is creating seeds [1/1954] 431s Rank 0: assembler memory usage: 125732 KiB 432s Rank 0 has 1 seeds 432s Rank 0 is creating seeds [1954/1954] (completed) 432s Rank 0: peak number of workers: 746, maximum: 32768 432s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 432s Rank 0 runtime statistics for seeding algorithm: 432s Rank 0 Skipped paths because of dead end for head: 0 432s Rank 0 Skipped paths because of dead end for tail: 0 432s Rank 0 Skipped paths because of two dead ends: 0 432s Rank 0 Skipped paths because of bubble weak component: 0 432s Rank 0 Skipped paths because of short length: 1952 432s Rank 0 Skipped paths because of bad ownership: 1 432s Rank 0 Skipped paths because of low coverage: 0 432s Rank 0 Eligible paths: 1 432s Rank 0: assembler memory usage: 125732 KiB 432s Rank 0 has 1 seeds to register. 432s Rank 0 registered 0/1 432s Rank 0 registered 0/1 432s Rank 0 registered its seeds 432s VirtualProcessor: completed jobs: 0 432s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 433s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 443s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 443s Rank 0 merged its seeds: 1 seeds -> 1 seeds 443s 443s *** 443s Step: Detection of assembly seeds 443s Date: Mon Jul 8 16:08:24 2024 443s Elapsed time: 12 seconds 443s Since beginning: 15 seconds 443s *** 443s 443s 443s Rank 0 is calculating library lengths [1/1] 443s Rank 0 detected 1737 library lengths 443s Rank 0 is calculating library lengths [1/1] (completed) 443s Rank 0: peak number of workers: 1, maximum: 32768 443s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 443s Rank 0: assembler memory usage: 162600 KiB 443s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 443s 443s Mode= 2 signalAverage= 9 443s CURRENT IS NOISE, 244 443s GOT HIT 212 443s 443s 443s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 443s 443s *** 443s Step: Estimation of outer distances for paired reads 443s Date: Mon Jul 8 16:08:24 2024 443s Elapsed time: 0 seconds 443s Since beginning: 15 seconds 443s *** 443s 443s 444s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 444s Rank 0 traversed 1000 nucleotide symbols 444s Rank 0: assembler memory usage: 166696 KiB 444s Rank 0 is extending seeds [1/1] (completed) 444s Rank 0 extended 1 seeds out of 1 (100.00%) 444s Rank 0: assembler memory usage: 158504 KiB 444s Rank 0 starting fusions 444s 444s *** 444s Step: Bidirectional extension of seeds 444s Date: Mon Jul 8 16:08:25 2024 444s Elapsed time: 1 seconds 444s Since beginning: 16 seconds 444s *** 444s 444s 444s Rank 0: starting clear step. cycleNumber= 0 444s Rank 0 adding 0 new fusions 444s Rank 0 cleared, 1 paths 444s Rank 0: starting distribution step 444s Rank 0 is distributing fusions [1/1] 444s Rank 0: assembler memory usage: 158504 KiB 444s Date: Mon Jul 8 16:08:25 2024 444s Rank 0 is distributing fusions [1/1] (completed) 444s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 444s Rank 0: assembler memory usage: 162600 KiB 444s Date: Mon Jul 8 16:08:25 2024 444s Rank 0 tells others to compute fusions. 444s Rank 0 FusionTaskCreator assignNextTask [0/2] 444s Rank 0: assembler memory usage: 162600 KiB 444s Date: Mon Jul 8 16:08:25 2024 444s Rank 0 FusionTaskCreator processWorkerResult [0/2] 444s Rank 0: assembler memory usage: 162600 KiB 444s Date: Mon Jul 8 16:08:25 2024 444s Rank 0 FusionTaskCreator [2/2] 444s Statistics: all paths: 1 eliminated during fusing: 0 444s Rank 0: assembler memory usage: 162600 KiB 444s VirtualProcessor: completed jobs: 2 444s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 444s Rank 0: starting clear step. cycleNumber= 1 445s Rank 0 adding 0 new fusions 445s Rank 0 cleared, 1 paths 445s Rank 0 is distributing fusions [1/1] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:26 2024 445s Rank 0 is distributing fusions [1/1] (completed) 445s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:26 2024 445s Rank 0 JoinerTaskCreator assignNextTask [0/2] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:26 2024 445s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:26 2024 445s Rank 0 JoinerTaskCreator [2/2] 445s Statistics: all paths: 1 eliminated during joining: 0 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:26 2024 445s VirtualProcessor: completed jobs: 2 445s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 445s Rank 0 adding 0 new fusions 445s Rank 0 cleared, 1 paths 445s Rank 0: starting distribution step 445s Rank 0 is distributing fusions [1/1] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:27 2024 445s Rank 0 is distributing fusions [1/1] (completed) 445s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:27 2024 445s Rank 0 tells others to compute fusions. 445s Rank 0 FusionTaskCreator assignNextTask [0/2] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:27 2024 445s Rank 0 FusionTaskCreator processWorkerResult [0/2] 445s Rank 0: assembler memory usage: 162600 KiB 445s Date: Mon Jul 8 16:08:27 2024 446s Rank 0 FusionTaskCreator [2/2] 446s Statistics: all paths: 1 eliminated during fusing: 0 446s Rank 0: assembler memory usage: 162600 KiB 446s VirtualProcessor: completed jobs: 2 446s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 446s Rank 0: starting clear step. cycleNumber= 2 446s Rank 0 adding 0 new fusions 446s Rank 0 cleared, 1 paths 446s Rank 0 is distributing fusions [1/1] 446s Rank 0: assembler memory usage: 162600 KiB 446s Date: Mon Jul 8 16:08:27 2024 446s Rank 0 is distributing fusions [1/1] (completed) 446s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 446s Rank 0: assembler memory usage: 162600 KiB 446s Date: Mon Jul 8 16:08:27 2024 446s Rank 0 JoinerTaskCreator assignNextTask [0/2] 446s Rank 0: assembler memory usage: 162600 KiB 446s Date: Mon Jul 8 16:08:27 2024 446s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 446s Rank 0: assembler memory usage: 162600 KiB 446s Date: Mon Jul 8 16:08:27 2024 446s Rank 0 JoinerTaskCreator [2/2] 446s Statistics: all paths: 1 eliminated during joining: 0 446s Rank 0: assembler memory usage: 162600 KiB 446s Date: Mon Jul 8 16:08:27 2024 446s VirtualProcessor: completed jobs: 2 446s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 447s Rank 0 adding 0 new fusions 447s Rank 0 cleared, 1 paths 447s Rank 0: starting distribution step 447s Rank 0 is distributing fusions [1/1] 447s Rank 0: assembler memory usage: 162600 KiB 447s Date: Mon Jul 8 16:08:28 2024 447s Rank 0 is distributing fusions [1/1] (completed) 447s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 447s Rank 0: assembler memory usage: 162600 KiB 447s Date: Mon Jul 8 16:08:28 2024 447s Rank 0 cycleNumber= 2 447s 447s *** 447s Step: Merging of redundant paths 447s Date: Mon Jul 8 16:08:28 2024 447s Elapsed time: 3 seconds 447s Since beginning: 19 seconds 447s *** 447s 447s 447s Rank 0 appended 1 elements 447s 447s *** 447s Step: Generation of contigs 447s Date: Mon Jul 8 16:08:28 2024 447s Elapsed time: 0 seconds 447s Since beginning: 19 seconds 447s *** 447s 447s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 447s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 447s Rank 0 ineligibleObjects: 0/970 (0.00%) 447s Rank 0: assembler memory usage: 162600 KiB 447s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 447s Rank 0 finished gathering scaffold links. 447s Rank 0 will write 1 contig lengths 447s Rank 0 will solve the scaffolding problem. 447s Welcome to GreedySolver v1.0 447s 1 vertices; 0 edges 447s 1 contigs >= 500 447s Edges in solution: 0 447s 447s Conflict statistics: 447s 1 scaffolds, 1 >= 500 447s Total: 1000 nucleotides 447s 447s *** 447s Step: Scaffolding of contigs 447s Date: Mon Jul 8 16:08:28 2024 447s Elapsed time: 0 seconds 447s Since beginning: 19 seconds 447s *** 447s 447s Rank 0 syncing with master 447s 447s *** 447s Step: Counting sequences to search 447s Date: Mon Jul 8 16:08:28 2024 447s Elapsed time: 0 seconds 447s Since beginning: 19 seconds 447s *** 447s 447s 447s Rank 0 will add colors, 0 sequences in 0 files to process 447s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 448s 448s *** 448s Step: Graph coloring 448s Date: Mon Jul 8 16:08:29 2024 448s Elapsed time: 1 seconds 448s Since beginning: 20 seconds 448s *** 448s 448s 448s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 448s Rank 0 shares its counts 448s Rank 0 computing contig abundances [1/1] [1/970] 448s Rank 0 computing contig abundances [1/1] [970/970] 448s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 448s 448s *** 448s Step: Counting contig biological abundances 448s Date: Mon Jul 8 16:08:29 2024 448s Elapsed time: 0 seconds 448s Since beginning: 20 seconds 448s *** 448s 448s 448s Rank 0 colored the graph with 0 real colors using 1 virtual colors 448s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 448s 448s *** 448s Step: Counting sequence biological abundances 448s Date: Mon Jul 8 16:08:29 2024 448s Elapsed time: 0 seconds 448s Since beginning: 20 seconds 448s *** 448s 448s 448s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 448s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 448s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 448s 448s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 448s Rank 0 is starting taxon syncing across the compute tribe. 