0s autopkgtest [23:56:48]: starting date and time: 2024-08-01 23:56:48+0000 0s autopkgtest [23:56:48]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [23:56:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.13b2y886/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:mpich,src:hwloc,src:slurm-wlm --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=mpich/4.2.0-9ubuntu3 hwloc/2.11.0-2 slurm-wlm/24.05.1-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-63.secgroup --name adt-oracular-amd64-ray-20240801-235647-juju-7f2275-prod-proposed-migration-environment-2-2df57bff-4151-4840-a0d3-d30af6d04837 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 71s autopkgtest [23:57:59]: testbed dpkg architecture: amd64 72s autopkgtest [23:58:00]: testbed apt version: 2.9.6 72s autopkgtest [23:58:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 73s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8552 B] 73s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [57.8 kB] 73s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [632 kB] 73s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [8756 B] 73s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [105 kB] 73s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [62.4 kB] 73s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [3700 B] 73s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [35.6 kB] 73s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6888 B] 73s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 73s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [671 kB] 73s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [283 kB] 73s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [20.7 kB] 73s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [4196 B] 73s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [12.1 kB] 73s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [552 B] 74s Fetched 2039 kB in 0s (5204 kB/s) 74s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [23:58:11]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 84s autopkgtest [23:58:12]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 86s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (dsc) [2192 B] 86s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (tar) [450 kB] 86s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (diff) [213 kB] 86s gpgv: Signature made Mon Apr 1 07:35:01 2024 UTC 86s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 86s gpgv: Can't check signature: No public key 86s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8build2.dsc: no acceptable signature found 86s autopkgtest [23:58:14]: testing package ray version 2.3.1-8build2 86s autopkgtest [23:58:14]: build not needed 87s autopkgtest [23:58:15]: test run-unit-test: preparing testbed 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 90s The following additional packages will be installed: 90s fontconfig libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdatrie1 90s libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 90s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 90s libibumad3 libice6 liblapack3 libllvm17t64 libmunge2 libopenmpi3t64 90s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 90s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 libpsm-infinipath1 90s libpsm2-2 librdmacm1t64 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 90s libucx0 libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 90s libxt6t64 mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common 90s r-base-core ray ray-doc ray-extra unzip x11-common xdg-utils zip 90s Suggested packages: 90s libhwloc-contrib-plugins tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler 90s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 90s Recommended packages: 90s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 90s libx11-protocol-perl x11-utils x11-xserver-utils 90s The following NEW packages will be installed: 90s autopkgtest-satdep fontconfig libamd-comgr2 libamdhip64-5 libblas3 libcairo2 90s libdatrie1 libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libfabric1 libgfortran5 90s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 90s libibumad3 libice6 liblapack3 libllvm17t64 libmunge2 libopenmpi3t64 90s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 90s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 libpsm-infinipath1 90s libpsm2-2 librdmacm1t64 libsm6 libtcl8.6 libthai-data libthai0 libtk8.6 90s libucx0 libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 90s libxt6t64 mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common 90s r-base-core ray ray-doc ray-extra unzip x11-common xdg-utils zip 90s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 94.0 MB/94.0 MB of archives. 90s After this operation, 307 MB of additional disk space will be used. 90s Get:1 /tmp/autopkgtest.8SVVik/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 90s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 90s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libllvm17t64 amd64 1:17.0.6-12 [26.2 MB] 90s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 90s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-amdgpu1 amd64 2.4.121-2 [20.7 kB] 90s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 90s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 90s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamdhip64-5 amd64 5.7.1-4 [9526 kB] 90s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 90s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB] 90s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 90s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 90s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 90s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libcairo2 amd64 1.18.0-3build1 [566 kB] 90s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 90s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 90s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 90s Get:18 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 90s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 librdmacm1t64 amd64 52.0-2 [70.7 kB] 90s Get:20 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfabric1 amd64 1.17.0-3build2 [657 kB] 91s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-5ubuntu1 [909 kB] 91s Get:22 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libhwloc15 amd64 2.11.0-2 [173 kB] 91s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 91s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB] 91s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 91s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 91s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 91s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 91s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 91s Get:30 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libhwloc-plugins amd64 2.11.0-2 [15.7 kB] 91s Get:31 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpmix2t64 amd64 5.0.1-4.1build1 [697 kB] 91s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libibumad3 amd64 52.0-2 [28.9 kB] 91s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libibmad5 amd64 52.0-2 [42.8 kB] 91s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 libucx0 amd64 1.17.0+ds-3 [1162 kB] 91s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 libopenmpi3t64 amd64 4.1.6-7ubuntu2 [2563 kB] 91s Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 91s Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 91s Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [233 kB] 91s Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [42.3 kB] 91s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [28.7 kB] 91s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 91s Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 91s Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB] 91s Get:44 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 91s Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 91s Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 91s Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 91s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 91s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-common all 4.1.6-7ubuntu2 [170 kB] 91s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 openmpi-bin amd64 4.1.6-7ubuntu2 [114 kB] 91s Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 zip amd64 3.0-14 [174 kB] 91s Get:52 http://ftpmaster.internal/ubuntu oracular/main amd64 unzip amd64 6.0-28ubuntu5 [180 kB] 91s Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 91s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 r-base-core amd64 4.4.1-1 [28.5 MB] 91s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 mpi-default-bin amd64 1.15build1 [2376 B] 91s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray amd64 2.3.1-8build2 [740 kB] 91s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray-doc all 2.3.1-8build2 [35.1 kB] 91s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 ray-extra all 2.3.1-8build2 [12.1 kB] 91s Preconfiguring packages ... 91s Fetched 94.0 MB in 1s (98.4 MB/s) 91s Selecting previously unselected package fontconfig. 92s (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 ... 74235 files and directories currently installed.) 92s Preparing to unpack .../00-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package libllvm17t64:amd64. 92s Preparing to unpack .../01-libllvm17t64_1%3a17.0.6-12_amd64.deb ... 92s Unpacking libllvm17t64:amd64 (1:17.0.6-12) ... 92s Selecting previously unselected package libamd-comgr2:amd64. 92s Preparing to unpack .../02-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 92s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 92s Selecting previously unselected package libdrm-amdgpu1:amd64. 92s Preparing to unpack .../03-libdrm-amdgpu1_2.4.121-2_amd64.deb ... 92s Unpacking libdrm-amdgpu1:amd64 (2.4.121-2) ... 92s Selecting previously unselected package libhsakmt1:amd64. 92s Preparing to unpack .../04-libhsakmt1_5.7.0-1build1_amd64.deb ... 92s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 92s Selecting previously unselected package libhsa-runtime64-1. 92s Preparing to unpack .../05-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 92s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 93s Selecting previously unselected package libamdhip64-5. 93s Preparing to unpack .../06-libamdhip64-5_5.7.1-4_amd64.deb ... 93s Unpacking libamdhip64-5 (5.7.1-4) ... 93s Selecting previously unselected package libblas3:amd64. 93s Preparing to unpack .../07-libblas3_3.12.0-3build1_amd64.deb ... 93s Unpacking libblas3:amd64 (3.12.0-3build1) ... 93s Selecting previously unselected package libpixman-1-0:amd64. 93s Preparing to unpack .../08-libpixman-1-0_0.42.2-1build1_amd64.deb ... 93s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ... 93s Selecting previously unselected package libxcb-render0:amd64. 93s Preparing to unpack .../09-libxcb-render0_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libxcb-shm0:amd64. 93s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libxrender1:amd64. 93s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 93s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 93s Selecting previously unselected package libcairo2:amd64. 93s Preparing to unpack .../12-libcairo2_1.18.0-3build1_amd64.deb ... 93s Unpacking libcairo2:amd64 (1.18.0-3build1) ... 93s Selecting previously unselected package libdatrie1:amd64. 93s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_amd64.deb ... 93s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 93s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 93s Preparing to unpack .../14-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 93s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 93s Selecting previously unselected package libpsm-infinipath1. 93s Preparing to unpack .../15-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 93s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 93s Selecting previously unselected package libpsm2-2. 93s Preparing to unpack .../16-libpsm2-2_11.2.185-2.1_amd64.deb ... 93s Unpacking libpsm2-2 (11.2.185-2.1) ... 93s Selecting previously unselected package librdmacm1t64:amd64. 93s Preparing to unpack .../17-librdmacm1t64_52.0-2_amd64.deb ... 93s Unpacking librdmacm1t64:amd64 (52.0-2) ... 93s Selecting previously unselected package libfabric1:amd64. 93s Preparing to unpack .../18-libfabric1_1.17.0-3build2_amd64.deb ... 93s Unpacking libfabric1:amd64 (1.17.0-3build2) ... 93s Selecting previously unselected package libgfortran5:amd64. 93s Preparing to unpack .../19-libgfortran5_14.1.0-5ubuntu1_amd64.deb ... 93s Unpacking libgfortran5:amd64 (14.1.0-5ubuntu1) ... 93s Selecting previously unselected package libhwloc15:amd64. 93s Preparing to unpack .../20-libhwloc15_2.11.0-2_amd64.deb ... 93s Unpacking libhwloc15:amd64 (2.11.0-2) ... 93s Selecting previously unselected package x11-common. 93s Preparing to unpack .../21-x11-common_1%3a7.7+23ubuntu3_all.deb ... 93s Unpacking x11-common (1:7.7+23ubuntu3) ... 93s Selecting previously unselected package libice6:amd64. 93s Preparing to unpack .../22-libice6_2%3a1.0.10-1build3_amd64.deb ... 