0s autopkgtest [01:14:32]: starting date and time: 2024-03-19 01:14:32+0000 0s autopkgtest [01:14:32]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [01:14:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ai_bsri4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-13.secgroup --name adt-noble-ppc64el-ray-20240319-011432-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 442s autopkgtest [01:21:54]: testbed dpkg architecture: ppc64el 442s autopkgtest [01:21:54]: testbed apt version: 2.7.12 442s autopkgtest [01:21:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 443s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 444s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 445s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 445s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 445s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 450s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [645 kB] 450s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 450s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 450s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 450s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4015 kB] 452s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 452s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.3 kB] 452s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 455s Fetched 9129 kB in 10s (895 kB/s) 456s Reading package lists... 458s Reading package lists... 459s Building dependency tree... 459s Reading state information... 459s Calculating upgrade... 459s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 459s Reading package lists... 460s Building dependency tree... 460s Reading state information... 460s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 461s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 461s Get:2 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 461s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 461s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 461s Get:5 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 464s Get:6 http://ftpmaster.internal/ubuntu noble/multiverse Sources [295 kB] 464s Get:7 http://ftpmaster.internal/ubuntu noble/main Sources [1377 kB] 465s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1377 kB] 465s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [14.9 MB] 467s Get:10 http://ftpmaster.internal/ubuntu noble/multiverse ppc64el Packages [185 kB] 471s Fetched 38.3 MB in 10s (3814 kB/s) 472s Reading package lists... 472s Reading package lists... 472s Building dependency tree... 472s Reading state information... 473s Calculating upgrade... 473s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 473s Reading package lists... 473s Building dependency tree... 473s Reading state information... 474s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 476s autopkgtest [01:22:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 476s autopkgtest [01:22:28]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 479s Get:1 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (dsc) [2114 B] 479s Get:2 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (tar) [450 kB] 479s Get:3 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (diff) [213 kB] 480s gpgv: Signature made Wed Dec 6 21:31:12 2023 UTC 480s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 480s gpgv: issuer "tille@debian.org" 480s gpgv: Can't check signature: No public key 480s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8.dsc: no acceptable signature found 480s autopkgtest [01:22:32]: testing package ray version 2.3.1-8 480s autopkgtest [01:22:32]: build not needed 481s autopkgtest [01:22:33]: test run-unit-test: preparing testbed 483s Reading package lists... 483s Building dependency tree... 483s Reading state information... 483s Starting pkgProblemResolver with broken count: 0 483s Starting 2 pkgProblemResolver with broken count: 0 483s Done 484s The following additional packages will be installed: 484s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 484s libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdatrie1 libdeflate0 484s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfontconfig1 484s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 484s libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 484s libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3t64 484s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 484s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 484s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 484s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 484s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 484s ray ray-doc ray-extra unzip x11-common xdg-utils zip 484s Suggested packages: 484s tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler elpa-ess r-doc-info 484s | r-doc-pdf r-mathlib r-base-html 484s Recommended packages: 484s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 484s libx11-protocol-perl x11-utils x11-xserver-utils 484s The following NEW packages will be installed: 484s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 484s fonts-dejavu-mono libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdatrie1 484s libdeflate0 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfontconfig1 484s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 484s libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 484s libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3t64 484s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 484s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 484s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 484s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 484s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 484s ray ray-doc ray-extra unzip x11-common xdg-utils zip 484s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 484s Need to get 94.3 MB/94.3 MB of archives. 484s After this operation, 341 MB of additional disk space will be used. 484s Get:1 /tmp/autopkgtest.YYRWq4/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 484s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 484s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 484s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 484s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 485s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 485s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 488s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 490s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 490s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 490s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 490s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 491s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 491s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 491s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 491s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 491s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 491s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 491s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 491s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 491s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 491s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 491s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 491s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 491s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 491s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 491s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 491s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 491s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 491s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 491s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 491s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 491s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 492s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 492s Get:35 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 492s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 492s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 492s Get:38 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 492s Get:39 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 492s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 492s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 492s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-7ubuntu1 [2721 kB] 492s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 492s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 492s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 492s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 492s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 492s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 492s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 492s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 492s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 492s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 492s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 492s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 492s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 493s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 493s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 493s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.13-2 [916 kB] 493s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 493s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-7ubuntu1 [170 kB] 493s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-7ubuntu1 [118 kB] 493s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 493s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 493s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 493s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 496s Get:66 http://ftpmaster.internal/ubuntu noble/universe ppc64el mpi-default-bin ppc64el 1.15 [2336 B] 496s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el ray ppc64el 2.3.1-8 [812 kB] 496s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el ray-doc all 2.3.1-8 [35.2 kB] 496s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el ray-extra all 2.3.1-8 [12.3 kB] 496s Preconfiguring packages ... 497s Fetched 94.3 MB in 12s (7761 kB/s) 497s Selecting previously unselected package fonts-dejavu-mono. 497s (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 ... 70095 files and directories currently installed.) 497s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 497s Unpacking fonts-dejavu-mono (2.37-8) ... 497s Selecting previously unselected package fonts-dejavu-core. 497s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 497s Unpacking fonts-dejavu-core (2.37-8) ... 497s Selecting previously unselected package fontconfig-config. 497s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 497s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 497s Selecting previously unselected package libfontconfig1:ppc64el. 497s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 497s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 497s Selecting previously unselected package fontconfig. 497s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 497s Unpacking fontconfig (2.15.0-1ubuntu1) ... 497s Selecting previously unselected package libllvm17:ppc64el. 497s Preparing to unpack .../05-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 497s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 498s Selecting previously unselected package libamd-comgr2:ppc64el. 498s Preparing to unpack .../06-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 498s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 499s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 499s Preparing to unpack .../07-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 499s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 499s Selecting previously unselected package libhsakmt1:ppc64el. 499s Preparing to unpack .../08-libhsakmt1_5.7.0-1_ppc64el.deb ... 499s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 499s Selecting previously unselected package libhsa-runtime64-1. 499s Preparing to unpack .../09-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 499s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 499s Selecting previously unselected package libamdhip64-5. 499s Preparing to unpack .../10-libamdhip64-5_5.2.3-12_ppc64el.deb ... 499s Unpacking libamdhip64-5 (5.2.3-12) ... 499s Selecting previously unselected package libblas3:ppc64el. 499s Preparing to unpack .../11-libblas3_3.12.0-3_ppc64el.deb ... 499s Unpacking libblas3:ppc64el (3.12.0-3) ... 499s Selecting previously unselected package libpixman-1-0:ppc64el. 499s Preparing to unpack .../12-libpixman-1-0_0.42.2-1_ppc64el.deb ... 499s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 499s Selecting previously unselected package libxcb-render0:ppc64el. 499s Preparing to unpack .../13-libxcb-render0_1.15-1_ppc64el.deb ... 499s Unpacking libxcb-render0:ppc64el (1.15-1) ... 499s Selecting previously unselected package libxcb-shm0:ppc64el. 499s Preparing to unpack .../14-libxcb-shm0_1.15-1_ppc64el.deb ... 