448s 448s *** 448s Step: Loading taxons 448s Date: Mon Jul 8 16:08:29 2024 448s Elapsed time: 0 seconds 448s Since beginning: 20 seconds 448s *** 448s 448s Rank 0 synced taxons across the grid with 1 poor slaves. 448s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 448s Rank 0 has 0 taxons after syncing with master 449s 449s 449s *** 449s Step: Loading tree 449s Date: Mon Jul 8 16:08:30 2024 449s Elapsed time: 1 seconds 449s Since beginning: 21 seconds 449s *** 449s 450s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 450s 450s Rank 0: counting ontology terms in the graph... 450s Rank 0: 0 have some biological signal 450s Number of dereferenced alternate handles: 0 450s Number of k-mer observations with gene ontology terms: 0 450s Rank 0: synced ontology term profiles with master 450s Rank 0: synchronization is complete! 450s Rank 0: ontology terms with biological signal: 0 450s Populated recursive values... 450s Gene ontology terms without depth information: 0 450s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 450s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 450s 450s *** 450s Step: Processing gene ontologies 450s Date: Mon Jul 8 16:08:31 2024 450s Elapsed time: 1 seconds 450s Since beginning: 22 seconds 450s *** 450s 450s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 450s [GenomeNeighbourhood] in final list: 0 450s 450s *** 450s Step: Computing neighbourhoods 450s Date: Mon Jul 8 16:08:31 2024 450s Elapsed time: 0 seconds 450s Since beginning: 22 seconds 450s *** 450s 450s Contigs >= 100 nt 450s Number: 1 450s Total length: 1000 450s Average: 1000 450s N50: 1000 450s Median: 1000 450s Largest: 1000 450s Contigs >= 500 nt 450s Number: 1 450s Total length: 1000 450s Average: 1000 450s N50: 1000 450s Median: 1000 450s Largest: 1000 450s Scaffolds >= 100 nt 450s Number: 1 450s Total length: 1000 450s Average: 1000 450s N50: 1000 450s Median: 1000 450s Largest: 1000 450s Scaffolds >= 500 nt 450s Number: 1 450s Total length: 1000 450s Average: 1000 450s N50: 1000 450s Median: 1000 450s Largest: 1000 450s 450s Rank 0 wrote test1/Contigs.fasta 450s Rank 0 wrote test1/Scaffolds.fasta 450s Check for test1/* 450s 450s 452s 452s ************************************************** 452s This program comes with ABSOLUTELY NO WARRANTY. 452s This is free software, and you are welcome to redistribute it 452s under certain conditions; see "LICENSE.txt" for details. 452s ************************************************** 452s 452s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 452s Centre de recherche en infectiologie de l'Université Laval 452s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 452s http://denovoassembler.sf.net/ 452s 452s References to cite: 452s 452s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 452s Ray Meta: scalable de novo metagenome assembly and profiling. 452s Genome Biology (BioMed Central Ltd). 452s 13:R122, Published: 22 December 2012 452s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 452s 452s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 452s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 452s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 452s November 2010, Volume 17, Issue 11, Pages 1519-1533. 452s http://dx.doi.org/doi:10.1089/cmb.2009.0238 452s 452s Ray version 2.3.1 452s License for Ray: GNU General Public License version 3 452s RayPlatform version: 2.0.1 452s License for RayPlatform: GNU Lesser General Public License version 3 452s 452s MAXKMERLENGTH: 32 452s Maximum coverage depth stored by CoverageDepth: 4294967295 452s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 452s FORCE_PACKING = n 452s ASSERT = n 452s HAVE_LIBZ = y 452s HAVE_LIBBZ2 = y 452s PROFILER_COLLECT = n 452s MINIRANKS = y 452s CLOCK_GETTIME = n 452s __linux__ = y 452s _MSC_VER = n 452s __GNUC__ = y 452s RAY_32_BITS = n 452s RAY_64_BITS = y 452s MPI standard version: MPI 3.1 452s MPI library: Open-MPI 4.1.6 452s Compiler: GNU gcc/g++ 13.2.0 452s MPI I/O: n 452s 452s 452s -k (to set the k-mer size) 452s Value: 31 452s 452s 452s Paired library # 0 452s -p (paired-end sequences) 452s Left sequences: SampleDirectory/s_6.first1000_1.fastq 452s Right sequences: SampleDirectory/s_6.first1000_2.fastq 452s Average length: automatic detection 452s Standard deviation: automatic detection 452s 452s Ray command: 452s mpiexec -n 1 Ray \ 452s -k \ 452s 31 \ 452s -detect-sequence-files \ 452s SampleDirectory \ 452s -o \ 452s test2 452s 452s Rank 0 wrote test2/RayCommand.txt 452s 452s k-mer length: 31 452s Rank 0: assembler memory usage: 41944 KiB 452s Rank 0: assembler memory usage: 107764 KiB 452s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3152 452s Rank 0: testing the network, please wait... 452s 452s Rank 0 is testing the network [0/1000] 452s Rank 0 is testing the network [1000/1000] 452s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 452s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 452s 452s Rank 0 wrote test2/NetworkTest.txt 452s 452s 452s *** 452s Step: Network testing 452s Date: Mon Jul 8 16:08:33 2024 452s Elapsed time: 0 seconds 452s Since beginning: 0 seconds 452s *** 452s 452s 452s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 452s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 452s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 452s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 452s Rank 0 wrote test2/NumberOfSequences.txt 452s Rank 0 wrote test2/SequencePartition.txt 452s 452s *** 452s Step: Counting sequences to assemble 452s Date: Mon Jul 8 16:08:33 2024 452s Elapsed time: 0 seconds 452s Since beginning: 0 seconds 452s *** 452s 452s 452s Rank 0 is loading sequence reads 452s Rank 0 : partition is [0;4107], 4108 sequence reads 452s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 452s Rank 0 has 0 sequence reads 452s Rank 0: assembler memory usage: 120644 KiB 452s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 452s Rank 0 has 4108 sequence reads (completed) 452s 452s *** 452s Step: Sequence loading 452s Date: Mon Jul 8 16:08:33 2024 452s Elapsed time: 0 seconds 452s Since beginning: 0 seconds 452s *** 452s 452s 452s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 452s Rank 0 created its Bloom filter 453s Rank 0 is counting k-mers in sequence reads [1/4108] 453s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 453s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 453s 453s 453s *** 453s Step: K-mer counting 453s Date: Mon Jul 8 16:08:34 2024 453s Elapsed time: 1 seconds 453s Since beginning: 1 seconds 453s *** 453s 453s 453s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 453s Rank 0 destroyed its Bloom filter 453s Rank 0 has 1954 k-mers (completed) 453s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 453s Rank 0: assembler memory usage: 117036 KiB 453s 453s 453s Rank 0: the minimum coverage is 3 453s Rank 0: the peak coverage is 3 453s Warning: no peak observed in the k-mer coverage distribution. 453s to deal with the sequencing error rate, try to lower the k-mer length (-k) 453s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 453s 453s *** 453s Step: Coverage distribution analysis 453s Date: Mon Jul 8 16:08:34 2024 453s Elapsed time: 0 seconds 453s Since beginning: 1 seconds 453s *** 453s 453s 453s 453s Rank 0 is adding edges [1/4108] 453s Rank 0 is adding edges [4108/4108] (completed) 453s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 453s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 453s 453s *** 453s Step: Graph construction 453s Date: Mon Jul 8 16:08:35 2024 453s Elapsed time: 1 seconds 453s Since beginning: 2 seconds 453s *** 453s 453s 453s Rank 0 has 1954 vertices (completed) 453s Rank 0: assembler memory usage: 117036 KiB 454s Rank 0 is purging edges [1/1954] 454s Rank 0 is purging edges [1954/1954] (completed) 454s Rank 0: assembler memory usage: 117564 KiB 454s VirtualProcessor: completed jobs: 1954 454s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 455s Rank 0 wrote test2/degreeDistribution.txt 455s 455s *** 455s Step: Null edge purging 455s Date: Mon Jul 8 16:08:36 2024 455s Elapsed time: 1 seconds 455s Since beginning: 3 seconds 455s *** 455s 455s 455s Rank 0 is selecting optimal read markers [1/4108] 455s Rank 0: assembler memory usage: 117564 KiB 455s Rank 0 is selecting optimal read markers [4108/4108] (completed) 455s Rank 0: peak number of workers: 599, maximum: 32768 455s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 455s Rank 0: assembler memory usage: 125692 KiB 455s Rank 0: Freeing unused assembler memory: 4096 KiB freed 455s Rank 0: assembler memory usage: 125692 KiB 455s 455s *** 455s Step: Selection of optimal read markers 455s Date: Mon Jul 8 16:08:36 2024 455s Elapsed time: 0 seconds 455s Since beginning: 3 seconds 455s *** 455s 455s 455s Rank 0: memory usage for optimal read markers= 4096 KiB 455s Rank 0 is creating seeds [1/1954] 455s Rank 0: assembler memory usage: 125692 KiB 456s Rank 0 has 1 seeds 456s Rank 0 is creating seeds [1954/1954] (completed) 456s Rank 0: peak number of workers: 746, maximum: 32768 456s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 456s Rank 0 runtime statistics for seeding algorithm: 456s Rank 0 Skipped paths because of dead end for head: 0 456s Rank 0 Skipped paths because of dead end for tail: 0 456s Rank 0 Skipped paths because of two dead ends: 0 456s Rank 0 Skipped paths because of bubble weak component: 0 456s Rank 0 Skipped paths because of short length: 1952 456s Rank 0 Skipped paths because of bad ownership: 1 456s Rank 0 Skipped paths because of low coverage: 0 456s Rank 0 Eligible paths: 1 456s Rank 0: assembler memory usage: 125692 KiB 456s Rank 0 has 1 seeds to register. 