93s Unpacking libice6:amd64 (2:1.0.10-1build3) ... 93s Selecting previously unselected package liblapack3:amd64. 93s Preparing to unpack .../23-liblapack3_3.12.0-3build1_amd64.deb ... 93s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 93s Selecting previously unselected package libmunge2:amd64. 93s Preparing to unpack .../24-libmunge2_0.5.15-4build1_amd64.deb ... 93s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 93s Selecting previously unselected package libpciaccess0:amd64. 93s Preparing to unpack .../25-libpciaccess0_0.17-3build1_amd64.deb ... 93s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 93s Selecting previously unselected package libxnvctrl0:amd64. 93s Preparing to unpack .../26-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 93s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 93s Selecting previously unselected package ocl-icd-libopencl1:amd64. 93s Preparing to unpack .../27-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 93s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 93s Selecting previously unselected package libhwloc-plugins:amd64. 93s Preparing to unpack .../28-libhwloc-plugins_2.11.0-2_amd64.deb ... 93s Unpacking libhwloc-plugins:amd64 (2.11.0-2) ... 93s Selecting previously unselected package libpmix2t64:amd64. 93s Preparing to unpack .../29-libpmix2t64_5.0.1-4.1build1_amd64.deb ... 93s Unpacking libpmix2t64:amd64 (5.0.1-4.1build1) ... 93s Selecting previously unselected package libibumad3:amd64. 93s Preparing to unpack .../30-libibumad3_52.0-2_amd64.deb ... 93s Unpacking libibumad3:amd64 (52.0-2) ... 93s Selecting previously unselected package libibmad5:amd64. 93s Preparing to unpack .../31-libibmad5_52.0-2_amd64.deb ... 93s Unpacking libibmad5:amd64 (52.0-2) ... 93s Selecting previously unselected package libucx0:amd64. 93s Preparing to unpack .../32-libucx0_1.17.0+ds-3_amd64.deb ... 93s Unpacking libucx0:amd64 (1.17.0+ds-3) ... 93s Selecting previously unselected package libopenmpi3t64:amd64. 93s Preparing to unpack .../33-libopenmpi3t64_4.1.6-7ubuntu2_amd64.deb ... 93s Unpacking libopenmpi3t64:amd64 (4.1.6-7ubuntu2) ... 94s Selecting previously unselected package libthai-data. 94s Preparing to unpack .../34-libthai-data_0.1.29-2build1_all.deb ... 94s Unpacking libthai-data (0.1.29-2build1) ... 94s Selecting previously unselected package libthai0:amd64. 94s Preparing to unpack .../35-libthai0_0.1.29-2build1_amd64.deb ... 94s Unpacking libthai0:amd64 (0.1.29-2build1) ... 94s Selecting previously unselected package libpango-1.0-0:amd64. 94s Preparing to unpack .../36-libpango-1.0-0_1.54.0+ds-1_amd64.deb ... 94s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-1) ... 94s Selecting previously unselected package libpangoft2-1.0-0:amd64. 94s Preparing to unpack .../37-libpangoft2-1.0-0_1.54.0+ds-1_amd64.deb ... 94s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... 94s Selecting previously unselected package libpangocairo-1.0-0:amd64. 94s Preparing to unpack .../38-libpangocairo-1.0-0_1.54.0+ds-1_amd64.deb ... 94s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... 94s Selecting previously unselected package libpaper1:amd64. 94s Preparing to unpack .../39-libpaper1_1.1.29build1_amd64.deb ... 94s Unpacking libpaper1:amd64 (1.1.29build1) ... 94s Selecting previously unselected package libpaper-utils. 94s Preparing to unpack .../40-libpaper-utils_1.1.29build1_amd64.deb ... 94s Unpacking libpaper-utils (1.1.29build1) ... 94s Selecting previously unselected package libsm6:amd64. 94s Preparing to unpack .../41-libsm6_2%3a1.2.3-1build3_amd64.deb ... 94s Unpacking libsm6:amd64 (2:1.2.3-1build3) ... 94s Selecting previously unselected package libtcl8.6:amd64. 94s Preparing to unpack .../42-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 94s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 94s Selecting previously unselected package libxft2:amd64. 94s Preparing to unpack .../43-libxft2_2.3.6-1build1_amd64.deb ... 94s Unpacking libxft2:amd64 (2.3.6-1build1) ... 94s Selecting previously unselected package libxss1:amd64. 94s Preparing to unpack .../44-libxss1_1%3a1.2.3-1build3_amd64.deb ... 94s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 94s Selecting previously unselected package libtk8.6:amd64. 94s Preparing to unpack .../45-libtk8.6_8.6.14-1build1_amd64.deb ... 94s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 94s Selecting previously unselected package libxt6t64:amd64. 94s Preparing to unpack .../46-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 94s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 94s Selecting previously unselected package openmpi-common. 94s Preparing to unpack .../47-openmpi-common_4.1.6-7ubuntu2_all.deb ... 94s Unpacking openmpi-common (4.1.6-7ubuntu2) ... 94s Selecting previously unselected package openmpi-bin. 94s Preparing to unpack .../48-openmpi-bin_4.1.6-7ubuntu2_amd64.deb ... 94s Unpacking openmpi-bin (4.1.6-7ubuntu2) ... 94s Selecting previously unselected package zip. 94s Preparing to unpack .../49-zip_3.0-14_amd64.deb ... 94s Unpacking zip (3.0-14) ... 94s Selecting previously unselected package unzip. 94s Preparing to unpack .../50-unzip_6.0-28ubuntu5_amd64.deb ... 94s Unpacking unzip (6.0-28ubuntu5) ... 94s Selecting previously unselected package xdg-utils. 94s Preparing to unpack .../51-xdg-utils_1.2.1-0ubuntu1_all.deb ... 94s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 94s Selecting previously unselected package r-base-core. 94s Preparing to unpack .../52-r-base-core_4.4.1-1_amd64.deb ... 94s Unpacking r-base-core (4.4.1-1) ... 95s Selecting previously unselected package mpi-default-bin. 95s Preparing to unpack .../53-mpi-default-bin_1.15build1_amd64.deb ... 95s Unpacking mpi-default-bin (1.15build1) ... 95s Selecting previously unselected package ray. 95s Preparing to unpack .../54-ray_2.3.1-8build2_amd64.deb ... 95s Unpacking ray (2.3.1-8build2) ... 95s Selecting previously unselected package ray-doc. 95s Preparing to unpack .../55-ray-doc_2.3.1-8build2_all.deb ... 95s Unpacking ray-doc (2.3.1-8build2) ... 95s Selecting previously unselected package ray-extra. 95s Preparing to unpack .../56-ray-extra_2.3.1-8build2_all.deb ... 95s Unpacking ray-extra (2.3.1-8build2) ... 95s Selecting previously unselected package autopkgtest-satdep. 95s Preparing to unpack .../57-1-autopkgtest-satdep.deb ... 95s Unpacking autopkgtest-satdep (0) ... 95s Setting up libpixman-1-0:amd64 (0.42.2-1build1) ... 95s Setting up libpaper1:amd64 (1.1.29build1) ... 95s 95s Creating config file /etc/papersize with new version 95s Setting up ray-doc (2.3.1-8build2) ... 95s Setting up libpciaccess0:amd64 (0.17-3build1) ... 95s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 97s Regenerating fonts cache... done. 97s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 97s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 97s Setting up libxcb-render0:amd64 (1.17.0-2) ... 97s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 97s Setting up unzip (6.0-28ubuntu5) ... 97s Setting up x11-common (1:7.7+23ubuntu3) ... 97s Setting up libibumad3:amd64 (52.0-2) ... 97s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 97s Setting up libibmad5:amd64 (52.0-2) ... 97s Setting up libpaper-utils (1.1.29build1) ... 97s Setting up libcairo2:amd64 (1.18.0-3build1) ... 97s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 97s Setting up zip (3.0-14) ... 97s Setting up libblas3:amd64 (3.12.0-3build1) ... 97s 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 97s Setting up libmunge2:amd64 (0.5.15-4build1) ... 97s Setting up libllvm17t64:amd64 (1:17.0.6-12) ... 97s Setting up libhwloc15:amd64 (2.11.0-2) ... 97s Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 97s Setting up libgfortran5:amd64 (14.1.0-5ubuntu1) ... 97s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 97s Setting up libpsm2-2 (11.2.185-2.1) ... 97s Setting up openmpi-common (4.1.6-7ubuntu2) ... 97s Setting up librdmacm1t64:amd64 (52.0-2) ... 97s Setting up libthai-data (0.1.29-2build1) ... 97s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 97s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 97s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 97s 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 97s Setting up xdg-utils (1.2.1-0ubuntu1) ... 97s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 97s Setting up libdrm-amdgpu1:amd64 (2.4.121-2) ... 97s Setting up libfabric1:amd64 (1.17.0-3build2) ... 97s Setting up libice6:amd64 (2:1.0.10-1build3) ... 97s Setting up liblapack3:amd64 (3.12.0-3build1) ... 97s 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 97s Setting up libxft2:amd64 (2.3.6-1build1) ... 97s Setting up libtk8.6:amd64 (8.6.14-1build1) ... 97s Setting up libhwloc-plugins:amd64 (2.11.0-2) ... 97s Setting up libthai0:amd64 (0.1.29-2build1) ... 97s Setting up libpmix2t64:amd64 (5.0.1-4.1build1) ... 97s Setting up libsm6:amd64 (2:1.2.3-1build3) ... 97s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 97s Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ... 97s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 97s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 97s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... 97s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... 97s Setting up libamdhip64-5 (5.7.1-4) ... 97s Setting up r-base-core (4.4.1-1) ... 98s 98s Creating config file /etc/R/Renviron with new version 98s Setting up libucx0:amd64 (1.17.0+ds-3) ... 98s Setting up ray-extra (2.3.1-8build2) ... 98s Setting up libopenmpi3t64:amd64 (4.1.6-7ubuntu2) ... 98s Setting up openmpi-bin (4.1.6-7ubuntu2) ... 98s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 98s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 98s Setting up mpi-default-bin (1.15build1) ... 98s Setting up ray (2.3.1-8build2) ... 98s Setting up autopkgtest-satdep (0) ... 98s Processing triggers for man-db (2.12.1-2) ... 99s Processing triggers for install-info (7.1-3build2) ... 99s Processing triggers for libc-bin (2.39-0ubuntu9) ... 103s (Reading database ... 76935 files and directories currently installed.) 103s Removing autopkgtest-satdep (0) ... 104s autopkgtest [23:58:32]: test run-unit-test: [----------------------- 105s 105s ************************************************** 105s This program comes with ABSOLUTELY NO WARRANTY. 105s This is free software, and you are welcome to redistribute it 105s under certain conditions; see "LICENSE.txt" for details. 105s ************************************************** 105s 105s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 105s Centre de recherche en infectiologie de l'Université Laval 105s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 105s http://denovoassembler.sf.net/ 105s 105s References to cite: 105s 105s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 105s Ray Meta: scalable de novo metagenome assembly and profiling. 105s Genome Biology (BioMed Central Ltd). 105s 13:R122, Published: 22 December 2012 105s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 105s 105s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 105s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 105s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 105s November 2010, Volume 17, Issue 11, Pages 1519-1533. 105s http://dx.doi.org/doi:10.1089/cmb.2009.0238 105s 105s Ray version 2.3.1 105s License for Ray: GNU General Public License version 3 105s RayPlatform version: 2.0.1 105s License for RayPlatform: GNU Lesser General Public License version 3 105s 105s MAXKMERLENGTH: 32 105s Maximum coverage depth stored by CoverageDepth: 4294967295 105s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 105s FORCE_PACKING = n 105s ASSERT = n 105s HAVE_LIBZ = y 105s HAVE_LIBBZ2 = y 105s PROFILER_COLLECT = n 105s MINIRANKS = y 105s CLOCK_GETTIME = n 105s __linux__ = y 105s _MSC_VER = n 105s __GNUC__ = y 105s RAY_32_BITS = n 105s RAY_64_BITS = y 105s MPI standard version: MPI 3.1 105s MPI library: Open-MPI 4.1.6 105s Compiler: GNU gcc/g++ 13.2.0 105s MPI I/O: n 105s 105s 105s -k (to set the k-mer size) 105s Value: 31 105s 105s 105s Paired library # 0 105s -p (paired-end sequences) 105s Left sequences: ecoli_1K_1.fq 105s Right sequences: ecoli_1K_2.fq 105s Average length: automatic detection 105s Standard deviation: automatic detection 105s 105s Ray command: 105s mpiexec -n 1 Ray \ 105s -k \ 105s 31 \ 105s -p \ 105s ecoli_1K_1.fq \ 105s ecoli_1K_2.fq \ 105s -o \ 105s test1 105s 105s Rank 0 wrote test1/RayCommand.txt 105s 105s k-mer length: 31 105s Rank 0: assembler memory usage: 42804 KiB 105s Rank 0: assembler memory usage: 108624 KiB 105s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2985 105s Rank 0: testing the network, please wait... 105s 105s Rank 0 is testing the network [0/1000] 105s Rank 0 is testing the network [1000/1000] 105s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 105s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 105s 105s Rank 0 wrote test1/NetworkTest.txt 105s 105s 105s *** 105s Step: Network testing 105s Date: Thu Aug 1 23:58:33 2024 105s Elapsed time: 0 seconds 105s Since beginning: 0 seconds 105s *** 105s 105s 105s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 105s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 105s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 105s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 105s Rank 0 wrote test1/NumberOfSequences.txt 105s Rank 0 wrote test1/SequencePartition.txt 105s 105s *** 105s Step: Counting sequences to assemble 105s Date: Thu Aug 1 23:58:33 2024 105s Elapsed time: 0 seconds 105s Since beginning: 0 seconds 105s *** 105s 105s 105s Rank 0 is loading sequence reads 105s Rank 0 : partition is [0;4107], 4108 sequence reads 105s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 105s Rank 0 has 0 sequence reads 105s Rank 0: assembler memory usage: 121500 KiB 105s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 105s Rank 0 has 4108 sequence reads (completed) 105s 105s *** 105s Step: Sequence loading 105s Date: Thu Aug 1 23:58:33 2024 105s Elapsed time: 0 seconds 105s Since beginning: 0 seconds 105s *** 105s 105s 105s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 105s Rank 0 created its Bloom filter 105s Rank 0 is counting k-mers in sequence reads [1/4108] 105s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 105s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 105s 105s 105s *** 105s Step: K-mer counting 105s Date: Thu Aug 1 23:58:33 2024 105s Elapsed time: 0 seconds 105s Since beginning: 0 seconds 105s *** 105s 105s 105s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 105s Rank 0 destroyed its Bloom filter 105s Rank 0 has 1954 k-mers (completed) 105s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 105s Rank 0: assembler memory usage: 117896 KiB 107s 107s 107s Rank 0: the minimum coverage is 3 107s Rank 0: the peak coverage is 3 107s Warning: no peak observed in the k-mer coverage distribution. 