499s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 499s Selecting previously unselected package libxrender1:ppc64el. 499s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 499s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 499s Selecting previously unselected package libcairo2:ppc64el. 499s Preparing to unpack .../16-libcairo2_1.18.0-1_ppc64el.deb ... 499s Unpacking libcairo2:ppc64el (1.18.0-1) ... 499s Selecting previously unselected package libdatrie1:ppc64el. 499s Preparing to unpack .../17-libdatrie1_0.2.13-3_ppc64el.deb ... 499s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 499s Selecting previously unselected package libdeflate0:ppc64el. 499s Preparing to unpack .../18-libdeflate0_1.19-1_ppc64el.deb ... 499s Unpacking libdeflate0:ppc64el (1.19-1) ... 499s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 499s Preparing to unpack .../19-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 499s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 499s Selecting previously unselected package librdmacm1t64:ppc64el. 499s Preparing to unpack .../20-librdmacm1t64_50.0-2_ppc64el.deb ... 499s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 499s Selecting previously unselected package libfabric1:ppc64el. 499s Preparing to unpack .../21-libfabric1_1.17.0-3_ppc64el.deb ... 499s Unpacking libfabric1:ppc64el (1.17.0-3) ... 499s Selecting previously unselected package libgfortran5:ppc64el. 499s Preparing to unpack .../22-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 499s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 499s Selecting previously unselected package libgomp1:ppc64el. 499s Preparing to unpack .../23-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 499s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 499s Selecting previously unselected package libgraphite2-3:ppc64el. 499s Preparing to unpack .../24-libgraphite2-3_1.3.14-2_ppc64el.deb ... 499s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 499s Selecting previously unselected package libharfbuzz0b:ppc64el. 499s Preparing to unpack .../25-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 499s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 499s Selecting previously unselected package libhwloc15:ppc64el. 499s Preparing to unpack .../26-libhwloc15_2.10.0-1_ppc64el.deb ... 499s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 499s Selecting previously unselected package x11-common. 499s Preparing to unpack .../27-x11-common_1%3a7.7+23ubuntu2_all.deb ... 499s Unpacking x11-common (1:7.7+23ubuntu2) ... 499s Selecting previously unselected package libice6:ppc64el. 499s Preparing to unpack .../28-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 499s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 499s Selecting previously unselected package libjpeg-turbo8:ppc64el. 499s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 499s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 499s Selecting previously unselected package libjpeg8:ppc64el. 499s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 499s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 499s Selecting previously unselected package liblapack3:ppc64el. 499s Preparing to unpack .../31-liblapack3_3.12.0-3_ppc64el.deb ... 499s Unpacking liblapack3:ppc64el (3.12.0-3) ... 499s Selecting previously unselected package liblerc4:ppc64el. 499s Preparing to unpack .../32-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 499s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 499s Selecting previously unselected package libmunge2:ppc64el. 499s Preparing to unpack .../33-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 499s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 499s Selecting previously unselected package libpciaccess0:ppc64el. 499s Preparing to unpack .../34-libpciaccess0_0.17-3_ppc64el.deb ... 499s Unpacking libpciaccess0:ppc64el (0.17-3) ... 499s Selecting previously unselected package libxnvctrl0:ppc64el. 499s Preparing to unpack .../35-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 499s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 499s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 499s Preparing to unpack .../36-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 499s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 499s Selecting previously unselected package libhwloc-plugins:ppc64el. 499s Preparing to unpack .../37-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 499s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 499s Selecting previously unselected package libpmix2t64:ppc64el. 499s Preparing to unpack .../38-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 499s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 499s Selecting previously unselected package libucx0:ppc64el. 499s Preparing to unpack .../39-libucx0_1.16.0+ds-4_ppc64el.deb ... 499s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 500s Selecting previously unselected package libopenmpi3t64:ppc64el. 500s Preparing to unpack .../40-libopenmpi3t64_4.1.6-7ubuntu1_ppc64el.deb ... 500s Unpacking libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 500s Selecting previously unselected package libthai-data. 500s Preparing to unpack .../41-libthai-data_0.1.29-2_all.deb ... 500s Unpacking libthai-data (0.1.29-2) ... 500s Selecting previously unselected package libthai0:ppc64el. 500s Preparing to unpack .../42-libthai0_0.1.29-2_ppc64el.deb ... 500s Unpacking libthai0:ppc64el (0.1.29-2) ... 500s Selecting previously unselected package libpango-1.0-0:ppc64el. 500s Preparing to unpack .../43-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 500s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 500s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 500s Preparing to unpack .../44-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 500s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 500s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 500s Preparing to unpack .../45-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 500s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 500s Selecting previously unselected package libpaper1:ppc64el. 500s Preparing to unpack .../46-libpaper1_1.1.29_ppc64el.deb ... 500s Unpacking libpaper1:ppc64el (1.1.29) ... 500s Selecting previously unselected package libpaper-utils. 500s Preparing to unpack .../47-libpaper-utils_1.1.29_ppc64el.deb ... 500s Unpacking libpaper-utils (1.1.29) ... 500s Selecting previously unselected package libsharpyuv0:ppc64el. 500s Preparing to unpack .../48-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 500s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 500s Selecting previously unselected package libsm6:ppc64el. 500s Preparing to unpack .../49-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 500s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 500s Selecting previously unselected package libtcl8.6:ppc64el. 500s Preparing to unpack .../50-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 500s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 500s Selecting previously unselected package libjbig0:ppc64el. 500s Preparing to unpack .../51-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 500s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 500s Selecting previously unselected package libwebp7:ppc64el. 500s Preparing to unpack .../52-libwebp7_1.3.2-0.4_ppc64el.deb ... 500s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 500s Selecting previously unselected package libtiff6:ppc64el. 500s Preparing to unpack .../53-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 500s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 500s Selecting previously unselected package libxft2:ppc64el. 500s Preparing to unpack .../54-libxft2_2.3.6-1_ppc64el.deb ... 500s Unpacking libxft2:ppc64el (2.3.6-1) ... 500s Selecting previously unselected package libxss1:ppc64el. 500s Preparing to unpack .../55-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 500s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 500s Selecting previously unselected package libtk8.6:ppc64el. 500s Preparing to unpack .../56-libtk8.6_8.6.13-2_ppc64el.deb ... 500s Unpacking libtk8.6:ppc64el (8.6.13-2) ... 500s Selecting previously unselected package libxt6:ppc64el. 500s Preparing to unpack .../57-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 500s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 500s Selecting previously unselected package openmpi-common. 500s Preparing to unpack .../58-openmpi-common_4.1.6-7ubuntu1_all.deb ... 500s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 500s Selecting previously unselected package openmpi-bin. 500s Preparing to unpack .../59-openmpi-bin_4.1.6-7ubuntu1_ppc64el.deb ... 500s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 500s Selecting previously unselected package zip. 500s Preparing to unpack .../60-zip_3.0-13_ppc64el.deb ... 500s Unpacking zip (3.0-13) ... 500s Selecting previously unselected package unzip. 500s Preparing to unpack .../61-unzip_6.0-28ubuntu3_ppc64el.deb ... 500s Unpacking unzip (6.0-28ubuntu3) ... 500s Selecting previously unselected package xdg-utils. 500s Preparing to unpack .../62-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 500s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 500s Selecting previously unselected package r-base-core. 500s Preparing to unpack .../63-r-base-core_4.3.2-1build1_ppc64el.deb ... 500s Unpacking r-base-core (4.3.2-1build1) ... 501s Selecting previously unselected package mpi-default-bin. 501s Preparing to unpack .../64-mpi-default-bin_1.15_ppc64el.deb ... 501s Unpacking mpi-default-bin (1.15) ... 501s Selecting previously unselected package ray. 501s Preparing to unpack .../65-ray_2.3.1-8_ppc64el.deb ... 501s Unpacking ray (2.3.1-8) ... 501s Selecting previously unselected package ray-doc. 501s Preparing to unpack .../66-ray-doc_2.3.1-8_all.deb ... 501s Unpacking ray-doc (2.3.1-8) ... 501s Selecting previously unselected package ray-extra. 501s Preparing to unpack .../67-ray-extra_2.3.1-8_all.deb ... 501s Unpacking ray-extra (2.3.1-8) ... 501s Selecting previously unselected package autopkgtest-satdep. 501s Preparing to unpack .../68-1-autopkgtest-satdep.deb ... 501s Unpacking autopkgtest-satdep (0) ... 501s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 501s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 501s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 501s Setting up libpaper1:ppc64el (1.1.29) ... 501s 501s Creating config file /etc/papersize with new version 501s Setting up ray-doc (2.3.1-8) ... 501s Setting up libpciaccess0:ppc64el (0.17-3) ... 501s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 501s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 501s Setting up libdatrie1:ppc64el (0.2.13-3) ... 501s Setting up libxcb-render0:ppc64el (1.15-1) ... 501s Setting up unzip (6.0-28ubuntu3) ... 501s Setting up x11-common (1:7.7+23ubuntu2) ... 502s Setting up libdeflate0:ppc64el (1.19-1) ... 502s Setting up libxcb-shm0:ppc64el (1.15-1) ... 502s Setting up libpaper-utils (1.1.29) ... 502s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 502s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 502s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 502s Setting up zip (3.0-13) ... 502s Setting up libblas3:ppc64el (3.12.0-3) ... 502s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 502s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 502s Setting up fonts-dejavu-mono (2.37-8) ... 502s Setting up libhwloc15:ppc64el (2.10.0-1) ... 502s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 502s Setting up fonts-dejavu-core (2.37-8) ... 502s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 502s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 502s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 502s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 502s Setting up openmpi-common (4.1.6-7ubuntu1) ... 502s Setting up librdmacm1t64:ppc64el (50.0-2) ... 502s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 502s Setting up libthai-data (0.1.29-2) ... 502s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 502s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 502s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 502s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 502s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 502s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 502s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 502s Setting up libfabric1:ppc64el (1.17.0-3) ... 502s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 502s Setting up liblapack3:ppc64el (3.12.0-3) ... 502s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 502s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 502s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 502s Setting up libthai0:ppc64el (0.1.29-2) ... 502s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 502s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 502s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 502s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 502s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 502s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 502s Setting up fontconfig (2.15.0-1ubuntu1) ... 