0s autopkgtest [11:14:36]: starting date and time: 2024-07-24 11:14:36+0000 0s autopkgtest [11:14:36]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [11:14:36]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bpcta82o/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.4-1 -- lxd -r lxd-armhf-10.145.243.202 lxd-armhf-10.145.243.202:autopkgtest/ubuntu/oracular/armhf 54s autopkgtest [11:15:30]: testbed dpkg architecture: armhf 55s autopkgtest [11:15:31]: testbed apt version: 2.9.6 55s autopkgtest [11:15:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 63s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [406 kB] 64s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [56.7 kB] 64s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 64s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 64s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [71.6 kB] 64s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1428 B] 64s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1368 B] 64s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf c-n-f Metadata [120 B] 64s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [396 kB] 64s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6916 B] 64s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [2072 B] 64s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 66s Fetched 1081 kB in 1s (1412 kB/s) 66s Reading package lists... 83s tee: /proc/self/fd/2: Permission denied 104s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 106s The following package was automatically installed and is no longer required: 106s python3-six 106s Use 'apt autoremove' to remove it. 106s The following packages will be upgraded: 106s cloud-init dmsetup gcc-14-base gdisk libbpf1 libdevmapper1.02.1 libgcc-s1 106s libpython3-stdlib libstdc++6 libudisks2-0 libxml2 logrotate netcat-openbsd 106s networkd-dispatcher python3 python3-launchpadlib python3-minimal 106s systemd-hwe-hwdb udisks2 107s 19 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 3270 kB of archives. 107s After this operation, 48.1 kB disk space will be freed. 107s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf python3-minimal armhf 3.12.4-1 [27.1 kB] 107s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf python3 armhf 3.12.4-1 [24.0 kB] 107s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libpython3-stdlib armhf 3.12.4-1 [9824 B] 107s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-14-base armhf 14.1.0-5ubuntu1 [49.8 kB] 107s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libstdc++6 armhf 14.1.0-5ubuntu1 [711 kB] 107s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libgcc-s1 armhf 14.1.0-5ubuntu1 [40.8 kB] 107s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf libdevmapper1.02.1 armhf 2:1.02.196-1ubuntu1 [135 kB] 107s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf dmsetup armhf 2:1.02.196-1ubuntu1 [81.3 kB] 107s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libbpf1 armhf 1:1.4.5-1 [151 kB] 107s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf libxml2 armhf 2.12.7+dfsg-3 [560 kB] 107s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf logrotate armhf 3.22.0-1 [51.5 kB] 107s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf netcat-openbsd armhf 1.226-1.1 [42.2 kB] 107s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf networkd-dispatcher all 2.2.4-1.1 [15.6 kB] 107s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf systemd-hwe-hwdb all 256.2.1 [3210 B] 107s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf udisks2 armhf 2.10.1-9ubuntu1 [277 kB] 107s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf libudisks2-0 armhf 2.10.1-9ubuntu1 [142 kB] 107s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf python3-launchpadlib all 2.0.0-1 [126 kB] 107s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf cloud-init all 24.3~1g6e4153b3-0ubuntu1 [592 kB] 107s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf gdisk armhf 1.0.10-2 [229 kB] 108s Preconfiguring packages ... 108s Fetched 3270 kB in 1s (4457 kB/s) 108s (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 ... 58436 files and directories currently installed.) 108s Preparing to unpack .../python3-minimal_3.12.4-1_armhf.deb ... 108s Unpacking python3-minimal (3.12.4-1) over (3.12.3-0ubuntu1) ... 108s Setting up python3-minimal (3.12.4-1) ... 108s (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 ... 58436 files and directories currently installed.) 108s Preparing to unpack .../python3_3.12.4-1_armhf.deb ... 108s Unpacking python3 (3.12.4-1) over (3.12.3-0ubuntu1) ... 108s Preparing to unpack .../libpython3-stdlib_3.12.4-1_armhf.deb ... 108s Unpacking libpython3-stdlib:armhf (3.12.4-1) over (3.12.3-0ubuntu1) ... 108s Preparing to unpack .../gcc-14-base_14.1.0-5ubuntu1_armhf.deb ... 108s Unpacking gcc-14-base:armhf (14.1.0-5ubuntu1) over (14.1.0-4ubuntu2) ... 108s Setting up gcc-14-base:armhf (14.1.0-5ubuntu1) ... 108s (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 ... 58436 files and directories currently installed.) 108s Preparing to unpack .../libstdc++6_14.1.0-5ubuntu1_armhf.deb ... 108s Unpacking libstdc++6:armhf (14.1.0-5ubuntu1) over (14.1.0-4ubuntu2) ... 108s Setting up libstdc++6:armhf (14.1.0-5ubuntu1) ... 108s (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 ... 58436 files and directories currently installed.) 108s Preparing to unpack .../libgcc-s1_14.1.0-5ubuntu1_armhf.deb ... 108s Unpacking libgcc-s1:armhf (14.1.0-5ubuntu1) over (14.1.0-4ubuntu2) ... 108s Setting up libgcc-s1:armhf (14.1.0-5ubuntu1) ... 108s (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 ... 58436 files and directories currently installed.) 108s Preparing to unpack .../00-libdevmapper1.02.1_2%3a1.02.196-1ubuntu1_armhf.deb ... 108s Unpacking libdevmapper1.02.1:armhf (2:1.02.196-1ubuntu1) over (2:1.02.185-3ubuntu4) ... 108s Preparing to unpack .../01-dmsetup_2%3a1.02.196-1ubuntu1_armhf.deb ... 108s Unpacking dmsetup (2:1.02.196-1ubuntu1) over (2:1.02.185-3ubuntu4) ... 108s Preparing to unpack .../02-libbpf1_1%3a1.4.5-1_armhf.deb ... 108s Unpacking libbpf1:armhf (1:1.4.5-1) over (1:1.4.3-1) ... 108s Preparing to unpack .../03-libxml2_2.12.7+dfsg-3_armhf.deb ... 108s Unpacking libxml2:armhf (2.12.7+dfsg-3) over (2.9.14+dfsg-1.3ubuntu3) ... 109s Preparing to unpack .../04-logrotate_3.22.0-1_armhf.deb ... 109s Unpacking logrotate (3.22.0-1) over (3.21.0-2build1) ... 109s Preparing to unpack .../05-netcat-openbsd_1.226-1.1_armhf.deb ... 109s Unpacking netcat-openbsd (1.226-1.1) over (1.226-1ubuntu2) ... 109s Preparing to unpack .../06-networkd-dispatcher_2.2.4-1.1_all.deb ... 109s Unpacking networkd-dispatcher (2.2.4-1.1) over (2.2.4-1) ... 