107s to deal with the sequencing error rate, try to lower the k-mer length (-k) 107s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 107s 107s *** 107s Step: Coverage distribution analysis 107s Date: Thu Aug 1 23:58:35 2024 107s Elapsed time: 2 seconds 107s Since beginning: 2 seconds 107s *** 107s 107s 107s 107s Rank 0 is adding edges [1/4108] 107s Rank 0 is adding edges [4108/4108] (completed) 107s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 107s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 107s 107s *** 107s Step: Graph construction 107s Date: Thu Aug 1 23:58:35 2024 107s Elapsed time: 0 seconds 107s Since beginning: 2 seconds 107s *** 107s 107s 107s Rank 0 has 1954 vertices (completed) 107s Rank 0: assembler memory usage: 117896 KiB 109s Rank 0 is purging edges [1/1954] 109s Rank 0 is purging edges [1954/1954] (completed) 109s Rank 0: assembler memory usage: 118424 KiB 109s VirtualProcessor: completed jobs: 1954 109s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 111s Rank 0 wrote test1/degreeDistribution.txt 111s 111s *** 111s Step: Null edge purging 111s Date: Thu Aug 1 23:58:39 2024 111s Elapsed time: 4 seconds 111s Since beginning: 6 seconds 111s *** 111s 111s 111s Rank 0 is selecting optimal read markers [1/4108] 111s Rank 0: assembler memory usage: 118424 KiB 112s Rank 0 is selecting optimal read markers [4108/4108] (completed) 112s Rank 0: peak number of workers: 599, maximum: 32768 112s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 112s Rank 0: assembler memory usage: 126552 KiB 112s Rank 0: Freeing unused assembler memory: 4096 KiB freed 112s Rank 0: assembler memory usage: 126552 KiB 112s 112s *** 112s Step: Selection of optimal read markers 112s Date: Thu Aug 1 23:58:40 2024 112s Elapsed time: 1 seconds 112s Since beginning: 7 seconds 112s *** 112s 112s 112s Rank 0: memory usage for optimal read markers= 4096 KiB 112s Rank 0 is creating seeds [1/1954] 112s Rank 0: assembler memory usage: 126552 KiB 113s Rank 0 has 1 seeds 113s Rank 0 is creating seeds [1954/1954] (completed) 113s Rank 0: peak number of workers: 746, maximum: 32768 113s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 113s Rank 0 runtime statistics for seeding algorithm: 113s Rank 0 Skipped paths because of dead end for head: 0 113s Rank 0 Skipped paths because of dead end for tail: 0 113s Rank 0 Skipped paths because of two dead ends: 0 113s Rank 0 Skipped paths because of bubble weak component: 0 113s Rank 0 Skipped paths because of short length: 1952 113s Rank 0 Skipped paths because of bad ownership: 1 113s Rank 0 Skipped paths because of low coverage: 0 113s Rank 0 Eligible paths: 1 113s Rank 0: assembler memory usage: 126552 KiB 113s Rank 0 has 1 seeds to register. 113s Rank 0 registered 0/1 113s Rank 0 registered 0/1 113s Rank 0 registered its seeds 113s VirtualProcessor: completed jobs: 0 113s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 115s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 125s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 125s Rank 0 merged its seeds: 1 seeds -> 1 seeds 125s 125s *** 125s Step: Detection of assembly seeds 125s Date: Thu Aug 1 23:58:53 2024 125s Elapsed time: 13 seconds 125s Since beginning: 20 seconds 125s *** 125s 125s 125s Rank 0 is calculating library lengths [1/1] 125s Rank 0 detected 1737 library lengths 125s Rank 0 is calculating library lengths [1/1] (completed) 125s Rank 0: peak number of workers: 1, maximum: 32768 125s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 125s Rank 0: assembler memory usage: 163420 KiB 125s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 125s 125s Mode= 2 signalAverage= 9 125s CURRENT IS NOISE, 244 125s GOT HIT 212 125s 125s 125s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 125s 125s *** 125s Step: Estimation of outer distances for paired reads 125s Date: Thu Aug 1 23:58:53 2024 125s Elapsed time: 0 seconds 125s Since beginning: 20 seconds 125s *** 125s 125s 125s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 125s Rank 0 traversed 1000 nucleotide symbols 125s Rank 0: assembler memory usage: 167516 KiB 125s Rank 0 is extending seeds [1/1] (completed) 125s Rank 0 extended 1 seeds out of 1 (100.00%) 125s Rank 0: assembler memory usage: 159324 KiB 125s Rank 0 starting fusions 125s 125s *** 125s Step: Bidirectional extension of seeds 125s Date: Thu Aug 1 23:58:53 2024 125s Elapsed time: 0 seconds 125s Since beginning: 20 seconds 125s *** 125s 125s 125s Rank 0: starting clear step. cycleNumber= 0 127s Rank 0 adding 0 new fusions 127s Rank 0 cleared, 1 paths 127s Rank 0: starting distribution step 127s Rank 0 is distributing fusions [1/1] 127s Rank 0: assembler memory usage: 159324 KiB 127s Date: Thu Aug 1 23:58:55 2024 127s Rank 0 is distributing fusions [1/1] (completed) 127s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 127s Rank 0: assembler memory usage: 163420 KiB 127s Date: Thu Aug 1 23:58:55 2024 127s Rank 0 tells others to compute fusions. 127s Rank 0 FusionTaskCreator assignNextTask [0/2] 127s Rank 0: assembler memory usage: 163420 KiB 127s Date: Thu Aug 1 23:58:55 2024 127s Rank 0 FusionTaskCreator processWorkerResult [0/2] 127s Rank 0: assembler memory usage: 163420 KiB 127s Date: Thu Aug 1 23:58:55 2024 127s Rank 0 FusionTaskCreator [2/2] 127s Statistics: all paths: 1 eliminated during fusing: 0 127s Rank 0: assembler memory usage: 163420 KiB 127s VirtualProcessor: completed jobs: 2 127s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 127s Rank 0: starting clear step. cycleNumber= 1 129s Rank 0 adding 0 new fusions 129s Rank 0 cleared, 1 paths 129s Rank 0 is distributing fusions [1/1] 129s Rank 0: assembler memory usage: 163420 KiB 129s Date: Thu Aug 1 23:58:57 2024 129s Rank 0 is distributing fusions [1/1] (completed) 129s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 129s Rank 0: assembler memory usage: 163420 KiB 129s Date: Thu Aug 1 23:58:57 2024 129s Rank 0 JoinerTaskCreator assignNextTask [0/2] 129s Rank 0: assembler memory usage: 163420 KiB 129s Date: Thu Aug 1 23:58:57 2024 129s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 129s Rank 0: assembler memory usage: 163420 KiB 129s Date: Thu Aug 1 23:58:57 2024 129s Rank 0 JoinerTaskCreator [2/2] 129s Statistics: all paths: 1 eliminated during joining: 0 129s Rank 0: assembler memory usage: 163420 KiB 129s Date: Thu Aug 1 23:58:57 2024 129s VirtualProcessor: completed jobs: 2 129s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 131s Rank 0 adding 0 new fusions 131s Rank 0 cleared, 1 paths 131s Rank 0: starting distribution step 131s Rank 0 is distributing fusions [1/1] 131s Rank 0: assembler memory usage: 163420 KiB 131s Date: Thu Aug 1 23:58:59 2024 131s Rank 0 is distributing fusions [1/1] (completed) 131s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 131s Rank 0: assembler memory usage: 163420 KiB 131s Date: Thu Aug 1 23:58:59 2024 131s Rank 0 tells others to compute fusions. 131s Rank 0 FusionTaskCreator assignNextTask [0/2] 131s Rank 0: assembler memory usage: 163420 KiB 131s Date: Thu Aug 1 23:58:59 2024 131s Rank 0 FusionTaskCreator processWorkerResult [0/2] 131s Rank 0: assembler memory usage: 163420 KiB 131s Date: Thu Aug 1 23:58:59 2024 131s Rank 0 FusionTaskCreator [2/2] 131s Statistics: all paths: 1 eliminated during fusing: 0 131s Rank 0: assembler memory usage: 163420 KiB 131s VirtualProcessor: completed jobs: 2 131s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 131s Rank 0: starting clear step. cycleNumber= 2 133s Rank 0 adding 0 new fusions 133s Rank 0 cleared, 1 paths 133s Rank 0 is distributing fusions [1/1] 133s Rank 0: assembler memory usage: 163420 KiB 133s Date: Thu Aug 1 23:59:01 2024 133s Rank 0 is distributing fusions [1/1] (completed) 133s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 133s Rank 0: assembler memory usage: 163420 KiB 133s Date: Thu Aug 1 23:59:01 2024 133s Rank 0 JoinerTaskCreator assignNextTask [0/2] 133s Rank 0: assembler memory usage: 163420 KiB 133s Date: Thu Aug 1 23:59:01 2024 133s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 133s Rank 0: assembler memory usage: 163420 KiB 133s Date: Thu Aug 1 23:59:01 2024 133s Rank 0 JoinerTaskCreator [2/2] 133s Statistics: all paths: 1 eliminated during joining: 0 133s Rank 0: assembler memory usage: 163420 KiB 133s Date: Thu Aug 1 23:59:01 2024 133s VirtualProcessor: completed jobs: 2 133s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 135s Rank 0 adding 0 new fusions 135s Rank 0 cleared, 1 paths 135s Rank 0: starting distribution step 135s Rank 0 is distributing fusions [1/1] 135s Rank 0: assembler memory usage: 163420 KiB 135s Date: Thu Aug 1 23:59:03 2024 135s Rank 0 is distributing fusions [1/1] (completed) 135s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 135s Rank 0: assembler memory usage: 163420 KiB 135s Date: Thu Aug 1 23:59:03 2024 135s Rank 0 cycleNumber= 2 135s 135s *** 135s Step: Merging of redundant paths 135s Date: Thu Aug 1 23:59:03 2024 135s Elapsed time: 10 seconds 135s Since beginning: 30 seconds 135s *** 135s 135s 135s Rank 0 appended 1 elements 135s 135s *** 135s Step: Generation of contigs 135s Date: Thu Aug 1 23:59:03 2024 135s Elapsed time: 0 seconds 135s Since beginning: 30 seconds 135s *** 135s 135s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 135s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 135s Rank 0 ineligibleObjects: 0/970 (0.00%) 135s Rank 0: assembler memory usage: 163420 KiB 135s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 135s Rank 0 finished gathering scaffold links. 135s Rank 0 will write 1 contig lengths 135s Rank 0 will solve the scaffolding problem. 135s Welcome to GreedySolver v1.0 135s 1 vertices; 0 edges 135s 1 contigs >= 500 135s Edges in solution: 0 135s 135s Conflict statistics: 135s 1 scaffolds, 1 >= 500 135s Total: 1000 nucleotides 135s 135s *** 135s Step: Scaffolding of contigs 135s Date: Thu Aug 1 23:59:03 2024 135s Elapsed time: 0 seconds 135s Since beginning: 30 seconds 135s *** 135s 135s Rank 0 syncing with master 135s 135s *** 135s Step: Counting sequences to search 135s Date: Thu Aug 1 23:59:03 2024 135s Elapsed time: 0 seconds 135s Since beginning: 30 seconds 135s *** 135s 135s 135s Rank 0 will add colors, 0 sequences in 0 files to process 135s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 137s 137s *** 137s Step: Graph coloring 137s Date: Thu Aug 1 23:59:05 2024 137s Elapsed time: 2 seconds 137s Since beginning: 32 seconds 137s *** 137s 137s 137s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 137s Rank 0 shares its counts 137s Rank 0 computing contig abundances [1/1] [1/970] 137s Rank 0 computing contig abundances [1/1] [970/970] 137s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 137s 137s *** 137s Step: Counting contig biological abundances 137s Date: Thu Aug 1 23:59:05 2024 137s Elapsed time: 0 seconds 137s Since beginning: 32 seconds 137s *** 137s 137s 137s Rank 0 colored the graph with 0 real colors using 1 virtual colors 137s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 137s 137s *** 137s Step: Counting sequence biological abundances 137s Date: Thu Aug 1 23:59:05 2024 137s Elapsed time: 0 seconds 137s Since beginning: 32 seconds 137s *** 137s 137s 137s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 137s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 139s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 139s 139s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 139s Rank 0 is starting taxon syncing across the compute tribe. 