456s Rank 0 registered 0/1 456s Rank 0 registered 0/1 456s Rank 0 registered its seeds 456s VirtualProcessor: completed jobs: 0 456s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 456s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 467s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 467s Rank 0 merged its seeds: 1 seeds -> 1 seeds 467s 467s *** 467s Step: Detection of assembly seeds 467s Date: Mon Jul 8 16:08:48 2024 467s Elapsed time: 12 seconds 467s Since beginning: 15 seconds 467s *** 467s 467s 467s Rank 0 is calculating library lengths [1/1] 467s Rank 0 detected 1737 library lengths 467s Rank 0 is calculating library lengths [1/1] (completed) 467s Rank 0: peak number of workers: 1, maximum: 32768 467s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 467s Rank 0: assembler memory usage: 162560 KiB 467s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 467s 467s Mode= 2 signalAverage= 9 467s CURRENT IS NOISE, 244 467s GOT HIT 212 467s 467s 467s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 467s 467s *** 467s Step: Estimation of outer distances for paired reads 467s Date: Mon Jul 8 16:08:48 2024 467s Elapsed time: 0 seconds 467s Since beginning: 15 seconds 467s *** 467s 467s 467s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 467s Rank 0 traversed 1000 nucleotide symbols 467s Rank 0: assembler memory usage: 166656 KiB 467s Rank 0 is extending seeds [1/1] (completed) 467s Rank 0 extended 1 seeds out of 1 (100.00%) 467s Rank 0: assembler memory usage: 158464 KiB 467s Rank 0 starting fusions 467s 467s *** 467s Step: Bidirectional extension of seeds 467s Date: Mon Jul 8 16:08:48 2024 467s Elapsed time: 0 seconds 467s Since beginning: 15 seconds 467s *** 467s 467s 467s Rank 0: starting clear step. cycleNumber= 0 468s Rank 0 adding 0 new fusions 468s Rank 0 cleared, 1 paths 468s Rank 0: starting distribution step 468s Rank 0 is distributing fusions [1/1] 468s Rank 0: assembler memory usage: 158464 KiB 468s Date: Mon Jul 8 16:08:49 2024 468s Rank 0 is distributing fusions [1/1] (completed) 468s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 468s Rank 0: assembler memory usage: 162560 KiB 468s Date: Mon Jul 8 16:08:49 2024 468s Rank 0 tells others to compute fusions. 468s Rank 0 FusionTaskCreator assignNextTask [0/2] 468s Rank 0: assembler memory usage: 162560 KiB 468s Date: Mon Jul 8 16:08:49 2024 468s Rank 0 FusionTaskCreator processWorkerResult [0/2] 468s Rank 0: assembler memory usage: 162560 KiB 468s Date: Mon Jul 8 16:08:49 2024 468s Rank 0 FusionTaskCreator [2/2] 468s Statistics: all paths: 1 eliminated during fusing: 0 468s Rank 0: assembler memory usage: 162560 KiB 468s VirtualProcessor: completed jobs: 2 468s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 468s Rank 0: starting clear step. cycleNumber= 1 469s Rank 0 adding 0 new fusions 469s Rank 0 cleared, 1 paths 469s Rank 0 is distributing fusions [1/1] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 is distributing fusions [1/1] (completed) 469s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 JoinerTaskCreator assignNextTask [0/2] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 JoinerTaskCreator [2/2] 469s Statistics: all paths: 1 eliminated during joining: 0 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s VirtualProcessor: completed jobs: 2 469s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 469s Rank 0 adding 0 new fusions 469s Rank 0 cleared, 1 paths 469s Rank 0: starting distribution step 469s Rank 0 is distributing fusions [1/1] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 is distributing fusions [1/1] (completed) 469s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 tells others to compute fusions. 469s Rank 0 FusionTaskCreator assignNextTask [0/2] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 FusionTaskCreator processWorkerResult [0/2] 469s Rank 0: assembler memory usage: 162560 KiB 469s Date: Mon Jul 8 16:08:50 2024 469s Rank 0 FusionTaskCreator [2/2] 469s Statistics: all paths: 1 eliminated during fusing: 0 469s Rank 0: assembler memory usage: 162560 KiB 469s VirtualProcessor: completed jobs: 2 469s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 469s Rank 0: starting clear step. cycleNumber= 2 470s Rank 0 adding 0 new fusions 470s Rank 0 cleared, 1 paths 470s Rank 0 is distributing fusions [1/1] 470s Rank 0: assembler memory usage: 162560 KiB 470s Date: Mon Jul 8 16:08:51 2024 470s Rank 0 is distributing fusions [1/1] (completed) 470s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 470s Rank 0: assembler memory usage: 162560 KiB 470s Date: Mon Jul 8 16:08:51 2024 470s Rank 0 JoinerTaskCreator assignNextTask [0/2] 470s Rank 0: assembler memory usage: 162560 KiB 470s Date: Mon Jul 8 16:08:51 2024 470s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 470s Rank 0: assembler memory usage: 162560 KiB 470s Date: Mon Jul 8 16:08:51 2024 470s Rank 0 JoinerTaskCreator [2/2] 470s Statistics: all paths: 1 eliminated during joining: 0 470s Rank 0: assembler memory usage: 162560 KiB 470s Date: Mon Jul 8 16:08:51 2024 470s VirtualProcessor: completed jobs: 2 470s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 471s Rank 0 adding 0 new fusions 471s Rank 0 cleared, 1 paths 471s Rank 0: starting distribution step 471s Rank 0 is distributing fusions [1/1] 471s Rank 0: assembler memory usage: 162560 KiB 471s Date: Mon Jul 8 16:08:52 2024 471s Rank 0 is distributing fusions [1/1] (completed) 471s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 471s Rank 0: assembler memory usage: 162560 KiB 471s Date: Mon Jul 8 16:08:52 2024 471s Rank 0 cycleNumber= 2 471s 471s *** 471s Step: Merging of redundant paths 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 4 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s 471s Rank 0 appended 1 elements 471s 471s *** 471s Step: Generation of contigs 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 471s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 471s Rank 0 ineligibleObjects: 0/970 (0.00%) 471s Rank 0: assembler memory usage: 162560 KiB 471s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 471s Rank 0 finished gathering scaffold links. 471s Rank 0 will write 1 contig lengths 471s Rank 0 will solve the scaffolding problem. 471s Welcome to GreedySolver v1.0 471s 1 vertices; 0 edges 471s 1 contigs >= 500 471s Edges in solution: 0 471s 471s Conflict statistics: 471s 1 scaffolds, 1 >= 500 471s Total: 1000 nucleotides 471s 471s *** 471s Step: Scaffolding of contigs 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s Rank 0 syncing with master 471s 471s *** 471s Step: Counting sequences to search 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s 471s Rank 0 will add colors, 0 sequences in 0 files to process 471s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 471s 471s *** 471s Step: Graph coloring 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s 471s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 471s Rank 0 shares its counts 471s Rank 0 computing contig abundances [1/1] [1/970] 471s Rank 0 computing contig abundances [1/1] [970/970] 471s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 471s 471s *** 471s Step: Counting contig biological abundances 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s 471s Rank 0 colored the graph with 0 real colors using 1 virtual colors 471s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 471s 471s *** 471s Step: Counting sequence biological abundances 471s Date: Mon Jul 8 16:08:52 2024 471s Elapsed time: 0 seconds 471s Since beginning: 19 seconds 471s *** 471s 471s 471s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 471s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 472s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 472s 472s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 472s Rank 0 is starting taxon syncing across the compute tribe. 472s 472s *** 472s Step: Loading taxons 472s Date: Mon Jul 8 16:08:53 2024 472s Elapsed time: 1 seconds 472s Since beginning: 20 seconds 472s *** 472s 472s Rank 0 synced taxons across the grid with 1 poor slaves. 472s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 472s Rank 0 has 0 taxons after syncing with master 473s 473s 473s *** 473s Step: Loading tree 473s Date: Mon Jul 8 16:08:54 2024 473s Elapsed time: 1 seconds 473s Since beginning: 21 seconds 473s *** 473s 473s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 473s 473s Rank 0: counting ontology terms in the graph... 474s Rank 0: 0 have some biological signal 474s Number of dereferenced alternate handles: 0 474s Number of k-mer observations with gene ontology terms: 0 474s Rank 0: synced ontology term profiles with master 474s Rank 0: synchronization is complete! 