109s Preparing to unpack .../07-systemd-hwe-hwdb_256.2.1_all.deb ... 109s Unpacking systemd-hwe-hwdb (256.2.1) over (255.1.3) ... 109s Preparing to unpack .../08-udisks2_2.10.1-9ubuntu1_armhf.deb ... 109s Unpacking udisks2 (2.10.1-9ubuntu1) over (2.10.1-9) ... 109s Preparing to unpack .../09-libudisks2-0_2.10.1-9ubuntu1_armhf.deb ... 109s Unpacking libudisks2-0:armhf (2.10.1-9ubuntu1) over (2.10.1-9) ... 109s Preparing to unpack .../10-python3-launchpadlib_2.0.0-1_all.deb ... 109s Unpacking python3-launchpadlib (2.0.0-1) over (1.11.0-6) ... 109s Preparing to unpack .../11-cloud-init_24.3~1g6e4153b3-0ubuntu1_all.deb ... 109s Unpacking cloud-init (24.3~1g6e4153b3-0ubuntu1) over (24.2-0ubuntu1) ... 109s Preparing to unpack .../12-gdisk_1.0.10-2_armhf.deb ... 109s Unpacking gdisk (1.0.10-2) over (1.0.10-1build1) ... 109s Setting up logrotate (3.22.0-1) ... 110s logrotate.service is a disabled or a static unit not running, not starting it. 110s Setting up netcat-openbsd (1.226-1.1) ... 110s Setting up gdisk (1.0.10-2) ... 110s Setting up systemd-hwe-hwdb (256.2.1) ... 110s Setting up libdevmapper1.02.1:armhf (2:1.02.196-1ubuntu1) ... 110s Setting up dmsetup (2:1.02.196-1ubuntu1) ... 110s Setting up libxml2:armhf (2.12.7+dfsg-3) ... 110s Setting up libbpf1:armhf (1:1.4.5-1) ... 110s Setting up libudisks2-0:armhf (2.10.1-9ubuntu1) ... 110s Setting up libpython3-stdlib:armhf (3.12.4-1) ... 110s Setting up udisks2 (2.10.1-9ubuntu1) ... 110s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 110s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 110s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 110s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 110s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 110s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 110s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 110s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 110s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 110s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 110s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 110s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 111s Setting up python3 (3.12.4-1) ... 111s Setting up networkd-dispatcher (2.2.4-1.1) ... 111s Setting up cloud-init (24.3~1g6e4153b3-0ubuntu1) ... 113s Setting up python3-launchpadlib (2.0.0-1) ... 113s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 113s Processing triggers for man-db (2.12.1-2) ... 114s Processing triggers for dbus (1.14.10-4ubuntu4) ... 114s Processing triggers for udev (256-1ubuntu1) ... 115s Processing triggers for initramfs-tools (0.142ubuntu30) ... 115s Processing triggers for libc-bin (2.39-0ubuntu9) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s The following packages will be REMOVED: 116s python3-six* 116s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 116s After this operation, 59.4 kB disk space will be freed. 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58436 files and directories currently installed.) 116s Removing python3-six (1.16.0-6) ... 119s autopkgtest [11:16:35]: rebooting testbed after setup commands that affected boot 186s autopkgtest [11:17:42]: testbed running kernel: Linux 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 16:55:18 UTC 2 213s autopkgtest [11:18:09]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 230s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (dsc) [2192 B] 230s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (tar) [450 kB] 230s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ray 2.3.1-8build2 (diff) [213 kB] 230s gpgv: Signature made Mon Apr 1 07:35:01 2024 UTC 230s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8build2.dsc: no acceptable signature found 231s autopkgtest [11:18:27]: testing package ray version 2.3.1-8build2 233s autopkgtest [11:18:29]: build not needed 235s autopkgtest [11:18:31]: test run-unit-test: preparing testbed 245s Reading package lists... 245s Building dependency tree... 245s Reading state information... 246s Starting pkgProblemResolver with broken count: 0 246s Starting 2 pkgProblemResolver with broken count: 0 246s Done 246s The following additional packages will be installed: 246s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 246s libcairo2 libdatrie1 libdeflate0 libevent-pthreads-2.1-7t64 libfabric1 246s libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 246s libharfbuzz0b libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 246s libjpeg8 liblapack3 liblerc4 libmunge2 libopenmpi3t64 libpango-1.0-0 246s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 246s libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 libsm6 libtcl8.6 246s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 246s libxft2 libxnvctrl0 libxrender1 libxss1 libxt6t64 mpi-default-bin 246s ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core ray ray-doc 246s ray-extra unzip x11-common xdg-utils zip 246s Suggested packages: 246s tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler elpa-ess r-doc-info 246s | r-doc-pdf r-mathlib r-base-html 246s Recommended packages: 246s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 246s libx11-protocol-perl x11-utils x11-xserver-utils 246s The following NEW packages will be installed: 246s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 246s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 246s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libfreetype6 246s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwloc-plugins 246s libhwloc15 libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 246s libmunge2 libopenmpi3t64 libpango-1.0-0 libpangocairo-1.0-0 246s libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpixman-1-0 246s libpmix2t64 librdmacm1t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data 246s libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 246s libxnvctrl0 libxrender1 libxss1 libxt6t64 mpi-default-bin ocl-icd-libopencl1 246s openmpi-bin openmpi-common r-base-core ray ray-doc ray-extra unzip 246s x11-common xdg-utils zip 246s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 246s Need to get 41.9 MB/41.9 MB of archives. 