139s 139s *** 139s Step: Loading taxons 139s Date: Thu Aug 1 23:59:07 2024 139s Elapsed time: 2 seconds 139s Since beginning: 34 seconds 139s *** 139s 139s Rank 0 synced taxons across the grid with 1 poor slaves. 139s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 139s Rank 0 has 0 taxons after syncing with master 141s 141s 141s *** 141s Step: Loading tree 141s Date: Thu Aug 1 23:59:09 2024 141s Elapsed time: 2 seconds 141s Since beginning: 36 seconds 141s *** 141s 143s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 143s 143s Rank 0: counting ontology terms in the graph... 145s Rank 0: 0 have some biological signal 145s Number of dereferenced alternate handles: 0 145s Number of k-mer observations with gene ontology terms: 0 145s Rank 0: synced ontology term profiles with master 145s Rank 0: synchronization is complete! 145s Rank 0: ontology terms with biological signal: 0 145s Populated recursive values... 145s Gene ontology terms without depth information: 0 145s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 145s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 145s 145s *** 145s Step: Processing gene ontologies 145s Date: Thu Aug 1 23:59:13 2024 145s Elapsed time: 4 seconds 145s Since beginning: 40 seconds 145s *** 145s 145s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 145s [GenomeNeighbourhood] in final list: 0 145s 145s *** 145s Step: Computing neighbourhoods 145s Date: Thu Aug 1 23:59:13 2024 145s Elapsed time: 0 seconds 145s Since beginning: 40 seconds 145s *** 145s 145s Contigs >= 100 nt 145s Number: 1 145s Total length: 1000 145s Average: 1000 145s N50: 1000 145s Median: 1000 145s Largest: 1000 145s Contigs >= 500 nt 145s Number: 1 145s Total length: 1000 145s Average: 1000 145s N50: 1000 145s Median: 1000 145s Largest: 1000 145s Scaffolds >= 100 nt 145s Number: 1 145s Total length: 1000 145s Average: 1000 145s N50: 1000 145s Median: 1000 145s Largest: 1000 145s Scaffolds >= 500 nt 145s Number: 1 145s Total length: 1000 145s Average: 1000 145s N50: 1000 145s Median: 1000 145s Largest: 1000 145s 145s Rank 0 wrote test1/Contigs.fasta 145s Rank 0 wrote test1/Scaffolds.fasta 145s Check for test1/* 145s 145s 145s 145s ************************************************** 145s This program comes with ABSOLUTELY NO WARRANTY. 145s This is free software, and you are welcome to redistribute it 145s under certain conditions; see "LICENSE.txt" for details. 145s ************************************************** 145s 145s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 145s Centre de recherche en infectiologie de l'Université Laval 145s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 145s http://denovoassembler.sf.net/ 145s 145s References to cite: 145s 145s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 145s Ray Meta: scalable de novo metagenome assembly and profiling. 145s Genome Biology (BioMed Central Ltd). 145s 13:R122, Published: 22 December 2012 145s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 145s 145s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 145s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 145s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 145s November 2010, Volume 17, Issue 11, Pages 1519-1533. 145s http://dx.doi.org/doi:10.1089/cmb.2009.0238 145s 145s Ray version 2.3.1 145s License for Ray: GNU General Public License version 3 145s RayPlatform version: 2.0.1 145s License for RayPlatform: GNU Lesser General Public License version 3 145s 145s MAXKMERLENGTH: 32 145s Maximum coverage depth stored by CoverageDepth: 4294967295 145s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 145s FORCE_PACKING = n 145s ASSERT = n 145s HAVE_LIBZ = y 145s HAVE_LIBBZ2 = y 145s PROFILER_COLLECT = n 145s MINIRANKS = y 145s CLOCK_GETTIME = n 145s __linux__ = y 145s _MSC_VER = n 145s __GNUC__ = y 145s RAY_32_BITS = n 145s RAY_64_BITS = y 145s MPI standard version: MPI 3.1 145s MPI library: Open-MPI 4.1.6 145s Compiler: GNU gcc/g++ 13.2.0 145s MPI I/O: n 145s 145s 145s -k (to set the k-mer size) 145s Value: 31 145s 145s 145s Paired library # 0 145s -p (paired-end sequences) 145s Left sequences: SampleDirectory/s_6.first1000_1.fastq 145s Right sequences: SampleDirectory/s_6.first1000_2.fastq 145s Average length: automatic detection 145s Standard deviation: automatic detection 145s 145s Ray command: 145s mpiexec -n 1 Ray \ 145s -k \ 145s 31 \ 145s -detect-sequence-files \ 145s SampleDirectory \ 145s -o \ 145s test2 145s 145s Rank 0 wrote test2/RayCommand.txt 145s 145s k-mer length: 31 145s Rank 0: assembler memory usage: 42808 KiB 146s Rank 0: assembler memory usage: 108624 KiB 146s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2994 146s Rank 0: testing the network, please wait... 146s 146s Rank 0 is testing the network [0/1000] 146s Rank 0 is testing the network [1000/1000] 146s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 146s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 146s 146s Rank 0 wrote test2/NetworkTest.txt 146s 146s 146s *** 146s Step: Network testing 146s Date: Thu Aug 1 23:59:14 2024 146s Elapsed time: 1 seconds 146s Since beginning: 1 seconds 146s *** 146s 146s 146s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 146s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 146s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 146s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 146s Rank 0 wrote test2/NumberOfSequences.txt 146s Rank 0 wrote test2/SequencePartition.txt 146s 146s *** 146s Step: Counting sequences to assemble 146s Date: Thu Aug 1 23:59:14 2024 146s Elapsed time: 0 seconds 146s Since beginning: 1 seconds 146s *** 146s 146s 146s Rank 0 is loading sequence reads 146s Rank 0 : partition is [0;4107], 4108 sequence reads 146s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 146s Rank 0 has 0 sequence reads 146s Rank 0: assembler memory usage: 121500 KiB 146s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 146s Rank 0 has 4108 sequence reads (completed) 146s 146s *** 146s Step: Sequence loading 146s Date: Thu Aug 1 23:59:14 2024 146s Elapsed time: 0 seconds 146s Since beginning: 1 seconds 146s *** 146s 146s 146s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 146s Rank 0 created its Bloom filter 146s Rank 0 is counting k-mers in sequence reads [1/4108] 146s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 146s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 146s 146s 146s *** 146s Step: K-mer counting 146s Date: Thu Aug 1 23:59:14 2024 146s Elapsed time: 0 seconds 146s Since beginning: 1 seconds 146s *** 146s 146s 146s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 146s Rank 0 destroyed its Bloom filter 146s Rank 0 has 1954 k-mers (completed) 146s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 146s Rank 0: assembler memory usage: 117896 KiB 148s 148s 148s Rank 0: the minimum coverage is 3 148s Rank 0: the peak coverage is 3 148s Warning: no peak observed in the k-mer coverage distribution. 148s to deal with the sequencing error rate, try to lower the k-mer length (-k) 148s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 148s 148s *** 148s Step: Coverage distribution analysis 148s Date: Thu Aug 1 23:59:16 2024 148s Elapsed time: 2 seconds 148s Since beginning: 3 seconds 148s *** 148s 148s 148s 148s Rank 0 is adding edges [1/4108] 148s Rank 0 is adding edges [4108/4108] (completed) 148s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 148s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 148s 148s *** 148s Step: Graph construction 148s Date: Thu Aug 1 23:59:16 2024 148s Elapsed time: 0 seconds 148s Since beginning: 3 seconds 148s *** 148s 148s 148s Rank 0 has 1954 vertices (completed) 148s Rank 0: assembler memory usage: 117896 KiB 150s Rank 0 is purging edges [1/1954] 150s Rank 0 is purging edges [1954/1954] (completed) 150s Rank 0: assembler memory usage: 118424 KiB 150s VirtualProcessor: completed jobs: 1954 150s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 152s Rank 0 wrote test2/degreeDistribution.txt 152s 152s *** 152s Step: Null edge purging 152s Date: Thu Aug 1 23:59:20 2024 152s Elapsed time: 4 seconds 152s Since beginning: 7 seconds 152s *** 152s 152s 152s Rank 0 is selecting optimal read markers [1/4108] 152s Rank 0: assembler memory usage: 118424 KiB 152s Rank 0 is selecting optimal read markers [4108/4108] (completed) 152s Rank 0: peak number of workers: 599, maximum: 32768 152s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 152s Rank 0: assembler memory usage: 126548 KiB 152s Rank 0: Freeing unused assembler memory: 4096 KiB freed 152s Rank 0: assembler memory usage: 126548 KiB 152s 152s *** 152s Step: Selection of optimal read markers 152s Date: Thu Aug 1 23:59:20 2024 152s Elapsed time: 0 seconds 152s Since beginning: 7 seconds 152s *** 152s 152s 152s Rank 0: memory usage for optimal read markers= 4096 KiB 152s Rank 0 is creating seeds [1/1954] 152s Rank 0: assembler memory usage: 126548 KiB 154s Rank 0 has 1 seeds 154s Rank 0 is creating seeds [1954/1954] (completed) 154s Rank 0: peak number of workers: 746, maximum: 32768 154s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 154s Rank 0 runtime statistics for seeding algorithm: 154s Rank 0 Skipped paths because of dead end for head: 0 154s Rank 0 Skipped paths because of dead end for tail: 0 154s Rank 0 Skipped paths because of two dead ends: 0 154s Rank 0 Skipped paths because of bubble weak component: 0 154s Rank 0 Skipped paths because of short length: 1952 154s Rank 0 Skipped paths because of bad ownership: 1 154s Rank 0 Skipped paths because of low coverage: 0 154s Rank 0 Eligible paths: 1 154s Rank 0: assembler memory usage: 126548 KiB 154s Rank 0 has 1 seeds to register. 154s Rank 0 registered 0/1 154s Rank 0 registered 0/1 154s Rank 0 registered its seeds 154s VirtualProcessor: completed jobs: 0 154s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 156s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 166s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 166s Rank 0 merged its seeds: 1 seeds -> 1 seeds 166s 166s *** 166s Step: Detection of assembly seeds 166s Date: Thu Aug 1 23:59:34 2024 166s Elapsed time: 14 seconds 166s Since beginning: 21 seconds 166s *** 166s 166s 166s Rank 0 is calculating library lengths [1/1] 166s Rank 0 detected 1737 library lengths 166s Rank 0 is calculating library lengths [1/1] (completed) 166s Rank 0: peak number of workers: 1, maximum: 32768 166s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 166s Rank 0: assembler memory usage: 163416 KiB 166s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 166s 166s Mode= 2 signalAverage= 9 166s CURRENT IS NOISE, 244 166s GOT HIT 212 166s 166s 166s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 166s 166s *** 166s Step: Estimation of outer distances for paired reads 166s Date: Thu Aug 1 23:59:34 2024 166s Elapsed time: 0 seconds 166s Since beginning: 21 seconds 166s *** 166s 166s 166s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 166s Rank 0 traversed 1000 nucleotide symbols 166s Rank 0: assembler memory usage: 167512 KiB 166s Rank 0 is extending seeds [1/1] (completed) 166s Rank 0 extended 1 seeds out of 1 (100.00%) 166s Rank 0: assembler memory usage: 159320 KiB 166s Rank 0 starting fusions 166s 166s *** 166s Step: Bidirectional extension of seeds 166s Date: Thu Aug 1 23:59:34 2024 166s Elapsed time: 0 seconds 166s Since beginning: 21 seconds 166s *** 166s 166s 166s Rank 0: starting clear step. cycleNumber= 0 168s Rank 0 adding 0 new fusions 168s Rank 0 cleared, 1 paths 168s Rank 0: starting distribution step 168s Rank 0 is distributing fusions [1/1] 168s Rank 0: assembler memory usage: 159320 KiB 168s Date: Thu Aug 1 23:59:36 2024 168s Rank 0 is distributing fusions [1/1] (completed) 168s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 168s Rank 0: assembler memory usage: 163416 KiB 168s Date: Thu Aug 1 23:59:36 2024 168s Rank 0 tells others to compute fusions. 168s Rank 0 FusionTaskCreator assignNextTask [0/2] 168s Rank 0: assembler memory usage: 163416 KiB 168s Date: Thu Aug 1 23:59:36 2024 168s Rank 0 FusionTaskCreator processWorkerResult [0/2] 168s Rank 0: assembler memory usage: 163416 KiB 168s Date: Thu Aug 1 23:59:36 2024 168s Rank 0 FusionTaskCreator [2/2] 168s Statistics: all paths: 1 eliminated during fusing: 0 168s Rank 0: assembler memory usage: 163416 KiB 168s VirtualProcessor: completed jobs: 2 168s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 168s Rank 0: starting clear step. cycleNumber= 1 170s Rank 0 adding 0 new fusions 170s Rank 0 cleared, 1 paths 170s Rank 0 is distributing fusions [1/1] 170s Rank 0: assembler memory usage: 163416 KiB 170s Date: Thu Aug 1 23:59:38 2024 170s Rank 0 is distributing fusions [1/1] (completed) 170s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 170s Rank 0: assembler memory usage: 163416 KiB 170s Date: Thu Aug 1 23:59:38 2024 170s Rank 0 JoinerTaskCreator assignNextTask [0/2] 170s Rank 0: assembler memory usage: 163416 KiB 170s Date: Thu Aug 1 23:59:38 2024 170s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 170s Rank 0: assembler memory usage: 163416 KiB 170s Date: Thu Aug 1 23:59:38 2024 170s Rank 0 JoinerTaskCreator [2/2] 170s Statistics: all paths: 1 eliminated during joining: 0 170s Rank 0: assembler memory usage: 163416 KiB 170s Date: Thu Aug 1 23:59:38 2024 170s VirtualProcessor: completed jobs: 2 170s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 172s Rank 0 adding 0 new fusions 172s Rank 0 cleared, 1 paths 172s Rank 0: starting distribution step 172s Rank 0 is distributing fusions [1/1] 172s Rank 0: assembler memory usage: 163416 KiB 172s Date: Thu Aug 1 23:59:40 2024 172s Rank 0 is distributing fusions [1/1] (completed) 172s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 172s Rank 0: assembler memory usage: 163416 KiB 172s Date: Thu Aug 1 23:59:40 2024 172s Rank 0 tells others to compute fusions. 