474s Rank 0: ontology terms with biological signal: 0 474s Populated recursive values... 474s Gene ontology terms without depth information: 0 474s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 474s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 474s 474s *** 474s Step: Processing gene ontologies 474s Date: Mon Jul 8 16:08:55 2024 474s Elapsed time: 1 seconds 474s Since beginning: 22 seconds 474s *** 474s 474s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 474s [GenomeNeighbourhood] in final list: 0 474s 474s *** 474s Step: Computing neighbourhoods 474s Date: Mon Jul 8 16:08:55 2024 474s Elapsed time: 0 seconds 474s Since beginning: 22 seconds 474s *** 474s 474s Contigs >= 100 nt 474s Number: 1 474s Total length: 1000 474s Average: 1000 474s N50: 1000 474s Median: 1000 474s Largest: 1000 474s Contigs >= 500 nt 474s Number: 1 474s Total length: 1000 474s Average: 1000 474s N50: 1000 474s Median: 1000 474s Largest: 1000 474s Scaffolds >= 100 nt 474s Number: 1 474s Total length: 1000 474s Average: 1000 474s N50: 1000 474s Median: 1000 474s Largest: 1000 474s Scaffolds >= 500 nt 474s Number: 1 474s Total length: 1000 474s Average: 1000 474s N50: 1000 474s Median: 1000 474s Largest: 1000 474s 474s Rank 0 wrote test2/Contigs.fasta 474s Rank 0 wrote test2/Scaffolds.fasta 474s Check for test2/* 474s 474s 477s 477s ************************************************** 477s This program comes with ABSOLUTELY NO WARRANTY. 477s This is free software, and you are welcome to redistribute it 477s under certain conditions; see "LICENSE.txt" for details. 477s ************************************************** 477s 477s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 477s Centre de recherche en infectiologie de l'Université Laval 477s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 477s http://denovoassembler.sf.net/ 477s 477s References to cite: 477s 477s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 477s Ray Meta: scalable de novo metagenome assembly and profiling. 477s Genome Biology (BioMed Central Ltd). 477s 13:R122, Published: 22 December 2012 477s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 477s 477s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 477s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 477s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 477s November 2010, Volume 17, Issue 11, Pages 1519-1533. 477s http://dx.doi.org/doi:10.1089/cmb.2009.0238 477s 477s Ray version 2.3.1 477s License for Ray: GNU General Public License version 3 477s RayPlatform version: 2.0.1 477s License for RayPlatform: GNU Lesser General Public License version 3 477s 477s MAXKMERLENGTH: 32 477s Maximum coverage depth stored by CoverageDepth: 4294967295 477s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 477s FORCE_PACKING = n 477s ASSERT = n 477s HAVE_LIBZ = y 477s HAVE_LIBBZ2 = y 477s PROFILER_COLLECT = n 477s MINIRANKS = y 477s CLOCK_GETTIME = n 477s __linux__ = y 477s _MSC_VER = n 477s __GNUC__ = y 477s RAY_32_BITS = n 477s RAY_64_BITS = y 477s MPI standard version: MPI 3.1 477s MPI library: Open-MPI 4.1.6 477s Compiler: GNU gcc/g++ 13.2.0 477s MPI I/O: n 477s 477s 477s -k (to set the k-mer size) 477s Value: 29 477s 477s 477s Paired library # 0 477s -p (paired-end sequences) 477s Left sequences: SampleDirectory/s_6.first1000_1.fastq 477s Right sequences: SampleDirectory/s_6.first1000_2.fastq 477s Average length: automatic detection 477s Standard deviation: automatic detection 477s 477s Ray command: 477s mpiexec -n 1 Ray \ 477s -k \ 477s 29 \ 477s -desable-recycling \ 477s -p \ 477s SampleDirectory/s_6.first1000_1.fastq \ 477s SampleDirectory/s_6.first1000_2.fastq 477s 477s Rank 0 wrote RayOutput/RayCommand.txt 477s 477s k-mer length: 29 477s Rank 0: assembler memory usage: 41928 KiB 477s Rank 0: assembler memory usage: 107764 KiB 477s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3158 477s Rank 0: testing the network, please wait... 477s 477s Rank 0 is testing the network [0/1000] 477s Rank 0 is testing the network [1000/1000] 477s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 477s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 477s 477s Rank 0 wrote RayOutput/NetworkTest.txt 477s 477s 477s *** 477s Step: Network testing 477s Date: Mon Jul 8 16:08:58 2024 477s Elapsed time: 0 seconds 477s Since beginning: 0 seconds 477s *** 477s 477s 477s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 477s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 477s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 477s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 477s Rank 0 wrote RayOutput/NumberOfSequences.txt 477s Rank 0 wrote RayOutput/SequencePartition.txt 477s 477s *** 477s Step: Counting sequences to assemble 477s Date: Mon Jul 8 16:08:58 2024 477s Elapsed time: 0 seconds 477s Since beginning: 0 seconds 477s *** 477s 477s 477s Rank 0 is loading sequence reads 477s Rank 0 : partition is [0;4107], 4108 sequence reads 477s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 477s Rank 0 has 0 sequence reads 477s Rank 0: assembler memory usage: 120644 KiB 477s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 477s Rank 0 has 4108 sequence reads (completed) 477s 477s *** 477s Step: Sequence loading 477s Date: Mon Jul 8 16:08:58 2024 477s Elapsed time: 0 seconds 477s Since beginning: 0 seconds 477s *** 477s 477s 477s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 477s Rank 0 created its Bloom filter 477s Rank 0 is counting k-mers in sequence reads [1/4108] 477s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 477s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 477s 477s 477s *** 477s Step: K-mer counting 477s Date: Mon Jul 8 16:08:58 2024 477s Elapsed time: 0 seconds 477s Since beginning: 0 seconds 477s *** 477s 477s 477s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 477s Rank 0 destroyed its Bloom filter 477s Rank 0 has 1958 k-mers (completed) 477s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 477s Rank 0: assembler memory usage: 117020 KiB 478s 478s 478s Rank 0: the minimum coverage is 3 478s Rank 0: the peak coverage is 3 478s Warning: no peak observed in the k-mer coverage distribution. 478s to deal with the sequencing error rate, try to lower the k-mer length (-k) 478s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 478s 478s *** 478s Step: Coverage distribution analysis 478s Date: Mon Jul 8 16:08:59 2024 478s Elapsed time: 1 seconds 478s Since beginning: 1 seconds 478s *** 478s 478s 478s 478s Rank 0 is adding edges [1/4108] 478s Rank 0 is adding edges [4108/4108] (completed) 478s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 478s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 478s 478s *** 478s Step: Graph construction 478s Date: Mon Jul 8 16:08:59 2024 478s Elapsed time: 0 seconds 478s Since beginning: 1 seconds 478s *** 478s 478s 478s Rank 0 has 1958 vertices (completed) 478s Rank 0: assembler memory usage: 117020 KiB 479s Rank 0 is purging edges [1/1958] 479s Rank 0 is purging edges [1958/1958] (completed) 479s Rank 0: assembler memory usage: 117548 KiB 479s VirtualProcessor: completed jobs: 1958 479s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 480s Rank 0 wrote RayOutput/degreeDistribution.txt 480s 480s *** 480s Step: Null edge purging 480s Date: Mon Jul 8 16:09:01 2024 480s Elapsed time: 2 seconds 480s Since beginning: 3 seconds 480s *** 480s 480s 480s Rank 0 is selecting optimal read markers [1/4108] 480s Rank 0: assembler memory usage: 117548 KiB 480s Rank 0 is selecting optimal read markers [4108/4108] (completed) 480s Rank 0: peak number of workers: 599, maximum: 32768 480s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 480s Rank 0: assembler memory usage: 125768 KiB 480s Rank 0: Freeing unused assembler memory: 4096 KiB freed 480s Rank 0: assembler memory usage: 125768 KiB 480s 480s *** 480s Step: Selection of optimal read markers 480s Date: Mon Jul 8 16:09:01 2024 480s Elapsed time: 0 seconds 480s Since beginning: 3 seconds 480s *** 480s 480s 480s Rank 0: memory usage for optimal read markers= 4096 KiB 480s Rank 0 is creating seeds [1/1958] 480s Rank 0: assembler memory usage: 125768 KiB 481s Rank 0 has 1 seeds 481s Rank 0 is creating seeds [1958/1958] (completed) 481s Rank 0: peak number of workers: 746, maximum: 32768 481s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 481s Rank 0 runtime statistics for seeding algorithm: 481s Rank 0 Skipped paths because of dead end for head: 0 481s Rank 0 Skipped paths because of dead end for tail: 0 481s Rank 0 Skipped paths because of two dead ends: 0 481s Rank 0 Skipped paths because of bubble weak component: 0 481s Rank 0 Skipped paths because of short length: 1956 481s Rank 0 Skipped paths because of bad ownership: 1 481s Rank 0 Skipped paths because of low coverage: 0 481s Rank 0 Eligible paths: 1 481s Rank 0: assembler memory usage: 125768 KiB 481s Rank 0 has 1 seeds to register. 