0s autopkgtest [15:31:25]: starting date and time: 2024-07-08 15:31:25+0000 0s autopkgtest [15:31:25]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [15:31:25]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jmsi_ftp/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-3@lcy02-37.secgroup --name adt-oracular-amd64-ray-20240708-153106-juju-7f2275-prod-proposed-migration-environment-3-cb8fbdba-0af6-4ed0-b577-f5faefe907b5 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 122s autopkgtest [15:33:27]: testbed dpkg architecture: amd64 126s autopkgtest [15:33:31]: testbed apt version: 2.9.6 126s autopkgtest [15:33:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 129s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 129s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [360 kB] 129s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 129s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3336 B] 129s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [107 kB] 129s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [78.4 kB] 129s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2592 B] 129s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 129s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 129s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 129s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [219 kB] 129s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [381 kB] 129s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9628 B] 129s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 129s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 129s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 129s Fetched 1398 kB in 0s (4673 kB/s) 129s Reading package lists... 145s Reading package lists... 146s Building dependency tree... 146s Reading state information... 148s Calculating upgrade... 148s The following packages will be upgraded: 148s libnetplan1 netplan-generator netplan.io python3-netplan 148s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 274 kB of archives. 148s After this operation, 1024 B of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 netplan-generator amd64 1.0.1-1ubuntu2 [59.5 kB] 148s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-netplan amd64 1.0.1-1ubuntu2 [22.6 kB] 148s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 netplan.io amd64 1.0.1-1ubuntu2 [66.2 kB] 148s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libnetplan1 amd64 1.0.1-1ubuntu2 [125 kB] 148s Fetched 274 kB in 0s (4024 kB/s) 148s (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 ... 74466 files and directories currently installed.) 148s Preparing to unpack .../netplan-generator_1.0.1-1ubuntu2_amd64.deb ... 148s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 148s Unpacking netplan-generator (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 148s Preparing to unpack .../python3-netplan_1.0.1-1ubuntu2_amd64.deb ... 148s Unpacking python3-netplan (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 148s Preparing to unpack .../netplan.io_1.0.1-1ubuntu2_amd64.deb ... 148s Unpacking netplan.io (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 148s Preparing to unpack .../libnetplan1_1.0.1-1ubuntu2_amd64.deb ... 148s Unpacking libnetplan1:amd64 (1.0.1-1ubuntu2) over (1.0.1-1ubuntu1) ... 148s Setting up libnetplan1:amd64 (1.0.1-1ubuntu2) ... 148s Setting up python3-netplan (1.0.1-1ubuntu2) ... 148s Setting up netplan-generator (1.0.1-1ubuntu2) ... 148s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 148s Setting up netplan.io (1.0.1-1ubuntu2) ... 148s Processing triggers for libc-bin (2.39-0ubuntu9) ... 148s Processing triggers for man-db (2.12.1-2) ... 148s Processing triggers for dbus (1.14.10-4ubuntu4) ... 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 149s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 151s Reading package lists... 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Calculating upgrade... 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s autopkgtest [15:34:32]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 187s autopkgtest [15:34:32]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 215s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (dsc) [2192 B] 215s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (tar) [450 kB] 215s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (diff) [213 kB] 215s gpgv: Signature made Mon Apr 1 07:35:01 2024 UTC 215s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 215s gpgv: Can't check signature: No public key 215s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8build2.dsc: no acceptable signature found 215s autopkgtest [15:35:00]: testing package ray version 2.3.1-8build2 215s autopkgtest [15:35:00]: build not needed 223s autopkgtest [15:35:08]: test run-unit-test: preparing testbed 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 233s Starting pkgProblemResolver with broken count: 0 233s Starting 2 pkgProblemResolver with broken count: 0 233s Done 234s The following additional packages will be installed: 234s fontconfig libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libcairo2 234s libdatrie1 libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 234s libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 234s libhwloc-plugins libhwloc15 libice6 liblapack3 libllvm17t64 libmunge2 234s libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 234s libpaper-utils libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 234s libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsm6 libtcl8.6 libthai-data 234s libthai0 libtk8.6 libucx0 libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 234s libxrender1 libxss1 libxt6t64 mpi-default-bin ocl-icd-libopencl1 openmpi-bin 234s openmpi-common r-base-core ray ray-doc ray-extra unzip x11-common xdg-utils 234s zip 234s Suggested packages: 234s libhwloc-contrib-plugins tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler 234s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 234s Recommended packages: 234s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 234s libx11-protocol-perl x11-utils x11-xserver-utils 234s The following NEW packages will be installed: 234s autopkgtest-satdep fontconfig libamd-comgr2 libamdhip64-5 libatomic1 234s libblas3 libcairo2 libdatrie1 libdrm-amdgpu1 libevent-pthreads-2.1-7t64 234s libfabric1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 234s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libice6 liblapack3 234s libllvm17t64 libmunge2 libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 234s libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpixman-1-0 234s libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsm6 libtcl8.6 234s libthai-data libthai0 libtk8.6 libucx0 libxcb-render0 libxcb-shm0 libxft2 234s libxnvctrl0 libxrender1 libxss1 libxt6t64 mpi-default-bin ocl-icd-libopencl1 234s openmpi-bin openmpi-common r-base-core ray ray-doc ray-extra unzip 234s x11-common xdg-utils zip 234s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 94.7 MB/94.7 MB of archives. 234s After this operation, 309 MB of additional disk space will be used. 234s Get:1 /tmp/autopkgtest.S0cIDE/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 234s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 234s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libllvm17t64 amd64 1:17.0.6-12 [26.2 MB] 234s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 234s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-amdgpu1 amd64 2.4.121-2 [20.7 kB] 234s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 234s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 234s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamdhip64-5 amd64 5.7.1-4 [9526 kB] 234s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libatomic1 amd64 14.1.0-1ubuntu1 [10.4 kB] 234s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 234s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB] 234s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 234s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 234s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 234s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libcairo2 amd64 1.18.0-3build1 [566 kB] 234s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 234s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 234s Get:18 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 234s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 234s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 librdmacm1t64 amd64 52.0-2 [70.7 kB] 234s Get:21 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfabric1 amd64 1.17.0-3build2 [657 kB] 234s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 234s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 234s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 234s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 234s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc15 amd64 2.10.0-1build1 [172 kB] 234s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 234s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB] 234s Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 234s Get:30 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 234s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 234s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 234s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 234s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc-plugins amd64 2.10.0-1build1 [15.7 kB] 234s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpmix2t64 amd64 5.0.1-4.1build1 [697 kB] 234s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 libucx0 amd64 1.16.0+ds-5ubuntu1 [1140 kB] 234s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 libopenmpi3t64 amd64 4.1.6-7ubuntu2 [2563 kB] 234s Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 234s Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 234s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [233 kB] 234s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [42.3 kB] 234s Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [28.7 kB] 234s Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 234s Get:44 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 234s Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB] 234s Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 234s Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 234s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 234s Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 234s Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 234s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-common all 4.1.6-7ubuntu2 [170 kB] 234s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-bin amd64 4.1.6-7ubuntu2 [114 kB] 234s Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 zip amd64 3.0-13build1 [175 kB] 234s Get:54 http://ftpmaster.internal/ubuntu oracular/main amd64 unzip amd64 6.0-28ubuntu5 [180 kB] 234s Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 234s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 r-base-core amd64 4.4.1-1 [28.5 MB] 235s Get:57 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 mpi-default-bin amd64 1.17 [2296 B] 235s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray amd64 2.3.1-8build2 [740 kB] 235s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray-doc all 2.3.1-8build2 [35.1 kB] 235s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray-extra all 2.3.1-8build2 [12.1 kB] 235s Preconfiguring packages ... 235s Fetched 94.7 MB in 1s (131 MB/s) 235s Selecting previously unselected package fontconfig. 235s (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 ... 74466 files and directories currently installed.) 235s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 235s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 235s Selecting previously unselected package libllvm17t64:amd64. 235s Preparing to unpack .../01-libllvm17t64_1%3a17.0.6-12_amd64.deb ... 235s Unpacking libllvm17t64:amd64 (1:17.0.6-12) ... 236s Selecting previously unselected package libamd-comgr2:amd64. 236s Preparing to unpack .../02-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 236s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 236s Selecting previously unselected package libdrm-amdgpu1:amd64. 236s Preparing to unpack .../03-libdrm-amdgpu1_2.4.121-2_amd64.deb ... 236s Unpacking libdrm-amdgpu1:amd64 (2.4.121-2) ... 236s Selecting previously unselected package libhsakmt1:amd64. 236s Preparing to unpack .../04-libhsakmt1_5.7.0-1build1_amd64.deb ... 236s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 236s Selecting previously unselected package libhsa-runtime64-1. 236s Preparing to unpack .../05-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 236s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 236s Selecting previously unselected package libamdhip64-5. 236s Preparing to unpack .../06-libamdhip64-5_5.7.1-4_amd64.deb ... 236s Unpacking libamdhip64-5 (5.7.1-4) ... 236s Selecting previously unselected package libatomic1:amd64. 236s Preparing to unpack .../07-libatomic1_14.1.0-1ubuntu1_amd64.deb ... 236s Unpacking libatomic1:amd64 (14.1.0-1ubuntu1) ... 236s Selecting previously unselected package libblas3:amd64. 236s Preparing to unpack .../08-libblas3_3.12.0-3build1_amd64.deb ... 236s Unpacking libblas3:amd64 (3.12.0-3build1) ... 236s Selecting previously unselected package libpixman-1-0:amd64. 