246s After this operation, 79.0 MB of additional disk space will be used. 246s Get:1 /tmp/autopkgtest.v5hz6Q/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B] 247s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libfreetype6 armhf 2.13.2+dfsg-1build3 [331 kB] 247s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 247s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 247s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 247s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 247s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB] 247s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 247s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libpixman-1-0 armhf 0.42.2-1build1 [193 kB] 247s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 247s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 247s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 247s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf libcairo2 armhf 1.18.0-3build1 [482 kB] 247s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 247s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 247s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf libevent-pthreads-2.1-7t64 armhf 2.1.12-stable-10 [7530 B] 247s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf librdmacm1t64 armhf 52.0-2 [63.2 kB] 247s Get:18 http://ftpmaster.internal/ubuntu oracular/universe armhf libfabric1 armhf 1.17.0-3build2 [419 kB] 247s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-5ubuntu1 [311 kB] 247s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf libgomp1 armhf 14.1.0-5ubuntu1 [125 kB] 247s Get:21 http://ftpmaster.internal/ubuntu oracular/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 247s Get:22 http://ftpmaster.internal/ubuntu oracular/main armhf libharfbuzz0b armhf 8.3.0-2build2 [446 kB] 247s Get:23 http://ftpmaster.internal/ubuntu oracular/universe armhf libhwloc15 armhf 2.10.0-1build1 [146 kB] 247s Get:24 http://ftpmaster.internal/ubuntu oracular/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 247s Get:25 http://ftpmaster.internal/ubuntu oracular/main armhf libice6 armhf 2:1.0.10-1build3 [35.4 kB] 247s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 247s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 247s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 247s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 247s Get:30 http://ftpmaster.internal/ubuntu oracular/universe armhf libmunge2 armhf 0.5.15-4build1 [17.1 kB] 247s Get:31 http://ftpmaster.internal/ubuntu oracular/main armhf libpciaccess0 armhf 0.17-3build1 [16.3 kB] 247s Get:32 http://ftpmaster.internal/ubuntu oracular/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu4 [11.6 kB] 247s Get:33 http://ftpmaster.internal/ubuntu oracular/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1build1 [34.5 kB] 247s Get:34 http://ftpmaster.internal/ubuntu oracular/universe armhf libhwloc-plugins armhf 2.10.0-1build1 [13.7 kB] 247s Get:35 http://ftpmaster.internal/ubuntu oracular/universe armhf libpmix2t64 armhf 5.0.1-4.1build1 [616 kB] 247s Get:36 http://ftpmaster.internal/ubuntu oracular/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu2 [2041 kB] 247s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf libthai-data all 0.1.29-2build1 [158 kB] 247s Get:38 http://ftpmaster.internal/ubuntu oracular/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 247s Get:39 http://ftpmaster.internal/ubuntu oracular/main armhf libpango-1.0-0 armhf 1.54.0+ds-1 [209 kB] 248s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf libpangoft2-1.0-0 armhf 1.54.0+ds-1 [36.4 kB] 248s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf libpangocairo-1.0-0 armhf 1.54.0+ds-1 [24.8 kB] 248s Get:42 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB] 248s Get:43 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper-utils armhf 1.1.29build1 [8184 B] 248s Get:44 http://ftpmaster.internal/ubuntu oracular/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 248s Get:45 http://ftpmaster.internal/ubuntu oracular/main armhf libsm6 armhf 2:1.2.3-1build3 [14.1 kB] 248s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf libtcl8.6 armhf 8.6.14+dfsg-1build1 [903 kB] 248s Get:47 http://ftpmaster.internal/ubuntu oracular/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 248s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 248s Get:49 http://ftpmaster.internal/ubuntu oracular/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu3 [178 kB] 248s Get:50 http://ftpmaster.internal/ubuntu oracular/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 248s Get:51 http://ftpmaster.internal/ubuntu oracular/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 248s Get:52 http://ftpmaster.internal/ubuntu oracular/main armhf libtk8.6 armhf 8.6.14-1build1 [681 kB] 248s Get:53 http://ftpmaster.internal/ubuntu oracular/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 248s Get:54 http://ftpmaster.internal/ubuntu oracular/universe armhf openmpi-common all 4.1.6-7ubuntu2 [170 kB] 248s Get:55 http://ftpmaster.internal/ubuntu oracular/universe armhf openmpi-bin armhf 4.1.6-7ubuntu2 [83.2 kB] 248s Get:56 http://ftpmaster.internal/ubuntu oracular/main armhf zip armhf 3.0-13build1 [163 kB] 248s Get:57 http://ftpmaster.internal/ubuntu oracular/main armhf unzip armhf 6.0-28ubuntu5 [167 kB] 248s Get:58 http://ftpmaster.internal/ubuntu oracular/main armhf xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 248s Get:59 http://ftpmaster.internal/ubuntu oracular/universe armhf r-base-core armhf 4.4.1-1 [28.1 MB] 249s Get:60 http://ftpmaster.internal/ubuntu oracular/universe armhf mpi-default-bin armhf 1.15build1 [2376 B] 249s Get:61 http://ftpmaster.internal/ubuntu oracular/universe armhf ray armhf 2.3.1-8build2 [839 kB] 249s Get:62 http://ftpmaster.internal/ubuntu oracular/universe armhf ray-doc all 2.3.1-8build2 [35.1 kB] 249s Get:63 http://ftpmaster.internal/ubuntu oracular/universe armhf ray-extra all 2.3.1-8build2 [12.1 kB] 249s Preconfiguring packages ... 249s Fetched 41.9 MB in 2s (18.4 MB/s) 249s Selecting previously unselected package libfreetype6:armhf. 249s (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 ... 58426 files and directories currently installed.) 249s Preparing to unpack .../00-libfreetype6_2.13.2+dfsg-1build3_armhf.deb ... 249s Unpacking libfreetype6:armhf (2.13.2+dfsg-1build3) ... 249s Selecting previously unselected package fonts-dejavu-mono. 249s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 249s Unpacking fonts-dejavu-mono (2.37-8) ... 249s Selecting previously unselected package fonts-dejavu-core. 249s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 249s Unpacking fonts-dejavu-core (2.37-8) ... 249s Selecting previously unselected package fontconfig-config. 249s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 250s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 250s Selecting previously unselected package libfontconfig1:armhf. 250s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 250s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 250s Selecting previously unselected package fontconfig. 