504s Regenerating fonts cache... done. 504s Setting up libxft2:ppc64el (2.3.6-1) ... 504s Setting up libtk8.6:ppc64el (8.6.13-2) ... 504s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 504s Setting up libcairo2:ppc64el (1.18.0-1) ... 504s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 504s Setting up libhsa-runtime64-1 (5.7.1-1) ... 504s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 504s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 504s Setting up libamdhip64-5 (5.2.3-12) ... 504s Setting up r-base-core (4.3.2-1build1) ... 504s 504s Creating config file /etc/R/Renviron with new version 504s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 504s Setting up ray-extra (2.3.1-8) ... 504s Setting up libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 504s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 504s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 504s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 504s Setting up mpi-default-bin (1.15) ... 504s Setting up ray (2.3.1-8) ... 504s Setting up autopkgtest-satdep (0) ... 504s Processing triggers for man-db (2.12.0-3) ... 505s Processing triggers for install-info (7.1-3) ... 505s Processing triggers for libc-bin (2.39-0ubuntu2) ... 510s (Reading database ... 72741 files and directories currently installed.) 510s Removing autopkgtest-satdep (0) ... 511s autopkgtest [01:23:03]: test run-unit-test: [----------------------- 511s 511s ************************************************** 511s This program comes with ABSOLUTELY NO WARRANTY. 511s This is free software, and you are welcome to redistribute it 511s under certain conditions; see "LICENSE.txt" for details. 511s ************************************************** 511s 511s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 511s Centre de recherche en infectiologie de l'Université Laval 511s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 511s http://denovoassembler.sf.net/ 511s 511s References to cite: 511s 511s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 511s Ray Meta: scalable de novo metagenome assembly and profiling. 511s Genome Biology (BioMed Central Ltd). 511s 13:R122, Published: 22 December 2012 511s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 511s 511s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 511s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 511s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 511s November 2010, Volume 17, Issue 11, Pages 1519-1533. 511s http://dx.doi.org/doi:10.1089/cmb.2009.0238 511s 511s Ray version 2.3.1 511s License for Ray: GNU General Public License version 3 511s RayPlatform version: 2.0.1 511s License for RayPlatform: GNU Lesser General Public License version 3 511s 511s MAXKMERLENGTH: 32 511s Maximum coverage depth stored by CoverageDepth: 4294967295 511s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 511s FORCE_PACKING = n 511s ASSERT = n 511s HAVE_LIBZ = y 511s HAVE_LIBBZ2 = y 511s PROFILER_COLLECT = n 511s MINIRANKS = y 511s CLOCK_GETTIME = n 511s __linux__ = y 511s _MSC_VER = n 511s __GNUC__ = y 511s RAY_32_BITS = n 511s RAY_64_BITS = y 511s MPI standard version: MPI 3.1 511s MPI library: Open-MPI 4.1.6 511s Compiler: GNU gcc/g++ 13.2.0 511s MPI I/O: n 511s 511s 511s -k (to set the k-mer size) 511s Value: 31 511s 511s 511s Paired library # 0 511s -p (paired-end sequences) 511s Left sequences: ecoli_1K_1.fq 511s Right sequences: ecoli_1K_2.fq 511s Average length: automatic detection 511s Standard deviation: automatic detection 511s 511s Ray command: 511s mpiexec -n 1 Ray \ 511s -k \ 511s 31 \ 511s -p \ 511s ecoli_1K_1.fq \ 511s ecoli_1K_2.fq \ 511s -o \ 511s test1 511s 511s Rank 0 wrote test1/RayCommand.txt 511s 511s k-mer length: 31 511s Rank 0: assembler memory usage: 46272 KiB 511s Rank 0: assembler memory usage: 112064 KiB 511s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3466 511s Rank 0: testing the network, please wait... 511s 511s Rank 0 is testing the network [0/1000] 511s Rank 0 is testing the network [1000/1000] 511s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 511s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 511s 511s Rank 0 wrote test1/NetworkTest.txt 511s 511s 511s *** 511s Step: Network testing 511s Date: Tue Mar 19 01:23:03 2024 511s Elapsed time: 0 seconds 511s Since beginning: 0 seconds 511s *** 511s 511s 511s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 511s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 511s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 511s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 511s Rank 0 wrote test1/NumberOfSequences.txt 511s Rank 0 wrote test1/SequencePartition.txt 511s 511s *** 511s Step: Counting sequences to assemble 511s Date: Tue Mar 19 01:23:03 2024 511s Elapsed time: 0 seconds 511s Since beginning: 0 seconds 511s *** 511s 511s 511s Rank 0 is loading sequence reads 511s Rank 0 : partition is [0;4107], 4108 sequence reads 511s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 511s Rank 0 has 0 sequence reads 511s Rank 0: assembler memory usage: 124992 KiB 511s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 511s Rank 0 has 4108 sequence reads (completed) 511s 511s *** 511s Step: Sequence loading 511s Date: Tue Mar 19 01:23:03 2024 511s Elapsed time: 0 seconds 511s Since beginning: 0 seconds 511s *** 511s 511s 511s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 511s Rank 0 created its Bloom filter 511s Rank 0 is counting k-mers in sequence reads [1/4108] 511s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 511s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 511s 511s 511s *** 511s Step: K-mer counting 511s Date: Tue Mar 19 01:23:03 2024 511s Elapsed time: 0 seconds 511s Since beginning: 0 seconds 511s *** 511s 511s 511s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 511s Rank 0 destroyed its Bloom filter 511s Rank 0 has 1954 k-mers (completed) 511s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 511s Rank 0: assembler memory usage: 121408 KiB 512s 512s 512s Rank 0: the minimum coverage is 3 512s Rank 0: the peak coverage is 3 512s Warning: no peak observed in the k-mer coverage distribution. 512s to deal with the sequencing error rate, try to lower the k-mer length (-k) 512s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 512s 512s *** 512s Step: Coverage distribution analysis 512s Date: Tue Mar 19 01:23:04 2024 512s Elapsed time: 1 seconds 512s Since beginning: 1 seconds 512s *** 512s 512s 512s 512s Rank 0 is adding edges [1/4108] 512s Rank 0 is adding edges [4108/4108] (completed) 512s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 512s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 512s 512s *** 512s Step: Graph construction 512s Date: Tue Mar 19 01:23:04 2024 512s Elapsed time: 0 seconds 512s Since beginning: 1 seconds 512s *** 512s 512s 512s Rank 0 has 1954 vertices (completed) 512s Rank 0: assembler memory usage: 121408 KiB 512s Rank 0 is purging edges [1/1954] 512s Rank 0 is purging edges [1954/1954] (completed) 512s Rank 0: assembler memory usage: 121792 KiB 512s VirtualProcessor: completed jobs: 1954 512s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 513s Rank 0 wrote test1/degreeDistribution.txt 513s 513s *** 513s Step: Null edge purging 513s Date: Tue Mar 19 01:23:05 2024 513s Elapsed time: 1 seconds 513s Since beginning: 2 seconds 513s *** 513s 513s 513s Rank 0 is selecting optimal read markers [1/4108] 513s Rank 0: assembler memory usage: 121792 KiB 513s Rank 0 is selecting optimal read markers [4108/4108] (completed) 513s Rank 0: peak number of workers: 599, maximum: 32768 513s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 513s Rank 0: assembler memory usage: 130112 KiB 513s Rank 0: Freeing unused assembler memory: 4096 KiB freed 513s Rank 0: assembler memory usage: 130112 KiB 513s 513s *** 513s Step: Selection of optimal read markers 513s Date: Tue Mar 19 01:23:05 2024 513s Elapsed time: 0 seconds 513s Since beginning: 2 seconds 513s *** 513s 513s 513s Rank 0: memory usage for optimal read markers= 4096 KiB 513s Rank 0 is creating seeds [1/1954] 513s Rank 0: assembler memory usage: 130112 KiB 514s Rank 0 has 1 seeds 514s Rank 0 is creating seeds [1954/1954] (completed) 514s Rank 0: peak number of workers: 746, maximum: 32768 514s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 514s Rank 0 runtime statistics for seeding algorithm: 514s Rank 0 Skipped paths because of dead end for head: 0 514s Rank 0 Skipped paths because of dead end for tail: 0 514s Rank 0 Skipped paths because of two dead ends: 0 514s Rank 0 Skipped paths because of bubble weak component: 0 514s Rank 0 Skipped paths because of short length: 1952 514s Rank 0 Skipped paths because of bad ownership: 1 514s Rank 0 Skipped paths because of low coverage: 0 514s Rank 0 Eligible paths: 1 514s Rank 0: assembler memory usage: 130112 KiB 514s Rank 0 has 1 seeds to register. 514s Rank 0 registered 0/1 514s Rank 0 registered 0/1 514s Rank 0 registered its seeds 514s VirtualProcessor: completed jobs: 0 514s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 514s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 524s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 524s Rank 0 merged its seeds: 1 seeds -> 1 seeds 524s 524s *** 524s Step: Detection of assembly seeds 524s Date: Tue Mar 19 01:23:16 2024 524s Elapsed time: 11 seconds 524s Since beginning: 13 seconds 524s *** 524s 524s 524s Rank 0 is calculating library lengths [1/1] 524s Rank 0 detected 1737 library lengths 524s Rank 0 is calculating library lengths [1/1] (completed) 524s Rank 0: peak number of workers: 1, maximum: 32768 524s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 524s Rank 0: assembler memory usage: 167040 KiB 524s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 524s 524s Mode= 2 signalAverage= 9 524s CURRENT IS NOISE, 244 524s GOT HIT 212 524s 524s 524s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 524s 524s *** 524s Step: Estimation of outer distances for paired reads 524s Date: Tue Mar 19 01:23:16 2024 524s Elapsed time: 0 seconds 524s Since beginning: 13 seconds 524s *** 524s 524s 524s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 524s Rank 0 traversed 1000 nucleotide symbols 524s Rank 0: assembler memory usage: 171136 KiB 524s Rank 0 is extending seeds [1/1] (completed) 524s Rank 0 extended 1 seeds out of 1 (100.00%) 524s Rank 0: assembler memory usage: 162944 KiB 524s Rank 0 starting fusions 524s 524s *** 524s Step: Bidirectional extension of seeds 524s Date: Tue Mar 19 01:23:16 2024 524s Elapsed time: 0 seconds 524s Since beginning: 13 seconds 524s *** 524s 524s 524s Rank 0: starting clear step. cycleNumber= 0 525s Rank 0 adding 0 new fusions 525s Rank 0 cleared, 1 paths 525s Rank 0: starting distribution step 525s Rank 0 is distributing fusions [1/1] 525s Rank 0: assembler memory usage: 162944 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 is distributing fusions [1/1] (completed) 525s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 tells others to compute fusions. 525s Rank 0 FusionTaskCreator assignNextTask [0/2] 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 FusionTaskCreator processWorkerResult [0/2] 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 FusionTaskCreator [2/2] 525s Statistics: all paths: 1 eliminated during fusing: 0 525s Rank 0: assembler memory usage: 167040 KiB 525s VirtualProcessor: completed jobs: 2 525s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 525s Rank 0: starting clear step. cycleNumber= 1 525s Rank 0 adding 0 new fusions 525s Rank 0 cleared, 1 paths 525s Rank 0 is distributing fusions [1/1] 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 is distributing fusions [1/1] (completed) 525s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 JoinerTaskCreator assignNextTask [0/2] 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s Rank 0 JoinerTaskCreator [2/2] 525s Statistics: all paths: 1 eliminated during joining: 0 525s Rank 0: assembler memory usage: 167040 KiB 525s Date: Tue Mar 19 01:23:17 2024 525s VirtualProcessor: completed jobs: 2 525s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 526s Rank 0 adding 0 new fusions 526s Rank 0 cleared, 1 paths 526s Rank 0: starting distribution step 526s Rank 0 is distributing fusions [1/1] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 is distributing fusions [1/1] (completed) 526s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 tells others to compute fusions. 