236s Preparing to unpack .../09-libpixman-1-0_0.42.2-1build1_amd64.deb ... 236s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ... 236s Selecting previously unselected package libxcb-render0:amd64. 236s Preparing to unpack .../10-libxcb-render0_1.17.0-2_amd64.deb ... 236s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 236s Selecting previously unselected package libxcb-shm0:amd64. 236s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_amd64.deb ... 236s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 236s Selecting previously unselected package libxrender1:amd64. 237s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 237s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 237s Selecting previously unselected package libcairo2:amd64. 237s Preparing to unpack .../13-libcairo2_1.18.0-3build1_amd64.deb ... 237s Unpacking libcairo2:amd64 (1.18.0-3build1) ... 237s Selecting previously unselected package libdatrie1:amd64. 237s Preparing to unpack .../14-libdatrie1_0.2.13-3build1_amd64.deb ... 237s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 237s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 237s Preparing to unpack .../15-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 237s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 237s Selecting previously unselected package libpsm-infinipath1. 237s Preparing to unpack .../16-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 237s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 237s Selecting previously unselected package libpsm2-2. 237s Preparing to unpack .../17-libpsm2-2_11.2.185-2.1_amd64.deb ... 237s Unpacking libpsm2-2 (11.2.185-2.1) ... 237s Selecting previously unselected package librdmacm1t64:amd64. 237s Preparing to unpack .../18-librdmacm1t64_52.0-2_amd64.deb ... 237s Unpacking librdmacm1t64:amd64 (52.0-2) ... 237s Selecting previously unselected package libfabric1:amd64. 237s Preparing to unpack .../19-libfabric1_1.17.0-3build2_amd64.deb ... 237s Unpacking libfabric1:amd64 (1.17.0-3build2) ... 237s Selecting previously unselected package libgfortran5:amd64. 237s Preparing to unpack .../20-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 237s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 237s Selecting previously unselected package libgomp1:amd64. 237s Preparing to unpack .../21-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 237s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 237s Selecting previously unselected package libgraphite2-3:amd64. 237s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 237s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 237s Selecting previously unselected package libharfbuzz0b:amd64. 237s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 237s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 237s Selecting previously unselected package libhwloc15:amd64. 237s Preparing to unpack .../24-libhwloc15_2.10.0-1build1_amd64.deb ... 237s Unpacking libhwloc15:amd64 (2.10.0-1build1) ... 237s Selecting previously unselected package x11-common. 237s Preparing to unpack .../25-x11-common_1%3a7.7+23ubuntu3_all.deb ... 237s Unpacking x11-common (1:7.7+23ubuntu3) ... 237s Selecting previously unselected package libice6:amd64. 237s Preparing to unpack .../26-libice6_2%3a1.0.10-1build3_amd64.deb ... 237s Unpacking libice6:amd64 (2:1.0.10-1build3) ... 237s Selecting previously unselected package liblapack3:amd64. 237s Preparing to unpack .../27-liblapack3_3.12.0-3build1_amd64.deb ... 237s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 237s Selecting previously unselected package libmunge2:amd64. 237s Preparing to unpack .../28-libmunge2_0.5.15-4build1_amd64.deb ... 237s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 237s Selecting previously unselected package libpciaccess0:amd64. 237s Preparing to unpack .../29-libpciaccess0_0.17-3build1_amd64.deb ... 237s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 237s Selecting previously unselected package libxnvctrl0:amd64. 237s Preparing to unpack .../30-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 237s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 237s Selecting previously unselected package ocl-icd-libopencl1:amd64. 237s Preparing to unpack .../31-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 237s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 237s Selecting previously unselected package libhwloc-plugins:amd64. 237s Preparing to unpack .../32-libhwloc-plugins_2.10.0-1build1_amd64.deb ... 237s Unpacking libhwloc-plugins:amd64 (2.10.0-1build1) ... 237s Selecting previously unselected package libpmix2t64:amd64. 237s Preparing to unpack .../33-libpmix2t64_5.0.1-4.1build1_amd64.deb ... 237s Unpacking libpmix2t64:amd64 (5.0.1-4.1build1) ... 237s Selecting previously unselected package libucx0:amd64. 237s Preparing to unpack .../34-libucx0_1.16.0+ds-5ubuntu1_amd64.deb ... 237s Unpacking libucx0:amd64 (1.16.0+ds-5ubuntu1) ... 237s Selecting previously unselected package libopenmpi3t64:amd64. 237s Preparing to unpack .../35-libopenmpi3t64_4.1.6-7ubuntu2_amd64.deb ... 237s Unpacking libopenmpi3t64:amd64 (4.1.6-7ubuntu2) ... 237s Selecting previously unselected package libthai-data. 237s Preparing to unpack .../36-libthai-data_0.1.29-2build1_all.deb ... 237s Unpacking libthai-data (0.1.29-2build1) ... 237s Selecting previously unselected package libthai0:amd64. 237s Preparing to unpack .../37-libthai0_0.1.29-2build1_amd64.deb ... 237s Unpacking libthai0:amd64 (0.1.29-2build1) ... 237s Selecting previously unselected package libpango-1.0-0:amd64. 237s Preparing to unpack .../38-libpango-1.0-0_1.54.0+ds-1_amd64.deb ... 237s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-1) ... 237s Selecting previously unselected package libpangoft2-1.0-0:amd64. 237s Preparing to unpack .../39-libpangoft2-1.0-0_1.54.0+ds-1_amd64.deb ... 237s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... 237s Selecting previously unselected package libpangocairo-1.0-0:amd64. 237s Preparing to unpack .../40-libpangocairo-1.0-0_1.54.0+ds-1_amd64.deb ... 237s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... 237s Selecting previously unselected package libpaper1:amd64. 237s Preparing to unpack .../41-libpaper1_1.1.29build1_amd64.deb ... 237s Unpacking libpaper1:amd64 (1.1.29build1) ... 238s Selecting previously unselected package libpaper-utils. 238s Preparing to unpack .../42-libpaper-utils_1.1.29build1_amd64.deb ... 238s Unpacking libpaper-utils (1.1.29build1) ... 238s Selecting previously unselected package libsm6:amd64. 238s Preparing to unpack .../43-libsm6_2%3a1.2.3-1build3_amd64.deb ... 238s Unpacking libsm6:amd64 (2:1.2.3-1build3) ... 238s Selecting previously unselected package libtcl8.6:amd64. 238s Preparing to unpack .../44-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 238s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 238s Selecting previously unselected package libxft2:amd64. 238s Preparing to unpack .../45-libxft2_2.3.6-1build1_amd64.deb ... 238s Unpacking libxft2:amd64 (2.3.6-1build1) ... 238s Selecting previously unselected package libxss1:amd64. 238s Preparing to unpack .../46-libxss1_1%3a1.2.3-1build3_amd64.deb ... 238s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 238s Selecting previously unselected package libtk8.6:amd64. 238s Preparing to unpack .../47-libtk8.6_8.6.14-1build1_amd64.deb ... 238s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 238s Selecting previously unselected package libxt6t64:amd64. 238s Preparing to unpack .../48-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 238s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 238s Selecting previously unselected package openmpi-common. 238s Preparing to unpack .../49-openmpi-common_4.1.6-7ubuntu2_all.deb ... 238s Unpacking openmpi-common (4.1.6-7ubuntu2) ... 238s Selecting previously unselected package openmpi-bin. 238s Preparing to unpack .../50-openmpi-bin_4.1.6-7ubuntu2_amd64.deb ... 238s Unpacking openmpi-bin (4.1.6-7ubuntu2) ... 238s Selecting previously unselected package zip. 238s Preparing to unpack .../51-zip_3.0-13build1_amd64.deb ... 238s Unpacking zip (3.0-13build1) ... 238s Selecting previously unselected package unzip. 238s Preparing to unpack .../52-unzip_6.0-28ubuntu5_amd64.deb ... 238s Unpacking unzip (6.0-28ubuntu5) ... 238s Selecting previously unselected package xdg-utils. 238s Preparing to unpack .../53-xdg-utils_1.2.1-0ubuntu1_all.deb ... 238s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 238s Selecting previously unselected package r-base-core. 238s Preparing to unpack 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(0.42.2-1build1) ... 239s Setting up libpaper1:amd64 (1.1.29build1) ... 239s 239s Creating config file /etc/papersize with new version 239s Setting up ray-doc (2.3.1-8build2) ... 239s Setting up libpciaccess0:amd64 (0.17-3build1) ... 239s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 241s Regenerating fonts cache... done. 241s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 241s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 241s Setting up libxcb-render0:amd64 (1.17.0-2) ... 241s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 241s Setting up unzip (6.0-28ubuntu5) ... 241s Setting up x11-common (1:7.7+23ubuntu3) ... 241s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 241s Setting up libpaper-utils (1.1.29build1) ... 241s Setting up libgomp1:amd64 (14.1.0-1ubuntu1) ... 241s Setting up libcairo2:amd64 (1.18.0-3build1) ... 241s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 241s Setting up zip (3.0-13build1) ... 241s Setting up libblas3:amd64 (3.12.0-3build1) ... 241s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 241s Setting up libmunge2:amd64 (0.5.15-4build1) ... 241s Setting up libllvm17t64:amd64 (1:17.0.6-12) ... 241s Setting up libhwloc15:amd64 (2.10.0-1build1) ... 241s Setting up libatomic1:amd64 (14.1.0-1ubuntu1) ... 241s Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 241s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 241s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 241s Setting up libpsm2-2 (11.2.185-2.1) ... 241s Setting up openmpi-common (4.1.6-7ubuntu2) ... 241s Setting up librdmacm1t64:amd64 (52.0-2) ... 241s Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ... 241s Setting up libthai-data (0.1.29-2build1) ... 241s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 241s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 241s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 241s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 241s Setting up xdg-utils (1.2.1-0ubuntu1) ... 241s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 241s Setting up libdrm-amdgpu1:amd64 (2.4.121-2) ... 241s Setting up libfabric1:amd64 (1.17.0-3build2) ... 241s Setting up libice6:amd64 (2:1.0.10-1build3) ... 241s Setting up liblapack3:amd64 (3.12.0-3build1) ... 241s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 241s Setting up libxft2:amd64 (2.3.6-1build1) ... 241s Setting up libtk8.6:amd64 (8.6.14-1build1) ... 241s Setting up libhwloc-plugins:amd64 (2.10.0-1build1) ... 241s Setting up libthai0:amd64 (0.1.29-2build1) ... 241s Setting up libpmix2t64:amd64 (5.0.1-4.1build1) ... 241s Setting up libsm6:amd64 (2:1.2.3-1build3) ... 241s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 241s Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ... 241s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 241s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 241s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... 241s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... 241s Setting up libamdhip64-5 (5.7.1-4) ... 241s Setting up r-base-core (4.4.1-1) ... 242s 242s Creating config file /etc/R/Renviron with new version 242s Setting up libucx0:amd64 (1.16.0+ds-5ubuntu1) ... 242s Setting up ray-extra (2.3.1-8build2) ... 242s Setting up libopenmpi3t64:amd64 (4.1.6-7ubuntu2) ... 242s Setting up openmpi-bin (4.1.6-7ubuntu2) ... 242s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 242s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 242s Setting up mpi-default-bin (1.17) ... 242s Setting up ray (2.3.1-8build2) ... 242s Setting up autopkgtest-satdep (0) ... 242s Processing triggers for man-db (2.12.1-2) ... 243s Processing triggers for install-info (7.1-3build2) ... 243s Processing triggers for libc-bin (2.39-0ubuntu9) ... 246s (Reading database ... 77171 files and directories currently installed.) 246s Removing autopkgtest-satdep (0) ... 259s autopkgtest [15:35:43]: test run-unit-test: [----------------------- 259s 259s ************************************************** 259s This program comes with ABSOLUTELY NO WARRANTY. 259s This is free software, and you are welcome to redistribute it 259s under certain conditions; see "LICENSE.txt" for details. 259s ************************************************** 259s 259s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 259s Centre de recherche en infectiologie de l'Université Laval 259s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 259s http://denovoassembler.sf.net/ 259s 259s References to cite: 259s 259s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 259s Ray Meta: scalable de novo metagenome assembly and profiling. 259s Genome Biology (BioMed Central Ltd). 