481s Rank 0 registered 0/1 481s Rank 0 registered 0/1 481s Rank 0 registered its seeds 481s VirtualProcessor: completed jobs: 0 481s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 481s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 491s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 491s Rank 0 merged its seeds: 1 seeds -> 1 seeds 491s 491s *** 491s Step: Detection of assembly seeds 491s Date: Mon Jul 8 16:09:12 2024 491s Elapsed time: 11 seconds 491s Since beginning: 14 seconds 491s *** 491s 491s 491s Rank 0 is calculating library lengths [1/1] 491s Rank 0 detected 1743 library lengths 491s Rank 0 is calculating library lengths [1/1] (completed) 491s Rank 0: peak number of workers: 1, maximum: 32768 491s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 491s Rank 0: assembler memory usage: 162636 KiB 491s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 491s 491s Mode= 2 signalAverage= 10 491s CURRENT IS NOISE, 244 491s GOT HIT 214 491s 491s 491s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 491s 491s *** 491s Step: Estimation of outer distances for paired reads 491s Date: Mon Jul 8 16:09:12 2024 491s Elapsed time: 0 seconds 491s Since beginning: 14 seconds 491s *** 491s 491s 491s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 491s Rank 0 traversed 1000 nucleotide symbols 491s Rank 0: assembler memory usage: 166732 KiB 491s Rank 0 is extending seeds [1/1] (completed) 491s Rank 0 extended 1 seeds out of 1 (100.00%) 491s Rank 0: assembler memory usage: 158540 KiB 491s Rank 0 starting fusions 491s 491s *** 491s Step: Bidirectional extension of seeds 491s Date: Mon Jul 8 16:09:12 2024 491s Elapsed time: 0 seconds 491s Since beginning: 14 seconds 491s *** 491s 491s 491s Rank 0: starting clear step. cycleNumber= 0 492s Rank 0 adding 0 new fusions 492s Rank 0 cleared, 1 paths 492s Rank 0: starting distribution step 492s Rank 0 is distributing fusions [1/1] 492s Rank 0: assembler memory usage: 158540 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 is distributing fusions [1/1] (completed) 492s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 tells others to compute fusions. 492s Rank 0 FusionTaskCreator assignNextTask [0/2] 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 FusionTaskCreator processWorkerResult [0/2] 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 FusionTaskCreator [2/2] 492s Statistics: all paths: 1 eliminated during fusing: 0 492s Rank 0: assembler memory usage: 162636 KiB 492s VirtualProcessor: completed jobs: 2 492s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 492s Rank 0: starting clear step. cycleNumber= 1 492s Rank 0 adding 0 new fusions 492s Rank 0 cleared, 1 paths 492s Rank 0 is distributing fusions [1/1] 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 is distributing fusions [1/1] (completed) 492s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 JoinerTaskCreator assignNextTask [0/2] 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 492s Rank 0: assembler memory usage: 162636 KiB 492s Date: Mon Jul 8 16:09:13 2024 492s Rank 0 JoinerTaskCreator [2/2] 492s Statistics: all paths: 1 eliminated during joining: 0 493s Rank 0: assembler memory usage: 162636 KiB 493s Date: Mon Jul 8 16:09:13 2024 493s VirtualProcessor: completed jobs: 2 493s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 493s Rank 0 adding 0 new fusions 493s Rank 0 cleared, 1 paths 493s Rank 0: starting distribution step 493s Rank 0 is distributing fusions [1/1] 493s Rank 0: assembler memory usage: 162636 KiB 493s Date: Mon Jul 8 16:09:14 2024 493s Rank 0 is distributing fusions [1/1] (completed) 493s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 493s Rank 0: assembler memory usage: 162636 KiB 493s Date: Mon Jul 8 16:09:14 2024 493s Rank 0 tells others to compute fusions. 493s Rank 0 FusionTaskCreator assignNextTask [0/2] 493s Rank 0: assembler memory usage: 162636 KiB 493s Date: Mon Jul 8 16:09:14 2024 493s Rank 0 FusionTaskCreator processWorkerResult [0/2] 493s Rank 0: assembler memory usage: 162636 KiB 493s Date: Mon Jul 8 16:09:14 2024 493s Rank 0 FusionTaskCreator [2/2] 493s Statistics: all paths: 1 eliminated during fusing: 0 493s Rank 0: assembler memory usage: 162636 KiB 493s VirtualProcessor: completed jobs: 2 493s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 493s Rank 0: starting clear step. cycleNumber= 2 494s Rank 0 adding 0 new fusions 494s Rank 0 cleared, 1 paths 494s Rank 0 is distributing fusions [1/1] 494s Rank 0: assembler memory usage: 162636 KiB 494s Date: Mon Jul 8 16:09:15 2024 494s Rank 0 is distributing fusions [1/1] (completed) 494s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 494s Rank 0: assembler memory usage: 162636 KiB 494s Date: Mon Jul 8 16:09:15 2024 494s Rank 0 JoinerTaskCreator assignNextTask [0/2] 494s Rank 0: assembler memory usage: 162636 KiB 494s Date: Mon Jul 8 16:09:15 2024 494s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 494s Rank 0: assembler memory usage: 162636 KiB 494s Date: Mon Jul 8 16:09:15 2024 494s Rank 0 JoinerTaskCreator [2/2] 494s Statistics: all paths: 1 eliminated during joining: 0 494s Rank 0: assembler memory usage: 162636 KiB 494s Date: Mon Jul 8 16:09:15 2024 494s VirtualProcessor: completed jobs: 2 494s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 495s Rank 0 adding 0 new fusions 495s Rank 0 cleared, 1 paths 495s Rank 0: starting distribution step 495s Rank 0 is distributing fusions [1/1] 495s Rank 0: assembler memory usage: 162636 KiB 495s Date: Mon Jul 8 16:09:15 2024 495s Rank 0 is distributing fusions [1/1] (completed) 495s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 495s Rank 0: assembler memory usage: 162636 KiB 495s Date: Mon Jul 8 16:09:15 2024 495s Rank 0 cycleNumber= 2 495s 495s *** 495s Step: Merging of redundant paths 495s Date: Mon Jul 8 16:09:15 2024 495s Elapsed time: 3 seconds 495s Since beginning: 17 seconds 495s *** 495s 495s 495s Rank 0 appended 1 elements 495s 495s *** 495s Step: Generation of contigs 495s Date: Mon Jul 8 16:09:15 2024 495s Elapsed time: 0 seconds 495s Since beginning: 17 seconds 495s *** 495s 495s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 495s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 495s Rank 0 ineligibleObjects: 0/972 (0.00%) 495s Rank 0: assembler memory usage: 162636 KiB 495s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 495s Rank 0 finished gathering scaffold links. 495s Rank 0 will write 1 contig lengths 495s Rank 0 will solve the scaffolding problem. 495s Welcome to GreedySolver v1.0 495s 1 vertices; 0 edges 495s 1 contigs >= 500 495s Edges in solution: 0 495s 495s Conflict statistics: 495s 1 scaffolds, 1 >= 500 495s Total: 1000 nucleotides 495s 495s *** 495s Step: Scaffolding of contigs 495s Date: Mon Jul 8 16:09:16 2024 495s Elapsed time: 1 seconds 495s Since beginning: 18 seconds 495s *** 495s 495s Rank 0 syncing with master 495s 495s *** 495s Step: Counting sequences to search 495s Date: Mon Jul 8 16:09:16 2024 495s Elapsed time: 0 seconds 495s Since beginning: 18 seconds 495s *** 495s 495s 495s Rank 0 will add colors, 0 sequences in 0 files to process 495s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 495s 495s *** 495s Step: Graph coloring 495s Date: Mon Jul 8 16:09:16 2024 495s Elapsed time: 0 seconds 495s Since beginning: 18 seconds 495s *** 495s 495s 495s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 495s Rank 0 shares its counts 495s Rank 0 computing contig abundances [1/1] [1/972] 495s Rank 0 computing contig abundances [1/1] [972/972] 495s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 495s 495s *** 495s Step: Counting contig biological abundances 495s Date: Mon Jul 8 16:09:16 2024 495s Elapsed time: 0 seconds 495s Since beginning: 18 seconds 495s *** 495s 495s 495s Rank 0 colored the graph with 0 real colors using 1 virtual colors 495s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 495s 495s *** 495s Step: Counting sequence biological abundances 495s Date: Mon Jul 8 16:09:16 2024 495s Elapsed time: 0 seconds 495s Since beginning: 18 seconds 495s *** 495s 495s 495s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 495s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 496s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 496s 496s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 496s Rank 0 is starting taxon syncing across the compute tribe. 496s 496s *** 496s Step: Loading taxons 496s Date: Mon Jul 8 16:09:17 2024 496s Elapsed time: 1 seconds 496s Since beginning: 19 seconds 496s *** 496s 496s Rank 0 synced taxons across the grid with 1 poor slaves. 496s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 496s Rank 0 has 0 taxons after syncing with master 497s 497s 497s *** 497s Step: Loading tree 497s Date: Mon Jul 8 16:09:18 2024 497s Elapsed time: 1 seconds 497s Since beginning: 20 seconds 497s *** 497s 497s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 497s 497s Rank 0: counting ontology terms in the graph... 498s Rank 0: 0 have some biological signal 498s Number of dereferenced alternate handles: 0 498s Number of k-mer observations with gene ontology terms: 0 498s Rank 0: synced ontology term profiles with master 498s Rank 0: synchronization is complete! 498s Rank 0: ontology terms with biological signal: 0 498s Populated recursive values... 