250s Preparing to unpack .../05-fontconfig_2.15.0-1.1ubuntu2_armhf.deb ... 250s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 250s Selecting previously unselected package libblas3:armhf. 250s Preparing to unpack .../06-libblas3_3.12.0-3build1_armhf.deb ... 250s Unpacking libblas3:armhf (3.12.0-3build1) ... 250s Selecting previously unselected package libpixman-1-0:armhf. 250s Preparing to unpack .../07-libpixman-1-0_0.42.2-1build1_armhf.deb ... 250s Unpacking libpixman-1-0:armhf (0.42.2-1build1) ... 250s Selecting previously unselected package libxcb-render0:armhf. 250s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 250s Unpacking libxcb-render0:armhf (1.17.0-2) ... 250s Selecting previously unselected package libxcb-shm0:armhf. 250s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 250s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 250s Selecting previously unselected package libxrender1:armhf. 250s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 250s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 250s Selecting previously unselected package libcairo2:armhf. 250s Preparing to unpack .../11-libcairo2_1.18.0-3build1_armhf.deb ... 250s Unpacking libcairo2:armhf (1.18.0-3build1) ... 250s Selecting previously unselected package libdatrie1:armhf. 250s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 250s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 250s Selecting previously unselected package libdeflate0:armhf. 250s Preparing to unpack .../13-libdeflate0_1.20-1_armhf.deb ... 250s Unpacking libdeflate0:armhf (1.20-1) ... 250s Selecting previously unselected package libevent-pthreads-2.1-7t64:armhf. 250s Preparing to unpack .../14-libevent-pthreads-2.1-7t64_2.1.12-stable-10_armhf.deb ... 250s Unpacking libevent-pthreads-2.1-7t64:armhf (2.1.12-stable-10) ... 250s Selecting previously unselected package librdmacm1t64:armhf. 250s Preparing to unpack .../15-librdmacm1t64_52.0-2_armhf.deb ... 250s Unpacking librdmacm1t64:armhf (52.0-2) ... 250s Selecting previously unselected package libfabric1:armhf. 250s Preparing to unpack .../16-libfabric1_1.17.0-3build2_armhf.deb ... 250s Unpacking libfabric1:armhf (1.17.0-3build2) ... 250s Selecting previously unselected package libgfortran5:armhf. 250s Preparing to unpack .../17-libgfortran5_14.1.0-5ubuntu1_armhf.deb ... 250s Unpacking libgfortran5:armhf (14.1.0-5ubuntu1) ... 250s Selecting previously unselected package libgomp1:armhf. 250s Preparing to unpack .../18-libgomp1_14.1.0-5ubuntu1_armhf.deb ... 250s Unpacking libgomp1:armhf (14.1.0-5ubuntu1) ... 250s Selecting previously unselected package libgraphite2-3:armhf. 250s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 250s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 250s Selecting previously unselected package libharfbuzz0b:armhf. 250s Preparing to unpack .../20-libharfbuzz0b_8.3.0-2build2_armhf.deb ... 250s Unpacking libharfbuzz0b:armhf (8.3.0-2build2) ... 250s Selecting previously unselected package libhwloc15:armhf. 250s Preparing to unpack .../21-libhwloc15_2.10.0-1build1_armhf.deb ... 250s Unpacking libhwloc15:armhf (2.10.0-1build1) ... 250s Selecting previously unselected package x11-common. 250s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu3_all.deb ... 250s Unpacking x11-common (1:7.7+23ubuntu3) ... 250s Selecting previously unselected package libice6:armhf. 250s Preparing to unpack .../23-libice6_2%3a1.0.10-1build3_armhf.deb ... 250s Unpacking libice6:armhf (2:1.0.10-1build3) ... 250s Selecting previously unselected package libjpeg-turbo8:armhf. 250s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 250s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 250s Selecting previously unselected package libjpeg8:armhf. 250s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_armhf.deb ... 250s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 250s Selecting previously unselected package liblapack3:armhf. 250s Preparing to unpack .../26-liblapack3_3.12.0-3build1_armhf.deb ... 250s Unpacking liblapack3:armhf (3.12.0-3build1) ... 250s Selecting previously unselected package liblerc4:armhf. 250s Preparing to unpack .../27-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 250s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 250s Selecting previously unselected package libmunge2:armhf. 250s Preparing to unpack .../28-libmunge2_0.5.15-4build1_armhf.deb ... 250s Unpacking libmunge2:armhf (0.5.15-4build1) ... 250s Selecting previously unselected package libpciaccess0:armhf. 250s Preparing to unpack .../29-libpciaccess0_0.17-3build1_armhf.deb ... 250s Unpacking libpciaccess0:armhf (0.17-3build1) ... 251s Selecting previously unselected package libxnvctrl0:armhf. 251s Preparing to unpack .../30-libxnvctrl0_510.47.03-0ubuntu4_armhf.deb ... 251s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu4) ... 251s Selecting previously unselected package ocl-icd-libopencl1:armhf. 251s Preparing to unpack .../31-ocl-icd-libopencl1_2.3.2-1build1_armhf.deb ... 251s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1build1) ... 251s Selecting previously unselected package libhwloc-plugins:armhf. 251s Preparing to unpack .../32-libhwloc-plugins_2.10.0-1build1_armhf.deb ... 251s Unpacking libhwloc-plugins:armhf (2.10.0-1build1) ... 251s Selecting previously unselected package libpmix2t64:armhf. 251s Preparing to unpack .../33-libpmix2t64_5.0.1-4.1build1_armhf.deb ... 251s Unpacking libpmix2t64:armhf (5.0.1-4.1build1) ... 251s Selecting previously unselected package libopenmpi3t64:armhf. 251s Preparing to unpack .../34-libopenmpi3t64_4.1.6-7ubuntu2_armhf.deb ... 251s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu2) ... 251s Selecting previously unselected package libthai-data. 251s Preparing to unpack .../35-libthai-data_0.1.29-2build1_all.deb ... 251s Unpacking libthai-data (0.1.29-2build1) ... 251s Selecting previously unselected package libthai0:armhf. 251s Preparing to unpack .../36-libthai0_0.1.29-2build1_armhf.deb ... 251s Unpacking libthai0:armhf (0.1.29-2build1) ... 251s Selecting previously unselected package libpango-1.0-0:armhf. 251s Preparing to unpack .../37-libpango-1.0-0_1.54.0+ds-1_armhf.deb ... 251s Unpacking libpango-1.0-0:armhf (1.54.0+ds-1) ... 251s Selecting previously unselected package libpangoft2-1.0-0:armhf. 251s Preparing to unpack .../38-libpangoft2-1.0-0_1.54.0+ds-1_armhf.deb ... 251s Unpacking libpangoft2-1.0-0:armhf (1.54.0+ds-1) ... 251s Selecting previously unselected package libpangocairo-1.0-0:armhf. 251s Preparing to unpack .../39-libpangocairo-1.0-0_1.54.0+ds-1_armhf.deb ... 251s Unpacking libpangocairo-1.0-0:armhf (1.54.0+ds-1) ... 