259s 13:R122, Published: 22 December 2012 259s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 259s 259s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 259s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 259s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 259s November 2010, Volume 17, Issue 11, Pages 1519-1533. 259s http://dx.doi.org/doi:10.1089/cmb.2009.0238 259s 259s Ray version 2.3.1 259s License for Ray: GNU General Public License version 3 259s RayPlatform version: 2.0.1 259s License for RayPlatform: GNU Lesser General Public License version 3 259s 259s MAXKMERLENGTH: 32 259s Maximum coverage depth stored by CoverageDepth: 4294967295 259s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 259s FORCE_PACKING = n 259s ASSERT = n 259s HAVE_LIBZ = y 259s HAVE_LIBBZ2 = y 259s PROFILER_COLLECT = n 259s MINIRANKS = y 259s CLOCK_GETTIME = n 259s __linux__ = y 259s _MSC_VER = n 259s __GNUC__ = y 259s RAY_32_BITS = n 259s RAY_64_BITS = y 259s MPI standard version: MPI 3.1 259s MPI library: Open-MPI 4.1.6 259s Compiler: GNU gcc/g++ 13.2.0 259s MPI I/O: n 259s 259s 259s -k (to set the k-mer size) 259s Value: 31 259s 259s 259s Paired library # 0 259s -p (paired-end sequences) 259s Left sequences: ecoli_1K_1.fq 259s Right sequences: ecoli_1K_2.fq 259s Average length: automatic detection 259s Standard deviation: automatic detection 259s 259s Ray command: 259s mpiexec -n 1 Ray \ 259s -k \ 259s 31 \ 259s -p \ 259s ecoli_1K_1.fq \ 259s ecoli_1K_2.fq \ 259s -o \ 259s test1 259s 259s Rank 0 wrote test1/RayCommand.txt 259s 259s k-mer length: 31 259s Rank 0: assembler memory usage: 42804 KiB 259s Rank 0: assembler memory usage: 108620 KiB 259s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3087 259s Rank 0: testing the network, please wait... 259s 259s Rank 0 is testing the network [0/1000] 259s Rank 0 is testing the network [1000/1000] 259s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 259s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 259s 259s Rank 0 wrote test1/NetworkTest.txt 259s 259s 259s *** 259s Step: Network testing 259s Date: Mon Jul 8 15:35:44 2024 259s Elapsed time: 0 seconds 259s Since beginning: 0 seconds 259s *** 259s 259s 259s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 259s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 259s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 259s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 259s Rank 0 wrote test1/NumberOfSequences.txt 259s Rank 0 wrote test1/SequencePartition.txt 259s 259s *** 259s Step: Counting sequences to assemble 259s Date: Mon Jul 8 15:35:44 2024 259s Elapsed time: 0 seconds 259s Since beginning: 0 seconds 259s *** 259s 259s 259s Rank 0 is loading sequence reads 259s Rank 0 : partition is [0;4107], 4108 sequence reads 259s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 259s Rank 0 has 0 sequence reads 259s Rank 0: assembler memory usage: 121496 KiB 259s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 259s Rank 0 has 4108 sequence reads (completed) 259s 259s *** 259s Step: Sequence loading 259s Date: Mon Jul 8 15:35:44 2024 259s Elapsed time: 0 seconds 259s Since beginning: 0 seconds 259s *** 259s 259s 259s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 259s Rank 0 created its Bloom filter 259s Rank 0 is counting k-mers in sequence reads [1/4108] 259s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 259s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 259s 259s 259s *** 259s Step: K-mer counting 259s Date: Mon Jul 8 15:35:44 2024 259s Elapsed time: 0 seconds 259s Since beginning: 0 seconds 259s *** 259s 259s 259s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 259s Rank 0 destroyed its Bloom filter 259s Rank 0 has 1954 k-mers (completed) 259s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 259s Rank 0: assembler memory usage: 117892 KiB 261s 261s 261s Rank 0: the minimum coverage is 3 261s Rank 0: the peak coverage is 3 261s Warning: no peak observed in the k-mer coverage distribution. 261s to deal with the sequencing error rate, try to lower the k-mer length (-k) 261s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 261s 261s *** 261s Step: Coverage distribution analysis 261s Date: Mon Jul 8 15:35:46 2024 261s Elapsed time: 2 seconds 261s Since beginning: 2 seconds 261s *** 261s 261s 261s 261s Rank 0 is adding edges [1/4108] 261s Rank 0 is adding edges [4108/4108] (completed) 261s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 261s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 261s 261s *** 261s Step: Graph construction 261s Date: Mon Jul 8 15:35:46 2024 261s Elapsed time: 0 seconds 261s Since beginning: 2 seconds 261s *** 261s 261s 261s Rank 0 has 1954 vertices (completed) 261s Rank 0: assembler memory usage: 117892 KiB 263s Rank 0 is purging edges [1/1954] 263s Rank 0 is purging edges [1954/1954] (completed) 263s Rank 0: assembler memory usage: 118420 KiB 263s VirtualProcessor: completed jobs: 1954 263s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 265s Rank 0 wrote test1/degreeDistribution.txt 265s 265s *** 265s Step: Null edge purging 265s Date: Mon Jul 8 15:35:50 2024 265s Elapsed time: 4 seconds 265s Since beginning: 6 seconds 265s *** 265s 265s 265s Rank 0 is selecting optimal read markers [1/4108] 265s Rank 0: assembler memory usage: 118420 KiB 266s Rank 0 is selecting optimal read markers [4108/4108] (completed) 266s Rank 0: peak number of workers: 599, maximum: 32768 266s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 266s Rank 0: assembler memory usage: 126584 KiB 266s Rank 0: Freeing unused assembler memory: 4096 KiB freed 266s Rank 0: assembler memory usage: 126584 KiB 266s 266s *** 266s Step: Selection of optimal read markers 266s Date: Mon Jul 8 15:35:51 2024 266s Elapsed time: 1 seconds 266s Since beginning: 7 seconds 266s *** 266s 266s 266s Rank 0: memory usage for optimal read markers= 4096 KiB 266s Rank 0 is creating seeds [1/1954] 266s Rank 0: assembler memory usage: 126584 KiB 268s Rank 0 has 1 seeds 268s Rank 0 is creating seeds [1954/1954] (completed) 268s Rank 0: peak number of workers: 746, maximum: 32768 268s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 268s Rank 0 runtime statistics for seeding algorithm: 268s Rank 0 Skipped paths because of dead end for head: 0 268s Rank 0 Skipped paths because of dead end for tail: 0 268s Rank 0 Skipped paths because of two dead ends: 0 268s Rank 0 Skipped paths because of bubble weak component: 0 268s Rank 0 Skipped paths because of short length: 1952 268s Rank 0 Skipped paths because of bad ownership: 1 268s Rank 0 Skipped paths because of low coverage: 0 268s Rank 0 Eligible paths: 1 268s Rank 0: assembler memory usage: 126584 KiB 268s Rank 0 has 1 seeds to register. 268s Rank 0 registered 0/1 268s Rank 0 registered 0/1 268s Rank 0 registered its seeds 268s VirtualProcessor: completed jobs: 0 268s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 270s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 279s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 279s Rank 0 merged its seeds: 1 seeds -> 1 seeds 279s 279s *** 279s Step: Detection of assembly seeds 279s Date: Mon Jul 8 15:36:05 2024 279s Elapsed time: 14 seconds 279s Since beginning: 21 seconds 279s *** 279s 279s 280s Rank 0 is calculating library lengths [1/1] 280s Rank 0 detected 1737 library lengths 280s Rank 0 is calculating library lengths [1/1] (completed) 280s Rank 0: peak number of workers: 1, maximum: 32768 280s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 280s Rank 0: assembler memory usage: 163452 KiB 280s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 280s 280s Mode= 2 signalAverage= 9 280s CURRENT IS NOISE, 244 280s GOT HIT 212 280s 280s 280s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 280s 280s *** 280s Step: Estimation of outer distances for paired reads 280s Date: Mon Jul 8 15:36:05 2024 280s Elapsed time: 0 seconds 280s Since beginning: 21 seconds 280s *** 280s 280s 280s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 280s Rank 0 traversed 1000 nucleotide symbols 280s Rank 0: assembler memory usage: 167548 KiB 280s Rank 0 is extending seeds [1/1] (completed) 280s Rank 0 extended 1 seeds out of 1 (100.00%) 280s Rank 0: assembler memory usage: 159356 KiB 280s Rank 0 starting fusions 280s 280s *** 280s Step: Bidirectional extension of seeds 280s Date: Mon Jul 8 15:36:05 2024 280s Elapsed time: 0 seconds 280s Since beginning: 21 seconds 280s *** 280s 280s 280s Rank 0: starting clear step. cycleNumber= 0 282s Rank 0 adding 0 new fusions 282s Rank 0 cleared, 1 paths 282s Rank 0: starting distribution step 282s Rank 0 is distributing fusions [1/1] 282s Rank 0: assembler memory usage: 159356 KiB 282s Date: Mon Jul 8 15:36:07 2024 282s Rank 0 is distributing fusions [1/1] (completed) 282s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 282s Rank 0: assembler memory usage: 163452 KiB 282s Date: Mon Jul 8 15:36:07 2024 282s Rank 0 tells others to compute fusions. 282s Rank 0 FusionTaskCreator assignNextTask [0/2] 282s Rank 0: assembler memory usage: 163452 KiB 282s Date: Mon Jul 8 15:36:07 2024 282s Rank 0 FusionTaskCreator processWorkerResult [0/2] 282s Rank 0: assembler memory usage: 163452 KiB 282s Date: Mon Jul 8 15:36:07 2024 282s Rank 0 FusionTaskCreator [2/2] 282s Statistics: all paths: 1 eliminated during fusing: 0 282s Rank 0: assembler memory usage: 163452 KiB 282s VirtualProcessor: completed jobs: 2 282s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 282s Rank 0: starting clear step. cycleNumber= 1 284s Rank 0 adding 0 new fusions 284s Rank 0 cleared, 1 paths 284s Rank 0 is distributing fusions [1/1] 284s Rank 0: assembler memory usage: 163452 KiB 284s Date: Mon Jul 8 15:36:09 2024 284s Rank 0 is distributing fusions [1/1] (completed) 284s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 284s Rank 0: assembler memory usage: 163452 KiB 284s Date: Mon Jul 8 15:36:09 2024 284s Rank 0 JoinerTaskCreator assignNextTask [0/2] 284s Rank 0: assembler memory usage: 163452 KiB 284s Date: Mon Jul 8 15:36:09 2024 284s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 284s Rank 0: assembler memory usage: 163452 KiB 284s Date: Mon Jul 8 15:36:09 2024 284s Rank 0 JoinerTaskCreator [2/2] 284s Statistics: all paths: 1 eliminated during joining: 0 284s Rank 0: assembler memory usage: 163452 KiB 284s Date: Mon Jul 8 15:36:09 2024 284s VirtualProcessor: completed jobs: 2 284s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 286s Rank 0 adding 0 new fusions 286s Rank 0 cleared, 1 paths 286s Rank 0: starting distribution step 286s Rank 0 is distributing fusions [1/1] 286s Rank 0: assembler memory usage: 163452 KiB 286s Date: Mon Jul 8 15:36:11 2024 286s Rank 0 is distributing fusions [1/1] (completed) 286s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 286s Rank 0: assembler memory usage: 163452 KiB 286s Date: Mon Jul 8 15:36:11 2024 286s Rank 0 tells others to compute fusions. 286s Rank 0 FusionTaskCreator assignNextTask [0/2] 286s Rank 0: assembler memory usage: 163452 KiB 286s Date: Mon Jul 8 15:36:11 2024 286s Rank 0 FusionTaskCreator processWorkerResult [0/2] 286s Rank 0: assembler memory usage: 163452 KiB 286s Date: Mon Jul 8 15:36:11 2024 286s Rank 0 FusionTaskCreator [2/2] 286s Statistics: all paths: 1 eliminated during fusing: 0 286s Rank 0: assembler memory usage: 163452 KiB 286s VirtualProcessor: completed jobs: 2 286s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 286s Rank 0: starting clear step. cycleNumber= 2 288s Rank 0 adding 0 new fusions 288s Rank 0 cleared, 1 paths 288s Rank 0 is distributing fusions [1/1] 288s Rank 0: assembler memory usage: 163452 KiB 288s Date: Mon Jul 8 15:36:13 2024 288s Rank 0 is distributing fusions [1/1] (completed) 288s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 288s Rank 0: assembler memory usage: 163452 KiB 288s Date: Mon Jul 8 15:36:13 2024 288s Rank 0 JoinerTaskCreator assignNextTask [0/2] 288s Rank 0: assembler memory usage: 163452 KiB 288s Date: Mon Jul 8 15:36:13 2024 288s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 288s Rank 0: assembler memory usage: 163452 KiB 288s Date: Mon Jul 8 15:36:13 2024 288s Rank 0 JoinerTaskCreator [2/2] 288s Statistics: all paths: 1 eliminated during joining: 0 288s Rank 0: assembler memory usage: 163452 KiB 288s Date: Mon Jul 8 15:36:13 2024 288s VirtualProcessor: completed jobs: 2 288s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 290s Rank 0 adding 0 new fusions 290s Rank 0 cleared, 1 paths 290s Rank 0: starting distribution step 290s Rank 0 is distributing fusions [1/1] 290s Rank 0: assembler memory usage: 163452 KiB 290s Date: Mon Jul 8 15:36:15 2024 290s Rank 0 is distributing fusions [1/1] (completed) 290s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 290s Rank 0: assembler memory usage: 163452 KiB 290s Date: Mon Jul 8 15:36:15 2024 290s Rank 0 cycleNumber= 2 290s 290s *** 290s Step: Merging of redundant paths 290s Date: Mon Jul 8 15:36:15 2024 290s Elapsed time: 10 seconds 290s Since beginning: 31 seconds 290s *** 290s 290s 290s Rank 0 appended 1 elements 290s 290s *** 290s Step: Generation of contigs 290s Date: Mon Jul 8 15:36:15 2024 290s Elapsed time: 0 seconds 290s Since beginning: 31 seconds 290s *** 290s 290s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 290s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 290s Rank 0 ineligibleObjects: 0/970 (0.00%) 290s Rank 0: assembler memory usage: 163452 KiB 290s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 290s Rank 0 finished gathering scaffold links. 