172s Rank 0 FusionTaskCreator assignNextTask [0/2] 172s Rank 0: assembler memory usage: 163416 KiB 172s Date: Thu Aug 1 23:59:40 2024 172s Rank 0 FusionTaskCreator processWorkerResult [0/2] 172s Rank 0: assembler memory usage: 163416 KiB 172s Date: Thu Aug 1 23:59:40 2024 172s Rank 0 FusionTaskCreator [2/2] 172s Statistics: all paths: 1 eliminated during fusing: 0 172s Rank 0: assembler memory usage: 163416 KiB 172s VirtualProcessor: completed jobs: 2 172s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 172s Rank 0: starting clear step. cycleNumber= 2 174s Rank 0 adding 0 new fusions 174s Rank 0 cleared, 1 paths 174s Rank 0 is distributing fusions [1/1] 174s Rank 0: assembler memory usage: 163416 KiB 174s Date: Thu Aug 1 23:59:42 2024 174s Rank 0 is distributing fusions [1/1] (completed) 174s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 174s Rank 0: assembler memory usage: 163416 KiB 174s Date: Thu Aug 1 23:59:42 2024 174s Rank 0 JoinerTaskCreator assignNextTask [0/2] 174s Rank 0: assembler memory usage: 163416 KiB 174s Date: Thu Aug 1 23:59:42 2024 174s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 174s Rank 0: assembler memory usage: 163416 KiB 174s Date: Thu Aug 1 23:59:42 2024 174s Rank 0 JoinerTaskCreator [2/2] 174s Statistics: all paths: 1 eliminated during joining: 0 174s Rank 0: assembler memory usage: 163416 KiB 174s Date: Thu Aug 1 23:59:42 2024 174s VirtualProcessor: completed jobs: 2 174s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 176s Rank 0 adding 0 new fusions 176s Rank 0 cleared, 1 paths 176s Rank 0: starting distribution step 176s Rank 0 is distributing fusions [1/1] 176s Rank 0: assembler memory usage: 163416 KiB 176s Date: Thu Aug 1 23:59:44 2024 176s Rank 0 is distributing fusions [1/1] (completed) 176s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 176s Rank 0: assembler memory usage: 163416 KiB 176s Date: Thu Aug 1 23:59:44 2024 176s Rank 0 cycleNumber= 2 176s 176s *** 176s Step: Merging of redundant paths 176s Date: Thu Aug 1 23:59:44 2024 176s Elapsed time: 10 seconds 176s Since beginning: 31 seconds 176s *** 176s 176s 176s Rank 0 appended 1 elements 176s 176s *** 176s Step: Generation of contigs 176s Date: Thu Aug 1 23:59:44 2024 176s Elapsed time: 0 seconds 176s Since beginning: 31 seconds 176s *** 176s 176s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 176s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 176s Rank 0 ineligibleObjects: 0/970 (0.00%) 176s Rank 0: assembler memory usage: 163416 KiB 176s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 176s Rank 0 finished gathering scaffold links. 176s Rank 0 will write 1 contig lengths 176s Rank 0 will solve the scaffolding problem. 176s Welcome to GreedySolver v1.0 176s 1 vertices; 0 edges 176s 1 contigs >= 500 176s Edges in solution: 0 176s 176s Conflict statistics: 176s 1 scaffolds, 1 >= 500 176s Total: 1000 nucleotides 176s 176s *** 176s Step: Scaffolding of contigs 176s Date: Thu Aug 1 23:59:44 2024 176s Elapsed time: 0 seconds 176s Since beginning: 31 seconds 176s *** 176s 176s Rank 0 syncing with master 176s 176s *** 176s Step: Counting sequences to search 176s Date: Thu Aug 1 23:59:44 2024 176s Elapsed time: 0 seconds 176s Since beginning: 31 seconds 176s *** 176s 176s 176s Rank 0 will add colors, 0 sequences in 0 files to process 176s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 178s 178s *** 178s Step: Graph coloring 178s Date: Thu Aug 1 23:59:46 2024 178s Elapsed time: 2 seconds 178s Since beginning: 33 seconds 178s *** 178s 178s 178s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 178s Rank 0 shares its counts 178s Rank 0 computing contig abundances [1/1] [1/970] 178s Rank 0 computing contig abundances [1/1] [970/970] 178s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 178s 178s *** 178s Step: Counting contig biological abundances 178s Date: Thu Aug 1 23:59:46 2024 178s Elapsed time: 0 seconds 178s Since beginning: 33 seconds 178s *** 178s 178s 178s Rank 0 colored the graph with 0 real colors using 1 virtual colors 178s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 178s 178s *** 178s Step: Counting sequence biological abundances 178s Date: Thu Aug 1 23:59:46 2024 178s Elapsed time: 0 seconds 178s Since beginning: 33 seconds 178s *** 178s 178s 178s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 178s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 180s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 180s 180s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 180s Rank 0 is starting taxon syncing across the compute tribe. 180s 180s *** 180s Step: Loading taxons 180s Date: Thu Aug 1 23:59:48 2024 180s Elapsed time: 2 seconds 180s Since beginning: 35 seconds 180s *** 180s 180s Rank 0 synced taxons across the grid with 1 poor slaves. 180s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 180s Rank 0 has 0 taxons after syncing with master 182s 182s 182s *** 182s Step: Loading tree 182s Date: Thu Aug 1 23:59:50 2024 182s Elapsed time: 2 seconds 182s Since beginning: 37 seconds 182s *** 182s 184s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 184s 184s Rank 0: counting ontology terms in the graph... 186s Rank 0: 0 have some biological signal 186s Number of dereferenced alternate handles: 0 186s Number of k-mer observations with gene ontology terms: 0 186s Rank 0: synced ontology term profiles with master 186s Rank 0: synchronization is complete! 186s Rank 0: ontology terms with biological signal: 0 186s Populated recursive values... 186s Gene ontology terms without depth information: 0 186s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 186s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 186s 186s *** 186s Step: Processing gene ontologies 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 4 seconds 186s Since beginning: 41 seconds 186s *** 186s 186s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 186s [GenomeNeighbourhood] in final list: 0 186s 186s *** 186s Step: Computing neighbourhoods 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 0 seconds 186s Since beginning: 41 seconds 186s *** 186s 186s Contigs >= 100 nt 186s Number: 1 186s Total length: 1000 186s Average: 1000 186s N50: 1000 186s Median: 1000 186s Largest: 1000 186s Contigs >= 500 nt 186s Number: 1 186s Total length: 1000 186s Average: 1000 186s N50: 1000 186s Median: 1000 186s Largest: 1000 186s Scaffolds >= 100 nt 186s Number: 1 186s Total length: 1000 186s Average: 1000 186s N50: 1000 186s Median: 1000 186s Largest: 1000 186s Scaffolds >= 500 nt 186s Number: 1 186s Total length: 1000 186s Average: 1000 186s N50: 1000 186s Median: 1000 186s Largest: 1000 186s 186s Rank 0 wrote test2/Contigs.fasta 186s Rank 0 wrote test2/Scaffolds.fasta 186s Check for test2/* 186s 186s 186s 186s ************************************************** 186s This program comes with ABSOLUTELY NO WARRANTY. 186s This is free software, and you are welcome to redistribute it 186s under certain conditions; see "LICENSE.txt" for details. 186s ************************************************** 186s 186s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 186s Centre de recherche en infectiologie de l'Université Laval 186s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 186s http://denovoassembler.sf.net/ 186s 186s References to cite: 186s 186s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 186s Ray Meta: scalable de novo metagenome assembly and profiling. 186s Genome Biology (BioMed Central Ltd). 186s 13:R122, Published: 22 December 2012 186s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 186s 186s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 186s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 186s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 186s November 2010, Volume 17, Issue 11, Pages 1519-1533. 186s http://dx.doi.org/doi:10.1089/cmb.2009.0238 186s 186s Ray version 2.3.1 186s License for Ray: GNU General Public License version 3 186s RayPlatform version: 2.0.1 186s License for RayPlatform: GNU Lesser General Public License version 3 186s 186s MAXKMERLENGTH: 32 186s Maximum coverage depth stored by CoverageDepth: 4294967295 186s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 186s FORCE_PACKING = n 186s ASSERT = n 186s HAVE_LIBZ = y 186s HAVE_LIBBZ2 = y 186s PROFILER_COLLECT = n 186s MINIRANKS = y 186s CLOCK_GETTIME = n 186s __linux__ = y 186s _MSC_VER = n 186s __GNUC__ = y 186s RAY_32_BITS = n 186s RAY_64_BITS = y 186s MPI standard version: MPI 3.1 186s MPI library: Open-MPI 4.1.6 186s Compiler: GNU gcc/g++ 13.2.0 186s MPI I/O: n 186s 186s 186s -k (to set the k-mer size) 186s Value: 29 186s 186s 186s Paired library # 0 186s -p (paired-end sequences) 186s Left sequences: SampleDirectory/s_6.first1000_1.fastq 186s Right sequences: SampleDirectory/s_6.first1000_2.fastq 186s Average length: automatic detection 186s Standard deviation: automatic detection 186s 186s Ray command: 186s mpiexec -n 1 Ray \ 186s -k \ 186s 29 \ 186s -desable-recycling \ 186s -p \ 186s SampleDirectory/s_6.first1000_1.fastq \ 186s SampleDirectory/s_6.first1000_2.fastq 186s 186s Rank 0 wrote RayOutput/RayCommand.txt 186s 186s k-mer length: 29 186s Rank 0: assembler memory usage: 42804 KiB 186s Rank 0: assembler memory usage: 108624 KiB 186s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3010 186s Rank 0: testing the network, please wait... 186s 186s Rank 0 is testing the network [0/1000] 186s Rank 0 is testing the network [1000/1000] 186s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 186s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 186s 186s Rank 0 wrote RayOutput/NetworkTest.txt 186s 186s 186s *** 186s Step: Network testing 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 0 seconds 186s Since beginning: 0 seconds 186s *** 186s 186s 186s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 186s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 186s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 186s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 186s Rank 0 wrote RayOutput/NumberOfSequences.txt 186s Rank 0 wrote RayOutput/SequencePartition.txt 186s 186s *** 186s Step: Counting sequences to assemble 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 0 seconds 186s Since beginning: 0 seconds 186s *** 186s 186s 186s Rank 0 is loading sequence reads 186s Rank 0 : partition is [0;4107], 4108 sequence reads 186s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 186s Rank 0 has 0 sequence reads 186s Rank 0: assembler memory usage: 121500 KiB 186s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 186s Rank 0 has 4108 sequence reads (completed) 186s 186s *** 186s Step: Sequence loading 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 0 seconds 186s Since beginning: 0 seconds 186s *** 186s 186s 186s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 186s Rank 0 created its Bloom filter 186s Rank 0 is counting k-mers in sequence reads [1/4108] 186s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 186s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 186s 186s 186s *** 186s Step: K-mer counting 186s Date: Thu Aug 1 23:59:54 2024 186s Elapsed time: 0 seconds 186s Since beginning: 0 seconds 186s *** 186s 186s 186s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 186s Rank 0 destroyed its Bloom filter 186s Rank 0 has 1958 k-mers (completed) 186s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 186s Rank 0: assembler memory usage: 117880 KiB 188s 188s 188s Rank 0: the minimum coverage is 3 188s Rank 0: the peak coverage is 3 188s Warning: no peak observed in the k-mer coverage distribution. 