498s Gene ontology terms without depth information: 0 498s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 498s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 498s 498s *** 498s Step: Processing gene ontologies 498s Date: Mon Jul 8 16:09:19 2024 498s Elapsed time: 1 seconds 498s Since beginning: 21 seconds 498s *** 498s 498s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 498s [GenomeNeighbourhood] in final list: 0 498s 498s *** 498s Step: Computing neighbourhoods 498s Date: Mon Jul 8 16:09:19 2024 498s Elapsed time: 0 seconds 498s Since beginning: 21 seconds 498s *** 498s 498s Contigs >= 100 nt 498s Number: 1 498s Total length: 1000 498s Average: 1000 498s N50: 1000 498s Median: 1000 498s Largest: 1000 498s Contigs >= 500 nt 498s Number: 1 498s Total length: 1000 498s Average: 1000 498s N50: 1000 498s Median: 1000 498s Largest: 1000 498s Scaffolds >= 100 nt 498s Number: 1 498s Total length: 1000 498s Average: 1000 498s N50: 1000 498s Median: 1000 498s Largest: 1000 498s Scaffolds >= 500 nt 498s Number: 1 498s Total length: 1000 498s Average: 1000 498s N50: 1000 498s Median: 1000 498s Largest: 1000 498s 498s Rank 0 wrote RayOutput/Contigs.fasta 498s Rank 0 wrote RayOutput/Scaffolds.fasta 498s Check for RayOutput/* 498s 498s 501s 501s ************************************************** 501s This program comes with ABSOLUTELY NO WARRANTY. 501s This is free software, and you are welcome to redistribute it 501s under certain conditions; see "LICENSE.txt" for details. 501s ************************************************** 501s 501s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 501s Centre de recherche en infectiologie de l'Université Laval 501s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 501s http://denovoassembler.sf.net/ 501s 501s References to cite: 501s 501s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 501s Ray Meta: scalable de novo metagenome assembly and profiling. 501s Genome Biology (BioMed Central Ltd). 501s 13:R122, Published: 22 December 2012 501s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 501s 501s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 501s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 501s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 501s November 2010, Volume 17, Issue 11, Pages 1519-1533. 501s http://dx.doi.org/doi:10.1089/cmb.2009.0238 501s 501s Ray version 2.3.1 501s License for Ray: GNU General Public License version 3 501s RayPlatform version: 2.0.1 501s License for RayPlatform: GNU Lesser General Public License version 3 501s 501s MAXKMERLENGTH: 32 501s Maximum coverage depth stored by CoverageDepth: 4294967295 501s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 501s FORCE_PACKING = n 501s ASSERT = n 501s HAVE_LIBZ = y 501s HAVE_LIBBZ2 = y 501s PROFILER_COLLECT = n 501s MINIRANKS = y 501s CLOCK_GETTIME = n 501s __linux__ = y 501s _MSC_VER = n 501s __GNUC__ = y 501s RAY_32_BITS = n 501s RAY_64_BITS = y 501s MPI standard version: MPI 3.1 501s MPI library: Open-MPI 4.1.6 501s Compiler: GNU gcc/g++ 13.2.0 501s MPI I/O: n 501s 501s 501s -k (to set the k-mer size) 501s Value: 31 501s 501s 501s Paired library # 0 501s -p (paired-end sequences) 501s Left sequences: ecoli_1K_1.fq 501s Right sequences: ecoli_1K_2.fq 501s Average length: automatic detection 501s Standard deviation: automatic detection 501s 501s Ray command: 501s mpiexec -n 2 Ray \ 501s -k \ 501s 31 \ 501s -p \ 501s ecoli_1K_1.fq \ 501s ecoli_1K_2.fq \ 501s -o \ 501s test3 501s 501s Rank 0 wrote test3/RayCommand.txt 501s 501s k-mer length: 31 501s Rank 1: assembler memory usage: 41924 KiB 501s Rank 0: assembler memory usage: 41920 KiB 501s Rank 0: assembler memory usage: 107768 KiB 501s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 3170 501s Rank 0: testing the network, please wait... 501s 501s Rank 1: assembler memory usage: 107760 KiB 501s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 3171 501s Rank 1 is testing the network [0/1000] 501s Rank 0 is testing the network [0/1000] 501s Rank 1 is testing the network [1000/1000] 501s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 501s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 501s Rank 0 is testing the network [1000/1000] 501s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 501s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 501s 501s Rank 0 wrote test3/NetworkTest.txt 501s 501s 501s *** 501s Step: Network testing 501s Date: Mon Jul 8 16:09:22 2024 501s Elapsed time: 0 seconds 501s Since beginning: 0 seconds 501s *** 501s 501s 501s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 501s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 501s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 501s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 501s Rank 0 wrote test3/NumberOfSequences.txt 501s Rank 0 wrote test3/SequencePartition.txt 501s 501s *** 501s Step: Counting sequences to assemble 501s Date: Mon Jul 8 16:09:22 2024 501s Elapsed time: 0 seconds 501s Since beginning: 0 seconds 501s *** 501s 501s 501s Rank 1 is loading sequence reads 501s Rank 0 is loading sequence reads 501s Rank 0 : partition is [0;2053], 2054 sequence reads 501s Rank 1 : partition is [2054;4107], 2054 sequence reads 501s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 501s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 501s Rank 0 has 0 sequence reads 501s Rank 0: assembler memory usage: 116560 KiB 501s Rank 1 has 0 sequence reads 501s Rank 1: assembler memory usage: 116540 KiB 501s Rank 0 has 2054 sequence reads (completed) 501s Rank 1 has 2054 sequence reads (completed) 501s 501s *** 501s Step: Sequence loading 501s Date: Mon Jul 8 16:09:22 2024 501s Elapsed time: 0 seconds 501s Since beginning: 0 seconds 501s *** 501s 501s 501s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 501s Rank 0 created its Bloom filter 501s Rank 0 is counting k-mers in sequence reads [1/2054] 501s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 501s Rank 1 created its Bloom filter 501s Rank 1 is counting k-mers in sequence reads [1/2054] 501s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 501s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 501s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 501s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 501s 501s 501s *** 501s Step: K-mer counting 501s Date: Mon Jul 8 16:09:22 2024 501s Elapsed time: 0 seconds 501s Since beginning: 0 seconds 501s *** 501s 501s 501s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 501s Rank 0 destroyed its Bloom filter 501s Rank 0 has 1032 k-mers (completed) 501s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 501s Rank 0: assembler memory usage: 112828 KiB 501s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 501s Rank 1 destroyed its Bloom filter 501s Rank 1 has 922 k-mers (completed) 501s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 501s Rank 1: assembler memory usage: 116540 KiB 502s 502s 502s Rank 0: the minimum coverage is 3 502s Rank 0: the peak coverage is 3 502s Warning: no peak observed in the k-mer coverage distribution. 502s to deal with the sequencing error rate, try to lower the k-mer length (-k) 502s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 502s 502s *** 502s Step: Coverage distribution analysis 502s Date: Mon Jul 8 16:09:23 2024 502s Elapsed time: 1 seconds 502s Since beginning: 1 seconds 502s *** 502s 502s 502s 502s Rank 0 is adding edges [1/2054] 502s Rank 1 is adding edges [1/2054] 502s Rank 1 is adding edges [2054/2054] (completed) 502s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 502s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 502s Rank 0 is adding edges [2054/2054] (completed) 502s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 502s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 502s 502s *** 502s Step: Graph construction 502s Date: Mon Jul 8 16:09:23 2024 502s Elapsed time: 0 seconds 502s Since beginning: 1 seconds 502s *** 502s 502s 502s Rank 0 has 1032 vertices (completed) 502s Rank 0: assembler memory usage: 112828 KiB 502s Rank 1 has 922 vertices (completed) 502s Rank 1: assembler memory usage: 116540 KiB 502s Rank 0 is purging edges [1/1032] 502s Rank 1 is purging edges [1/922] 502s Rank 0 is purging edges [1032/1032] (completed) 502s Rank 0: assembler memory usage: 113096 KiB 502s VirtualProcessor: completed jobs: 1032 502s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 502s Rank 1 is purging edges [922/922] (completed) 502s Rank 1: assembler memory usage: 116540 KiB 502s VirtualProcessor: completed jobs: 922 502s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 503s Rank 0 wrote test3/degreeDistribution.txt 503s 503s *** 503s Step: Null edge purging 503s Date: Mon Jul 8 16:09:24 2024 503s Elapsed time: 1 seconds 503s Since beginning: 2 seconds 503s *** 503s 503s 503s Rank 1 is selecting optimal read markers [1/2054] 503s Rank 1: assembler memory usage: 116540 KiB 503s Rank 0 is selecting optimal read markers [1/2054] 503s Rank 0: assembler memory usage: 113096 KiB 503s Rank 1 is selecting optimal read markers [2054/2054] (completed) 503s Rank 1: peak number of workers: 1121, maximum: 32768 503s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 503s Rank 1: assembler memory usage: 