290s Rank 0 will write 1 contig lengths 290s Rank 0 will solve the scaffolding problem. 290s Welcome to GreedySolver v1.0 290s 1 vertices; 0 edges 290s 1 contigs >= 500 290s Edges in solution: 0 290s 290s Conflict statistics: 290s 1 scaffolds, 1 >= 500 290s Total: 1000 nucleotides 290s 290s *** 290s Step: Scaffolding of contigs 290s Date: Mon Jul 8 15:36:15 2024 290s Elapsed time: 0 seconds 290s Since beginning: 31 seconds 290s *** 290s 290s Rank 0 syncing with master 290s 290s *** 290s Step: Counting sequences to search 290s Date: Mon Jul 8 15:36:15 2024 290s Elapsed time: 0 seconds 290s Since beginning: 31 seconds 290s *** 290s 290s 290s Rank 0 will add colors, 0 sequences in 0 files to process 290s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 292s 292s *** 292s Step: Graph coloring 292s Date: Mon Jul 8 15:36:17 2024 292s Elapsed time: 2 seconds 292s Since beginning: 33 seconds 292s *** 292s 292s 292s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 292s Rank 0 shares its counts 292s Rank 0 computing contig abundances [1/1] [1/970] 292s Rank 0 computing contig abundances [1/1] [970/970] 292s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 292s 292s *** 292s Step: Counting contig biological abundances 292s Date: Mon Jul 8 15:36:17 2024 292s Elapsed time: 0 seconds 292s Since beginning: 33 seconds 292s *** 292s 292s 292s Rank 0 colored the graph with 0 real colors using 1 virtual colors 292s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 292s 292s *** 292s Step: Counting sequence biological abundances 292s Date: Mon Jul 8 15:36:17 2024 292s Elapsed time: 0 seconds 292s Since beginning: 33 seconds 292s *** 292s 292s 292s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 292s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 294s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 294s 294s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 294s Rank 0 is starting taxon syncing across the compute tribe. 294s 294s *** 294s Step: Loading taxons 294s Date: Mon Jul 8 15:36:19 2024 294s Elapsed time: 2 seconds 294s Since beginning: 35 seconds 294s *** 294s 294s Rank 0 synced taxons across the grid with 1 poor slaves. 294s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 294s Rank 0 has 0 taxons after syncing with master 296s 296s 296s *** 296s Step: Loading tree 296s Date: Mon Jul 8 15:36:21 2024 296s Elapsed time: 2 seconds 296s Since beginning: 37 seconds 296s *** 296s 298s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 298s 298s Rank 0: counting ontology terms in the graph... 300s Rank 0: 0 have some biological signal 300s Number of dereferenced alternate handles: 0 300s Number of k-mer observations with gene ontology terms: 0 300s Rank 0: synced ontology term profiles with master 300s Rank 0: synchronization is complete! 305s Rank 0: ontology terms with biological signal: 0 305s Populated recursive values... 305s Gene ontology terms without depth information: 0 305s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 305s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 305s 305s *** 305s Step: Processing gene ontologies 305s Date: Mon Jul 8 15:36:25 2024 305s Elapsed time: 4 seconds 305s Since beginning: 41 seconds 311s *** 311s 311s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 311s [GenomeNeighbourhood] in final list: 0 311s 311s *** 311s Step: Computing neighbourhoods 311s Date: Mon Jul 8 15:36:25 2024 311s Elapsed time: 0 seconds 311s Since beginning: 41 seconds 311s *** 311s 311s Contigs >= 100 nt 311s Number: 1 311s Total length: 1000 311s Average: 1000 311s N50: 1000 311s Median: 1000 311s Largest: 1000 311s Contigs >= 500 nt 311s Number: 1 311s Total length: 1000 311s Average: 1000 311s N50: 1000 311s Median: 1000 311s Largest: 1000 311s Scaffolds >= 100 nt 311s Number: 1 311s Total length: 1000 311s Average: 1000 311s N50: 1000 311s Median: 1000 311s Largest: 1000 311s Scaffolds >= 500 nt 311s Number: 1 311s Total length: 1000 311s Average: 1000 311s N50: 1000 311s Median: 1000 311s Largest: 1000 311s 311s Rank 0 wrote test1/Contigs.fasta 311s Rank 0 wrote test1/Scaffolds.fasta 311s Check for test1/* 311s 311s 311s 311s ************************************************** 311s This program comes with ABSOLUTELY NO WARRANTY. 311s This is free software, and you are welcome to redistribute it 311s under certain conditions; see "LICENSE.txt" for details. 311s ************************************************** 311s 311s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 311s Centre de recherche en infectiologie de l'Université Laval 311s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 311s http://denovoassembler.sf.net/ 311s 311s References to cite: 311s 311s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 311s Ray Meta: scalable de novo metagenome assembly and profiling. 311s Genome Biology (BioMed Central Ltd). 311s 13:R122, Published: 22 December 2012 311s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 311s 311s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 311s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 311s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 311s November 2010, Volume 17, Issue 11, Pages 1519-1533. 311s http://dx.doi.org/doi:10.1089/cmb.2009.0238 311s 311s Ray version 2.3.1 311s License for Ray: GNU General Public License version 3 311s RayPlatform version: 2.0.1 311s License for RayPlatform: GNU Lesser General Public License version 3 311s 311s MAXKMERLENGTH: 32 311s Maximum coverage depth stored by CoverageDepth: 4294967295 311s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 311s FORCE_PACKING = n 311s ASSERT = n 311s HAVE_LIBZ = y 311s HAVE_LIBBZ2 = y 311s PROFILER_COLLECT = n 311s MINIRANKS = y 311s CLOCK_GETTIME = n 311s __linux__ = y 311s _MSC_VER = n 311s __GNUC__ = y 311s RAY_32_BITS = n 311s RAY_64_BITS = y 311s MPI standard version: MPI 3.1 311s MPI library: Open-MPI 4.1.6 311s Compiler: GNU gcc/g++ 13.2.0 311s MPI I/O: n 311s 311s 311s -k (to set the k-mer size) 311s Value: 31 311s 311s 311s Paired library # 0 311s -p (paired-end sequences) 311s Left sequences: SampleDirectory/s_6.first1000_1.fastq 311s Right sequences: SampleDirectory/s_6.first1000_2.fastq 311s Average length: automatic detection 311s Standard deviation: automatic detection 311s 311s Ray command: 311s mpiexec -n 1 Ray \ 311s -k \ 311s 31 \ 311s -detect-sequence-files \ 311s SampleDirectory \ 311s -o \ 311s test2 311s 311s Rank 0 wrote test2/RayCommand.txt 311s 311s k-mer length: 31 311s Rank 0: assembler memory usage: 42828 KiB 311s Rank 0: assembler memory usage: 108500 KiB 311s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3095 311s Rank 0: testing the network, please wait... 311s 311s Rank 0 is testing the network [0/1000] 311s Rank 0 is testing the network [1000/1000] 311s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 311s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 311s 311s Rank 0 wrote test2/NetworkTest.txt 311s 311s 311s *** 311s Step: Network testing 311s Date: Mon Jul 8 15:36:25 2024 311s Elapsed time: 0 seconds 311s Since beginning: 0 seconds 311s *** 311s 311s 311s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 311s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 311s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 311s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 311s Rank 0 wrote test2/NumberOfSequences.txt 311s Rank 0 wrote test2/SequencePartition.txt 311s 311s *** 311s Step: Counting sequences to assemble 311s Date: Mon Jul 8 15:36:25 2024 311s Elapsed time: 0 seconds 311s Since beginning: 0 seconds 311s *** 311s 311s 311s Rank 0 is loading sequence reads 311s Rank 0 : partition is [0;4107], 4108 sequence reads 311s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 311s Rank 0 has 0 sequence reads 311s Rank 0: assembler memory usage: 121496 KiB 311s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 311s Rank 0 has 4108 sequence reads (completed) 311s 311s *** 311s Step: Sequence loading 311s Date: Mon Jul 8 15:36:25 2024 311s Elapsed time: 0 seconds 311s Since beginning: 0 seconds 311s *** 311s 311s 311s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 311s Rank 0 created its Bloom filter 311s Rank 0 is counting k-mers in sequence reads [1/4108] 311s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 311s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 311s 311s 311s *** 311s Step: K-mer counting 311s Date: Mon Jul 8 15:36:25 2024 311s Elapsed time: 0 seconds 311s Since beginning: 0 seconds 311s *** 311s 311s 311s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 311s Rank 0 destroyed its Bloom filter 311s Rank 0 has 1954 k-mers (completed) 311s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 311s Rank 0: assembler memory usage: 117888 KiB 311s 311s 311s Rank 0: the minimum coverage is 3 311s Rank 0: the peak coverage is 3 311s Warning: no peak observed in the k-mer coverage distribution. 311s to deal with the sequencing error rate, try to lower the k-mer length (-k) 311s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 311s 311s *** 311s Step: Coverage distribution analysis 311s Date: Mon Jul 8 15:36:27 2024 311s Elapsed time: 2 seconds 311s Since beginning: 2 seconds 311s *** 311s 311s 311s 311s Rank 0 is adding edges [1/4108] 311s Rank 0 is adding edges [4108/4108] (completed) 311s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 311s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 311s 311s *** 311s Step: Graph construction 311s Date: Mon Jul 8 15:36:28 2024 311s Elapsed time: 1 seconds 311s Since beginning: 3 seconds 311s *** 311s 311s 311s Rank 0 has 1954 vertices (completed) 311s Rank 0: assembler memory usage: 117888 KiB 311s Rank 0 is purging edges [1/1954] 311s Rank 0 is purging edges [1954/1954] (completed) 311s Rank 0: assembler memory usage: 118416 KiB 311s VirtualProcessor: completed jobs: 1954 311s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 311s Rank 0 wrote test2/degreeDistribution.txt 311s 311s *** 311s Step: Null edge purging 311s Date: Mon Jul 8 15:36:31 2024 311s Elapsed time: 3 seconds 311s Since beginning: 6 seconds 311s *** 311s 311s 311s Rank 0 is selecting optimal read markers [1/4108] 311s Rank 0: assembler memory usage: 118416 KiB 311s Rank 0 is selecting optimal read markers [4108/4108] (completed) 311s Rank 0: peak number of workers: 599, maximum: 32768 311s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 311s Rank 0: assembler memory usage: 126544 KiB 311s Rank 0: Freeing unused assembler memory: 4096 KiB freed 311s Rank 0: assembler memory usage: 126544 KiB 311s 311s *** 311s Step: Selection of optimal read markers 311s Date: Mon Jul 8 15:36:32 2024 311s Elapsed time: 1 seconds 311s Since beginning: 7 seconds 311s *** 311s 311s 311s Rank 0: memory usage for optimal read markers= 4096 KiB 311s Rank 0 is creating seeds [1/1954] 311s Rank 0: assembler memory usage: 126544 KiB 311s Rank 0 has 1 seeds 311s Rank 0 is creating seeds [1954/1954] (completed) 311s Rank 0: peak number of workers: 746, maximum: 32768 311s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 311s Rank 0 runtime statistics for seeding algorithm: 311s Rank 0 Skipped paths because of dead end for head: 0 311s Rank 0 Skipped paths because of dead end for tail: 0 311s Rank 0 Skipped paths because of two dead ends: 0 311s Rank 0 Skipped paths because of bubble weak component: 0 311s Rank 0 Skipped paths because of short length: 1952 311s Rank 0 Skipped paths because of bad ownership: 1 311s Rank 0 Skipped paths because of low coverage: 0 311s Rank 0 Eligible paths: 1 311s Rank 0: assembler memory usage: 126544 KiB 311s Rank 0 has 1 seeds to register. 311s Rank 0 registered 0/1 311s Rank 0 registered 0/1 311s Rank 0 registered its seeds 311s VirtualProcessor: completed jobs: 0 311s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 311s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 320s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 320s Rank 0 merged its seeds: 1 seeds -> 1 seeds 320s 320s *** 320s Step: Detection of assembly seeds 320s Date: Mon Jul 8 15:36:46 2024 320s Elapsed time: 14 seconds 321s Since beginning: 21 seconds 321s *** 321s 321s 321s Rank 0 is calculating library lengths [1/1] 321s Rank 0 detected 1737 library lengths 321s Rank 0 is calculating library lengths [1/1] (completed) 321s Rank 0: peak number of workers: 1, maximum: 32768 321s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 321s Rank 0: assembler memory usage: 163412 KiB 321s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 321s 321s Mode= 2 signalAverage= 9 321s CURRENT IS NOISE, 244 321s GOT HIT 212 321s 321s 321s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 321s 321s *** 321s Step: Estimation of outer distances for paired reads 321s Date: Mon Jul 8 15:36:46 2024 321s Elapsed time: 0 seconds 321s Since beginning: 21 seconds 321s *** 321s 321s 321s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 321s Rank 0 traversed 1000 nucleotide symbols 321s Rank 0: assembler memory usage: 167508 KiB 321s Rank 0 is extending seeds [1/1] (completed) 321s Rank 0 extended 1 seeds out of 1 (100.00%) 321s Rank 0: assembler memory usage: 159316 KiB 321s Rank 0 starting fusions 321s 321s *** 321s Step: Bidirectional extension of seeds 321s Date: Mon Jul 8 15:36:46 2024 321s Elapsed time: 0 seconds 321s Since beginning: 21 seconds 321s *** 321s 321s 321s Rank 0: starting clear step. cycleNumber= 0 323s Rank 0 adding 0 new fusions 323s Rank 0 cleared, 1 paths 323s Rank 0: starting distribution step 323s Rank 0 is distributing fusions [1/1] 323s Rank 0: assembler memory usage: 159316 KiB 323s Date: Mon Jul 8 15:36:48 2024 323s Rank 0 is distributing fusions [1/1] (completed) 323s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 323s Rank 0: assembler memory usage: 163412 KiB 323s Date: Mon Jul 8 15:36:48 2024 323s Rank 0 tells others to compute fusions. 