188s to deal with the sequencing error rate, try to lower the k-mer length (-k) 188s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 188s 188s *** 188s Step: Coverage distribution analysis 188s Date: Thu Aug 1 23:59:56 2024 188s Elapsed time: 2 seconds 188s Since beginning: 2 seconds 188s *** 188s 188s 188s 189s Rank 0 is adding edges [1/4108] 189s Rank 0 is adding edges [4108/4108] (completed) 189s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 189s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 189s 189s *** 189s Step: Graph construction 189s Date: Thu Aug 1 23:59:57 2024 189s Elapsed time: 1 seconds 189s Since beginning: 3 seconds 189s *** 189s 189s 189s Rank 0 has 1958 vertices (completed) 189s Rank 0: assembler memory usage: 117880 KiB 191s Rank 0 is purging edges [1/1958] 191s Rank 0 is purging edges [1958/1958] (completed) 191s Rank 0: assembler memory usage: 118412 KiB 191s VirtualProcessor: completed jobs: 1958 191s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 193s Rank 0 wrote RayOutput/degreeDistribution.txt 193s 193s *** 193s Step: Null edge purging 193s Date: Fri Aug 2 00:00:01 2024 193s Elapsed time: 4 seconds 193s Since beginning: 7 seconds 193s *** 193s 193s 193s Rank 0 is selecting optimal read markers [1/4108] 193s Rank 0: assembler memory usage: 118412 KiB 193s Rank 0 is selecting optimal read markers [4108/4108] (completed) 193s Rank 0: peak number of workers: 599, maximum: 32768 193s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 193s Rank 0: assembler memory usage: 126624 KiB 193s Rank 0: Freeing unused assembler memory: 4096 KiB freed 193s Rank 0: assembler memory usage: 126624 KiB 193s 193s *** 193s Step: Selection of optimal read markers 193s Date: Fri Aug 2 00:00:01 2024 193s Elapsed time: 0 seconds 193s Since beginning: 7 seconds 193s *** 193s 193s 193s Rank 0: memory usage for optimal read markers= 4096 KiB 193s Rank 0 is creating seeds [1/1958] 193s Rank 0: assembler memory usage: 126624 KiB 195s Rank 0 has 1 seeds 195s Rank 0 is creating seeds [1958/1958] (completed) 195s Rank 0: peak number of workers: 746, maximum: 32768 195s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 195s Rank 0 runtime statistics for seeding algorithm: 195s Rank 0 Skipped paths because of dead end for head: 0 195s Rank 0 Skipped paths because of dead end for tail: 0 195s Rank 0 Skipped paths because of two dead ends: 0 195s Rank 0 Skipped paths because of bubble weak component: 0 195s Rank 0 Skipped paths because of short length: 1956 195s Rank 0 Skipped paths because of bad ownership: 1 195s Rank 0 Skipped paths because of low coverage: 0 195s Rank 0 Eligible paths: 1 195s Rank 0: assembler memory usage: 126624 KiB 195s Rank 0 has 1 seeds to register. 195s Rank 0 registered 0/1 195s Rank 0 registered 0/1 195s Rank 0 registered its seeds 195s VirtualProcessor: completed jobs: 0 195s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 197s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 207s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 207s Rank 0 merged its seeds: 1 seeds -> 1 seeds 207s 207s *** 207s Step: Detection of assembly seeds 207s Date: Fri Aug 2 00:00:15 2024 207s Elapsed time: 14 seconds 207s Since beginning: 21 seconds 207s *** 207s 207s 207s Rank 0 is calculating library lengths [1/1] 207s Rank 0 detected 1743 library lengths 207s Rank 0 is calculating library lengths [1/1] (completed) 207s Rank 0: peak number of workers: 1, maximum: 32768 207s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 207s Rank 0: assembler memory usage: 163492 KiB 207s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 207s 207s Mode= 2 signalAverage= 10 207s CURRENT IS NOISE, 244 207s GOT HIT 214 207s 207s 207s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 207s 207s *** 207s Step: Estimation of outer distances for paired reads 207s Date: Fri Aug 2 00:00:15 2024 207s Elapsed time: 0 seconds 207s Since beginning: 21 seconds 207s *** 207s 207s 207s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 207s Rank 0 traversed 1000 nucleotide symbols 207s Rank 0: assembler memory usage: 167588 KiB 207s Rank 0 is extending seeds [1/1] (completed) 207s Rank 0 extended 1 seeds out of 1 (100.00%) 207s Rank 0: assembler memory usage: 159396 KiB 207s Rank 0 starting fusions 207s 207s *** 207s Step: Bidirectional extension of seeds 207s Date: Fri Aug 2 00:00:15 2024 207s Elapsed time: 0 seconds 207s Since beginning: 21 seconds 207s *** 207s 207s 207s Rank 0: starting clear step. cycleNumber= 0 209s Rank 0 adding 0 new fusions 209s Rank 0 cleared, 1 paths 209s Rank 0: starting distribution step 209s Rank 0 is distributing fusions [1/1] 209s Rank 0: assembler memory usage: 159396 KiB 209s Date: Fri Aug 2 00:00:17 2024 209s Rank 0 is distributing fusions [1/1] (completed) 209s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 209s Rank 0: assembler memory usage: 163492 KiB 209s Date: Fri Aug 2 00:00:17 2024 209s Rank 0 tells others to compute fusions. 209s Rank 0 FusionTaskCreator assignNextTask [0/2] 209s Rank 0: assembler memory usage: 163492 KiB 209s Date: Fri Aug 2 00:00:17 2024 209s Rank 0 FusionTaskCreator processWorkerResult [0/2] 209s Rank 0: assembler memory usage: 163492 KiB 209s Date: Fri Aug 2 00:00:17 2024 209s Rank 0 FusionTaskCreator [2/2] 209s Statistics: all paths: 1 eliminated during fusing: 0 209s Rank 0: assembler memory usage: 163492 KiB 209s VirtualProcessor: completed jobs: 2 209s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 209s Rank 0: starting clear step. cycleNumber= 1 211s Rank 0 adding 0 new fusions 211s Rank 0 cleared, 1 paths 211s Rank 0 is distributing fusions [1/1] 211s Rank 0: assembler memory usage: 163492 KiB 211s Date: Fri Aug 2 00:00:19 2024 211s Rank 0 is distributing fusions [1/1] (completed) 211s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 211s Rank 0: assembler memory usage: 163492 KiB 211s Date: Fri Aug 2 00:00:19 2024 211s Rank 0 JoinerTaskCreator assignNextTask [0/2] 211s Rank 0: assembler memory usage: 163492 KiB 211s Date: Fri Aug 2 00:00:19 2024 211s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 211s Rank 0: assembler memory usage: 163492 KiB 211s Date: Fri Aug 2 00:00:19 2024 211s Rank 0 JoinerTaskCreator [2/2] 211s Statistics: all paths: 1 eliminated during joining: 0 211s Rank 0: assembler memory usage: 163492 KiB 211s Date: Fri Aug 2 00:00:19 2024 211s VirtualProcessor: completed jobs: 2 211s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 213s Rank 0 adding 0 new fusions 213s Rank 0 cleared, 1 paths 213s Rank 0: starting distribution step 213s Rank 0 is distributing fusions [1/1] 213s Rank 0: assembler memory usage: 163492 KiB 213s Date: Fri Aug 2 00:00:21 2024 213s Rank 0 is distributing fusions [1/1] (completed) 213s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 213s Rank 0: assembler memory usage: 163492 KiB 213s Date: Fri Aug 2 00:00:21 2024 213s Rank 0 tells others to compute fusions. 213s Rank 0 FusionTaskCreator assignNextTask [0/2] 213s Rank 0: assembler memory usage: 163492 KiB 213s Date: Fri Aug 2 00:00:21 2024 213s Rank 0 FusionTaskCreator processWorkerResult [0/2] 213s Rank 0: assembler memory usage: 163492 KiB 213s Date: Fri Aug 2 00:00:21 2024 213s Rank 0 FusionTaskCreator [2/2] 213s Statistics: all paths: 1 eliminated during fusing: 0 213s Rank 0: assembler memory usage: 163492 KiB 213s VirtualProcessor: completed jobs: 2 213s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 213s Rank 0: starting clear step. cycleNumber= 2 215s Rank 0 adding 0 new fusions 215s Rank 0 cleared, 1 paths 215s Rank 0 is distributing fusions [1/1] 215s Rank 0: assembler memory usage: 163492 KiB 215s Date: Fri Aug 2 00:00:23 2024 215s Rank 0 is distributing fusions [1/1] (completed) 215s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 215s Rank 0: assembler memory usage: 163492 KiB 215s Date: Fri Aug 2 00:00:23 2024 215s Rank 0 JoinerTaskCreator assignNextTask [0/2] 215s Rank 0: assembler memory usage: 163492 KiB 215s Date: Fri Aug 2 00:00:23 2024 215s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 215s Rank 0: assembler memory usage: 163492 KiB 215s Date: Fri Aug 2 00:00:23 2024 215s Rank 0 JoinerTaskCreator [2/2] 215s Statistics: all paths: 1 eliminated during joining: 0 215s Rank 0: assembler memory usage: 163492 KiB 215s Date: Fri Aug 2 00:00:23 2024 215s VirtualProcessor: completed jobs: 2 215s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 217s Rank 0 adding 0 new fusions 217s Rank 0 cleared, 1 paths 217s Rank 0: starting distribution step 217s Rank 0 is distributing fusions [1/1] 217s Rank 0: assembler memory usage: 163492 KiB 217s Date: Fri Aug 2 00:00:25 2024 217s Rank 0 is distributing fusions [1/1] (completed) 217s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 217s Rank 0: assembler memory usage: 163492 KiB 217s Date: Fri Aug 2 00:00:25 2024 217s Rank 0 cycleNumber= 2 217s 217s *** 217s Step: Merging of redundant paths 217s Date: Fri Aug 2 00:00:25 2024 217s Elapsed time: 10 seconds 217s Since beginning: 31 seconds 217s *** 217s 217s 217s Rank 0 appended 1 elements 217s 217s *** 217s Step: Generation of contigs 217s Date: Fri Aug 2 00:00:25 2024 217s Elapsed time: 0 seconds 217s Since beginning: 31 seconds 217s *** 217s 217s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 217s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 217s Rank 0 ineligibleObjects: 0/972 (0.00%) 217s Rank 0: assembler memory usage: 163492 KiB 217s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 217s Rank 0 finished gathering scaffold links. 217s Rank 0 will write 1 contig lengths 217s Rank 0 will solve the scaffolding problem. 217s Welcome to GreedySolver v1.0 217s 1 vertices; 0 edges 217s 1 contigs >= 500 217s Edges in solution: 0 217s 217s Conflict statistics: 217s 1 scaffolds, 1 >= 500 217s Total: 1000 nucleotides 217s 217s *** 217s Step: Scaffolding of contigs 217s Date: Fri Aug 2 00:00:25 2024 217s Elapsed time: 0 seconds 217s Since beginning: 31 seconds 217s *** 217s 217s Rank 0 syncing with master 217s 217s *** 217s Step: Counting sequences to search 217s Date: Fri Aug 2 00:00:25 2024 217s Elapsed time: 0 seconds 217s Since beginning: 31 seconds 217s *** 217s 217s 217s Rank 0 will add colors, 0 sequences in 0 files to process 217s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 219s 219s *** 219s Step: Graph coloring 219s Date: Fri Aug 2 00:00:27 2024 219s Elapsed time: 2 seconds 219s Since beginning: 33 seconds 219s *** 219s 219s 219s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 219s Rank 0 shares its counts 219s Rank 0 computing contig abundances [1/1] [1/972] 219s Rank 0 computing contig abundances [1/1] [972/972] 219s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 219s 219s *** 219s Step: Counting contig biological abundances 219s Date: Fri Aug 2 00:00:27 2024 219s Elapsed time: 0 seconds 219s Since beginning: 33 seconds 219s *** 219s 219s 219s Rank 0 colored the graph with 0 real colors using 1 virtual colors 219s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 219s 219s *** 219s Step: Counting sequence biological abundances 219s Date: Fri Aug 2 00:00:27 2024 219s Elapsed time: 0 seconds 219s Since beginning: 33 seconds 219s *** 219s 219s 219s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 219s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 221s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 221s 221s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 221s Rank 0 is starting taxon syncing across the compute tribe. 221s 221s *** 221s Step: Loading taxons 221s Date: Fri Aug 2 00:00:29 2024 221s Elapsed time: 2 seconds 221s Since beginning: 35 seconds 221s *** 221s 221s Rank 0 synced taxons across the grid with 1 poor slaves. 221s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 221s Rank 0 has 0 taxons after syncing with master 223s 223s 223s *** 223s Step: Loading tree 223s Date: Fri Aug 2 00:00:31 2024 223s Elapsed time: 2 seconds 223s Since beginning: 37 seconds 223s *** 223s 225s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 225s 225s Rank 0: counting ontology terms in the graph... 227s Rank 0: 0 have some biological signal 227s Number of dereferenced alternate handles: 0 227s Number of k-mer observations with gene ontology terms: 0 227s Rank 0: synced ontology term profiles with master 227s Rank 0: synchronization is complete! 227s Rank 0: ontology terms with biological signal: 0 227s Populated recursive values... 227s Gene ontology terms without depth information: 0 227s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 227s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 227s 227s *** 227s Step: Processing gene ontologies 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 4 seconds 227s Since beginning: 41 seconds 227s *** 227s 227s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 227s [GenomeNeighbourhood] in final list: 0 227s 227s *** 227s Step: Computing neighbourhoods 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 0 seconds 227s Since beginning: 41 seconds 227s *** 227s 227s Contigs >= 100 nt 227s Number: 1 227s Total length: 1000 227s Average: 1000 227s N50: 1000 227s Median: 1000 227s Largest: 1000 227s Contigs >= 500 nt 227s Number: 1 227s Total length: 1000 227s Average: 1000 227s N50: 1000 227s Median: 1000 227s Largest: 1000 227s Scaffolds >= 100 nt 227s Number: 1 227s Total length: 1000 227s Average: 1000 227s N50: 1000 227s Median: 1000 227s Largest: 1000 227s Scaffolds >= 500 nt 227s Number: 1 227s Total length: 1000 227s Average: 1000 227s N50: 1000 227s Median: 1000 227s Largest: 1000 227s 227s Rank 0 wrote RayOutput/Contigs.fasta 227s Rank 0 wrote RayOutput/Scaffolds.fasta 227s Check for RayOutput/* 227s 227s 227s 227s ************************************************** 227s This program comes with ABSOLUTELY NO WARRANTY. 227s This is free software, and you are welcome to redistribute it 227s under certain conditions; see "LICENSE.txt" for details. 