526s Rank 0 FusionTaskCreator assignNextTask [0/2] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 FusionTaskCreator processWorkerResult [0/2] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 FusionTaskCreator [2/2] 526s Statistics: all paths: 1 eliminated during fusing: 0 526s Rank 0: assembler memory usage: 167040 KiB 526s VirtualProcessor: completed jobs: 2 526s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 526s Rank 0: starting clear step. cycleNumber= 2 526s Rank 0 adding 0 new fusions 526s Rank 0 cleared, 1 paths 526s Rank 0 is distributing fusions [1/1] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 is distributing fusions [1/1] (completed) 526s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 JoinerTaskCreator assignNextTask [0/2] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s Rank 0 JoinerTaskCreator [2/2] 526s Statistics: all paths: 1 eliminated during joining: 0 526s Rank 0: assembler memory usage: 167040 KiB 526s Date: Tue Mar 19 01:23:18 2024 526s VirtualProcessor: completed jobs: 2 526s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 527s Rank 0 adding 0 new fusions 527s Rank 0 cleared, 1 paths 527s Rank 0: starting distribution step 527s Rank 0 is distributing fusions [1/1] 527s Rank 0: assembler memory usage: 167040 KiB 527s Date: Tue Mar 19 01:23:19 2024 527s Rank 0 is distributing fusions [1/1] (completed) 527s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 527s Rank 0: assembler memory usage: 167040 KiB 527s Date: Tue Mar 19 01:23:19 2024 527s Rank 0 cycleNumber= 2 527s 527s *** 527s Step: Merging of redundant paths 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 3 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s 527s Rank 0 appended 1 elements 527s 527s *** 527s Step: Generation of contigs 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 527s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 527s Rank 0 ineligibleObjects: 0/970 (0.00%) 527s Rank 0: assembler memory usage: 167040 KiB 527s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 527s Rank 0 finished gathering scaffold links. 527s Rank 0 will write 1 contig lengths 527s Rank 0 will solve the scaffolding problem. 527s Welcome to GreedySolver v1.0 527s 1 vertices; 0 edges 527s 1 contigs >= 500 527s Edges in solution: 0 527s 527s Conflict statistics: 527s 1 scaffolds, 1 >= 500 527s Total: 1000 nucleotides 527s 527s *** 527s Step: Scaffolding of contigs 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s Rank 0 syncing with master 527s 527s *** 527s Step: Counting sequences to search 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s 527s Rank 0 will add colors, 0 sequences in 0 files to process 527s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 527s 527s *** 527s Step: Graph coloring 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s 527s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 527s Rank 0 shares its counts 527s Rank 0 computing contig abundances [1/1] [1/970] 527s Rank 0 computing contig abundances [1/1] [970/970] 527s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 527s 527s *** 527s Step: Counting contig biological abundances 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s 527s Rank 0 colored the graph with 0 real colors using 1 virtual colors 527s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 527s 527s *** 527s Step: Counting sequence biological abundances 527s Date: Tue Mar 19 01:23:19 2024 527s Elapsed time: 0 seconds 527s Since beginning: 16 seconds 527s *** 527s 527s 527s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 527s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 528s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 528s 528s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 528s Rank 0 is starting taxon syncing across the compute tribe. 528s 528s *** 528s Step: Loading taxons 528s Date: Tue Mar 19 01:23:20 2024 528s Elapsed time: 1 seconds 528s Since beginning: 17 seconds 528s *** 528s 528s Rank 0 synced taxons across the grid with 1 poor slaves. 528s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 528s Rank 0 has 0 taxons after syncing with master 528s 528s 528s *** 528s Step: Loading tree 528s Date: Tue Mar 19 01:23:20 2024 528s Elapsed time: 0 seconds 528s Since beginning: 17 seconds 528s *** 528s 529s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 529s 529s Rank 0: counting ontology terms in the graph... 529s Rank 0: 0 have some biological signal 529s Number of dereferenced alternate handles: 0 529s Number of k-mer observations with gene ontology terms: 0 529s Rank 0: synced ontology term profiles with master 529s Rank 0: synchronization is complete! 529s Rank 0: ontology terms with biological signal: 0 529s Populated recursive values... 529s Gene ontology terms without depth information: 0 529s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 529s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 529s 529s *** 529s Step: Processing gene ontologies 529s Date: Tue Mar 19 01:23:21 2024 529s Elapsed time: 1 seconds 529s Since beginning: 18 seconds 529s *** 529s 529s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 529s [GenomeNeighbourhood] in final list: 0 529s 529s *** 529s Step: Computing neighbourhoods 529s Date: Tue Mar 19 01:23:21 2024 529s Elapsed time: 0 seconds 529s Since beginning: 18 seconds 529s *** 529s 529s Contigs >= 100 nt 529s Number: 1 529s Total length: 1000 529s Average: 1000 529s N50: 1000 529s Median: 1000 529s Largest: 1000 529s Contigs >= 500 nt 529s Number: 1 529s Total length: 1000 529s Average: 1000 529s N50: 1000 529s Median: 1000 529s Largest: 1000 529s Scaffolds >= 100 nt 529s Number: 1 529s Total length: 1000 529s Average: 1000 529s N50: 1000 529s Median: 1000 529s Largest: 1000 529s Scaffolds >= 500 nt 529s Number: 1 529s Total length: 1000 529s Average: 1000 529s N50: 1000 529s Median: 1000 529s Largest: 1000 529s 529s Rank 0 wrote test1/Contigs.fasta 529s Rank 0 wrote test1/Scaffolds.fasta 529s Check for test1/* 529s 529s 529s 529s ************************************************** 529s This program comes with ABSOLUTELY NO WARRANTY. 529s This is free software, and you are welcome to redistribute it 529s under certain conditions; see "LICENSE.txt" for details. 529s ************************************************** 529s 529s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 529s Centre de recherche en infectiologie de l'Université Laval 529s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 529s http://denovoassembler.sf.net/ 529s 529s References to cite: 529s 529s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 529s Ray Meta: scalable de novo metagenome assembly and profiling. 529s Genome Biology (BioMed Central Ltd). 529s 13:R122, Published: 22 December 2012 529s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 529s 529s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 529s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 529s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 529s November 2010, Volume 17, Issue 11, Pages 1519-1533. 529s http://dx.doi.org/doi:10.1089/cmb.2009.0238 529s 529s Ray version 2.3.1 529s License for Ray: GNU General Public License version 3 529s RayPlatform version: 2.0.1 529s License for RayPlatform: GNU Lesser General Public License version 3 529s 529s MAXKMERLENGTH: 32 529s Maximum coverage depth stored by CoverageDepth: 4294967295 529s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 529s FORCE_PACKING = n 529s ASSERT = n 529s HAVE_LIBZ = y 529s HAVE_LIBBZ2 = y 529s PROFILER_COLLECT = n 529s MINIRANKS = y 529s CLOCK_GETTIME = n 529s __linux__ = y 529s _MSC_VER = n 529s __GNUC__ = y 529s RAY_32_BITS = n 529s RAY_64_BITS = y 529s MPI standard version: MPI 3.1 529s MPI library: Open-MPI 4.1.6 529s Compiler: GNU gcc/g++ 13.2.0 529s MPI I/O: n 529s 529s 529s -k (to set the k-mer size) 529s Value: 31 529s 529s 529s Paired library # 0 529s -p (paired-end sequences) 529s Left sequences: SampleDirectory/s_6.first1000_1.fastq 529s Right sequences: SampleDirectory/s_6.first1000_2.fastq 529s Average length: automatic detection 529s Standard deviation: automatic detection 529s 529s Ray command: 529s mpiexec -n 1 Ray \ 529s -k \ 529s 31 \ 529s -detect-sequence-files \ 529s SampleDirectory \ 529s -o \ 529s test2 529s 529s Rank 0 wrote test2/RayCommand.txt 529s 529s k-mer length: 31 529s Rank 0: assembler memory usage: 46272 KiB 529s Rank 0: assembler memory usage: 112064 KiB 529s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3472 529s Rank 0: testing the network, please wait... 529s 529s Rank 0 is testing the network [0/1000] 529s Rank 0 is testing the network [1000/1000] 529s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 529s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 529s 529s Rank 0 wrote test2/NetworkTest.txt 529s 529s 529s *** 529s Step: Network testing 529s Date: Tue Mar 19 01:23:21 2024 529s Elapsed time: 0 seconds 529s Since beginning: 0 seconds 529s *** 529s 529s 529s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 529s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 529s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 529s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 529s Rank 0 wrote test2/NumberOfSequences.txt 529s Rank 0 wrote test2/SequencePartition.txt 529s 529s *** 529s Step: Counting sequences to assemble 529s Date: Tue Mar 19 01:23:21 2024 529s Elapsed time: 0 seconds 529s Since beginning: 0 seconds 529s *** 529s 529s 529s Rank 0 is loading sequence reads 529s Rank 0 : partition is [0;4107], 4108 sequence reads 529s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 529s Rank 0 has 0 sequence reads 529s Rank 0: assembler memory usage: 124992 KiB 529s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 529s Rank 0 has 4108 sequence reads (completed) 529s 529s *** 529s Step: Sequence loading 529s Date: Tue Mar 19 01:23:21 2024 529s Elapsed time: 0 seconds 529s Since beginning: 0 seconds 529s *** 529s 529s 529s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 529s Rank 0 created its Bloom filter 530s Rank 0 is counting k-mers in sequence reads [1/4108] 530s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 530s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 530s 530s 530s *** 530s Step: K-mer counting 530s Date: Tue Mar 19 01:23:22 2024 530s Elapsed time: 1 seconds 530s Since beginning: 1 seconds 530s *** 530s 530s 530s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 530s Rank 0 destroyed its Bloom filter 530s Rank 0 has 1954 k-mers (completed) 530s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 530s Rank 0: assembler memory usage: 121408 KiB 530s 530s 530s Rank 0: the minimum coverage is 3 530s Rank 0: the peak coverage is 3 530s Warning: no peak observed in the k-mer coverage distribution. 530s to deal with the sequencing error rate, try to lower the k-mer length (-k) 530s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 530s 530s *** 530s Step: Coverage distribution analysis 530s Date: Tue Mar 19 01:23:22 2024 530s Elapsed time: 0 seconds 530s Since beginning: 1 seconds 530s *** 530s 530s 530s 531s Rank 0 is adding edges [1/4108] 531s Rank 0 is adding edges [4108/4108] (completed) 531s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 531s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 531s 531s *** 531s Step: Graph construction 531s Date: Tue Mar 19 01:23:22 2024 531s Elapsed time: 0 seconds 531s Since beginning: 1 seconds 531s *** 531s 531s 531s Rank 0 has 1954 vertices (completed) 531s Rank 0: assembler memory usage: 121408 KiB 531s Rank 0 is purging edges [1/1954] 531s Rank 0 is purging edges [1954/1954] (completed) 531s Rank 0: assembler memory usage: 121792 KiB 531s VirtualProcessor: completed jobs: 1954 531s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 531s Rank 0 wrote test2/degreeDistribution.txt 531s 531s *** 531s Step: Null edge purging 531s Date: Tue Mar 19 01:23:23 2024 531s Elapsed time: 1 seconds 531s Since beginning: 2 seconds 531s *** 531s 531s 531s Rank 0 is selecting optimal read markers [1/4108] 531s Rank 0: assembler memory usage: 121792 KiB 532s Rank 0 is selecting optimal read markers [4108/4108] (completed) 532s Rank 0: peak number of workers: 599, maximum: 32768 532s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 532s Rank 0: assembler memory usage: 130048 KiB 532s Rank 0: Freeing unused assembler memory: 4096 KiB freed 532s Rank 0: assembler memory usage: 130048 KiB 532s 532s *** 532s Step: Selection of optimal read markers 532s Date: Tue Mar 19 01:23:24 2024 532s Elapsed time: 1 seconds 532s Since beginning: 3 seconds 532s *** 532s 532s 532s Rank 0: memory usage for optimal read markers= 4096 KiB 532s Rank 0 is creating seeds [1/1954] 532s Rank 0: assembler memory usage: 130048 KiB 532s Rank 0 has 1 seeds 532s Rank 0 is creating seeds [1954/1954] (completed) 532s Rank 0: peak number of workers: 746, maximum: 32768 532s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 532s Rank 0 runtime statistics for seeding algorithm: 532s Rank 0 Skipped paths because of dead end for head: 0 532s Rank 0 Skipped paths because of dead end for tail: 0 532s Rank 0 Skipped paths because of two dead ends: 0 532s Rank 0 Skipped paths because of bubble weak component: 0 532s Rank 0 Skipped paths because of short length: 1952 532s Rank 0 Skipped paths because of bad ownership: 1 532s Rank 0 Skipped paths because of low coverage: 0 532s Rank 0 Eligible paths: 1 532s Rank 0: assembler memory usage: 130048 KiB 532s Rank 0 has 1 seeds to register. 