323s Rank 0 FusionTaskCreator assignNextTask [0/2] 323s Rank 0: assembler memory usage: 163412 KiB 323s Date: Mon Jul 8 15:36:48 2024 323s Rank 0 FusionTaskCreator processWorkerResult [0/2] 323s Rank 0: assembler memory usage: 163412 KiB 323s Date: Mon Jul 8 15:36:48 2024 323s Rank 0 FusionTaskCreator [2/2] 323s Statistics: all paths: 1 eliminated during fusing: 0 323s Rank 0: assembler memory usage: 163412 KiB 323s VirtualProcessor: completed jobs: 2 323s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 323s Rank 0: starting clear step. cycleNumber= 1 325s Rank 0 adding 0 new fusions 325s Rank 0 cleared, 1 paths 325s Rank 0 is distributing fusions [1/1] 325s Rank 0: assembler memory usage: 163412 KiB 325s Date: Mon Jul 8 15:36:50 2024 325s Rank 0 is distributing fusions [1/1] (completed) 325s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 325s Rank 0: assembler memory usage: 163412 KiB 325s Date: Mon Jul 8 15:36:50 2024 325s Rank 0 JoinerTaskCreator assignNextTask [0/2] 325s Rank 0: assembler memory usage: 163412 KiB 325s Date: Mon Jul 8 15:36:50 2024 325s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 325s Rank 0: assembler memory usage: 163412 KiB 325s Date: Mon Jul 8 15:36:50 2024 325s Rank 0 JoinerTaskCreator [2/2] 325s Statistics: all paths: 1 eliminated during joining: 0 325s Rank 0: assembler memory usage: 163412 KiB 325s Date: Mon Jul 8 15:36:50 2024 325s VirtualProcessor: completed jobs: 2 325s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 327s Rank 0 adding 0 new fusions 327s Rank 0 cleared, 1 paths 327s Rank 0: starting distribution step 327s Rank 0 is distributing fusions [1/1] 327s Rank 0: assembler memory usage: 163412 KiB 327s Date: Mon Jul 8 15:36:52 2024 327s Rank 0 is distributing fusions [1/1] (completed) 327s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 327s Rank 0: assembler memory usage: 163412 KiB 327s Date: Mon Jul 8 15:36:52 2024 327s Rank 0 tells others to compute fusions. 327s Rank 0 FusionTaskCreator assignNextTask [0/2] 327s Rank 0: assembler memory usage: 163412 KiB 327s Date: Mon Jul 8 15:36:52 2024 327s Rank 0 FusionTaskCreator processWorkerResult [0/2] 327s Rank 0: assembler memory usage: 163412 KiB 327s Date: Mon Jul 8 15:36:52 2024 327s Rank 0 FusionTaskCreator [2/2] 327s Statistics: all paths: 1 eliminated during fusing: 0 327s Rank 0: assembler memory usage: 163412 KiB 327s VirtualProcessor: completed jobs: 2 327s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 327s Rank 0: starting clear step. cycleNumber= 2 329s Rank 0 adding 0 new fusions 329s Rank 0 cleared, 1 paths 329s Rank 0 is distributing fusions [1/1] 329s Rank 0: assembler memory usage: 163412 KiB 329s Date: Mon Jul 8 15:36:54 2024 329s Rank 0 is distributing fusions [1/1] (completed) 329s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 329s Rank 0: assembler memory usage: 163412 KiB 329s Date: Mon Jul 8 15:36:54 2024 329s Rank 0 JoinerTaskCreator assignNextTask [0/2] 329s Rank 0: assembler memory usage: 163412 KiB 329s Date: Mon Jul 8 15:36:54 2024 329s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 329s Rank 0: assembler memory usage: 163412 KiB 329s Date: Mon Jul 8 15:36:54 2024 329s Rank 0 JoinerTaskCreator [2/2] 329s Statistics: all paths: 1 eliminated during joining: 0 329s Rank 0: assembler memory usage: 163412 KiB 329s Date: Mon Jul 8 15:36:54 2024 329s VirtualProcessor: completed jobs: 2 329s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 331s Rank 0 adding 0 new fusions 331s Rank 0 cleared, 1 paths 331s Rank 0: starting distribution step 331s Rank 0 is distributing fusions [1/1] 331s Rank 0: assembler memory usage: 163412 KiB 331s Date: Mon Jul 8 15:36:56 2024 331s Rank 0 is distributing fusions [1/1] (completed) 331s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 331s Rank 0: assembler memory usage: 163412 KiB 331s Date: Mon Jul 8 15:36:56 2024 331s Rank 0 cycleNumber= 2 331s 331s *** 331s Step: Merging of redundant paths 331s Date: Mon Jul 8 15:36:56 2024 331s Elapsed time: 10 seconds 331s Since beginning: 31 seconds 331s *** 331s 331s 331s Rank 0 appended 1 elements 331s 331s *** 331s Step: Generation of contigs 331s Date: Mon Jul 8 15:36:56 2024 331s Elapsed time: 0 seconds 331s Since beginning: 31 seconds 331s *** 331s 331s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 331s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 331s Rank 0 ineligibleObjects: 0/970 (0.00%) 331s Rank 0: assembler memory usage: 163412 KiB 331s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 331s Rank 0 finished gathering scaffold links. 331s Rank 0 will write 1 contig lengths 331s Rank 0 will solve the scaffolding problem. 331s Welcome to GreedySolver v1.0 331s 1 vertices; 0 edges 331s 1 contigs >= 500 331s Edges in solution: 0 331s 331s Conflict statistics: 331s 1 scaffolds, 1 >= 500 331s Total: 1000 nucleotides 331s 331s *** 331s Step: Scaffolding of contigs 331s Date: Mon Jul 8 15:36:56 2024 331s Elapsed time: 0 seconds 331s Since beginning: 31 seconds 331s *** 331s 331s Rank 0 syncing with master 331s 331s *** 331s Step: Counting sequences to search 331s Date: Mon Jul 8 15:36:56 2024 331s Elapsed time: 0 seconds 331s Since beginning: 31 seconds 331s *** 331s 331s 331s Rank 0 will add colors, 0 sequences in 0 files to process 331s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 333s 333s *** 333s Step: Graph coloring 333s Date: Mon Jul 8 15:36:58 2024 333s Elapsed time: 2 seconds 333s Since beginning: 33 seconds 333s *** 333s 333s 333s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 333s Rank 0 shares its counts 333s Rank 0 computing contig abundances [1/1] [1/970] 333s Rank 0 computing contig abundances [1/1] [970/970] 333s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 333s 333s *** 333s Step: Counting contig biological abundances 333s Date: Mon Jul 8 15:36:58 2024 333s Elapsed time: 0 seconds 333s Since beginning: 33 seconds 333s *** 333s 333s 333s Rank 0 colored the graph with 0 real colors using 1 virtual colors 333s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 333s 333s *** 333s Step: Counting sequence biological abundances 333s Date: Mon Jul 8 15:36:58 2024 333s Elapsed time: 0 seconds 333s Since beginning: 33 seconds 333s *** 333s 333s 333s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 333s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 335s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 335s 335s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 335s Rank 0 is starting taxon syncing across the compute tribe. 335s 335s *** 335s Step: Loading taxons 335s Date: Mon Jul 8 15:37:00 2024 335s Elapsed time: 2 seconds 335s Since beginning: 35 seconds 335s *** 335s 335s Rank 0 synced taxons across the grid with 1 poor slaves. 335s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 335s Rank 0 has 0 taxons after syncing with master 337s 337s 337s *** 337s Step: Loading tree 337s Date: Mon Jul 8 15:37:02 2024 337s Elapsed time: 2 seconds 337s Since beginning: 37 seconds 337s *** 337s 339s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 339s 339s Rank 0: counting ontology terms in the graph... 341s Rank 0: 0 have some biological signal 341s Number of dereferenced alternate handles: 0 341s Number of k-mer observations with gene ontology terms: 0 341s Rank 0: synced ontology term profiles with master 341s Rank 0: synchronization is complete! 341s Rank 0: ontology terms with biological signal: 0 341s Populated recursive values... 341s Gene ontology terms without depth information: 0 341s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 341s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 341s 341s *** 341s Step: Processing gene ontologies 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 4 seconds 341s Since beginning: 41 seconds 341s *** 341s 341s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 341s [GenomeNeighbourhood] in final list: 0 341s 341s *** 341s Step: Computing neighbourhoods 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 0 seconds 341s Since beginning: 41 seconds 341s *** 341s 341s Contigs >= 100 nt 341s Number: 1 341s Total length: 1000 341s Average: 1000 341s N50: 1000 341s Median: 1000 341s Largest: 1000 341s Contigs >= 500 nt 341s Number: 1 341s Total length: 1000 341s Average: 1000 341s N50: 1000 341s Median: 1000 341s Largest: 1000 341s Scaffolds >= 100 nt 341s Number: 1 341s Total length: 1000 341s Average: 1000 341s N50: 1000 341s Median: 1000 341s Largest: 1000 341s Scaffolds >= 500 nt 341s Number: 1 341s Total length: 1000 341s Average: 1000 341s N50: 1000 341s Median: 1000 341s Largest: 1000 341s 341s Rank 0 wrote test2/Contigs.fasta 341s Rank 0 wrote test2/Scaffolds.fasta 341s Check for test2/* 341s 341s 341s 341s ************************************************** 341s This program comes with ABSOLUTELY NO WARRANTY. 341s This is free software, and you are welcome to redistribute it 341s under certain conditions; see "LICENSE.txt" for details. 341s ************************************************** 341s 341s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 341s Centre de recherche en infectiologie de l'Université Laval 341s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 341s http://denovoassembler.sf.net/ 341s 341s References to cite: 341s 341s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 341s Ray Meta: scalable de novo metagenome assembly and profiling. 341s Genome Biology (BioMed Central Ltd). 341s 13:R122, Published: 22 December 2012 341s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 341s 341s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 341s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 341s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 341s November 2010, Volume 17, Issue 11, Pages 1519-1533. 341s http://dx.doi.org/doi:10.1089/cmb.2009.0238 341s 341s Ray version 2.3.1 341s License for Ray: GNU General Public License version 3 341s RayPlatform version: 2.0.1 341s License for RayPlatform: GNU Lesser General Public License version 3 341s 341s MAXKMERLENGTH: 32 341s Maximum coverage depth stored by CoverageDepth: 4294967295 341s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 341s FORCE_PACKING = n 341s ASSERT = n 341s HAVE_LIBZ = y 341s HAVE_LIBBZ2 = y 341s PROFILER_COLLECT = n 341s MINIRANKS = y 341s CLOCK_GETTIME = n 341s __linux__ = y 341s _MSC_VER = n 341s __GNUC__ = y 341s RAY_32_BITS = n 341s RAY_64_BITS = y 341s MPI standard version: MPI 3.1 341s MPI library: Open-MPI 4.1.6 341s Compiler: GNU gcc/g++ 13.2.0 341s MPI I/O: n 341s 341s 341s -k (to set the k-mer size) 341s Value: 29 341s 341s 341s Paired library # 0 341s -p (paired-end sequences) 341s Left sequences: SampleDirectory/s_6.first1000_1.fastq 341s Right sequences: SampleDirectory/s_6.first1000_2.fastq 341s Average length: automatic detection 341s Standard deviation: automatic detection 341s 341s Ray command: 341s mpiexec -n 1 Ray \ 341s -k \ 341s 29 \ 341s -desable-recycling \ 341s -p \ 341s SampleDirectory/s_6.first1000_1.fastq \ 341s SampleDirectory/s_6.first1000_2.fastq 341s 341s Rank 0 wrote RayOutput/RayCommand.txt 341s 341s k-mer length: 29 341s Rank 0: assembler memory usage: 42804 KiB 341s Rank 0: assembler memory usage: 108620 KiB 341s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3105 341s Rank 0: testing the network, please wait... 341s 341s Rank 0 is testing the network [0/1000] 341s Rank 0 is testing the network [1000/1000] 341s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 341s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 341s 341s Rank 0 wrote RayOutput/NetworkTest.txt 341s 341s 341s *** 341s Step: Network testing 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 0 seconds 341s Since beginning: 0 seconds 341s *** 341s 341s 341s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 341s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 341s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 341s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 341s Rank 0 wrote RayOutput/NumberOfSequences.txt 341s Rank 0 wrote RayOutput/SequencePartition.txt 341s 341s *** 341s Step: Counting sequences to assemble 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 0 seconds 341s Since beginning: 0 seconds 341s *** 341s 341s 341s Rank 0 is loading sequence reads 341s Rank 0 : partition is [0;4107], 4108 sequence reads 341s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 341s Rank 0 has 0 sequence reads 341s Rank 0: assembler memory usage: 121496 KiB 341s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 341s Rank 0 has 4108 sequence reads (completed) 341s 341s *** 341s Step: Sequence loading 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 0 seconds 341s Since beginning: 0 seconds 341s *** 341s 341s 341s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 341s Rank 0 created its Bloom filter 341s Rank 0 is counting k-mers in sequence reads [1/4108] 341s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 341s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 341s 341s 341s *** 341s Step: K-mer counting 341s Date: Mon Jul 8 15:37:06 2024 341s Elapsed time: 0 seconds 341s Since beginning: 0 seconds 341s *** 341s 341s 341s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 341s Rank 0 destroyed its Bloom filter 341s Rank 0 has 1958 k-mers (completed) 341s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 341s Rank 0: assembler memory usage: 117876 KiB 343s 343s 343s Rank 0: the minimum coverage is 3 343s Rank 0: the peak coverage is 3 343s Warning: no peak observed in the k-mer coverage distribution. 