124220 KiB 503s Rank 1: Freeing unused assembler memory: 4096 KiB freed 503s Rank 1: assembler memory usage: 124220 KiB 503s Rank 0 is selecting optimal read markers [2054/2054] (completed) 503s Rank 0: peak number of workers: 1135, maximum: 32768 503s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 503s Rank 0: assembler memory usage: 121300 KiB 503s Rank 0: Freeing unused assembler memory: 4096 KiB freed 503s Rank 0: assembler memory usage: 121300 KiB 503s 503s *** 503s Step: Selection of optimal read markers 503s Date: Mon Jul 8 16:09:24 2024 503s Elapsed time: 0 seconds 503s Since beginning: 2 seconds 503s *** 503s 503s 503s Rank 0: memory usage for optimal read markers= 4096 KiB 503s Rank 1: memory usage for optimal read markers= 4096 KiB 503s Rank 1 is creating seeds [1/922] 503s Rank 1: assembler memory usage: 124220 KiB 503s Rank 0 is creating seeds [1/1032] 503s Rank 0: assembler memory usage: 121300 KiB 504s Rank 1 has 1 seeds 504s Rank 1 is creating seeds [922/922] (completed) 504s Rank 1: peak number of workers: 916, maximum: 32768 504s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 504s Rank 1 runtime statistics for seeding algorithm: 504s Rank 1 Skipped paths because of dead end for head: 0 504s Rank 1 Skipped paths because of dead end for tail: 0 504s Rank 1 Skipped paths because of two dead ends: 0 504s Rank 1 Skipped paths because of bubble weak component: 0 504s Rank 1 Skipped paths because of short length: 921 504s Rank 1 Skipped paths because of bad ownership: 0 504s Rank 1 Skipped paths because of low coverage: 0 504s Rank 1 Eligible paths: 1 504s Rank 1: assembler memory usage: 124220 KiB 504s Rank 0 has 0 seeds 504s Rank 0 is creating seeds [1032/1032] (completed) 504s Rank 0: peak number of workers: 998, maximum: 32768 504s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 504s Rank 0 runtime statistics for seeding algorithm: 504s Rank 0 Skipped paths because of dead end for head: 0 504s Rank 0 Skipped paths because of dead end for tail: 0 504s Rank 0 Skipped paths because of two dead ends: 0 504s Rank 0 Skipped paths because of bubble weak component: 0 504s Rank 0 Skipped paths because of short length: 1031 504s Rank 0 Skipped paths because of bad ownership: 1 504s Rank 0 Skipped paths because of low coverage: 0 504s Rank 0 Eligible paths: 0 504s Rank 0: assembler memory usage: 121300 KiB 504s Rank 0 registered -1/0 504s Rank 0 registered its seeds 504s Rank 1 has 1 seeds to register. 504s Rank 1 registered 0/1 504s Rank 1 registered 0/1 504s VirtualProcessor: completed jobs: 0 504s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 504s Rank 1 registered its seeds 504s VirtualProcessor: completed jobs: 0 504s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 506s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 506s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 515s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 515s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 515s Rank 0 merged its seeds: 0 seeds -> 0 seeds 515s Rank 1 merged its seeds: 1 seeds -> 1 seeds 515s 515s *** 515s Step: Detection of assembly seeds 515s Date: Mon Jul 8 16:09:36 2024 515s Elapsed time: 12 seconds 515s Since beginning: 14 seconds 515s *** 515s 515s 515s Rank 0 detected 0 library lengths 515s Rank 0 is calculating library lengths [0/0] (completed) 515s Rank 0: peak number of workers: 0, maximum: 32768 515s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 515s Rank 0: assembler memory usage: 125396 KiB 515s Rank 1 is calculating library lengths [1/1] 515s Rank 1 detected 1737 library lengths 515s Rank 1 is calculating library lengths [1/1] (completed) 515s Rank 1: peak number of workers: 1, maximum: 32768 515s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7985 virtual messages generated 7985 real messages (100%) 515s Rank 1: assembler memory usage: 156992 KiB 515s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 515s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 515s 515s Mode= 2 signalAverage= 9 515s CURRENT IS NOISE, 244 515s GOT HIT 212 515s 515s 515s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 515s 515s *** 515s Step: Estimation of outer distances for paired reads 515s Date: Mon Jul 8 16:09:36 2024 515s Elapsed time: 0 seconds 515s Since beginning: 14 seconds 515s *** 515s 515s 515s Rank 0 is extending seeds [0/0] (completed) 515s Rank 0 extended 0 seeds out of 0 (0.00%) 515s Rank 0: assembler memory usage: 125396 KiB 515s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 515s Rank 1 traversed 1000 nucleotide symbols 515s Rank 1: assembler memory usage: 161088 KiB 515s Rank 1 is extending seeds [1/1] (completed) 515s Rank 1 extended 1 seeds out of 1 (100.00%) 515s Rank 1: assembler memory usage: 161088 KiB 515s Rank 0 starting fusions 515s 515s *** 515s Step: Bidirectional extension of seeds 515s Date: Mon Jul 8 16:09:36 2024 515s Elapsed time: 0 seconds 515s Since beginning: 14 seconds 515s *** 515s 515s 515s Rank 0: starting clear step. cycleNumber= 0 516s Rank 1 adding 0 new fusions 516s Rank 1 cleared, 1 paths 516s Rank 0 adding 0 new fusions 516s Rank 0 cleared, 0 paths 516s Rank 0: starting distribution step 516s Rank 0 is distributing fusions [0/0] (completed) 516s Rank 1 is distributing fusions [1/1] 516s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 516s Rank 1: assembler memory usage: 161088 KiB 516s Rank 0: assembler memory usage: 125396 KiB 516s Date: Mon Jul 8 16:09:37 2024 516s Date: Mon Jul 8 16:09:37 2024 516s Rank 1 is distributing fusions [1/1] (completed) 516s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 516s Rank 1: assembler memory usage: 161088 KiB 516s Date: Mon Jul 8 16:09:37 2024 516s Rank 0 tells others to compute fusions. 516s Rank 1 FusionTaskCreator assignNextTask [0/2] 516s Rank 0 FusionTaskCreator [0/0] 516s Rank 1: assembler memory usage: 161088 KiB 516s Date: Mon Jul 8 16:09:37 2024 516s Statistics: all paths: 0 eliminated during fusing: 0 516s Rank 0: assembler memory usage: 125396 KiB 516s VirtualProcessor: completed jobs: 0 516s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 516s Rank 1 FusionTaskCreator processWorkerResult [0/2] 516s Rank 1: assembler memory usage: 161088 KiB 516s Date: Mon Jul 8 16:09:37 2024 516s Rank 1 FusionTaskCreator [2/2] 516s Statistics: all paths: 1 eliminated during fusing: 0 516s Rank 1: assembler memory usage: 161088 KiB 516s VirtualProcessor: completed jobs: 2 516s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10895 virtual messages generated 10895 real messages (100%) 516s Rank 0: starting clear step. cycleNumber= 1 517s Rank 1 adding 0 new fusions 517s Rank 1 cleared, 1 paths 517s Rank 0 adding 0 new fusions 517s Rank 0 cleared, 0 paths 517s Rank 1 is distributing fusions [1/1] 517s Rank 0 is distributing fusions [0/0] (completed) 517s Rank 1: assembler memory usage: 161088 KiB 517s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 517s Rank 0: assembler memory usage: 125396 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 is distributing fusions [1/1] (completed) 517s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 517s Rank 1: assembler memory usage: 161088 KiB 517s Rank 0 JoinerTaskCreator [0/0] 517s Statistics: all paths: 0 eliminated during joining: 0 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 JoinerTaskCreator assignNextTask [0/2] 517s Rank 0: assembler memory usage: 125396 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1: assembler memory usage: 161088 KiB 517s VirtualProcessor: completed jobs: 0 517s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 517s Rank 1: assembler memory usage: 161088 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 JoinerTaskCreator [2/2] 517s Statistics: all paths: 1 eliminated during joining: 0 517s Rank 1: assembler memory usage: 161088 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s VirtualProcessor: completed jobs: 2 517s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13805 virtual messages generated 13805 real messages (100%) 517s Rank 0 adding 0 new fusions 517s Rank 0 cleared, 0 paths 517s Rank 1 adding 0 new fusions 517s Rank 1 cleared, 1 paths 517s Rank 0: starting distribution step 517s Rank 0 is distributing fusions [0/0] (completed) 517s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 517s Rank 0: assembler memory usage: 125396 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 is distributing fusions [1/1] 517s Rank 1: assembler memory usage: 161088 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 is distributing fusions [1/1] (completed) 517s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 517s Rank 1: assembler memory usage: 161088 KiB 517s Rank 0 tells others to compute fusions. 