532s Rank 0 registered 0/1 532s Rank 0 registered 0/1 532s Rank 0 registered its seeds 532s VirtualProcessor: completed jobs: 0 532s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 533s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 543s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 543s Rank 0 merged its seeds: 1 seeds -> 1 seeds 543s 543s *** 543s Step: Detection of assembly seeds 543s Date: Tue Mar 19 01:23:35 2024 543s Elapsed time: 11 seconds 543s Since beginning: 14 seconds 543s *** 543s 543s 543s Rank 0 is calculating library lengths [1/1] 543s Rank 0 detected 1737 library lengths 543s Rank 0 is calculating library lengths [1/1] (completed) 543s Rank 0: peak number of workers: 1, maximum: 32768 543s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 543s Rank 0: assembler memory usage: 166976 KiB 543s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 543s 543s Mode= 2 signalAverage= 9 543s CURRENT IS NOISE, 244 543s GOT HIT 212 543s 543s 543s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 543s 543s *** 543s Step: Estimation of outer distances for paired reads 543s Date: Tue Mar 19 01:23:35 2024 543s Elapsed time: 0 seconds 543s Since beginning: 14 seconds 543s *** 543s 543s 543s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 543s Rank 0 traversed 1000 nucleotide symbols 543s Rank 0: assembler memory usage: 171072 KiB 543s Rank 0 is extending seeds [1/1] (completed) 543s Rank 0 extended 1 seeds out of 1 (100.00%) 543s Rank 0: assembler memory usage: 162880 KiB 543s Rank 0 starting fusions 543s 543s *** 543s Step: Bidirectional extension of seeds 543s Date: Tue Mar 19 01:23:35 2024 543s Elapsed time: 0 seconds 543s Since beginning: 14 seconds 543s *** 543s 543s 543s Rank 0: starting clear step. cycleNumber= 0 544s Rank 0 adding 0 new fusions 544s Rank 0 cleared, 1 paths 544s Rank 0: starting distribution step 544s Rank 0 is distributing fusions [1/1] 544s Rank 0: assembler memory usage: 162880 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 is distributing fusions [1/1] (completed) 544s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 tells others to compute fusions. 544s Rank 0 FusionTaskCreator assignNextTask [0/2] 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 FusionTaskCreator processWorkerResult [0/2] 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 FusionTaskCreator [2/2] 544s Statistics: all paths: 1 eliminated during fusing: 0 544s Rank 0: assembler memory usage: 166976 KiB 544s VirtualProcessor: completed jobs: 2 544s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 544s Rank 0: starting clear step. cycleNumber= 1 544s Rank 0 adding 0 new fusions 544s Rank 0 cleared, 1 paths 544s Rank 0 is distributing fusions [1/1] 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 is distributing fusions [1/1] (completed) 544s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 JoinerTaskCreator assignNextTask [0/2] 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s Rank 0 JoinerTaskCreator [2/2] 544s Statistics: all paths: 1 eliminated during joining: 0 544s Rank 0: assembler memory usage: 166976 KiB 544s Date: Tue Mar 19 01:23:36 2024 544s VirtualProcessor: completed jobs: 2 544s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 545s Rank 0 adding 0 new fusions 545s Rank 0 cleared, 1 paths 545s Rank 0: starting distribution step 545s Rank 0 is distributing fusions [1/1] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 is distributing fusions [1/1] (completed) 545s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 tells others to compute fusions. 545s Rank 0 FusionTaskCreator assignNextTask [0/2] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 FusionTaskCreator processWorkerResult [0/2] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 FusionTaskCreator [2/2] 545s Statistics: all paths: 1 eliminated during fusing: 0 545s Rank 0: assembler memory usage: 166976 KiB 545s VirtualProcessor: completed jobs: 2 545s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 545s Rank 0: starting clear step. cycleNumber= 2 545s Rank 0 adding 0 new fusions 545s Rank 0 cleared, 1 paths 545s Rank 0 is distributing fusions [1/1] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 is distributing fusions [1/1] (completed) 545s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 JoinerTaskCreator assignNextTask [0/2] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 JoinerTaskCreator [2/2] 545s Statistics: all paths: 1 eliminated during joining: 0 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s VirtualProcessor: completed jobs: 2 545s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 545s Rank 0 adding 0 new fusions 545s Rank 0 cleared, 1 paths 545s Rank 0: starting distribution step 545s Rank 0 is distributing fusions [1/1] 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 is distributing fusions [1/1] (completed) 545s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 545s Rank 0: assembler memory usage: 166976 KiB 545s Date: Tue Mar 19 01:23:37 2024 545s Rank 0 cycleNumber= 2 545s 545s *** 545s Step: Merging of redundant paths 545s Date: Tue Mar 19 01:23:37 2024 545s Elapsed time: 2 seconds 545s Since beginning: 16 seconds 545s *** 545s 545s 545s Rank 0 appended 1 elements 545s 545s *** 545s Step: Generation of contigs 545s Date: Tue Mar 19 01:23:37 2024 545s Elapsed time: 0 seconds 545s Since beginning: 16 seconds 545s *** 545s 546s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 546s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 546s Rank 0 ineligibleObjects: 0/970 (0.00%) 546s Rank 0: assembler memory usage: 166976 KiB 546s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 546s Rank 0 finished gathering scaffold links. 546s Rank 0 will write 1 contig lengths 546s Rank 0 will solve the scaffolding problem. 546s Welcome to GreedySolver v1.0 546s 1 vertices; 0 edges 546s 1 contigs >= 500 546s Edges in solution: 0 546s 546s Conflict statistics: 546s 1 scaffolds, 1 >= 500 546s Total: 1000 nucleotides 546s 546s *** 546s Step: Scaffolding of contigs 546s Date: Tue Mar 19 01:23:38 2024 546s Elapsed time: 1 seconds 546s Since beginning: 17 seconds 546s *** 546s 546s Rank 0 syncing with master 546s 546s *** 546s Step: Counting sequences to search 546s Date: Tue Mar 19 01:23:38 2024 546s Elapsed time: 0 seconds 546s Since beginning: 17 seconds 546s *** 546s 546s 546s Rank 0 will add colors, 0 sequences in 0 files to process 546s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 546s 546s *** 546s Step: Graph coloring 546s Date: Tue Mar 19 01:23:38 2024 546s Elapsed time: 0 seconds 546s Since beginning: 17 seconds 546s *** 546s 546s 546s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 546s Rank 0 shares its counts 546s Rank 0 computing contig abundances [1/1] [1/970] 546s Rank 0 computing contig abundances [1/1] [970/970] 546s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 546s 546s *** 546s Step: Counting contig biological abundances 546s Date: Tue Mar 19 01:23:38 2024 546s Elapsed time: 0 seconds 546s Since beginning: 17 seconds 546s *** 546s 546s 546s Rank 0 colored the graph with 0 real colors using 1 virtual colors 546s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 546s 546s *** 546s Step: Counting sequence biological abundances 546s Date: Tue Mar 19 01:23:38 2024 546s Elapsed time: 0 seconds 546s Since beginning: 17 seconds 546s *** 546s 546s 546s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 546s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 547s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 547s 547s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 547s Rank 0 is starting taxon syncing across the compute tribe. 547s 547s *** 547s Step: Loading taxons 547s Date: Tue Mar 19 01:23:39 2024 547s Elapsed time: 1 seconds 547s Since beginning: 18 seconds 547s *** 547s 547s Rank 0 synced taxons across the grid with 1 poor slaves. 547s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 547s Rank 0 has 0 taxons after syncing with master 547s 547s 547s *** 547s Step: Loading tree 547s Date: Tue Mar 19 01:23:39 2024 547s Elapsed time: 0 seconds 547s Since beginning: 18 seconds 547s *** 547s 547s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 547s 547s Rank 0: counting ontology terms in the graph... 548s Rank 0: 0 have some biological signal 548s Number of dereferenced alternate handles: 0 548s Number of k-mer observations with gene ontology terms: 0 548s Rank 0: synced ontology term profiles with master 548s Rank 0: synchronization is complete! 548s Rank 0: ontology terms with biological signal: 0 548s Populated recursive values... 548s Gene ontology terms without depth information: 0 548s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 548s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 548s 548s *** 548s Step: Processing gene ontologies 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 1 seconds 548s Since beginning: 19 seconds 548s *** 548s 548s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 548s [GenomeNeighbourhood] in final list: 0 548s 548s *** 548s Step: Computing neighbourhoods 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 0 seconds 548s Since beginning: 19 seconds 548s *** 548s 548s Contigs >= 100 nt 548s Number: 1 548s Total length: 1000 548s Average: 1000 548s N50: 1000 548s Median: 1000 548s Largest: 1000 548s Contigs >= 500 nt 548s Number: 1 548s Total length: 1000 548s Average: 1000 548s N50: 1000 548s Median: 1000 548s Largest: 1000 548s Scaffolds >= 100 nt 548s Number: 1 548s Total length: 1000 548s Average: 1000 548s N50: 1000 548s Median: 1000 548s Largest: 1000 548s Scaffolds >= 500 nt 548s Number: 1 548s Total length: 1000 548s Average: 1000 548s N50: 1000 548s Median: 1000 548s Largest: 1000 548s 548s Rank 0 wrote test2/Contigs.fasta 548s Rank 0 wrote test2/Scaffolds.fasta 548s Check for test2/* 548s 548s 548s 548s ************************************************** 548s This program comes with ABSOLUTELY NO WARRANTY. 548s This is free software, and you are welcome to redistribute it 548s under certain conditions; see "LICENSE.txt" for details. 548s ************************************************** 548s 548s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 548s Centre de recherche en infectiologie de l'Université Laval 548s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 548s http://denovoassembler.sf.net/ 548s 548s References to cite: 548s 548s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 548s Ray Meta: scalable de novo metagenome assembly and profiling. 548s Genome Biology (BioMed Central Ltd). 548s 13:R122, Published: 22 December 2012 548s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 548s 548s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 548s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 548s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 548s November 2010, Volume 17, Issue 11, Pages 1519-1533. 548s http://dx.doi.org/doi:10.1089/cmb.2009.0238 548s 548s Ray version 2.3.1 548s License for Ray: GNU General Public License version 3 548s RayPlatform version: 2.0.1 548s License for RayPlatform: GNU Lesser General Public License version 3 548s 548s MAXKMERLENGTH: 32 548s Maximum coverage depth stored by CoverageDepth: 4294967295 548s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 548s FORCE_PACKING = n 548s ASSERT = n 548s HAVE_LIBZ = y 548s HAVE_LIBBZ2 = y 548s PROFILER_COLLECT = n 548s MINIRANKS = y 548s CLOCK_GETTIME = n 548s __linux__ = y 548s _MSC_VER = n 548s __GNUC__ = y 548s RAY_32_BITS = n 548s RAY_64_BITS = y 548s MPI standard version: MPI 3.1 548s MPI library: Open-MPI 4.1.6 548s Compiler: GNU gcc/g++ 13.2.0 548s MPI I/O: n 548s 548s 548s -k (to set the k-mer size) 548s Value: 29 548s 548s 548s Paired library # 0 548s -p (paired-end sequences) 548s Left sequences: SampleDirectory/s_6.first1000_1.fastq 548s Right sequences: SampleDirectory/s_6.first1000_2.fastq 548s Average length: automatic detection 548s Standard deviation: automatic detection 548s 548s Ray command: 548s mpiexec -n 1 Ray \ 548s -k \ 548s 29 \ 548s -desable-recycling \ 548s -p \ 548s SampleDirectory/s_6.first1000_1.fastq \ 548s SampleDirectory/s_6.first1000_2.fastq 548s 548s Rank 0 wrote RayOutput/RayCommand.txt 548s 548s k-mer length: 29 548s Rank 0: assembler memory usage: 46272 KiB 548s Rank 0: assembler memory usage: 112064 KiB 548s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3478 548s Rank 0: testing the network, please wait... 548s 548s Rank 0 is testing the network [0/1000] 548s Rank 0 is testing the network [1000/1000] 548s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 548s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 548s 548s Rank 0 wrote RayOutput/NetworkTest.txt 548s 548s 548s *** 548s Step: Network testing 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 0 seconds 548s Since beginning: 0 seconds 548s *** 548s 548s 548s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 548s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 548s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 548s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 548s Rank 0 wrote RayOutput/NumberOfSequences.txt 548s Rank 0 wrote RayOutput/SequencePartition.txt 548s 548s *** 548s Step: Counting sequences to assemble 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 0 seconds 548s Since beginning: 0 seconds 548s *** 548s 548s 548s Rank 0 is loading sequence reads 548s Rank 0 : partition is [0;4107], 4108 sequence reads 548s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 548s Rank 0 has 0 sequence reads 548s Rank 0: assembler memory usage: 124992 KiB 548s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 548s Rank 0 has 4108 sequence reads (completed) 548s 548s *** 548s Step: Sequence loading 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 0 seconds 548s Since beginning: 0 seconds 548s *** 548s 548s 548s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 548s Rank 0 created its Bloom filter 548s Rank 0 is counting k-mers in sequence reads [1/4108] 548s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 548s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 548s 548s 548s *** 548s Step: K-mer counting 548s Date: Tue Mar 19 01:23:40 2024 548s Elapsed time: 0 seconds 548s Since beginning: 0 seconds 548s *** 548s 548s 548s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 548s Rank 0 destroyed its Bloom filter 548s Rank 0 has 1958 k-mers (completed) 548s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 548s Rank 0: assembler memory usage: 121408 KiB 549s 549s 549s Rank 0: the minimum coverage is 3 549s Rank 0: the peak coverage is 3 549s Warning: no peak observed in the k-mer coverage distribution. 