343s to deal with the sequencing error rate, try to lower the k-mer length (-k) 343s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 343s 343s *** 343s Step: Coverage distribution analysis 343s Date: Mon Jul 8 15:37:08 2024 343s Elapsed time: 2 seconds 343s Since beginning: 2 seconds 343s *** 343s 343s 343s 344s Rank 0 is adding edges [1/4108] 344s Rank 0 is adding edges [4108/4108] (completed) 344s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 344s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 344s 344s *** 344s Step: Graph construction 344s Date: Mon Jul 8 15:37:09 2024 344s Elapsed time: 1 seconds 344s Since beginning: 3 seconds 344s *** 344s 344s 344s Rank 0 has 1958 vertices (completed) 344s Rank 0: assembler memory usage: 117876 KiB 346s Rank 0 is purging edges [1/1958] 346s Rank 0 is purging edges [1958/1958] (completed) 346s Rank 0: assembler memory usage: 118408 KiB 346s VirtualProcessor: completed jobs: 1958 346s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 348s Rank 0 wrote RayOutput/degreeDistribution.txt 348s 348s *** 348s Step: Null edge purging 348s Date: Mon Jul 8 15:37:13 2024 348s Elapsed time: 4 seconds 348s Since beginning: 7 seconds 348s *** 348s 348s 348s Rank 0 is selecting optimal read markers [1/4108] 348s Rank 0: assembler memory usage: 118408 KiB 348s Rank 0 is selecting optimal read markers [4108/4108] (completed) 348s Rank 0: peak number of workers: 599, maximum: 32768 348s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 348s Rank 0: assembler memory usage: 126620 KiB 348s Rank 0: Freeing unused assembler memory: 4096 KiB freed 348s Rank 0: assembler memory usage: 126620 KiB 348s 348s *** 348s Step: Selection of optimal read markers 348s Date: Mon Jul 8 15:37:13 2024 348s Elapsed time: 0 seconds 348s Since beginning: 7 seconds 348s *** 348s 348s 348s Rank 0: memory usage for optimal read markers= 4096 KiB 348s Rank 0 is creating seeds [1/1958] 348s Rank 0: assembler memory usage: 126620 KiB 350s Rank 0 has 1 seeds 350s Rank 0 is creating seeds [1958/1958] (completed) 350s Rank 0: peak number of workers: 746, maximum: 32768 350s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 350s Rank 0 runtime statistics for seeding algorithm: 350s Rank 0 Skipped paths because of dead end for head: 0 350s Rank 0 Skipped paths because of dead end for tail: 0 350s Rank 0 Skipped paths because of two dead ends: 0 350s Rank 0 Skipped paths because of bubble weak component: 0 350s Rank 0 Skipped paths because of short length: 1956 350s Rank 0 Skipped paths because of bad ownership: 1 350s Rank 0 Skipped paths because of low coverage: 0 350s Rank 0 Eligible paths: 1 350s Rank 0: assembler memory usage: 126620 KiB 350s Rank 0 has 1 seeds to register. 350s Rank 0 registered 0/1 350s Rank 0 registered 0/1 350s Rank 0 registered its seeds 350s VirtualProcessor: completed jobs: 0 350s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 352s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 361s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 361s Rank 0 merged its seeds: 1 seeds -> 1 seeds 361s 361s *** 361s Step: Detection of assembly seeds 361s Date: Mon Jul 8 15:37:27 2024 361s Elapsed time: 14 seconds 361s Since beginning: 21 seconds 361s *** 361s 361s 362s Rank 0 is calculating library lengths [1/1] 362s Rank 0 detected 1743 library lengths 362s Rank 0 is calculating library lengths [1/1] (completed) 362s Rank 0: peak number of workers: 1, maximum: 32768 362s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 362s Rank 0: assembler memory usage: 163488 KiB 362s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 362s 362s Mode= 2 signalAverage= 10 362s CURRENT IS NOISE, 244 362s GOT HIT 214 362s 362s 362s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 362s 362s *** 362s Step: Estimation of outer distances for paired reads 362s Date: Mon Jul 8 15:37:27 2024 362s Elapsed time: 0 seconds 362s Since beginning: 21 seconds 362s *** 362s 362s 362s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 362s Rank 0 traversed 1000 nucleotide symbols 362s Rank 0: assembler memory usage: 167584 KiB 362s Rank 0 is extending seeds [1/1] (completed) 362s Rank 0 extended 1 seeds out of 1 (100.00%) 362s Rank 0: assembler memory usage: 159392 KiB 362s Rank 0 starting fusions 362s 362s *** 362s Step: Bidirectional extension of seeds 362s Date: Mon Jul 8 15:37:27 2024 362s Elapsed time: 0 seconds 362s Since beginning: 21 seconds 362s *** 362s 362s 362s Rank 0: starting clear step. cycleNumber= 0 364s Rank 0 adding 0 new fusions 364s Rank 0 cleared, 1 paths 364s Rank 0: starting distribution step 364s Rank 0 is distributing fusions [1/1] 364s Rank 0: assembler memory usage: 159392 KiB 364s Date: Mon Jul 8 15:37:29 2024 364s Rank 0 is distributing fusions [1/1] (completed) 364s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 364s Rank 0: assembler memory usage: 163488 KiB 364s Date: Mon Jul 8 15:37:29 2024 364s Rank 0 tells others to compute fusions. 364s Rank 0 FusionTaskCreator assignNextTask [0/2] 364s Rank 0: assembler memory usage: 163488 KiB 364s Date: Mon Jul 8 15:37:29 2024 364s Rank 0 FusionTaskCreator processWorkerResult [0/2] 364s Rank 0: assembler memory usage: 163488 KiB 364s Date: Mon Jul 8 15:37:29 2024 364s Rank 0 FusionTaskCreator [2/2] 364s Statistics: all paths: 1 eliminated during fusing: 0 364s Rank 0: assembler memory usage: 163488 KiB 364s VirtualProcessor: completed jobs: 2 364s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 364s Rank 0: starting clear step. cycleNumber= 1 366s Rank 0 adding 0 new fusions 366s Rank 0 cleared, 1 paths 366s Rank 0 is distributing fusions [1/1] 366s Rank 0: assembler memory usage: 163488 KiB 366s Date: Mon Jul 8 15:37:31 2024 366s Rank 0 is distributing fusions [1/1] (completed) 366s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 366s Rank 0: assembler memory usage: 163488 KiB 366s Date: Mon Jul 8 15:37:31 2024 366s Rank 0 JoinerTaskCreator assignNextTask [0/2] 366s Rank 0: assembler memory usage: 163488 KiB 366s Date: Mon Jul 8 15:37:31 2024 366s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 366s Rank 0: assembler memory usage: 163488 KiB 366s Date: Mon Jul 8 15:37:31 2024 366s Rank 0 JoinerTaskCreator [2/2] 366s Statistics: all paths: 1 eliminated during joining: 0 366s Rank 0: assembler memory usage: 163488 KiB 366s Date: Mon Jul 8 15:37:31 2024 366s VirtualProcessor: completed jobs: 2 366s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 380s Rank 0 adding 0 new fusions 380s Rank 0 cleared, 1 paths 380s Rank 0: starting distribution step 380s Rank 0 is distributing fusions [1/1] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:33 2024 380s Rank 0 is distributing fusions [1/1] (completed) 380s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:33 2024 380s Rank 0 tells others to compute fusions. 380s Rank 0 FusionTaskCreator assignNextTask [0/2] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:33 2024 380s Rank 0 FusionTaskCreator processWorkerResult [0/2] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:33 2024 380s Rank 0 FusionTaskCreator [2/2] 380s Statistics: all paths: 1 eliminated during fusing: 0 380s Rank 0: assembler memory usage: 163488 KiB 380s VirtualProcessor: completed jobs: 2 380s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 380s Rank 0: starting clear step. cycleNumber= 2 380s Rank 0 adding 0 new fusions 380s Rank 0 cleared, 1 paths 380s Rank 0 is distributing fusions [1/1] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:35 2024 380s Rank 0 is distributing fusions [1/1] (completed) 380s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:35 2024 380s Rank 0 JoinerTaskCreator assignNextTask [0/2] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:35 2024 380s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:35 2024 380s Rank 0 JoinerTaskCreator [2/2] 380s Statistics: all paths: 1 eliminated during joining: 0 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:35 2024 380s VirtualProcessor: completed jobs: 2 380s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 380s Rank 0 adding 0 new fusions 380s Rank 0 cleared, 1 paths 380s Rank 0: starting distribution step 380s Rank 0 is distributing fusions [1/1] 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:37 2024 380s Rank 0 is distributing fusions [1/1] (completed) 380s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 380s Rank 0: assembler memory usage: 163488 KiB 380s Date: Mon Jul 8 15:37:37 2024 380s Rank 0 cycleNumber= 2 380s 380s *** 380s Step: Merging of redundant paths 380s Date: Mon Jul 8 15:37:37 2024 380s Elapsed time: 10 seconds 380s Since beginning: 31 seconds 380s *** 380s 380s 380s Rank 0 appended 1 elements 380s 380s *** 380s Step: Generation of contigs 380s Date: Mon Jul 8 15:37:37 2024 380s Elapsed time: 0 seconds 380s Since beginning: 31 seconds 380s *** 380s 380s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 380s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 380s Rank 0 ineligibleObjects: 0/972 (0.00%) 380s Rank 0: assembler memory usage: 163488 KiB 380s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 380s Rank 0 finished gathering scaffold links. 380s Rank 0 will write 1 contig lengths 380s Rank 0 will solve the scaffolding problem. 380s Welcome to GreedySolver v1.0 380s 1 vertices; 0 edges 380s 1 contigs >= 500 380s Edges in solution: 0 380s 380s Conflict statistics: 380s 1 scaffolds, 1 >= 500 380s Total: 1000 nucleotides 380s 380s *** 380s Step: Scaffolding of contigs 380s Date: Mon Jul 8 15:37:37 2024 380s Elapsed time: 0 seconds 380s Since beginning: 31 seconds 380s *** 380s 380s Rank 0 syncing with master 380s 380s *** 380s Step: Counting sequences to search 380s Date: Mon Jul 8 15:37:37 2024 380s Elapsed time: 0 seconds 380s Since beginning: 31 seconds 380s *** 380s 380s 380s Rank 0 will add colors, 0 sequences in 0 files to process 380s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 380s 380s *** 380s Step: Graph coloring 380s Date: Mon Jul 8 15:37:39 2024 380s Elapsed time: 2 seconds 380s Since beginning: 33 seconds 380s *** 380s 380s 380s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 380s Rank 0 shares its counts 380s Rank 0 computing contig abundances [1/1] [1/972] 380s Rank 0 computing contig abundances [1/1] [972/972] 380s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 380s 380s *** 380s Step: Counting contig biological abundances 380s Date: Mon Jul 8 15:37:39 2024 380s Elapsed time: 0 seconds 380s Since beginning: 33 seconds 380s *** 380s 380s 380s Rank 0 colored the graph with 0 real colors using 1 virtual colors 380s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 380s 380s *** 380s Step: Counting sequence biological abundances 380s Date: Mon Jul 8 15:37:39 2024 380s Elapsed time: 0 seconds 380s Since beginning: 33 seconds 380s *** 380s 380s 380s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 380s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 380s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 380s 380s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 380s Rank 0 is starting taxon syncing across the compute tribe. 380s 380s *** 380s Step: Loading taxons 380s Date: Mon Jul 8 15:37:41 2024 380s Elapsed time: 2 seconds 380s Since beginning: 35 seconds 380s *** 380s 380s Rank 0 synced taxons across the grid with 1 poor slaves. 380s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 380s Rank 0 has 0 taxons after syncing with master 380s 380s 380s *** 380s Step: Loading tree 380s Date: Mon Jul 8 15:37:43 2024 380s Elapsed time: 2 seconds 380s Since beginning: 37 seconds 380s *** 380s 380s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 380s 380s Rank 0: counting ontology terms in the graph... 382s Rank 0: 0 have some biological signal 382s Number of dereferenced alternate handles: 0 382s Number of k-mer observations with gene ontology terms: 0 382s Rank 0: synced ontology term profiles with master 382s Rank 0: synchronization is complete! 382s Rank 0: ontology terms with biological signal: 0 382s Populated recursive values... 382s Gene ontology terms without depth information: 0 382s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 384s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 384s 384s *** 384s Step: Processing gene ontologies 384s Date: Mon Jul 8 15:37:47 2024 384s Elapsed time: 4 seconds 384s Since beginning: 41 seconds 384s *** 385s 385s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 385s [GenomeNeighbourhood] in final list: 0 385s 385s *** 385s Step: Computing neighbourhoods 385s Date: Mon Jul 8 15:37:47 2024 385s Elapsed time: 0 seconds 385s Since beginning: 41 seconds 385s *** 385s 385s Contigs >= 100 nt 385s Number: 1 385s Total length: 1000 385s Average: 1000 385s N50: 1000 385s Median: 1000 385s Largest: 1000 385s Contigs >= 500 nt 385s Number: 1 385s Total length: 1000 385s Average: 1000 385s N50: 1000 385s Median: 1000 385s Largest: 1000 385s Scaffolds >= 100 nt 385s Number: 1 385s Total length: 1000 385s Average: 1000 385s N50: 1000 385s Median: 1000 385s Largest: 1000 385s Scaffolds >= 500 nt 385s Number: 1 385s Total length: 1000 385s Average: 1000 385s N50: 1000 385s Median: 1000 385s Largest: 1000 385s 385s Rank 0 wrote RayOutput/Contigs.fasta 385s Rank 0 wrote RayOutput/Scaffolds.fasta 385s Check for RayOutput/* 385s 385s 385s 385s ************************************************** 385s This program comes with ABSOLUTELY NO WARRANTY. 