251s Selecting previously unselected package libpaper1:armhf. 251s Preparing to unpack .../40-libpaper1_1.1.29build1_armhf.deb ... 251s Unpacking libpaper1:armhf (1.1.29build1) ... 251s Selecting previously unselected package libpaper-utils. 251s Preparing to unpack .../41-libpaper-utils_1.1.29build1_armhf.deb ... 251s Unpacking libpaper-utils (1.1.29build1) ... 251s Selecting previously unselected package libsharpyuv0:armhf. 251s Preparing to unpack .../42-libsharpyuv0_1.4.0-0.1_armhf.deb ... 251s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 251s Selecting previously unselected package libsm6:armhf. 251s Preparing to unpack .../43-libsm6_2%3a1.2.3-1build3_armhf.deb ... 251s Unpacking libsm6:armhf (2:1.2.3-1build3) ... 251s Selecting previously unselected package libtcl8.6:armhf. 251s Preparing to unpack .../44-libtcl8.6_8.6.14+dfsg-1build1_armhf.deb ... 251s Unpacking libtcl8.6:armhf (8.6.14+dfsg-1build1) ... 251s Selecting previously unselected package libjbig0:armhf. 251s Preparing to unpack .../45-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 251s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 251s Selecting previously unselected package libwebp7:armhf. 251s Preparing to unpack .../46-libwebp7_1.4.0-0.1_armhf.deb ... 251s Unpacking libwebp7:armhf (1.4.0-0.1) ... 251s Selecting previously unselected package libtiff6:armhf. 251s Preparing to unpack .../47-libtiff6_4.5.1+git230720-4ubuntu3_armhf.deb ... 251s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu3) ... 251s Selecting previously unselected package libxft2:armhf. 251s Preparing to unpack .../48-libxft2_2.3.6-1build1_armhf.deb ... 251s Unpacking libxft2:armhf (2.3.6-1build1) ... 251s Selecting previously unselected package libxss1:armhf. 251s Preparing to unpack .../49-libxss1_1%3a1.2.3-1build3_armhf.deb ... 251s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 251s Selecting previously unselected package libtk8.6:armhf. 251s Preparing to unpack .../50-libtk8.6_8.6.14-1build1_armhf.deb ... 251s Unpacking libtk8.6:armhf (8.6.14-1build1) ... 251s Selecting previously unselected package libxt6t64:armhf. 251s Preparing to unpack .../51-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 251s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 251s Selecting previously unselected package openmpi-common. 251s Preparing to unpack .../52-openmpi-common_4.1.6-7ubuntu2_all.deb ... 251s Unpacking openmpi-common (4.1.6-7ubuntu2) ... 251s Selecting previously unselected package openmpi-bin. 251s Preparing to unpack .../53-openmpi-bin_4.1.6-7ubuntu2_armhf.deb ... 251s Unpacking openmpi-bin (4.1.6-7ubuntu2) ... 251s Selecting previously unselected package zip. 251s Preparing to unpack .../54-zip_3.0-13build1_armhf.deb ... 251s Unpacking zip (3.0-13build1) ... 251s Selecting previously unselected package unzip. 251s Preparing to unpack .../55-unzip_6.0-28ubuntu5_armhf.deb ... 251s Unpacking unzip (6.0-28ubuntu5) ... 251s Selecting previously unselected package xdg-utils. 251s Preparing to unpack .../56-xdg-utils_1.2.1-0ubuntu1_all.deb ... 251s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 251s Selecting previously unselected package r-base-core. 251s Preparing to unpack .../57-r-base-core_4.4.1-1_armhf.deb ... 251s Unpacking r-base-core (4.4.1-1) ... 252s Selecting previously unselected package mpi-default-bin. 252s Preparing to unpack .../58-mpi-default-bin_1.15build1_armhf.deb ... 252s Unpacking mpi-default-bin (1.15build1) ... 252s Selecting previously unselected package ray. 252s Preparing to unpack .../59-ray_2.3.1-8build2_armhf.deb ... 252s Unpacking ray (2.3.1-8build2) ... 252s Selecting previously unselected package ray-doc. 252s Preparing to unpack .../60-ray-doc_2.3.1-8build2_all.deb ... 252s Unpacking ray-doc (2.3.1-8build2) ... 252s Selecting previously unselected package ray-extra. 252s Preparing to unpack .../61-ray-extra_2.3.1-8build2_all.deb ... 252s Unpacking ray-extra (2.3.1-8build2) ... 252s Selecting previously unselected package autopkgtest-satdep. 252s Preparing to unpack .../62-1-autopkgtest-satdep.deb ... 252s Unpacking autopkgtest-satdep (0) ... 252s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 252s Setting up libpixman-1-0:armhf (0.42.2-1build1) ... 252s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 252s Setting up libpaper1:armhf (1.1.29build1) ... 252s 252s Creating config file /etc/papersize with new version 252s Setting up ray-doc (2.3.1-8build2) ... 252s Setting up libpciaccess0:armhf (0.17-3build1) ... 252s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 252s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 252s Setting up libdatrie1:armhf (0.2.13-3build1) ... 252s Setting up libxcb-render0:armhf (1.17.0-2) ... 252s Setting up libevent-pthreads-2.1-7t64:armhf (2.1.12-stable-10) ... 252s Setting up unzip (6.0-28ubuntu5) ... 252s Setting up x11-common (1:7.7+23ubuntu3) ... 253s Setting up libdeflate0:armhf (1.20-1) ... 253s Setting up libxcb-shm0:armhf (1.17.0-2) ... 253s Setting up libpaper-utils (1.1.29build1) ... 253s Setting up libgomp1:armhf (14.1.0-5ubuntu1) ... 253s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 253s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu4) ... 253s Setting up zip (3.0-13build1) ... 253s Setting up libblas3:armhf (3.12.0-3build1) ... 253s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 253s Setting up libmunge2:armhf (0.5.15-4build1) ... 253s Setting up libfreetype6:armhf (2.13.2+dfsg-1build3) ... 253s Setting up fonts-dejavu-mono (2.37-8) ... 253s Setting up libhwloc15:armhf (2.10.0-1build1) ... 253s Setting up libtcl8.6:armhf (8.6.14+dfsg-1build1) ... 253s Setting up fonts-dejavu-core (2.37-8) ... 253s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 253s Setting up libgfortran5:armhf (14.1.0-5ubuntu1) ... 253s Setting up libwebp7:armhf (1.4.0-0.1) ... 253s Setting up ocl-icd-libopencl1:armhf (2.3.2-1build1) ... 253s Setting up openmpi-common (4.1.6-7ubuntu2) ... 253s Setting up librdmacm1t64:armhf (52.0-2) ... 253s Setting up libharfbuzz0b:armhf (8.3.0-2build2) ... 253s Setting up libthai-data (0.1.29-2build1) ... 253s Setting up libxss1:armhf (1:1.2.3-1build3) ... 253s Setting up xdg-utils (1.2.1-0ubuntu1) ... 253s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 253s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 253s Setting up libfabric1:armhf (1.17.0-3build2) ... 253s Setting up libice6:armhf (2:1.0.10-1build3) ... 253s Setting up liblapack3:armhf (3.12.0-3build1) ... 253s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 253s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 253s Setting up libhwloc-plugins:armhf (2.10.0-1build1) ... 