549s to deal with the sequencing error rate, try to lower the k-mer length (-k) 549s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 549s 549s *** 549s Step: Coverage distribution analysis 549s Date: Tue Mar 19 01:23:41 2024 549s Elapsed time: 1 seconds 549s Since beginning: 1 seconds 549s *** 549s 549s 549s 549s Rank 0 is adding edges [1/4108] 549s Rank 0 is adding edges [4108/4108] (completed) 549s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 549s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 549s 549s *** 549s Step: Graph construction 549s Date: Tue Mar 19 01:23:41 2024 549s Elapsed time: 0 seconds 549s Since beginning: 1 seconds 549s *** 549s 549s 549s Rank 0 has 1958 vertices (completed) 549s Rank 0: assembler memory usage: 121408 KiB 550s Rank 0 is purging edges [1/1958] 550s Rank 0 is purging edges [1958/1958] (completed) 550s Rank 0: assembler memory usage: 121792 KiB 550s VirtualProcessor: completed jobs: 1958 550s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 550s Rank 0 wrote RayOutput/degreeDistribution.txt 550s 550s *** 550s Step: Null edge purging 550s Date: Tue Mar 19 01:23:42 2024 550s Elapsed time: 1 seconds 550s Since beginning: 2 seconds 550s *** 550s 550s 550s Rank 0 is selecting optimal read markers [1/4108] 550s Rank 0: assembler memory usage: 121792 KiB 551s Rank 0 is selecting optimal read markers [4108/4108] (completed) 551s Rank 0: peak number of workers: 599, maximum: 32768 551s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 551s Rank 0: assembler memory usage: 130112 KiB 551s Rank 0: Freeing unused assembler memory: 4096 KiB freed 551s Rank 0: assembler memory usage: 130112 KiB 551s 551s *** 551s Step: Selection of optimal read markers 551s Date: Tue Mar 19 01:23:42 2024 551s Elapsed time: 0 seconds 551s Since beginning: 2 seconds 551s *** 551s 551s 551s Rank 0: memory usage for optimal read markers= 4096 KiB 551s Rank 0 is creating seeds [1/1958] 551s Rank 0: assembler memory usage: 130112 KiB 551s Rank 0 has 1 seeds 551s Rank 0 is creating seeds [1958/1958] (completed) 551s Rank 0: peak number of workers: 746, maximum: 32768 551s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 551s Rank 0 runtime statistics for seeding algorithm: 551s Rank 0 Skipped paths because of dead end for head: 0 551s Rank 0 Skipped paths because of dead end for tail: 0 551s Rank 0 Skipped paths because of two dead ends: 0 551s Rank 0 Skipped paths because of bubble weak component: 0 551s Rank 0 Skipped paths because of short length: 1956 551s Rank 0 Skipped paths because of bad ownership: 1 551s Rank 0 Skipped paths because of low coverage: 0 551s Rank 0 Eligible paths: 1 551s Rank 0: assembler memory usage: 130112 KiB 551s Rank 0 has 1 seeds to register. 551s Rank 0 registered 0/1 551s Rank 0 registered 0/1 551s Rank 0 registered its seeds 551s VirtualProcessor: completed jobs: 0 551s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 551s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 561s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 561s Rank 0 merged its seeds: 1 seeds -> 1 seeds 561s 561s *** 561s Step: Detection of assembly seeds 561s Date: Tue Mar 19 01:23:53 2024 561s Elapsed time: 11 seconds 561s Since beginning: 13 seconds 561s *** 561s 561s 561s Rank 0 is calculating library lengths [1/1] 561s Rank 0 detected 1743 library lengths 561s Rank 0 is calculating library lengths [1/1] (completed) 561s Rank 0: peak number of workers: 1, maximum: 32768 561s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 561s Rank 0: assembler memory usage: 167040 KiB 561s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 561s 561s Mode= 2 signalAverage= 10 561s CURRENT IS NOISE, 244 561s GOT HIT 214 561s 561s 561s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 561s 561s *** 561s Step: Estimation of outer distances for paired reads 561s Date: Tue Mar 19 01:23:53 2024 561s Elapsed time: 0 seconds 561s Since beginning: 13 seconds 561s *** 561s 561s 561s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 561s Rank 0 traversed 1000 nucleotide symbols 561s Rank 0: assembler memory usage: 171136 KiB 561s Rank 0 is extending seeds [1/1] (completed) 561s Rank 0 extended 1 seeds out of 1 (100.00%) 561s Rank 0: assembler memory usage: 162944 KiB 561s Rank 0 starting fusions 561s 561s *** 561s Step: Bidirectional extension of seeds 561s Date: Tue Mar 19 01:23:53 2024 561s Elapsed time: 0 seconds 561s Since beginning: 13 seconds 561s *** 561s 561s 561s Rank 0: starting clear step. cycleNumber= 0 562s Rank 0 adding 0 new fusions 562s Rank 0 cleared, 1 paths 562s Rank 0: starting distribution step 562s Rank 0 is distributing fusions [1/1] 562s Rank 0: assembler memory usage: 162944 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 is distributing fusions [1/1] (completed) 562s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 tells others to compute fusions. 562s Rank 0 FusionTaskCreator assignNextTask [0/2] 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 FusionTaskCreator processWorkerResult [0/2] 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 FusionTaskCreator [2/2] 562s Statistics: all paths: 1 eliminated during fusing: 0 562s Rank 0: assembler memory usage: 167040 KiB 562s VirtualProcessor: completed jobs: 2 562s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 562s Rank 0: starting clear step. cycleNumber= 1 562s Rank 0 adding 0 new fusions 562s Rank 0 cleared, 1 paths 562s Rank 0 is distributing fusions [1/1] 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 is distributing fusions [1/1] (completed) 562s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 JoinerTaskCreator assignNextTask [0/2] 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s Rank 0 JoinerTaskCreator [2/2] 562s Statistics: all paths: 1 eliminated during joining: 0 562s Rank 0: assembler memory usage: 167040 KiB 562s Date: Tue Mar 19 01:23:54 2024 562s VirtualProcessor: completed jobs: 2 562s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 563s Rank 0 adding 0 new fusions 563s Rank 0 cleared, 1 paths 563s Rank 0: starting distribution step 563s Rank 0 is distributing fusions [1/1] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 is distributing fusions [1/1] (completed) 563s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 tells others to compute fusions. 563s Rank 0 FusionTaskCreator assignNextTask [0/2] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 FusionTaskCreator processWorkerResult [0/2] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 FusionTaskCreator [2/2] 563s Statistics: all paths: 1 eliminated during fusing: 0 563s Rank 0: assembler memory usage: 167040 KiB 563s VirtualProcessor: completed jobs: 2 563s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 563s Rank 0: starting clear step. cycleNumber= 2 563s Rank 0 adding 0 new fusions 563s Rank 0 cleared, 1 paths 563s Rank 0 is distributing fusions [1/1] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 is distributing fusions [1/1] (completed) 563s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 JoinerTaskCreator assignNextTask [0/2] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s Rank 0 JoinerTaskCreator [2/2] 563s Statistics: all paths: 1 eliminated during joining: 0 563s Rank 0: assembler memory usage: 167040 KiB 563s Date: Tue Mar 19 01:23:55 2024 563s VirtualProcessor: completed jobs: 2 563s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 564s Rank 0 adding 0 new fusions 564s Rank 0 cleared, 1 paths 564s Rank 0: starting distribution step 564s Rank 0 is distributing fusions [1/1] 564s Rank 0: assembler memory usage: 167040 KiB 564s Date: Tue Mar 19 01:23:56 2024 564s Rank 0 is distributing fusions [1/1] (completed) 564s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 564s Rank 0: assembler memory usage: 167040 KiB 564s Date: Tue Mar 19 01:23:56 2024 564s Rank 0 cycleNumber= 2 564s 564s *** 564s Step: Merging of redundant paths 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 3 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s 564s Rank 0 appended 1 elements 564s 564s *** 564s Step: Generation of contigs 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 564s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 564s Rank 0 ineligibleObjects: 0/972 (0.00%) 564s Rank 0: assembler memory usage: 167040 KiB 564s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 564s Rank 0 finished gathering scaffold links. 564s Rank 0 will write 1 contig lengths 564s Rank 0 will solve the scaffolding problem. 564s Welcome to GreedySolver v1.0 564s 1 vertices; 0 edges 564s 1 contigs >= 500 564s Edges in solution: 0 564s 564s Conflict statistics: 564s 1 scaffolds, 1 >= 500 564s Total: 1000 nucleotides 564s 564s *** 564s Step: Scaffolding of contigs 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s Rank 0 syncing with master 564s 564s *** 564s Step: Counting sequences to search 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s 564s Rank 0 will add colors, 0 sequences in 0 files to process 564s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 564s 564s *** 564s Step: Graph coloring 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s 564s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 564s Rank 0 shares its counts 564s Rank 0 computing contig abundances [1/1] [1/972] 564s Rank 0 computing contig abundances [1/1] [972/972] 564s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 564s 564s *** 564s Step: Counting contig biological abundances 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s 564s Rank 0 colored the graph with 0 real colors using 1 virtual colors 564s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 564s 564s *** 564s Step: Counting sequence biological abundances 564s Date: Tue Mar 19 01:23:56 2024 564s Elapsed time: 0 seconds 564s Since beginning: 16 seconds 564s *** 564s 564s 564s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 564s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 565s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 565s 565s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 565s Rank 0 is starting taxon syncing across the compute tribe. 565s 565s *** 565s Step: Loading taxons 565s Date: Tue Mar 19 01:23:57 2024 565s Elapsed time: 1 seconds 565s Since beginning: 17 seconds 565s *** 565s 565s Rank 0 synced taxons across the grid with 1 poor slaves. 565s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 565s Rank 0 has 0 taxons after syncing with master 565s 565s 565s *** 565s Step: Loading tree 565s Date: Tue Mar 19 01:23:57 2024 565s Elapsed time: 0 seconds 565s Since beginning: 17 seconds 565s *** 565s 566s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 566s 566s Rank 0: counting ontology terms in the graph... 566s Rank 0: 0 have some biological signal 566s Number of dereferenced alternate handles: 0 566s Number of k-mer observations with gene ontology terms: 0 566s Rank 0: synced ontology term profiles with master 566s Rank 0: synchronization is complete! 566s Rank 0: ontology terms with biological signal: 0 566s Populated recursive values... 566s Gene ontology terms without depth information: 0 566s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 566s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 566s 566s *** 566s Step: Processing gene ontologies 566s Date: Tue Mar 19 01:23:58 2024 566s Elapsed time: 1 seconds 566s Since beginning: 18 seconds 566s *** 566s 566s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 566s [GenomeNeighbourhood] in final list: 0 566s 566s *** 566s Step: Computing neighbourhoods 566s Date: Tue Mar 19 01:23:58 2024 566s Elapsed time: 0 seconds 566s Since beginning: 18 seconds 566s *** 566s 566s Contigs >= 100 nt 566s Number: 1 566s Total length: 1000 566s Average: 1000 566s N50: 1000 566s Median: 1000 566s Largest: 1000 566s Contigs >= 500 nt 566s Number: 1 566s Total length: 1000 566s Average: 1000 566s N50: 1000 566s Median: 1000 566s Largest: 1000 566s Scaffolds >= 100 nt 566s Number: 1 566s Total length: 1000 566s Average: 1000 566s N50: 1000 566s Median: 1000 566s Largest: 1000 566s Scaffolds >= 500 nt 566s Number: 1 566s Total length: 1000 566s Average: 1000 566s N50: 1000 566s Median: 1000 566s Largest: 1000 566s 566s Rank 0 wrote RayOutput/Contigs.fasta 566s Rank 0 wrote RayOutput/Scaffolds.fasta 566s Check for RayOutput/* 566s 566s 566s 566s ************************************************** 566s This program comes with ABSOLUTELY NO WARRANTY. 