517s Rank 0 FusionTaskCreator [0/0] 517s Statistics: all paths: 0 eliminated during fusing: 0 517s Rank 0: assembler memory usage: 125396 KiB 517s VirtualProcessor: completed jobs: 0 517s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 FusionTaskCreator assignNextTask [0/2] 517s Rank 1: assembler memory usage: 161088 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 FusionTaskCreator processWorkerResult [0/2] 517s Rank 1: assembler memory usage: 161088 KiB 517s Date: Mon Jul 8 16:09:38 2024 517s Rank 1 FusionTaskCreator [2/2] 517s Statistics: all paths: 1 eliminated during fusing: 0 517s Rank 1: assembler memory usage: 161088 KiB 517s VirtualProcessor: completed jobs: 2 517s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16715 virtual messages generated 16715 real messages (100%) 517s Rank 0: starting clear step. cycleNumber= 2 518s Rank 0 adding 0 new fusions 518s Rank 0 cleared, 0 paths 518s Rank 0 is distributing fusions [0/0] (completed) 518s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 518s Rank 0: assembler memory usage: 125396 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s Rank 0 JoinerTaskCreator [0/0] 518s Statistics: all paths: 0 eliminated during joining: 0 518s Rank 0: assembler memory usage: 125396 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s VirtualProcessor: completed jobs: 0 518s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 518s Rank 1 adding 0 new fusions 518s Rank 1 cleared, 1 paths 518s Rank 1 is distributing fusions [1/1] 518s Rank 1: assembler memory usage: 161088 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s Rank 1 is distributing fusions [1/1] (completed) 518s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 518s Rank 1: assembler memory usage: 161088 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s Rank 1 JoinerTaskCreator assignNextTask [0/2] 518s Rank 1: assembler memory usage: 161088 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 518s Rank 1: assembler memory usage: 161088 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s Rank 1 JoinerTaskCreator [2/2] 518s Statistics: all paths: 1 eliminated during joining: 0 518s Rank 1: assembler memory usage: 161088 KiB 518s Date: Mon Jul 8 16:09:39 2024 518s VirtualProcessor: completed jobs: 2 518s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19625 virtual messages generated 19625 real messages (100%) 519s Rank 0 adding 0 new fusions 519s Rank 0 cleared, 0 paths 519s Rank 1 adding 0 new fusions 519s Rank 1 cleared, 1 paths 519s Rank 0: starting distribution step 519s Rank 0 is distributing fusions [0/0] (completed) 519s Rank 1 is distributing fusions [1/1] 519s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 519s Rank 1: assembler memory usage: 161088 KiB 519s Date: Mon Jul 8 16:09:40 2024 519s Rank 0: assembler memory usage: 125396 KiB 519s Date: Mon Jul 8 16:09:40 2024 519s Rank 1 is distributing fusions [1/1] (completed) 519s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 519s Rank 1: assembler memory usage: 161088 KiB 519s Date: Mon Jul 8 16:09:40 2024 519s Rank 0 cycleNumber= 2 519s 519s *** 519s Step: Merging of redundant paths 519s Date: Mon Jul 8 16:09:40 2024 519s Elapsed time: 4 seconds 519s Since beginning: 18 seconds 519s *** 519s 519s 519s Rank 0 appended 0 elements 519s Rank 1 appended 1 elements 519s 519s *** 519s Step: Generation of contigs 519s Date: Mon Jul 8 16:09:40 2024 519s Elapsed time: 0 seconds 519s Since beginning: 18 seconds 519s *** 519s 519s Rank 0 finished gathering scaffold links. 519s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 519s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 519s Rank 0 ineligibleObjects: 0/970 (0.00%) 519s Rank 1: assembler memory usage: 161088 KiB 519s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 519s Rank 1 finished gathering scaffold links. 519s Rank 0 will write 1 contig lengths 519s Rank 0 will solve the scaffolding problem. 519s Welcome to GreedySolver v1.0 519s 1 vertices; 0 edges 519s 1 contigs >= 500 519s Edges in solution: 0 519s 519s Conflict statistics: 519s 1 scaffolds, 1 >= 500 519s Total: 1000 nucleotides 519s 519s *** 519s Step: Scaffolding of contigs 519s Date: Mon Jul 8 16:09:40 2024 519s Elapsed time: 0 seconds 519s Since beginning: 18 seconds 519s *** 519s 519s Rank 0 syncing with master 519s 519s Rank 1 syncing with master 519s *** 519s Step: Counting sequences to search 519s Date: Mon Jul 8 16:09:40 2024 519s Elapsed time: 0 seconds 519s Since beginning: 18 seconds 519s *** 519s 519s 519s Rank 1 will add colors, 0 sequences in 0 files to process 519s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 519s Rank 0 will add colors, 0 sequences in 0 files to process 519s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 520s 520s *** 520s Step: Graph coloring 520s Date: Mon Jul 8 16:09:40 2024 520s Elapsed time: 0 seconds 520s Since beginning: 18 seconds 520s *** 520s 520s 520s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 520s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 520s Rank 0 shares its counts 520s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 520s Rank 1 computing contig abundances [1/1] [1/970] 520s Rank 1 computing contig abundances [1/1] [970/970] 520s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 520s 520s *** 520s Step: Counting contig biological abundances 520s Date: Mon Jul 8 16:09:40 2024 520s Elapsed time: 0 seconds 520s Since beginning: 18 seconds 520s *** 520s 520s 520s Rank 1 colored the graph with 0 real colors using 1 virtual colors 520s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 520s Rank 0 colored the graph with 0 real colors using 1 virtual colors 520s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 520s 520s *** 520s Step: Counting sequence biological abundances 520s Date: Mon Jul 8 16:09:40 2024 520s Elapsed time: 0 seconds 520s Since beginning: 18 seconds 520s *** 520s 520s 520s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 520s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 520s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 520s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 520s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 520s 520s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 520s 520s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 520s Rank 0 is starting taxon syncing across the compute tribe. 520s 520s *** 520s Step: Loading taxons 520s Date: Mon Jul 8 16:09:41 2024 520s Elapsed time: 1 seconds 520s Since beginning: 19 seconds 520s *** 520s 520s Rank 0 synced taxons across the grid with 2 poor slaves. 520s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 520s Rank 1 has 0 taxons after syncing with master 520s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 520s Rank 0 has 0 taxons after syncing with master 521s 521s 521s 521s *** 521s Step: Loading tree 521s Date: Mon Jul 8 16:09:42 2024 521s Elapsed time: 1 seconds 521s Since beginning: 20 seconds 521s *** 521s 521s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 521s 521s Rank 1: counting ontology terms in the graph... 521s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 521s 521s Rank 0: counting ontology terms in the graph... 522s Rank 0: 0 have some biological signal 522s Number of dereferenced alternate handles: 0 522s Number of k-mer observations with gene ontology terms: 0 522s Rank 0: synced ontology term profiles with master 522s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 522s Rank 0: synchronization is complete! 522s Rank 0: ontology terms with biological signal: 0 522s Populated recursive values... 522s Gene ontology terms without depth information: 0 522s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 522s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 522s 522s *** 522s Step: Processing gene ontologies 522s Date: Mon Jul 8 16:09:43 2024 522s Elapsed time: 1 seconds 522s Since beginning: 21 seconds 522s *** 522s 522s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 522s [GenomeNeighbourhood] in final list: 0 522s 522s *** 522s Step: Computing neighbourhoods 522s Date: Mon Jul 8 16:09:43 2024 522s Elapsed time: 0 seconds 522s Since beginning: 21 seconds 522s *** 522s 522s Contigs >= 100 nt 522s Number: 1 522s Total length: 1000 522s Average: 1000 522s N50: 1000 522s Median: 1000 522s Largest: 1000 522s Contigs >= 500 nt 522s Number: 1 522s Total length: 1000 522s Average: 1000 522s N50: 1000 522s Median: 1000 522s Largest: 1000 522s Scaffolds >= 100 nt 522s Number: 1 522s Total length: 1000 522s Average: 1000 522s N50: 1000 522s Median: 1000 522s Largest: 1000 522s Scaffolds >= 500 nt 522s Number: 1 522s Total length: 1000 522s Average: 1000 522s N50: 1000 522s Median: 1000 522s Largest: 1000 522s 522s Rank 0 wrote test3/Contigs.fasta 522s Rank 0 wrote test3/Scaffolds.fasta 522s Check for test3/* 522s 522s 522s Rank 1: 0 have some biological signal 522s Number of dereferenced alternate handles: 0 522s Number of k-mer observations with gene ontology terms: 0 522s Rank 1: synced ontology term profiles with master 522s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 526s autopkgtest [16:09:47]: test run-unit-test: -----------------------] 527s run-unit-test PASS 527s autopkgtest [16:09:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 529s autopkgtest [16:09:50]: @@@@@@@@@@@@@@@@@@@@ summary 529s run-unit-test PASS 633s nova [W] Skipping flock in bos03-arm64 633s Creating nova instance adt-oracular-arm64-ray-20240708-160100-juju-7f2275-prod-proposed-migration-environment-2-8428d008-8138-45d1-bbb7-3e9f2f6022af from image adt/ubuntu-oracular-arm64-server-20240708.img (UUID 84b7272a-8ade-4c46-a865-17c686a9cf9b)...