385s This is free software, and you are welcome to redistribute it 385s under certain conditions; see "LICENSE.txt" for details. 385s ************************************************** 385s 385s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 385s Centre de recherche en infectiologie de l'Université Laval 385s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 385s http://denovoassembler.sf.net/ 385s 385s References to cite: 385s 385s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 385s Ray Meta: scalable de novo metagenome assembly and profiling. 385s Genome Biology (BioMed Central Ltd). 385s 13:R122, Published: 22 December 2012 385s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 385s 385s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 385s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 385s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 385s November 2010, Volume 17, Issue 11, Pages 1519-1533. 385s http://dx.doi.org/doi:10.1089/cmb.2009.0238 385s 385s Ray version 2.3.1 385s License for Ray: GNU General Public License version 3 385s RayPlatform version: 2.0.1 385s License for RayPlatform: GNU Lesser General Public License version 3 385s 385s MAXKMERLENGTH: 32 385s Maximum coverage depth stored by CoverageDepth: 4294967295 385s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 385s FORCE_PACKING = n 385s ASSERT = n 385s HAVE_LIBZ = y 385s HAVE_LIBBZ2 = y 385s PROFILER_COLLECT = n 385s MINIRANKS = y 385s CLOCK_GETTIME = n 385s __linux__ = y 385s _MSC_VER = n 385s __GNUC__ = y 385s RAY_32_BITS = n 385s RAY_64_BITS = y 385s MPI standard version: MPI 3.1 385s MPI library: Open-MPI 4.1.6 385s Compiler: GNU gcc/g++ 13.2.0 385s MPI I/O: n 385s 385s 385s -k (to set the k-mer size) 385s Value: 31 385s 385s 385s Paired library # 0 385s -p (paired-end sequences) 385s Left sequences: ecoli_1K_1.fq 385s Right sequences: ecoli_1K_2.fq 385s Average length: automatic detection 385s Standard deviation: automatic detection 385s 385s Ray command: 385s mpiexec -n 2 Ray \ 385s -k \ 385s 31 \ 385s -p \ 385s ecoli_1K_1.fq \ 385s ecoli_1K_2.fq \ 385s -o \ 385s test3 385s 385s Rank 0 wrote test3/RayCommand.txt 385s 385s k-mer length: 31 385s Rank 1: assembler memory usage: 42860 KiB 385s Rank 0: assembler memory usage: 42876 KiB 385s Rank 0: assembler memory usage: 108548 KiB 385s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 3116 385s Rank 0: testing the network, please wait... 385s 385s Rank 1: assembler memory usage: 108532 KiB 385s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 3117 385s Rank 0 is testing the network [0/1000] 385s Rank 1 is testing the network [0/1000] 385s Rank 1 is testing the network [1000/1000] 385s Rank 0 is testing the network [1000/1000] 385s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 385s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 385s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 385s 385s Rank 0 wrote test3/NetworkTest.txt 385s 385s 385s *** 385s Step: Network testing 385s Date: Mon Jul 8 15:37:47 2024 385s Elapsed time: 0 seconds 385s Since beginning: 0 seconds 385s *** 385s 385s 385s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 385s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 385s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 385s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 385s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 385s Rank 0 wrote test3/NumberOfSequences.txt 385s Rank 0 wrote test3/SequencePartition.txt 385s 385s *** 385s Step: Counting sequences to assemble 385s Date: Mon Jul 8 15:37:47 2024 385s Elapsed time: 0 seconds 385s Since beginning: 0 seconds 385s *** 385s 385s 385s Rank 0 is loading sequence reads 385s Rank 0 : partition is [0;2053], 2054 sequence reads 385s Rank 1 is loading sequence reads 385s Rank 1 : partition is [2054;4107], 2054 sequence reads 385s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 385s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 385s Rank 0 has 0 sequence reads 385s Rank 0: assembler memory usage: 117416 KiB 385s Rank 1 has 0 sequence reads 385s Rank 1: assembler memory usage: 117400 KiB 385s Rank 0 has 2054 sequence reads (completed) 385s 385s *** 385s Step: Sequence loading 385s Date: Mon Jul 8 15:37:47 2024 385s Elapsed time: 0 seconds 385s Since beginning: 0 seconds 385s *** 385s 385s 385s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 385s Rank 1 has 2054 sequence reads (completed) 385s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 385s Rank 0 created its Bloom filter 385s Rank 0 is counting k-mers in sequence reads [1/2054] 385s Rank 1 created its Bloom filter 385s Rank 1 is counting k-mers in sequence reads [1/2054] 385s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 385s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 385s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 385s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 385s 385s 385s *** 385s Step: K-mer counting 385s Date: Mon Jul 8 15:37:47 2024 385s Elapsed time: 0 seconds 385s Since beginning: 0 seconds 385s *** 385s 385s 385s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 385s Rank 0 destroyed its Bloom filter 385s Rank 0 has 1032 k-mers (completed) 385s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 385s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 385s Rank 0: assembler memory usage: 113684 KiB 385s Rank 1 destroyed its Bloom filter 385s Rank 1 has 922 k-mers (completed) 385s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 385s Rank 1: assembler memory usage: 117400 KiB 385s 385s 385s Rank 0: the minimum coverage is 3 385s Rank 0: the peak coverage is 3 385s Warning: no peak observed in the k-mer coverage distribution. 385s to deal with the sequencing error rate, try to lower the k-mer length (-k) 385s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 385s 385s *** 385s Step: Coverage distribution analysis 385s Date: Mon Jul 8 15:37:49 2024 385s Elapsed time: 2 seconds 385s Since beginning: 2 seconds 385s *** 385s 385s 385s 385s Rank 0 is adding edges [1/2054] 385s Rank 1 is adding edges [1/2054] 385s Rank 1 is adding edges [2054/2054] (completed) 385s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 385s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 385s Rank 0 is adding edges [2054/2054] (completed) 385s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 385s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 385s 385s *** 385s Step: Graph construction 385s Date: Mon Jul 8 15:37:49 2024 385s Elapsed time: 0 seconds 385s Since beginning: 2 seconds 385s *** 385s 385s 385s Rank 1 has 922 vertices (completed) 385s Rank 1: assembler memory usage: 117400 KiB 385s Rank 0 has 1032 vertices (completed) 385s Rank 0: assembler memory usage: 113684 KiB 386s Rank 1 is purging edges [1/922] 386s Rank 0 is purging edges [1/1032] 386s Rank 1 is purging edges [922/922] (completed) 386s Rank 1: assembler memory usage: 117400 KiB 386s VirtualProcessor: completed jobs: 922 386s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 386s Rank 0 is purging edges [1032/1032] (completed) 386s Rank 0: assembler memory usage: 113952 KiB 386s VirtualProcessor: completed jobs: 1032 386s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 388s Rank 0 wrote test3/degreeDistribution.txt 388s 388s *** 388s Step: Null edge purging 388s Date: Mon Jul 8 15:37:53 2024 388s Elapsed time: 4 seconds 388s Since beginning: 6 seconds 388s *** 388s 388s 388s Rank 1 is selecting optimal read markers [1/2054] 388s Rank 0 is selecting optimal read markers [1/2054] 388s Rank 1: assembler memory usage: 117400 KiB 388s Rank 0: assembler memory usage: 113952 KiB 389s Rank 1 is selecting optimal read markers [2054/2054] (completed) 389s Rank 1: peak number of workers: 1121, maximum: 32768 389s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 389s Rank 1: assembler memory usage: 125080 KiB 389s Rank 1: Freeing unused assembler memory: 4096 KiB freed 389s Rank 1: assembler memory usage: 125080 KiB 389s Rank 0 is selecting optimal read markers [2054/2054] (completed) 389s Rank 0: peak number of workers: 1135, maximum: 32768 389s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 389s Rank 0: assembler memory usage: 122156 KiB 389s Rank 0: Freeing unused assembler memory: 4096 KiB freed 389s Rank 0: assembler memory usage: 122156 KiB 389s 389s *** 389s Step: Selection of optimal read markers 389s Date: Mon Jul 8 15:37:54 2024 389s Elapsed time: 1 seconds 389s Since beginning: 7 seconds 389s *** 389s 389s 389s Rank 0: memory usage for optimal read markers= 4096 KiB 389s Rank 1: memory usage for optimal read markers= 4096 KiB 389s Rank 1 is creating seeds [1/922] 389s Rank 1: assembler memory usage: 125080 KiB 389s Rank 0 is creating seeds [1/1032] 389s Rank 0: assembler memory usage: 122156 KiB 391s Rank 1 has 1 seeds 391s Rank 1 is creating seeds [922/922] (completed) 391s Rank 1: peak number of workers: 916, maximum: 32768 391s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 391s Rank 1 runtime statistics for seeding algorithm: 391s Rank 1 Skipped paths because of dead end for head: 0 391s Rank 1 Skipped paths because of dead end for tail: 0 391s Rank 1 Skipped paths because of two dead ends: 0 391s Rank 1 Skipped paths because of bubble weak component: 0 391s Rank 1 Skipped paths because of short length: 921 391s Rank 1 Skipped paths because of bad ownership: 0 391s Rank 1 Skipped paths because of low coverage: 0 391s Rank 1 Eligible paths: 1 391s Rank 1: assembler memory usage: 125080 KiB 391s Rank 0 has 0 seeds 391s Rank 0 is creating seeds [1032/1032] (completed) 391s Rank 0: peak number of workers: 998, maximum: 32768 391s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 391s Rank 0 runtime statistics for seeding algorithm: 391s Rank 0 Skipped paths because of dead end for head: 0 391s Rank 0 Skipped paths because of dead end for tail: 0 391s Rank 0 Skipped paths because of two dead ends: 0 391s Rank 0 Skipped paths because of bubble weak component: 0 391s Rank 0 Skipped paths because of short length: 1031 391s Rank 0 Skipped paths because of bad ownership: 1 391s Rank 0 Skipped paths because of low coverage: 0 391s Rank 0 Eligible paths: 0 391s Rank 0: assembler memory usage: 122156 KiB 391s Rank 1 has 1 seeds to register. 391s Rank 1 registered 0/1 391s Rank 0 registered -1/0 391s Rank 0 registered its seeds 391s Rank 1 registered 0/1 391s Rank 1 registered its seeds 391s VirtualProcessor: completed jobs: 0 391s VirtualProcessor: completed jobs: 0 391s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 391s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 393s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 393s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 402s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 402s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 402s Rank 0 merged its seeds: 0 seeds -> 0 seeds 402s Rank 1 merged its seeds: 1 seeds -> 1 seeds 402s 402s *** 402s Step: Detection of assembly seeds 402s Date: Mon Jul 8 15:38:08 2024 402s Elapsed time: 14 seconds 402s Since beginning: 21 seconds 402s *** 402s 402s 402s Rank 0 detected 0 library lengths 402s Rank 0 is calculating library lengths [0/0] (completed) 402s Rank 0: peak number of workers: 0, maximum: 32768 402s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 402s Rank 0: assembler memory usage: 126252 KiB 403s Rank 1 is calculating library lengths [1/1] 403s Rank 1 detected 1737 library lengths 403s Rank 1 is calculating library lengths [1/1] (completed) 403s Rank 1: peak number of workers: 1, maximum: 32768 403s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7987 virtual messages generated 7987 real messages (100%) 403s Rank 1: assembler memory usage: 157852 KiB 403s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 403s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 403s 403s Mode= 2 signalAverage= 9 403s CURRENT IS NOISE, 244 403s GOT HIT 212 403s 403s 403s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 403s 403s *** 403s Step: Estimation of outer distances for paired reads 403s Date: Mon Jul 8 15:38:08 2024 403s Elapsed time: 0 seconds 403s Since beginning: 21 seconds 403s *** 403s 403s 403s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 403s Rank 0 is extending seeds [0/0] (completed) 403s Rank 0 extended 0 seeds out of 0 (0.00%) 403s Rank 0: assembler memory usage: 126252 KiB 403s Rank 1 traversed 1000 nucleotide symbols 403s Rank 1: assembler memory usage: 161948 KiB 403s Rank 1 is extending seeds [1/1] (completed) 403s Rank 1 extended 1 seeds out of 1 (100.00%) 403s Rank 1: assembler memory usage: 161948 KiB 403s Rank 0 starting fusions 403s 403s *** 403s Step: Bidirectional extension of seeds 403s Date: Mon Jul 8 15:38:08 2024 403s Elapsed time: 0 seconds 403s Since beginning: 21 seconds 403s *** 403s 403s 403s Rank 0: starting clear step. cycleNumber= 0 405s Rank 0 adding 0 new fusions 405s Rank 0 cleared, 0 paths 405s Rank 1 adding 0 new fusions 405s Rank 1 cleared, 1 paths 405s Rank 0: starting distribution step 405s Rank 1 is distributing fusions [1/1] 405s Rank 0 is distributing fusions [0/0] (completed) 405s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 405s Rank 1: assembler memory usage: 161948 KiB 405s Date: Mon Jul 8 15:38:10 2024 405s Rank 1 is distributing fusions [1/1] (completed) 405s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 405s Rank 1: assembler memory usage: 161948 KiB 405s Date: Mon Jul 8 15:38:10 2024 405s Rank 1 FusionTaskCreator assignNextTask [0/2] 405s Rank 1: assembler memory usage: 161948 KiB 405s Date: Mon Jul 8 15:38:10 2024 405s Rank 0: assembler memory usage: 126252 KiB 405s Date: Mon Jul 8 15:38:10 2024 405s Rank 0 tells others to compute fusions. 