566s This is free software, and you are welcome to redistribute it 566s under certain conditions; see "LICENSE.txt" for details. 566s ************************************************** 566s 566s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 566s Centre de recherche en infectiologie de l'Université Laval 566s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 566s http://denovoassembler.sf.net/ 566s 566s References to cite: 566s 566s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 566s Ray Meta: scalable de novo metagenome assembly and profiling. 566s Genome Biology (BioMed Central Ltd). 566s 13:R122, Published: 22 December 2012 566s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 566s 566s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 566s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 566s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 566s November 2010, Volume 17, Issue 11, Pages 1519-1533. 566s http://dx.doi.org/doi:10.1089/cmb.2009.0238 566s 566s Ray version 2.3.1 566s License for Ray: GNU General Public License version 3 566s RayPlatform version: 2.0.1 566s License for RayPlatform: GNU Lesser General Public License version 3 566s 566s MAXKMERLENGTH: 32 566s Maximum coverage depth stored by CoverageDepth: 4294967295 566s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 566s FORCE_PACKING = n 566s ASSERT = n 566s HAVE_LIBZ = y 566s HAVE_LIBBZ2 = y 566s PROFILER_COLLECT = n 566s MINIRANKS = y 566s CLOCK_GETTIME = n 566s __linux__ = y 566s _MSC_VER = n 566s __GNUC__ = y 566s RAY_32_BITS = n 566s RAY_64_BITS = y 566s MPI standard version: MPI 3.1 566s MPI library: Open-MPI 4.1.6 566s Compiler: GNU gcc/g++ 13.2.0 566s MPI I/O: n 566s 566s 566s -k (to set the k-mer size) 566s Value: 31 566s 566s 566s Paired library # 0 566s -p (paired-end sequences) 566s Left sequences: ecoli_1K_1.fq 566s Right sequences: ecoli_1K_2.fq 566s Average length: automatic detection 566s Standard deviation: automatic detection 566s 566s Ray command: 566s mpiexec -n 2 Ray \ 566s -k \ 566s 31 \ 566s -p \ 566s ecoli_1K_1.fq \ 566s ecoli_1K_2.fq \ 566s -o \ 566s test3 566s 566s Rank 0 wrote test3/RayCommand.txt 566s 566s k-mer length: 31 566s Rank 1: assembler memory usage: 46336 KiB 566s Rank 0: assembler memory usage: 46336 KiB 566s Rank 0: assembler memory usage: 112192 KiB 566s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 3487 566s Rank 0: testing the network, please wait... 566s 566s Rank 1: assembler memory usage: 112192 KiB 566s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 3488 566s Rank 1 is testing the network [0/1000] 566s Rank 0 is testing the network [0/1000] 566s Rank 1 is testing the network [1000/1000] 566s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 566s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 8 microseconds (10^-6 seconds) 566s Rank 0 is testing the network [1000/1000] 566s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 566s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 11 microseconds (10^-6 seconds) 566s 566s Rank 0 wrote test3/NetworkTest.txt 566s 566s 566s *** 566s Step: Network testing 566s Date: Tue Mar 19 01:23:58 2024 566s Elapsed time: 0 seconds 566s Since beginning: 0 seconds 566s *** 566s 566s 566s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 566s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 566s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 566s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 566s Rank 0 wrote test3/NumberOfSequences.txt 566s Rank 0 wrote test3/SequencePartition.txt 566s 566s *** 566s Step: Counting sequences to assemble 566s Date: Tue Mar 19 01:23:58 2024 566s Elapsed time: 0 seconds 566s Since beginning: 0 seconds 566s *** 566s 566s 566s Rank 1 is loading sequence reads 566s Rank 1 : partition is [2054;4107], 2054 sequence reads 566s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 566s Rank 0 is loading sequence reads 566s Rank 0 : partition is [0;2053], 2054 sequence reads 566s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 566s Rank 1 has 0 sequence reads 566s Rank 0 has 0 sequence reads 566s Rank 1: assembler memory usage: 121024 KiB 566s Rank 0: assembler memory usage: 121024 KiB 566s Rank 0 has 2054 sequence reads (completed) 566s Rank 1 has 2054 sequence reads (completed) 566s 566s *** 566s Step: Sequence loading 566s Date: Tue Mar 19 01:23:58 2024 566s Elapsed time: 0 seconds 566s Since beginning: 0 seconds 566s *** 566s 566s 566s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 566s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 566s Rank 1 created its Bloom filter 566s Rank 0 created its Bloom filter 566s Rank 1 is counting k-mers in sequence reads [1/2054] 566s Rank 0 is counting k-mers in sequence reads [1/2054] 567s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 567s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 567s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 567s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 567s 567s 567s *** 567s Step: K-mer counting 567s Date: Tue Mar 19 01:23:59 2024 567s Elapsed time: 1 seconds 567s Since beginning: 1 seconds 567s *** 567s 567s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 567s 567s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 567s Rank 0 destroyed its Bloom filter 567s Rank 0 has 1032 k-mers (completed) 567s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 567s Rank 1 destroyed its Bloom filter 567s Rank 1 has 922 k-mers (completed) 567s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 567s Rank 1: assembler memory usage: 121024 KiB 567s Rank 0: assembler memory usage: 117312 KiB 568s 568s 568s Rank 0: the minimum coverage is 3 568s Rank 0: the peak coverage is 3 568s Warning: no peak observed in the k-mer coverage distribution. 568s to deal with the sequencing error rate, try to lower the k-mer length (-k) 568s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 568s 568s *** 568s Step: Coverage distribution analysis 568s Date: Tue Mar 19 01:24:00 2024 568s Elapsed time: 1 seconds 568s Since beginning: 2 seconds 568s Rank 1 is adding edges [1/2054] 568s *** 568s 568s 568s 568s Rank 0 is adding edges [1/2054] 569s Rank 1 is adding edges [2054/2054] (completed) 569s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 569s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 569s Rank 0 is adding edges [2054/2054] (completed) 569s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 569s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 569s 569s *** 569s Step: Graph construction 569s Date: Tue Mar 19 01:24:01 2024 569s Elapsed time: 1 seconds 569s Since beginning: 3 seconds 569s *** 569s 569s 569s Rank 1 has 922 vertices (completed) 569s Rank 1: assembler memory usage: 121024 KiB 569s Rank 0 has 1032 vertices (completed) 569s Rank 0: assembler memory usage: 117312 KiB 570s Rank 1 is purging edges [1/922] 570s Rank 0 is purging edges [1/1032] 570s Rank 1 is purging edges [922/922] (completed) 570s Rank 1: assembler memory usage: 121024 KiB 570s VirtualProcessor: completed jobs: 922 570s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 570s Rank 0 is purging edges [1032/1032] (completed) 570s Rank 0: assembler memory usage: 117504 KiB 570s VirtualProcessor: completed jobs: 1032 570s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 571s Rank 0 wrote test3/degreeDistribution.txt 571s 571s *** 571s Step: Null edge purging 571s Date: Tue Mar 19 01:24:02 2024 571s Elapsed time: 1 seconds 571s Since beginning: 4 seconds 571s *** 571s 571s 571s Rank 0 is selecting optimal read markers [1/2054] 571s Rank 0: assembler memory usage: 117504 KiB 571s Rank 1 is selecting optimal read markers [1/2054] 571s Rank 1: assembler memory usage: 121024 KiB 572s Rank 1 is selecting optimal read markers [2054/2054] (completed) 572s Rank 1: peak number of workers: 1121, maximum: 32768 572s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 572s Rank 1: assembler memory usage: 128704 KiB 572s Rank 1: Freeing unused assembler memory: 4096 KiB freed 572s Rank 1: assembler memory usage: 128704 KiB 572s Rank 0 is selecting optimal read markers [2054/2054] (completed) 572s Rank 0: peak number of workers: 1135, maximum: 32768 572s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 572s Rank 0: assembler memory usage: 125760 KiB 572s Rank 0: Freeing unused assembler memory: 4096 KiB freed 572s Rank 0: assembler memory usage: 125760 KiB 572s 572s *** 572s Step: Selection of optimal read markers 572s Date: Tue Mar 19 01:24:04 2024 572s Elapsed time: 2 seconds 572s Since beginning: 6 seconds 572s *** 572s 572s 572s Rank 0: memory usage for optimal read markers= 4096 KiB 572s Rank 1: memory usage for optimal read markers= 4096 KiB 572s Rank 0 is creating seeds [1/1032] 572s Rank 1 is creating seeds [1/922] 572s Rank 1: assembler memory usage: 128704 KiB 572s Rank 0: assembler memory usage: 125760 KiB 573s Rank 1 has 1 seeds 573s Rank 1 is creating seeds [922/922] (completed) 573s Rank 1: peak number of workers: 916, maximum: 32768 573s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 573s Rank 1 runtime statistics for seeding algorithm: 573s Rank 1 Skipped paths because of dead end for head: 0 573s Rank 1 Skipped paths because of dead end for tail: 0 573s Rank 1 Skipped paths because of two dead ends: 0 573s Rank 1 Skipped paths because of bubble weak component: 0 573s Rank 1 Skipped paths because of short length: 921 573s Rank 1 Skipped paths because of bad ownership: 0 573s Rank 1 Skipped paths because of low coverage: 0 573s Rank 1 Eligible paths: 1 573s Rank 1: assembler memory usage: 128704 KiB 573s Rank 0 has 0 seeds 573s Rank 0 is creating seeds [1032/1032] (completed) 573s Rank 0: peak number of workers: 998, maximum: 32768 573s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 573s Rank 0 runtime statistics for seeding algorithm: 573s Rank 0 Skipped paths because of dead end for head: 0 573s Rank 0 Skipped paths because of dead end for tail: 0 573s Rank 0 Skipped paths because of two dead ends: 0 573s Rank 0 Skipped paths because of bubble weak component: 0 573s Rank 0 Skipped paths because of short length: 1031 573s Rank 0 Skipped paths because of bad ownership: 1 573s Rank 0 Skipped paths because of low coverage: 0 573s Rank 0 Eligible paths: 0 573s Rank 0: assembler memory usage: 125760 KiB 573s Rank 1 has 1 seeds to register. 573s Rank 0 registered -1/0 573s Rank 0 registered its seeds 573s Rank 1 registered 0/1 573s Rank 1 registered 0/1 573s Rank 1 registered its seeds 573s VirtualProcessor: completed jobs: 0 573s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 573s VirtualProcessor: completed jobs: 0 573s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 574s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 574s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 584s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 584s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 584s Rank 0 merged its seeds: 0 seeds -> 0 seeds 584s Rank 1 merged its seeds: 1 seeds -> 1 seeds 584s 584s *** 584s Step: Detection of assembly seeds 584s Date: Tue Mar 19 01:24:16 2024 584s Elapsed time: 12 seconds 584s Since beginning: 18 seconds 584s *** 584s 584s 584s Rank 0 detected 0 library lengths 584s Rank 0 is calculating library lengths [0/0] (completed) 584s Rank 0: peak number of workers: 0, maximum: 32768 584s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 584s Rank 0: assembler memory usage: 129856 KiB 584s Rank 1 is calculating library lengths [1/1] 584s Rank 1 detected 1737 library lengths 584s Rank 1 is calculating library lengths [1/1] (completed) 584s Rank 1: peak number of workers: 1, maximum: 32768 584s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7985 virtual messages generated 7985 real messages (100%) 584s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 584s Rank 1: assembler memory usage: 161536 KiB 584s 584s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 584s Mode= 2 signalAverage= 9 584s CURRENT IS NOISE, 244 584s GOT HIT 212 584s 584s 584s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 584s 584s *** 584s Step: Estimation of outer distances for paired reads 584s Date: Tue Mar 19 01:24:16 2024 584s Elapsed time: 0 seconds 584s Since beginning: 18 seconds 584s *** 584s 584s 584s Rank 0 is extending seeds [0/0] (completed) 584s Rank 0 extended 0 seeds out of 0 (0.00%) 584s Rank 0: assembler memory usage: 129856 KiB 584s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 589s Rank 1 traversed 1000 nucleotide symbols 589s Rank 1: assembler memory usage: 165632 KiB 589s Rank 1 is extending seeds [1/1] (completed) 589s Rank 1 extended 1 seeds out of 1 (100.00%) 589s Rank 1: assembler memory usage: 165632 KiB 589s Rank 0 starting fusions 589s 589s *** 589s Step: Bidirectional extension of seeds 589s Date: Tue Mar 19 01:24:21 2024 589s Elapsed time: 5 seconds 589s Since beginning: 23 seconds 589s *** 589s 589s 589s Rank 0: starting clear step. cycleNumber= 0 590s Rank 1 adding 0 new fusions 590s Rank 1 cleared, 1 paths 590s Rank 0 adding 0 new fusions 590s Rank 0 cleared, 0 paths 590s Rank 0: starting distribution step 590s Rank 0 is distributing fusions [0/0] (completed) 590s Rank 1 is distributing fusions [1/1] 590s Rank 1: assembler memory usage: 165632 KiB 590s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 590s Rank 0: assembler memory usage: 129856 KiB 590s Date: Tue Mar 19 01:24:22 2024 590s Date: Tue Mar 19 01:24:22 2024 590s Rank 1 is distributing fusions [1/1] (completed) 590s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 590s Rank 1: assembler memory usage: 165632 KiB 590s Date: Tue Mar 19 01:24:22 2024 590s Rank 0 tells others to compute fusions. 