253s Setting up libthai0:armhf (0.1.29-2build1) ... 253s Setting up libpmix2t64:armhf (5.0.1-4.1build1) ... 253s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu2) ... 253s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu3) ... 253s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 253s Setting up libsm6:armhf (2:1.2.3-1build3) ... 253s Setting up openmpi-bin (4.1.6-7ubuntu2) ... 253s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 253s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 253s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 255s Regenerating fonts cache... done. 255s Setting up libxft2:armhf (2.3.6-1build1) ... 255s Setting up libtk8.6:armhf (8.6.14-1build1) ... 255s Setting up libpango-1.0-0:armhf (1.54.0+ds-1) ... 255s Setting up mpi-default-bin (1.15build1) ... 255s Setting up libcairo2:armhf (1.18.0-3build1) ... 255s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 255s Setting up ray (2.3.1-8build2) ... 255s Setting up libpangoft2-1.0-0:armhf (1.54.0+ds-1) ... 255s Setting up libpangocairo-1.0-0:armhf (1.54.0+ds-1) ... 255s Setting up r-base-core (4.4.1-1) ... 255s 255s Creating config file /etc/R/Renviron with new version 255s Setting up ray-extra (2.3.1-8build2) ... 255s Setting up autopkgtest-satdep (0) ... 255s Processing triggers for man-db (2.12.1-2) ... 256s Processing triggers for install-info (7.1-3build2) ... 256s Processing triggers for libc-bin (2.39-0ubuntu9) ... 277s (Reading database ... 61149 files and directories currently installed.) 277s Removing autopkgtest-satdep (0) ... 283s autopkgtest [11:19:19]: test run-unit-test: [----------------------- 285s 285s ************************************************** 285s This program comes with ABSOLUTELY NO WARRANTY. 285s This is free software, and you are welcome to redistribute it 285s under certain conditions; see "LICENSE.txt" for details. 285s ************************************************** 285s 285s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 285s Centre de recherche en infectiologie de l'Université Laval 285s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 285s http://denovoassembler.sf.net/ 285s 285s References to cite: 285s 285s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 285s Ray Meta: scalable de novo metagenome assembly and profiling. 285s Genome Biology (BioMed Central Ltd). 285s 13:R122, Published: 22 December 2012 285s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 285s 285s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 285s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 285s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 285s November 2010, Volume 17, Issue 11, Pages 1519-1533. 285s http://dx.doi.org/doi:10.1089/cmb.2009.0238 285s 285s Ray version 2.3.1 285s License for Ray: GNU General Public License version 3 285s RayPlatform version: 2.0.1 285s License for RayPlatform: GNU Lesser General Public License version 3 285s 285s MAXKMERLENGTH: 32 285s Maximum coverage depth stored by CoverageDepth: 4294967295 285s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 285s FORCE_PACKING = n 285s ASSERT = n 285s HAVE_LIBZ = y 285s HAVE_LIBBZ2 = y 285s PROFILER_COLLECT = n 285s MINIRANKS = y 285s CLOCK_GETTIME = n 285s __linux__ = y 285s _MSC_VER = n 285s __GNUC__ = y 285s RAY_32_BITS = y 285s RAY_64_BITS = n 285s MPI standard version: MPI 3.1 285s MPI library: Open-MPI 4.1.6 285s Compiler: GNU gcc/g++ 13.2.0 285s MPI I/O: n 285s 285s 285s -k (to set the k-mer size) 285s Value: 31 285s 285s 285s Paired library # 0 285s -p (paired-end sequences) 285s Left sequences: ecoli_1K_1.fq 285s Right sequences: ecoli_1K_2.fq 285s Average length: automatic detection 285s Standard deviation: automatic detection 285s 285s Ray command: 285s mpiexec -n 1 Ray \ 285s -k \ 285s 31 \ 285s -p \ 285s ecoli_1K_1.fq \ 285s ecoli_1K_2.fq \ 285s -o \ 285s test1 285s 285s Rank 0 wrote test1/RayCommand.txt 285s 285s k-mer length: 31 285s Rank 0: assembler memory usage: 41156 KiB 285s Rank 0: assembler memory usage: 106828 KiB 285s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2236 285s Rank 0: testing the network, please wait... 285s 285s Rank 0 is testing the network [0/1000] 285s Rank 0 is testing the network [1000/1000] 285s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 285s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 285s 285s Rank 0 wrote test1/NetworkTest.txt 285s 285s 285s *** 285s Step: Network testing 285s Date: Wed Jul 24 11:19:21 2024 285s Elapsed time: 0 seconds 285s Since beginning: 0 seconds 285s *** 285s 285s 285s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 285s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 285s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 285s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 285s Rank 0 wrote test1/NumberOfSequences.txt 285s Rank 0 wrote test1/SequencePartition.txt 285s 285s *** 285s Step: Counting sequences to assemble 285s Date: Wed Jul 24 11:19:21 2024 285s Elapsed time: 0 seconds 285s Since beginning: 0 seconds 285s *** 285s 285s 285s Rank 0 is loading sequence reads 285s Rank 0 : partition is [0;4107], 4108 sequence reads 285s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 285s Rank 0 has 0 sequence reads 285s Rank 0: assembler memory usage: 115660 KiB 285s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 285s Rank 0 has 4108 sequence reads (completed) 285s 285s *** 285s Step: Sequence loading 285s Date: Wed Jul 24 11:19:21 2024 285s Elapsed time: 0 seconds 285s Since beginning: 0 seconds 285s *** 285s 285s 285s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 285s Rank 0 created its Bloom filter 286s Rank 0 is counting k-mers in sequence reads [1/4108] 286s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 286s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 286s 286s 286s *** 286s Step: K-mer counting 286s Date: Wed Jul 24 11:19:22 2024 286s Elapsed time: 1 seconds 286s Since beginning: 1 seconds 286s *** 286s 286s 286s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 286s Rank 0 destroyed its Bloom filter 286s Rank 0 has 1954 k-mers (completed) 286s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 286s Rank 0: assembler memory usage: 114804 KiB 295s 295s 295s Rank 0: the minimum coverage is 3 295s Rank 0: the peak coverage is 3 295s Warning: no peak observed in the k-mer coverage distribution. 