405s Rank 0 FusionTaskCreator [0/0] 405s Statistics: all paths: 0 eliminated during fusing: 0 405s Rank 0: assembler memory usage: 126252 KiB 405s VirtualProcessor: completed jobs: 0 405s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 405s Rank 1 FusionTaskCreator processWorkerResult [0/2] 405s Rank 1: assembler memory usage: 161948 KiB 405s Date: Mon Jul 8 15:38:10 2024 405s Rank 1 FusionTaskCreator [2/2] 405s Statistics: all paths: 1 eliminated during fusing: 0 405s Rank 1: assembler memory usage: 161948 KiB 405s VirtualProcessor: completed jobs: 2 405s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10897 virtual messages generated 10897 real messages (100%) 405s Rank 0: starting clear step. cycleNumber= 1 407s Rank 0 adding 0 new fusions 407s Rank 0 cleared, 0 paths 407s Rank 1 adding 0 new fusions 407s Rank 1 cleared, 1 paths 407s Rank 0 is distributing fusions [0/0] (completed) 407s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 407s Rank 1 is distributing fusions [1/1] 407s Rank 0: assembler memory usage: 126252 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 1: assembler memory usage: 161948 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 1 is distributing fusions [1/1] (completed) 407s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 407s Rank 1: assembler memory usage: 161948 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 0 JoinerTaskCreator [0/0] 407s Statistics: all paths: 0 eliminated during joining: 0 407s Rank 1 JoinerTaskCreator assignNextTask [0/2] 407s Rank 0: assembler memory usage: 126252 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 1: assembler memory usage: 161948 KiB 407s VirtualProcessor: completed jobs: 0 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 407s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 407s Rank 1: assembler memory usage: 161948 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s Rank 1 JoinerTaskCreator [2/2] 407s Statistics: all paths: 1 eliminated during joining: 0 407s Rank 1: assembler memory usage: 161948 KiB 407s Date: Mon Jul 8 15:38:12 2024 407s VirtualProcessor: completed jobs: 2 407s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13807 virtual messages generated 13807 real messages (100%) 409s Rank 1 adding 0 new fusions 409s Rank 1 cleared, 1 paths 409s Rank 0 adding 0 new fusions 409s Rank 0 cleared, 0 paths 409s Rank 0: starting distribution step 409s Rank 0 is distributing fusions [0/0] (completed) 409s Rank 1 is distributing fusions [1/1] 409s Rank 1: assembler memory usage: 161948 KiB 409s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 409s Date: Mon Jul 8 15:38:14 2024 409s Rank 0: assembler memory usage: 126252 KiB 409s Date: Mon Jul 8 15:38:14 2024 409s Rank 1 is distributing fusions [1/1] (completed) 409s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 409s Rank 1: assembler memory usage: 161948 KiB 409s Date: Mon Jul 8 15:38:14 2024 409s Rank 0 tells others to compute fusions. 409s Rank 0 FusionTaskCreator [0/0] 409s Statistics: all paths: 0 eliminated during fusing: 0 409s Rank 1 FusionTaskCreator assignNextTask [0/2] 409s Rank 0: assembler memory usage: 126252 KiB 409s Rank 1: assembler memory usage: 161948 KiB 409s Date: Mon Jul 8 15:38:14 2024 409s VirtualProcessor: completed jobs: 0 409s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 409s Rank 1 FusionTaskCreator processWorkerResult [0/2] 409s Rank 1: assembler memory usage: 161948 KiB 409s Date: Mon Jul 8 15:38:14 2024 409s Rank 1 FusionTaskCreator [2/2] 409s Statistics: all paths: 1 eliminated during fusing: 0 409s Rank 1: assembler memory usage: 161948 KiB 409s VirtualProcessor: completed jobs: 2 409s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16717 virtual messages generated 16717 real messages (100%) 409s Rank 0: starting clear step. cycleNumber= 2 411s Rank 0 adding 0 new fusions 411s Rank 0 cleared, 0 paths 411s Rank 1 adding 0 new fusions 411s Rank 1 cleared, 1 paths 411s Rank 0 is distributing fusions [0/0] (completed) 411s Rank 1 is distributing fusions [1/1] 411s Rank 1: assembler memory usage: 161948 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 411s Rank 0: assembler memory usage: 126252 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s Rank 1 is distributing fusions [1/1] (completed) 411s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 411s Rank 1: assembler memory usage: 161948 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s Rank 0 JoinerTaskCreator [0/0] 411s Rank 1 JoinerTaskCreator assignNextTask [0/2] 411s Rank 1: assembler memory usage: 161948 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s Statistics: all paths: 0 eliminated during joining: 0 411s Rank 0: assembler memory usage: 126252 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s VirtualProcessor: completed jobs: 0 411s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 411s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 411s Rank 1: assembler memory usage: 161948 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s Rank 1 JoinerTaskCreator [2/2] 411s Statistics: all paths: 1 eliminated during joining: 0 411s Rank 1: assembler memory usage: 161948 KiB 411s Date: Mon Jul 8 15:38:16 2024 411s VirtualProcessor: completed jobs: 2 411s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19627 virtual messages generated 19627 real messages (100%) 413s Rank 0 adding 0 new fusions 413s Rank 0 cleared, 0 paths 413s Rank 1 adding 0 new fusions 413s Rank 1 cleared, 1 paths 413s Rank 0: starting distribution step 413s Rank 0 is distributing fusions [0/0] (completed) 413s Rank 1 is distributing fusions [1/1] 413s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 413s Rank 1: assembler memory usage: 161948 KiB 413s Date: Mon Jul 8 15:38:18 2024 413s Rank 0: assembler memory usage: 126252 KiB 413s Date: Mon Jul 8 15:38:18 2024 413s Rank 1 is distributing fusions [1/1] (completed) 413s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 413s Rank 1: assembler memory usage: 161948 KiB 413s Date: Mon Jul 8 15:38:18 2024 413s Rank 0 cycleNumber= 2 413s 413s *** 413s Step: Merging of redundant paths 413s Date: Mon Jul 8 15:38:18 2024 413s Elapsed time: 10 seconds 413s Since beginning: 31 seconds 413s *** 413s 413s 413s Rank 1 appended 1 elements 413s Rank 0 appended 0 elements 413s 413s *** 413s Step: Generation of contigs 413s Date: Mon Jul 8 15:38:18 2024 413s Elapsed time: 0 seconds 413s Since beginning: 31 seconds 413s *** 413s 413s Rank 0 finished gathering scaffold links. 413s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 413s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 413s Rank 0 ineligibleObjects: 0/970 (0.00%) 413s Rank 1: assembler memory usage: 161948 KiB 413s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 413s Rank 1 finished gathering scaffold links. 413s Rank 0 will write 1 contig lengths 413s Rank 0 will solve the scaffolding problem. 413s Welcome to GreedySolver v1.0 413s 1 vertices; 0 edges 413s 1 contigs >= 500 413s Edges in solution: 0 413s 413s Conflict statistics: 413s 1 scaffolds, 1 >= 500 413s Total: 1000 nucleotides 413s 413s *** 413s Step: Scaffolding of contigs 413s Date: Mon Jul 8 15:38:18 2024 413s Rank 1 syncing with master 413s Rank 1 will add colors, 0 sequences in 0 files to process 413s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 413s Elapsed time: 0 seconds 413s Since beginning: 31 seconds 413s *** 413s 413s Rank 0 syncing with master 413s 413s *** 413s Step: Counting sequences to search 413s Date: Mon Jul 8 15:38:18 2024 413s Elapsed time: 0 seconds 413s Since beginning: 31 seconds 413s *** 413s 413s 413s Rank 0 will add colors, 0 sequences in 0 files to process 413s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 415s 415s *** 415s Step: Graph coloring 415s Date: Mon Jul 8 15:38:20 2024 415s Elapsed time: 2 seconds 415s Since beginning: 33 seconds 415s *** 415s 415s 415s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 415s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 415s Rank 0 shares its counts 415s Rank 1 computing contig abundances [1/1] [1/970] 415s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 415s Rank 1 computing contig abundances [1/1] [970/970] 415s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 415s 415s *** 415s Step: Counting contig biological abundances 415s Date: Mon Jul 8 15:38:20 2024 415s Elapsed time: 0 seconds 415s Since beginning: 33 seconds 415s *** 415s Rank 1 colored the graph with 0 real colors using 1 virtual colors 415s 415s 415s Rank 0 colored the graph with 0 real colors using 1 virtual colors 415s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 415s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 415s 415s *** 415s Step: Counting sequence biological abundances 415s Date: Mon Jul 8 15:38:20 2024 415s Elapsed time: 0 seconds 415s Since beginning: 33 seconds 415s *** 415s 415s 415s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 415s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 415s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 415s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 417s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 417s 417s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 417s 417s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 417s Rank 0 is starting taxon syncing across the compute tribe. 417s 417s *** 417s Step: Loading taxons 417s Date: Mon Jul 8 15:38:22 2024 417s Elapsed time: 2 seconds 417s Since beginning: 35 seconds 417s *** 417s 417s Rank 0 synced taxons across the grid with 2 poor slaves. 417s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 417s Rank 1 has 0 taxons after syncing with master 417s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 417s Rank 0 has 0 taxons after syncing with master 419s 419s 419s 419s *** 419s Step: Loading tree 419s Date: Mon Jul 8 15:38:24 2024 419s Elapsed time: 2 seconds 419s Since beginning: 37 seconds 419s *** 419s 421s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 421s 421s Rank 0: counting ontology terms in the graph... 421s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 421s 421s Rank 1: counting ontology terms in the graph... 423s Rank 0: 0 have some biological signal 423s Number of dereferenced alternate handles: 0 423s Number of k-mer observations with gene ontology terms: 0 423s Rank 0: synced ontology term profiles with master 423s Rank 1: 0 have some biological signal 423s Number of dereferenced alternate handles: 0 423s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 423s Rank 0: synchronization is complete! 423s Rank 0: ontology terms with biological signal: 0 423s Populated recursive values... 423s Gene ontology terms without depth information: 0 423s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 423s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 423s 423s *** 423s Step: Processing gene ontologies 423s Date: Mon Jul 8 15:38:28 2024 423s Number of k-mer observations with gene ontology terms: 0 423s Rank 1: synced ontology term profiles with master 423s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 423s Elapsed time: 4 seconds 423s Since beginning: 41 seconds 423s *** 423s 423s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 423s [GenomeNeighbourhood] in final list: 0 423s 423s *** 423s Step: Computing neighbourhoods 423s Date: Mon Jul 8 15:38:28 2024 423s Elapsed time: 0 seconds 423s Since beginning: 41 seconds 423s *** 423s 423s Contigs >= 100 nt 423s Number: 1 423s Total length: 1000 423s Average: 1000 423s N50: 1000 423s Median: 1000 423s Largest: 1000 423s Contigs >= 500 nt 423s Number: 1 423s Total length: 1000 423s Average: 1000 423s N50: 1000 423s Median: 1000 423s Largest: 1000 423s Scaffolds >= 100 nt 423s Number: 1 423s Total length: 1000 423s Average: 1000 423s N50: 1000 423s Median: 1000 423s Largest: 1000 423s Scaffolds >= 500 nt 423s Number: 1 423s Total length: 1000 423s Average: 1000 423s N50: 1000 423s Median: 1000 423s Largest: 1000 423s 423s Rank 0 wrote test3/Contigs.fasta 423s Rank 0 wrote test3/Scaffolds.fasta 423s Check for test3/* 423s 423s 423s autopkgtest [15:38:28]: test run-unit-test: -----------------------] 425s autopkgtest [15:38:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 425s run-unit-test PASS 428s autopkgtest [15:38:33]: @@@@@@@@@@@@@@@@@@@@ summary 428s run-unit-test PASS 489s nova [W] Skipping flock for amd64 489s Creating nova instance adt-oracular-amd64-ray-20240708-153106-juju-7f2275-prod-proposed-migration-environment-3-cb8fbdba-0af6-4ed0-b577-f5faefe907b5 from image adt/ubuntu-oracular-amd64-server-20240708.img (UUID a0fb9aef-f002-4c41-8539-53542ad6f0d4)...