590s Rank 0 FusionTaskCreator [0/0] 590s Rank 1 FusionTaskCreator assignNextTask [0/2] 590s Statistics: all paths: 0 eliminated during fusing: 0 590s Rank 1: assembler memory usage: 165632 KiB 590s Date: Tue Mar 19 01:24:22 2024 590s Rank 0: assembler memory usage: 129856 KiB 590s VirtualProcessor: completed jobs: 0 590s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 590s Rank 1 FusionTaskCreator processWorkerResult [0/2] 590s Rank 1: assembler memory usage: 165632 KiB 590s Date: Tue Mar 19 01:24:22 2024 590s Rank 1 FusionTaskCreator [2/2] 590s Statistics: all paths: 1 eliminated during fusing: 0 590s Rank 1: assembler memory usage: 165632 KiB 590s VirtualProcessor: completed jobs: 2 590s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10895 virtual messages generated 10895 real messages (100%) 590s Rank 0: starting clear step. cycleNumber= 1 591s Rank 0 adding 0 new fusions 591s Rank 0 cleared, 0 paths 591s Rank 1 adding 0 new fusions 591s Rank 1 cleared, 1 paths 591s Rank 0 is distributing fusions [0/0] (completed) 591s Rank 1 is distributing fusions [1/1] 591s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 591s Rank 1: assembler memory usage: 165632 KiB 591s Rank 0: assembler memory usage: 129856 KiB 591s Date: Tue Mar 19 01:24:23 2024 591s Date: Tue Mar 19 01:24:23 2024 591s Rank 1 is distributing fusions [1/1] (completed) 591s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 591s Rank 1: assembler memory usage: 165632 KiB 591s Date: Tue Mar 19 01:24:23 2024 591s Rank 0 JoinerTaskCreator [0/0] 591s Rank 1 JoinerTaskCreator assignNextTask [0/2] 591s Rank 1: assembler memory usage: 165632 KiB 591s Statistics: all paths: 0 eliminated during joining: 0 591s Rank 0: assembler memory usage: 129856 KiB 591s Date: Tue Mar 19 01:24:23 2024 591s VirtualProcessor: completed jobs: 0 591s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 591s Date: Tue Mar 19 01:24:23 2024 591s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 591s Rank 1: assembler memory usage: 165632 KiB 591s Date: Tue Mar 19 01:24:23 2024 591s Rank 1 JoinerTaskCreator [2/2] 591s Statistics: all paths: 1 eliminated during joining: 0 591s Rank 1: assembler memory usage: 165632 KiB 592s Date: Tue Mar 19 01:24:23 2024 592s VirtualProcessor: completed jobs: 2 592s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13805 virtual messages generated 13805 real messages (100%) 592s Rank 0 adding 0 new fusions 592s Rank 1 adding 0 new fusions 592s Rank 1 cleared, 1 paths 592s Rank 0 cleared, 0 paths 592s Rank 0: starting distribution step 592s Rank 0 is distributing fusions [0/0] (completed) 592s Rank 1 is distributing fusions [1/1] 592s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 592s Rank 0: assembler memory usage: 129856 KiB 592s Rank 1: assembler memory usage: 165632 KiB 592s Date: Tue Mar 19 01:24:24 2024 592s Date: Tue Mar 19 01:24:24 2024 592s Rank 1 is distributing fusions [1/1] (completed) 592s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 592s Rank 1: assembler memory usage: 165632 KiB 592s Date: Tue Mar 19 01:24:24 2024 592s Rank 0 tells others to compute fusions. 592s Rank 0 FusionTaskCreator [0/0] 592s Rank 1 FusionTaskCreator assignNextTask [0/2] 592s Rank 1: assembler memory usage: 165632 KiB 592s Statistics: all paths: 0 eliminated during fusing: 0 592s Rank 0: assembler memory usage: 129856 KiB 592s Date: Tue Mar 19 01:24:24 2024 592s VirtualProcessor: completed jobs: 0 592s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 592s Rank 1 FusionTaskCreator processWorkerResult [0/2] 592s Rank 1: assembler memory usage: 165632 KiB 592s Date: Tue Mar 19 01:24:24 2024 592s Rank 1 FusionTaskCreator [2/2] 592s Statistics: all paths: 1 eliminated during fusing: 0 592s Rank 1: assembler memory usage: 165632 KiB 592s VirtualProcessor: completed jobs: 2 592s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16715 virtual messages generated 16715 real messages (100%) 593s Rank 0: starting clear step. cycleNumber= 2 593s Rank 1 adding 0 new fusions 593s Rank 0 adding 0 new fusions 593s Rank 1 cleared, 1 paths 593s Rank 0 cleared, 0 paths 593s Rank 0 is distributing fusions [0/0] (completed) 593s Rank 1 is distributing fusions [1/1] 593s Rank 1: assembler memory usage: 165632 KiB 593s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 593s Date: Tue Mar 19 01:24:25 2024 593s Rank 0: assembler memory usage: 129856 KiB 593s Date: Tue Mar 19 01:24:25 2024 593s Rank 1 is distributing fusions [1/1] (completed) 593s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 593s Rank 1: assembler memory usage: 165632 KiB 593s Date: Tue Mar 19 01:24:25 2024 593s Rank 0 JoinerTaskCreator [0/0] 593s Statistics: all paths: 0 eliminated during joining: 0 593s Rank 1 JoinerTaskCreator assignNextTask [0/2] 593s Rank 0: assembler memory usage: 129856 KiB 593s Rank 1: assembler memory usage: 165632 KiB 593s Date: Tue Mar 19 01:24:25 2024 593s Date: Tue Mar 19 01:24:25 2024 593s VirtualProcessor: completed jobs: 0 593s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 593s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 593s Rank 1: assembler memory usage: 165632 KiB 593s Date: Tue Mar 19 01:24:25 2024 593s Rank 1 JoinerTaskCreator [2/2] 593s Statistics: all paths: 1 eliminated during joining: 0 593s Rank 1: assembler memory usage: 165632 KiB 593s Date: Tue Mar 19 01:24:25 2024 593s VirtualProcessor: completed jobs: 2 594s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19625 virtual messages generated 19625 real messages (100%) 594s Rank 1 adding 0 new fusions 594s Rank 0 adding 0 new fusions 594s Rank 1 cleared, 1 paths 594s Rank 0 cleared, 0 paths 594s Rank 0: starting distribution step 594s Rank 0 is distributing fusions [0/0] (completed) 594s Rank 1 is distributing fusions [1/1] 594s Rank 1: assembler memory usage: 165632 KiB 594s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 594s Rank 0: assembler memory usage: 129856 KiB 594s Date: Tue Mar 19 01:24:26 2024 594s Date: Tue Mar 19 01:24:26 2024 594s Rank 1 is distributing fusions [1/1] (completed) 594s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 594s Rank 1: assembler memory usage: 165632 KiB 594s Date: Tue Mar 19 01:24:26 2024 594s Rank 0 cycleNumber= 2 594s 594s *** 594s Step: Merging of redundant paths 594s Date: Tue Mar 19 01:24:26 2024 594s Elapsed time: 5 seconds 594s Since beginning: 28 seconds 594s *** 594s 594s 594s Rank 0 appended 0 elements 594s Rank 1 appended 1 elements 594s 594s *** 594s Step: Generation of contigs 594s Date: Tue Mar 19 01:24:26 2024 594s Elapsed time: 0 seconds 594s Since beginning: 28 seconds 594s *** 594s 594s Rank 0 finished gathering scaffold links. 594s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 595s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 595s Rank 0 ineligibleObjects: 0/970 (0.00%) 595s Rank 1: assembler memory usage: 165632 KiB 595s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 595s Rank 0 will write 1 contig lengths 595s Rank 1 finished gathering scaffold links. 595s Rank 0 will solve the scaffolding problem. 595s Welcome to GreedySolver v1.0 595s 1 vertices; 0 edges 595s 1 contigs >= 500 595s Edges in solution: 0 595s 595s Conflict statistics: 595s 1 scaffolds, 1 >= 500 595s Total: 1000 nucleotides 595s 595s *** 595s Step: Scaffolding of contigs 595s Date: Tue Mar 19 01:24:27 2024 595s Elapsed time: 1 seconds 595s Since beginning: 29 seconds 595s *** 595s 595s Rank 0 syncing with master 595s Rank 1 syncing with master 595s 595s *** 595s Step: Counting sequences to search 595s Date: Tue Mar 19 01:24:27 2024 595s Elapsed time: 0 seconds 595s Since beginning: 29 seconds 595s *** 595s 595s 595s Rank 0 will add colors, 0 sequences in 0 files to process 595s Rank 1 will add colors, 0 sequences in 0 files to process 595s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 595s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 596s 596s *** 596s Step: Graph coloring 596s Date: Tue Mar 19 01:24:28 2024 596s Elapsed time: 1 seconds 596s Since beginning: 30 seconds 596s *** 596s 596s 596s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 596s Rank 0 shares its counts 596s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 596s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 596s Rank 1 computing contig abundances [1/1] [1/970] 596s Rank 1 computing contig abundances [1/1] [970/970] 596s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 596s 596s *** 596s Step: Counting contig biological abundances 596s Date: Tue Mar 19 01:24:28 2024 596s Elapsed time: 0 seconds 596s Since beginning: 30 seconds 596s *** 596s 596s 596s Rank 1 colored the graph with 0 real colors using 1 virtual colors 596s Rank 0 colored the graph with 0 real colors using 1 virtual colors 596s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 596s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 596s 596s *** 596s Step: Counting sequence biological abundances 596s Date: Tue Mar 19 01:24:28 2024 596s Elapsed time: 0 seconds 596s Since beginning: 30 seconds 596s *** 596s 596s 596s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 596s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 596s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 596s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 597s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 597s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 597s 597s 597s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 597s Rank 0 is starting taxon syncing across the compute tribe. 597s 597s *** 597s Step: Loading taxons 597s Date: Tue Mar 19 01:24:29 2024 597s Elapsed time: 1 seconds 597s Since beginning: 31 seconds 597s *** 597s 597s Rank 0 synced taxons across the grid with 2 poor slaves. 597s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 597s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 597s Rank 0 has 0 taxons after syncing with master 597s Rank 1 has 0 taxons after syncing with master 598s 598s 598s 598s *** 598s Step: Loading tree 598s Date: Tue Mar 19 01:24:30 2024 598s Elapsed time: 1 seconds 598s Since beginning: 32 seconds 598s *** 598s 599s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 599s 599s Rank 0: counting ontology terms in the graph... 599s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 599s 599s Rank 1: counting ontology terms in the graph... 599s Rank 0: 0 have some biological signal 599s Number of dereferenced alternate handles: 0 599s Number of k-mer observations with gene ontology terms: 0 600s Rank 1: 0 have some biological signal 600s Rank 0: synced ontology term profiles with master 600s Number of dereferenced alternate handles: 0 600s Number of k-mer observations with gene ontology terms: 0 600s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 600s Rank 1: synced ontology term profiles with master 600s Rank 0: synchronization is complete! 600s Rank 0: ontology terms with biological signal: 0 600s Populated recursive values... 600s Gene ontology terms without depth information: 0 600s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 600s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 600s 600s *** 600s Step: Processing gene ontologies 600s Date: Tue Mar 19 01:24:32 2024 600s Elapsed time: 2 seconds 600s Since beginning: 34 seconds 600s *** 600s 600s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 600s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 600s [GenomeNeighbourhood] in final list: 0 600s 600s *** 600s Step: Computing neighbourhoods 600s Date: Tue Mar 19 01:24:32 2024 600s Elapsed time: 0 seconds 600s Since beginning: 34 seconds 600s *** 600s 600s Contigs >= 100 nt 600s Number: 1 600s Total length: 1000 600s Average: 1000 600s N50: 1000 600s Median: 1000 600s Largest: 1000 600s Contigs >= 500 nt 600s Number: 1 600s Total length: 1000 600s Average: 1000 600s N50: 1000 600s Median: 1000 600s Largest: 1000 600s Scaffolds >= 100 nt 600s Number: 1 600s Total length: 1000 600s Average: 1000 600s N50: 1000 600s Median: 1000 600s Largest: 1000 600s Scaffolds >= 500 nt 600s Number: 1 600s Total length: 1000 600s Average: 1000 600s N50: 1000 600s Median: 1000 600s Largest: 1000 600s 600s Rank 0 wrote test3/Contigs.fasta 600s Rank 0 wrote test3/Scaffolds.fasta 600s Check for test3/* 600s 600s 600s autopkgtest [01:24:32]: test run-unit-test: -----------------------] 601s autopkgtest [01:24:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 601s run-unit-test PASS 601s autopkgtest [01:24:33]: @@@@@@@@@@@@@@@@@@@@ summary 601s run-unit-test PASS 628s Creating nova instance adt-noble-ppc64el-ray-20240319-011432-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 1492b190-05c5-462d-b1de-84bc330afe32)...