295s to deal with the sequencing error rate, try to lower the k-mer length (-k) 295s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 295s 295s *** 295s Step: Coverage distribution analysis 295s Date: Wed Jul 24 11:19:31 2024 295s Elapsed time: 9 seconds 295s Since beginning: 10 seconds 295s *** 295s 295s 295s 296s Rank 0 is adding edges [1/4108] 296s Rank 0 is adding edges [4108/4108] (completed) 296s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 296s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 296s 296s *** 296s Step: Graph construction 296s Date: Wed Jul 24 11:19:32 2024 296s Elapsed time: 1 seconds 296s Since beginning: 11 seconds 296s *** 296s 296s 296s Rank 0 has 1954 vertices (completed) 296s Rank 0: assembler memory usage: 114804 KiB 305s Rank 0 is purging edges [1/1954] 305s Rank 0 is purging edges [1954/1954] (completed) 305s Rank 0: assembler memory usage: 115340 KiB 305s VirtualProcessor: completed jobs: 1954 305s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 315s Rank 0 wrote test1/degreeDistribution.txt 315s 315s *** 315s Step: Null edge purging 315s Date: Wed Jul 24 11:19:51 2024 315s Elapsed time: 19 seconds 315s Since beginning: 30 seconds 315s *** 315s 315s 315s Rank 0 is selecting optimal read markers [1/4108] 315s Rank 0: assembler memory usage: 115340 KiB 316s Rank 0 is selecting optimal read markers [4108/4108] (completed) 316s Rank 0: peak number of workers: 599, maximum: 32768 316s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 316s Rank 0: assembler memory usage: 123540 KiB 316s Rank 0: Freeing unused assembler memory: 4096 KiB freed 316s Rank 0: assembler memory usage: 119440 KiB 316s 316s *** 316s Step: Selection of optimal read markers 316s Date: Wed Jul 24 11:19:51 2024 316s Elapsed time: 0 seconds 316s Since beginning: 30 seconds 316s *** 316s 316s 316s Rank 0: memory usage for optimal read markers= 4096 KiB 316s Rank 0 is creating seeds [1/1954] 316s Rank 0: assembler memory usage: 119440 KiB 325s Rank 0 has 1 seeds 325s Rank 0 is creating seeds [1954/1954] (completed) 325s Rank 0: peak number of workers: 746, maximum: 32768 325s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 325s Rank 0 runtime statistics for seeding algorithm: 325s Rank 0 Skipped paths because of dead end for head: 0 325s Rank 0 Skipped paths because of dead end for tail: 0 325s Rank 0 Skipped paths because of two dead ends: 0 325s Rank 0 Skipped paths because of bubble weak component: 0 325s Rank 0 Skipped paths because of short length: 1952 325s Rank 0 Skipped paths because of bad ownership: 1 325s Rank 0 Skipped paths because of low coverage: 0 325s Rank 0 Eligible paths: 1 325s Rank 0: assembler memory usage: 119572 KiB 325s Rank 0 has 1 seeds to register. 325s Rank 0 registered 0/1 325s Rank 0 registered 0/1 325s Rank 0 registered its seeds 325s VirtualProcessor: completed jobs: 0 325s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 334s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 344s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 344s Rank 0 merged its seeds: 1 seeds -> 1 seeds 344s 344s *** 344s Step: Detection of assembly seeds 344s Date: Wed Jul 24 11:20:20 2024 344s Elapsed time: 29 seconds 344s Since beginning: 59 seconds 344s *** 344s 344s 344s Rank 0 is calculating library lengths [1/1] 344s Rank 0 detected 1737 library lengths 344s Rank 0 is calculating library lengths [1/1] (completed) 344s Rank 0: peak number of workers: 1, maximum: 32768 344s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 344s Rank 0: assembler memory usage: 152344 KiB 344s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 344s 344s Mode= 2 signalAverage= 9 344s CURRENT IS NOISE, 244 344s GOT HIT 212 344s 344s 344s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 344s 344s *** 344s Step: Estimation of outer distances for paired reads 344s Date: Wed Jul 24 11:20:20 2024 344s Elapsed time: 0 seconds 344s Since beginning: 59 seconds 344s *** 344s 344s 345s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 345s Rank 0 traversed 1000 nucleotide symbols 345s Rank 0: assembler memory usage: 156444 KiB 345s Rank 0 is extending seeds [1/1] (completed) 345s Rank 0 extended 1 seeds out of 1 (100.00%) 345s Rank 0: assembler memory usage: 152344 KiB 345s Rank 0 starting fusions 345s 345s *** 345s Step: Bidirectional extension of seeds 345s Date: Wed Jul 24 11:20:21 2024 345s Elapsed time: 1 seconds 345s Since beginning: 1 minutes, 0 seconds 345s *** 345s 345s 345s Rank 0: starting clear step. cycleNumber= 0 354s Rank 0 adding 0 new fusions 354s Rank 0 cleared, 1 paths 354s Rank 0: starting distribution step 354s Rank 0 is distributing fusions [1/1] 354s Rank 0: assembler memory usage: 152344 KiB 354s Date: Wed Jul 24 11:20:30 2024 354s Rank 0 is distributing fusions [1/1] (completed) 354s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 354s Rank 0: assembler memory usage: 156444 KiB 354s Date: Wed Jul 24 11:20:30 2024 354s Rank 0 tells others to compute fusions. 354s Rank 0 FusionTaskCreator assignNextTask [0/2] 354s Rank 0: assembler memory usage: 156444 KiB 354s Date: Wed Jul 24 11:20:30 2024 354s Rank 0 FusionTaskCreator processWorkerResult [0/2] 354s Rank 0: assembler memory usage: 156444 KiB 354s Date: Wed Jul 24 11:20:30 2024 354s Rank 0 FusionTaskCreator [2/2] 354s Statistics: all paths: 1 eliminated during fusing: 0 354s Rank 0: assembler memory usage: 156444 KiB 354s VirtualProcessor: completed jobs: 2 354s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 354s Rank 0: starting clear step. cycleNumber= 1 363s Rank 0 adding 0 new fusions 363s Rank 0 cleared, 1 paths 363s Rank 0 is distributing fusions [1/1] 363s Rank 0: assembler memory usage: 152344 KiB 363s Date: Wed Jul 24 11:20:39 2024 363s Rank 0 is distributing fusions [1/1] (completed) 363s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 363s Rank 0: assembler memory usage: 156444 KiB 363s Date: Wed Jul 24 11:20:39 2024 363s Rank 0 JoinerTaskCreator assignNextTask [0/2] 363s Rank 0: assembler memory usage: 156444 KiB 363s Date: Wed Jul 24 11:20:39 2024 363s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 363s Rank 0: assembler memory usage: 156444 KiB 363s Date: Wed Jul 24 11:20:39 2024 363s Rank 0 JoinerTaskCreator [2/2] 363s Statistics: all paths: 1 eliminated during joining: 0 363s Rank 0: assembler memory usage: 156444 KiB 363s Date: Wed Jul 24 11:20:39 2024 363s VirtualProcessor: completed jobs: 2 363s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 372s Rank 0 adding 0 new fusions 372s Rank 0 cleared, 1 paths 372s Rank 0: starting distribution step 372s Rank 0 is distributing fusions [1/1] 372s Rank 0: assembler memory usage: 152344 KiB 372s Date: Wed Jul 24 11:20:48 2024 372s Rank 0 is distributing fusions [1/1] (completed) 372s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 372s Rank 0: assembler memory usage: 156444 KiB 372s Date: Wed Jul 24 11:20:48 2024 372s Rank 0 tells others to compute fusions. 