227s ************************************************** 227s 227s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 227s Centre de recherche en infectiologie de l'Université Laval 227s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 227s http://denovoassembler.sf.net/ 227s 227s References to cite: 227s 227s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 227s Ray Meta: scalable de novo metagenome assembly and profiling. 227s Genome Biology (BioMed Central Ltd). 227s 13:R122, Published: 22 December 2012 227s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 227s 227s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 227s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 227s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 227s November 2010, Volume 17, Issue 11, Pages 1519-1533. 227s http://dx.doi.org/doi:10.1089/cmb.2009.0238 227s 227s Ray version 2.3.1 227s License for Ray: GNU General Public License version 3 227s RayPlatform version: 2.0.1 227s License for RayPlatform: GNU Lesser General Public License version 3 227s 227s MAXKMERLENGTH: 32 227s Maximum coverage depth stored by CoverageDepth: 4294967295 227s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 227s FORCE_PACKING = n 227s ASSERT = n 227s HAVE_LIBZ = y 227s HAVE_LIBBZ2 = y 227s PROFILER_COLLECT = n 227s MINIRANKS = y 227s CLOCK_GETTIME = n 227s __linux__ = y 227s _MSC_VER = n 227s __GNUC__ = y 227s RAY_32_BITS = n 227s RAY_64_BITS = y 227s MPI standard version: MPI 3.1 227s MPI library: Open-MPI 4.1.6 227s Compiler: GNU gcc/g++ 13.2.0 227s MPI I/O: n 227s 227s 227s -k (to set the k-mer size) 227s Value: 31 227s 227s 227s Paired library # 0 227s -p (paired-end sequences) 227s Left sequences: ecoli_1K_1.fq 227s Right sequences: ecoli_1K_2.fq 227s Average length: automatic detection 227s Standard deviation: automatic detection 227s 227s Ray command: 227s mpiexec -n 2 Ray \ 227s -k \ 227s 31 \ 227s -p \ 227s ecoli_1K_1.fq \ 227s ecoli_1K_2.fq \ 227s -o \ 227s test3 227s 227s Rank 0 wrote test3/RayCommand.txt 227s 227s k-mer length: 31 227s Rank 1: assembler memory usage: 42860 KiB 227s Rank 0: assembler memory usage: 42848 KiB 227s Rank 1: assembler memory usage: 108532 KiB 227s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 3079 227s Rank 0: assembler memory usage: 108520 KiB 227s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 3078 227s Rank 0: testing the network, please wait... 227s 227s Rank 0 is testing the network [0/1000] 227s Rank 1 is testing the network [0/1000] 227s Rank 1 is testing the network [1000/1000] 227s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 227s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 227s Rank 0 is testing the network [1000/1000] 227s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 227s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 227s 227s Rank 0 wrote test3/NetworkTest.txt 227s 227s 227s *** 227s Step: Network testing 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 0 seconds 227s Since beginning: 0 seconds 227s *** 227s 227s 227s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 227s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 227s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 227s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 227s Rank 0 wrote test3/NumberOfSequences.txt 227s Rank 0 wrote test3/SequencePartition.txt 227s 227s *** 227s Step: Counting sequences to assemble 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 0 seconds 227s Since beginning: 0 seconds 227s *** 227s 227s 227s Rank 0 is loading sequence reads 227s Rank 0 : partition is [0;2053], 2054 sequence reads 227s Rank 1 is loading sequence reads 227s Rank 1 : partition is [2054;4107], 2054 sequence reads 227s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 227s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 227s Rank 0 has 0 sequence reads 227s Rank 0: assembler memory usage: 117416 KiB 227s Rank 1 has 0 sequence reads 227s Rank 1: assembler memory usage: 117400 KiB 227s Rank 0 has 2054 sequence reads (completed) 227s Rank 1 has 2054 sequence reads (completed) 227s 227s *** 227s Step: Sequence loading 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 0 seconds 227s Since beginning: 0 seconds 227s *** 227s 227s 227s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 227s Rank 0 created its Bloom filter 227s Rank 0 is counting k-mers in sequence reads [1/2054] 227s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 227s Rank 1 created its Bloom filter 227s Rank 1 is counting k-mers in sequence reads [1/2054] 227s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 227s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 227s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 227s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 227s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 227s Rank 1 destroyed its Bloom filter 227s Rank 1 has 922 k-mers (completed) 227s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 227s Rank 1: assembler memory usage: 117400 KiB 227s 227s 227s *** 227s Step: K-mer counting 227s Date: Fri Aug 2 00:00:35 2024 227s Elapsed time: 0 seconds 227s Since beginning: 0 seconds 227s *** 227s 227s 227s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 227s Rank 0 destroyed its Bloom filter 227s Rank 0 has 1032 k-mers (completed) 227s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 227s Rank 0: assembler memory usage: 113684 KiB 229s 229s 229s Rank 0: the minimum coverage is 3 229s Rank 0: the peak coverage is 3 229s Warning: no peak observed in the k-mer coverage distribution. 229s to deal with the sequencing error rate, try to lower the k-mer length (-k) 229s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 229s 229s *** 229s Step: Coverage distribution analysis 229s Date: Fri Aug 2 00:00:37 2024 229s Elapsed time: 2 seconds 229s Since beginning: 2 seconds 229s *** 229s 229s 229s 229s Rank 0 is adding edges [1/2054] 229s Rank 1 is adding edges [1/2054] 229s Rank 1 is adding edges [2054/2054] (completed) 229s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 229s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 229s Rank 0 is adding edges [2054/2054] (completed) 229s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 229s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 229s 229s *** 229s Step: Graph construction 229s Date: Fri Aug 2 00:00:37 2024 229s Elapsed time: 0 seconds 229s Since beginning: 2 seconds 229s *** 229s 229s 229s Rank 1 has 922 vertices (completed) 229s Rank 0 has 1032 vertices (completed) 229s Rank 0: assembler memory usage: 113684 KiB 229s Rank 1: assembler memory usage: 117400 KiB 231s Rank 1 is purging edges [1/922] 231s Rank 0 is purging edges [1/1032] 231s Rank 1 is purging edges [922/922] (completed) 231s Rank 1: assembler memory usage: 117400 KiB 231s VirtualProcessor: completed jobs: 922 231s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 231s Rank 0 is purging edges [1032/1032] (completed) 231s Rank 0: assembler memory usage: 113956 KiB 231s VirtualProcessor: completed jobs: 1032 231s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 233s Rank 0 wrote test3/degreeDistribution.txt 233s 233s *** 233s Step: Null edge purging 233s Date: Fri Aug 2 00:00:41 2024 233s Elapsed time: 4 seconds 233s Since beginning: 6 seconds 233s *** 233s 233s 233s Rank 0 is selecting optimal read markers [1/2054] 233s Rank 1 is selecting optimal read markers [1/2054] 233s Rank 1: assembler memory usage: 117400 KiB 233s Rank 0: assembler memory usage: 113956 KiB 234s Rank 1 is selecting optimal read markers [2054/2054] (completed) 234s Rank 1: peak number of workers: 1121, maximum: 32768 234s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 234s Rank 1: assembler memory usage: 125080 KiB 234s Rank 1: Freeing unused assembler memory: 4096 KiB freed 234s Rank 1: assembler memory usage: 125080 KiB 234s Rank 0 is selecting optimal read markers [2054/2054] (completed) 234s Rank 0: peak number of workers: 1135, maximum: 32768 234s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 234s Rank 0: assembler memory usage: 122164 KiB 234s Rank 0: Freeing unused assembler memory: 4096 KiB freed 234s Rank 0: assembler memory usage: 122164 KiB 234s 234s *** 234s Step: Selection of optimal read markers 234s Date: Fri Aug 2 00:00:42 2024 234s Elapsed time: 1 seconds 234s Since beginning: 7 seconds 234s *** 234s 234s 234s Rank 1: memory usage for optimal read markers= 4096 KiB 234s Rank 0: memory usage for optimal read markers= 4096 KiB 234s Rank 1 is creating seeds [1/922] 234s Rank 1: assembler memory usage: 125080 KiB 234s Rank 0 is creating seeds [1/1032] 234s Rank 0: assembler memory usage: 122164 KiB 236s Rank 1 has 1 seeds 236s Rank 1 is creating seeds [922/922] (completed) 236s Rank 1: peak number of workers: 916, maximum: 32768 236s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 236s Rank 1 runtime statistics for seeding algorithm: 236s Rank 1 Skipped paths because of dead end for head: 0 236s Rank 1 Skipped paths because of dead end for tail: 0 236s Rank 1 Skipped paths because of two dead ends: 0 236s Rank 1 Skipped paths because of bubble weak component: 0 236s Rank 1 Skipped paths because of short length: 921 236s Rank 1 Skipped paths because of bad ownership: 0 236s Rank 1 Skipped paths because of low coverage: 0 236s Rank 1 Eligible paths: 1 236s Rank 1: assembler memory usage: 125080 KiB 236s Rank 0 has 0 seeds 236s Rank 0 is creating seeds [1032/1032] (completed) 236s Rank 0: peak number of workers: 998, maximum: 32768 236s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 236s Rank 0 runtime statistics for seeding algorithm: 236s Rank 0 Skipped paths because of dead end for head: 0 236s Rank 0 Skipped paths because of dead end for tail: 0 236s Rank 0 Skipped paths because of two dead ends: 0 236s Rank 0 Skipped paths because of bubble weak component: 0 236s Rank 0 Skipped paths because of short length: 1031 236s Rank 0 Skipped paths because of bad ownership: 1 236s Rank 0 Skipped paths because of low coverage: 0 236s Rank 0 Eligible paths: 0 236s Rank 0: assembler memory usage: 122164 KiB 236s Rank 1 has 1 seeds to register. 236s Rank 0 registered -1/0 236s Rank 0 registered its seeds 236s Rank 1 registered 0/1 236s VirtualProcessor: completed jobs: 0 236s Rank 1 registered 0/1 236s Rank 1 registered its seeds 236s VirtualProcessor: completed jobs: 0 236s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 236s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 238s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 238s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 248s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 248s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 248s Rank 0 merged its seeds: 0 seeds -> 0 seeds 248s Rank 1 merged its seeds: 1 seeds -> 1 seeds 248s 248s *** 248s Step: Detection of assembly seeds 248s Date: Fri Aug 2 00:00:56 2024 248s Elapsed time: 14 seconds 248s Since beginning: 21 seconds 248s *** 248s 248s 248s Rank 0 detected 0 library lengths 248s Rank 0 is calculating library lengths [0/0] (completed) 248s Rank 0: peak number of workers: 0, maximum: 32768 248s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 248s Rank 0: assembler memory usage: 126260 KiB 248s Rank 1 is calculating library lengths [1/1] 248s Rank 1 detected 1737 library lengths 248s Rank 1 is calculating library lengths [1/1] (completed) 248s Rank 1: peak number of workers: 1, maximum: 32768 248s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7983 virtual messages generated 7983 real messages (100%) 248s Rank 1: assembler memory usage: 157852 KiB 248s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 248s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 248s 248s Mode= 2 signalAverage= 9 248s CURRENT IS NOISE, 244 248s GOT HIT 212 248s 248s 248s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 248s 248s *** 248s Step: Estimation of outer distances for paired reads 248s Date: Fri Aug 2 00:00:56 2024 248s Elapsed time: 0 seconds 248s Since beginning: 21 seconds 248s *** 248s 248s 248s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 248s Rank 0 is extending seeds [0/0] (completed) 248s Rank 0 extended 0 seeds out of 0 (0.00%) 248s Rank 0: assembler memory usage: 126260 KiB 248s Rank 1 traversed 1000 nucleotide symbols 248s Rank 1: assembler memory usage: 161948 KiB 248s Rank 1 is extending seeds [1/1] (completed) 248s Rank 1 extended 1 seeds out of 1 (100.00%) 248s Rank 1: assembler memory usage: 161948 KiB 248s Rank 0 starting fusions 248s 248s *** 248s Step: Bidirectional extension of seeds 248s Date: Fri Aug 2 00:00:56 2024 248s Elapsed time: 0 seconds 248s Since beginning: 21 seconds 248s *** 248s 248s 248s Rank 0: starting clear step. cycleNumber= 0 250s Rank 0 adding 0 new fusions 250s Rank 0 cleared, 0 paths 250s Rank 0: starting distribution step 250s Rank 1 adding 0 new fusions 250s Rank 1 cleared, 1 paths 250s Rank 0 is distributing fusions [0/0] (completed) 250s Rank 1 is distributing fusions [1/1] 250s Rank 1: assembler memory usage: 161948 KiB 250s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 250s Rank 0: assembler memory usage: 126260 KiB 250s Date: Fri Aug 2 00:00:58 2024 250s Date: Fri Aug 2 00:00:58 2024 250s Rank 1 is distributing fusions [1/1] (completed) 250s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 250s Rank 1: assembler memory usage: 161948 KiB 250s Date: Fri Aug 2 00:00:58 2024 250s Rank 0 tells others to compute fusions. 250s Rank 0 FusionTaskCreator [0/0] 250s Statistics: all paths: 0 eliminated during fusing: 0 250s Rank 1 FusionTaskCreator assignNextTask [0/2] 250s Rank 0: assembler memory usage: 126260 KiB 250s VirtualProcessor: completed jobs: 0 250s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 250s Rank 1: assembler memory usage: 161948 KiB 250s Date: Fri Aug 2 00:00:58 2024 250s Rank 1 FusionTaskCreator processWorkerResult [0/2] 250s Rank 1: assembler memory usage: 161948 KiB 250s Date: Fri Aug 2 00:00:58 2024 250s Rank 1 FusionTaskCreator [2/2] 250s Statistics: all paths: 1 eliminated during fusing: 0 250s Rank 1: assembler memory usage: 161948 KiB 250s VirtualProcessor: completed jobs: 2 250s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10893 virtual messages generated 10893 real messages (100%) 250s Rank 0: starting clear step. cycleNumber= 1 252s Rank 1 adding 0 new fusions 252s Rank 1 cleared, 1 paths 252s Rank 0 adding 0 new fusions 252s Rank 0 cleared, 0 paths 252s Rank 1 is distributing fusions [1/1] 252s Rank 0 is distributing fusions [0/0] (completed) 252s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 252s Rank 1: assembler memory usage: 161948 KiB 252s Rank 0: assembler memory usage: 126260 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s Date: Fri Aug 2 00:01:00 2024 252s Rank 1 is distributing fusions [1/1] (completed) 252s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 252s Rank 1: assembler memory usage: 161948 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s Rank 0 JoinerTaskCreator [0/0] 252s Statistics: all paths: 0 eliminated during joining: 0 252s Rank 1 JoinerTaskCreator assignNextTask [0/2] 252s Rank 0: assembler memory usage: 126260 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s VirtualProcessor: completed jobs: 0 252s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 252s Rank 1: assembler memory usage: 161948 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 252s Rank 1: assembler memory usage: 161948 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s Rank 1 JoinerTaskCreator [2/2] 252s Statistics: all paths: 1 eliminated during joining: 0 252s Rank 1: assembler memory usage: 161948 KiB 252s Date: Fri Aug 2 00:01:00 2024 252s VirtualProcessor: completed jobs: 2 252s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13803 virtual messages generated 13803 real messages (100%) 254s Rank 1 adding 0 new fusions 254s Rank 1 cleared, 1 paths 254s Rank 0 adding 0 new fusions 254s Rank 0 cleared, 0 paths 254s Rank 0: starting distribution step 254s Rank 1 is distributing fusions [1/1] 254s Rank 0 is distributing fusions [0/0] (completed) 254s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 254s Rank 1: assembler memory usage: 161948 KiB 254s Date: Fri Aug 2 00:01:02 2024 254s Rank 0: assembler memory usage: 126260 KiB 254s Date: Fri Aug 2 00:01:02 2024 254s Rank 1 is distributing fusions [1/1] (completed) 254s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 254s Rank 1: assembler memory usage: 161948 KiB 254s Date: Fri Aug 2 00:01:02 2024 254s Rank 0 tells others to compute fusions. 254s Rank 1 FusionTaskCreator assignNextTask [0/2] 254s Rank 0 FusionTaskCreator [0/0] 254s Statistics: all paths: 0 eliminated during fusing: 0 254s Rank 0: assembler memory usage: 126260 KiB 254s VirtualProcessor: completed jobs: 0 254s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 254s Rank 1: assembler memory usage: 161948 KiB 254s Date: Fri Aug 2 00:01:02 2024 254s Rank 1 FusionTaskCreator processWorkerResult [0/2] 254s Rank 1: assembler memory usage: 161948 KiB 254s Date: Fri Aug 2 00:01:02 2024 254s Rank 1 FusionTaskCreator [2/2] 254s Statistics: all paths: 1 eliminated during fusing: 0 254s Rank 1: assembler memory usage: 161948 KiB 254s VirtualProcessor: completed jobs: 2 254s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16713 virtual messages generated 16713 real messages (100%) 254s Rank 0: starting clear step. cycleNumber= 2 256s Rank 1 adding 0 new fusions 256s Rank 1 cleared, 1 paths 256s Rank 0 adding 0 new fusions 256s Rank 0 cleared, 0 paths 256s Rank 1 is distributing fusions [1/1] 256s Rank 0 is distributing fusions [0/0] (completed) 256s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 256s Rank 0: assembler memory usage: 126260 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s Rank 1: assembler memory usage: 161948 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s Rank 1 is distributing fusions [1/1] (completed) 256s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 256s Rank 1: assembler memory usage: 161948 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s Rank 0 JoinerTaskCreator [0/0] 256s Rank 1 JoinerTaskCreator assignNextTask [0/2] 256s Statistics: all paths: 0 eliminated during joining: 0 256s Rank 1: assembler memory usage: 161948 KiB 256s Rank 0: assembler memory usage: 126260 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s VirtualProcessor: completed jobs: 0 256s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 256s Date: Fri Aug 2 00:01:04 2024 256s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 256s Rank 1: assembler memory usage: 161948 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s Rank 1 JoinerTaskCreator [2/2] 256s Statistics: all paths: 1 eliminated during joining: 0 256s Rank 1: assembler memory usage: 161948 KiB 256s Date: Fri Aug 2 00:01:04 2024 256s VirtualProcessor: completed jobs: 2 256s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19623 virtual messages generated 19623 real messages (100%) 258s Rank 0 adding 0 new fusions 258s Rank 0 cleared, 0 paths 258s Rank 1 adding 0 new fusions 258s Rank 1 cleared, 1 paths 258s Rank 0: starting distribution step 258s Rank 0 is distributing fusions [0/0] (completed) 258s Rank 1 is distributing fusions [1/1] 258s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 258s Rank 1: assembler memory usage: 161948 KiB 258s Date: Fri Aug 2 00:01:06 2024 258s Rank 0: assembler memory usage: 126260 KiB 258s Date: Fri Aug 2 00:01:06 2024 258s Rank 1 is distributing fusions [1/1] (completed) 258s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 258s Rank 1: assembler memory usage: 161948 KiB 258s Date: Fri Aug 2 00:01:06 2024 258s Rank 0 cycleNumber= 2 258s 258s *** 258s Step: Merging of redundant paths 258s Date: Fri Aug 2 00:01:06 2024 258s Elapsed time: 10 seconds 258s Since beginning: 31 seconds 258s *** 258s 258s 258s Rank 0 appended 0 elements 258s Rank 1 appended 1 elements 258s 258s *** 258s Step: Generation of contigs 258s Date: Fri Aug 2 00:01:06 2024 258s Elapsed time: 0 seconds 258s Since beginning: 31 seconds 258s *** 258s 258s Rank 0 finished gathering scaffold links. 258s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 258s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 258s Rank 0 ineligibleObjects: 0/970 (0.00%) 258s Rank 1: assembler memory usage: 161948 KiB 258s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 258s Rank 1 finished gathering scaffold links. 258s Rank 0 will write 1 contig lengths 258s Rank 0 will solve the scaffolding problem. 258s Welcome to GreedySolver v1.0 258s 1 vertices; 0 edges 258s 1 contigs >= 500 258s Edges in solution: 0 258s 258s Conflict statistics: 258s 1 scaffolds, 1 >= 500 258s Total: 1000 nucleotides 258s 258s *** 258s Step: Scaffolding of contigs 258s Date: Fri Aug 2 00:01:06 2024 258s Elapsed time: 0 seconds 258s Since beginning: 31 seconds 258s *** 258s 258s Rank 1 syncing with master 258s Rank 0 syncing with master 258s 258s *** 258s Step: Counting sequences to search 258s Date: Fri Aug 2 00:01:06 2024 258s Elapsed time: 0 seconds 258s Since beginning: 31 seconds 258s *** 258s 258s 258s Rank 1 will add colors, 0 sequences in 0 files to process 258s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 258s Rank 0 will add colors, 0 sequences in 0 files to process 258s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 260s 260s *** 260s Step: Graph coloring 260s Date: Fri Aug 2 00:01:08 2024 260s Elapsed time: 2 seconds 260s Since beginning: 33 seconds 260s *** 260s 260s 260s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 260s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 260s Rank 1 computing contig abundances [1/1] [1/970] 260s Rank 0 shares its counts 260s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 260s Rank 1 computing contig abundances [1/1] [970/970] 260s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 260s 260s *** 260s Step: Counting contig biological abundances 260s Date: Fri Aug 2 00:01:08 2024 260s Elapsed time: 0 seconds 260s Since beginning: 33 seconds 260s *** 260s Rank 1 colored the graph with 0 real colors using 1 virtual colors 260s 260s 260s Rank 0 colored the graph with 0 real colors using 1 virtual colors 260s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 260s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 260s 260s *** 260s Step: Counting sequence biological abundances 260s Date: Fri Aug 2 00:01:08 2024 260s Elapsed time: 0 seconds 260s Since beginning: 33 seconds 260s *** 260s 260s 260s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 260s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 260s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 260s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 262s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 262s 262s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 262s 262s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 262s Rank 0 is starting taxon syncing across the compute tribe. 262s 262s *** 262s Step: Loading taxons 262s Date: Fri Aug 2 00:01:10 2024 262s Elapsed time: 2 seconds 262s Since beginning: 35 seconds 262s *** 262s 262s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 262s Rank 1 has 0 taxons after syncing with master 262s Rank 0 synced taxons across the grid with 2 poor slaves. 262s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 262s Rank 0 has 0 taxons after syncing with master 264s 264s 264s 264s *** 264s Step: Loading tree 264s Date: Fri Aug 2 00:01:12 2024 264s Elapsed time: 2 seconds 264s Since beginning: 37 seconds 264s *** 264s 266s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 266s 266s Rank 0: counting ontology terms in the graph... 266s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 266s 266s Rank 1: counting ontology terms in the graph... 268s Rank 0: 0 have some biological signal 268s Number of dereferenced alternate handles: 0 268s Number of k-mer observations with gene ontology terms: 0 268s Rank 0: synced ontology term profiles with master 268s Rank 1: 0 have some biological signal 268s Number of dereferenced alternate handles: 0 268s Number of k-mer observations with gene ontology terms: 0 268s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 268s Rank 1: synced ontology term profiles with master 268s Rank 0: synchronization is complete! 268s Rank 0: ontology terms with biological signal: 0 268s Populated recursive values... 268s Gene ontology terms without depth information: 0 268s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 268s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 268s 268s *** 268s Step: Processing gene ontologies 268s Date: Fri Aug 2 00:01:16 2024 268s Elapsed time: 4 seconds 268s Since beginning: 41 seconds 268s *** 268s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 268s 268s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 268s [GenomeNeighbourhood] in final list: 0 268s 268s *** 268s Step: Computing neighbourhoods 268s Date: Fri Aug 2 00:01:16 2024 268s Elapsed time: 0 seconds 268s Since beginning: 41 seconds 268s *** 268s 268s Contigs >= 100 nt 268s Number: 1 268s Total length: 1000 268s Average: 1000 268s N50: 1000 268s Median: 1000 268s Largest: 1000 268s Contigs >= 500 nt 268s Number: 1 268s Total length: 1000 268s Average: 1000 268s N50: 1000 268s Median: 1000 268s Largest: 1000 268s Scaffolds >= 100 nt 268s Number: 1 268s Total length: 1000 268s Average: 1000 268s N50: 1000 268s Median: 1000 268s Largest: 1000 268s Scaffolds >= 500 nt 268s Number: 1 268s Total length: 1000 268s Average: 1000 268s N50: 1000 268s Median: 1000 268s Largest: 1000 268s 268s Rank 0 wrote test3/Contigs.fasta 268s Rank 0 wrote test3/Scaffolds.fasta 268s Check for test3/* 268s 268s 268s autopkgtest [00:01:16]: test run-unit-test: -----------------------] 268s run-unit-test PASS 268s autopkgtest [00:01:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 269s autopkgtest [00:01:17]: @@@@@@@@@@@@@@@@@@@@ summary 269s run-unit-test PASS 280s nova [W] Skipping flock for amd64 280s Creating nova instance adt-oracular-amd64-ray-20240801-235647-juju-7f2275-prod-proposed-migration-environment-2-2df57bff-4151-4840-a0d3-d30af6d04837 from image adt/ubuntu-oracular-amd64-server-20240801.img (UUID aebffe7b-12cf-44b5-a8f7-6038922fec62)...