372s Rank 0 FusionTaskCreator assignNextTask [0/2] 372s Rank 0: assembler memory usage: 156444 KiB 372s Date: Wed Jul 24 11:20:48 2024 372s Rank 0 FusionTaskCreator processWorkerResult [0/2] 372s Rank 0: assembler memory usage: 156444 KiB 372s Date: Wed Jul 24 11:20:48 2024 372s Rank 0 FusionTaskCreator [2/2] 372s Statistics: all paths: 1 eliminated during fusing: 0 372s Rank 0: assembler memory usage: 156444 KiB 372s VirtualProcessor: completed jobs: 2 372s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 372s Rank 0: starting clear step. cycleNumber= 2 382s Rank 0 adding 0 new fusions 382s Rank 0 cleared, 1 paths 382s Rank 0 is distributing fusions [1/1] 382s Rank 0: assembler memory usage: 152344 KiB 382s Date: Wed Jul 24 11:20:58 2024 382s Rank 0 is distributing fusions [1/1] (completed) 382s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 382s Rank 0: assembler memory usage: 156444 KiB 382s Date: Wed Jul 24 11:20:58 2024 382s Rank 0 JoinerTaskCreator assignNextTask [0/2] 382s Rank 0: assembler memory usage: 156444 KiB 382s Date: Wed Jul 24 11:20:58 2024 382s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 382s Rank 0: assembler memory usage: 156444 KiB 382s Date: Wed Jul 24 11:20:58 2024 382s Rank 0 JoinerTaskCreator [2/2] 382s Statistics: all paths: 1 eliminated during joining: 0 382s Rank 0: assembler memory usage: 156444 KiB 382s Date: Wed Jul 24 11:20:58 2024 382s VirtualProcessor: completed jobs: 2 382s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 391s Rank 0 adding 0 new fusions 391s Rank 0 cleared, 1 paths 391s Rank 0: starting distribution step 391s Rank 0 is distributing fusions [1/1] 391s Rank 0: assembler memory usage: 152344 KiB 391s Date: Wed Jul 24 11:21:07 2024 391s Rank 0 is distributing fusions [1/1] (completed) 391s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 391s Rank 0: assembler memory usage: 156444 KiB 391s Date: Wed Jul 24 11:21:07 2024 391s Rank 0 cycleNumber= 2 391s 391s *** 391s Step: Merging of redundant paths 391s Date: Wed Jul 24 11:21:07 2024 391s Elapsed time: 46 seconds 391s Since beginning: 1 minutes, 46 seconds 391s *** 391s 391s 391s Rank 0 appended 1 elements 391s 391s *** 391s Step: Generation of contigs 391s Date: Wed Jul 24 11:21:07 2024 391s Elapsed time: 0 seconds 391s Since beginning: 1 minutes, 46 seconds 391s *** 391s 391s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 391s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 391s Rank 0 ineligibleObjects: 0/970 (0.00%) 391s Rank 0: assembler memory usage: 156444 KiB 391s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 391s Rank 0 finished gathering scaffold links. 391s Rank 0 will write 1 contig lengths 391s Rank 0 will solve the scaffolding problem. 391s Welcome to GreedySolver v1.0 391s 1 vertices; 0 edges 391s 1 contigs >= 500 391s Edges in solution: 0 391s 391s Conflict statistics: 391s 1 scaffolds, 1 >= 500 391s Total: 1000 nucleotides 391s 391s *** 391s Step: Scaffolding of contigs 391s Date: Wed Jul 24 11:21:07 2024 391s Elapsed time: 0 seconds 391s Since beginning: 1 minutes, 46 seconds 391s *** 391s 391s Rank 0 syncing with master 391s 391s *** 391s Step: Counting sequences to search 391s Date: Wed Jul 24 11:21:07 2024 391s Elapsed time: 0 seconds 391s Since beginning: 1 minutes, 46 seconds 391s *** 391s 391s 391s Rank 0 will add colors, 0 sequences in 0 files to process 391s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 400s 400s *** 400s Step: Graph coloring 400s Date: Wed Jul 24 11:21:16 2024 400s Elapsed time: 9 seconds 400s Since beginning: 1 minutes, 55 seconds 400s *** 400s 400s 400s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 400s Rank 0 shares its counts 400s Rank 0 computing contig abundances [1/1] [1/970] 400s Rank 0 computing contig abundances [1/1] [970/970] 400s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 400s 400s *** 400s Step: Counting contig biological abundances 400s Date: Wed Jul 24 11:21:16 2024 400s Elapsed time: 0 seconds 400s Since beginning: 1 minutes, 55 seconds 400s *** 400s 400s 400s Rank 0 colored the graph with 0 real colors using 1 virtual colors 400s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 400s 400s *** 400s Step: Counting sequence biological abundances 400s Date: Wed Jul 24 11:21:16 2024 400s Elapsed time: 0 seconds 400s Since beginning: 1 minutes, 55 seconds 400s *** 400s 400s 400s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 400s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 410s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 410s 410s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 410s Rank 0 is starting taxon syncing across the compute tribe. 410s 410s *** 410s Step: Loading taxons 410s Date: Wed Jul 24 11:21:26 2024 410s Elapsed time: 10 seconds 410s Since beginning: 2 minutes, 5 seconds 410s *** 410s 410s Rank 0 synced taxons across the grid with 1 poor slaves. 410s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 410s Rank 0 has 0 taxons after syncing with master 419s 419s 419s *** 419s Step: Loading tree 419s Date: Wed Jul 24 11:21:35 2024 419s Elapsed time: 9 seconds 419s Since beginning: 2 minutes, 14 seconds 419s *** 419s 428s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 428s 428s Rank 0: counting ontology terms in the graph... 437s Rank 0: 0 have some biological signal 437s Number of dereferenced alternate handles: 0 437s Number of k-mer observations with gene ontology terms: 0 437s Rank 0: synced ontology term profiles with master 437s Rank 0: synchronization is complete! 437s Rank 0: ontology terms with biological signal: 0 437s Populated recursive values... 437s Gene ontology terms without depth information: 0 437s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 437s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 437s 437s *** 437s Step: Processing gene ontologies 437s Date: Wed Jul 24 11:21:53 2024 437s Elapsed time: 18 seconds 437s Since beginning: 2 minutes, 32 seconds 437s *** 437s 437s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 437s [GenomeNeighbourhood] in final list: 0 437s 437s *** 437s Step: Computing neighbourhoods 437s Date: Wed Jul 24 11:21:53 2024 437s Elapsed time: 0 seconds 437s Since beginning: 2 minutes, 32 seconds 437s *** 437s 437s Contigs >= 100 nt 437s Number: 1 437s Total length: 1000 437s Average: 1000 437s N50: 1000 437s Median: 1000 437s Largest: 1000 437s Contigs >= 500 nt 437s Number: 1 437s Total length: 1000 437s Average: 1000 437s N50: 1000 437s Median: 1000 437s Largest: 1000 437s Scaffolds >= 100 nt 437s Number: 1 437s Total length: 1000 437s Average: 1000 437s N50: 1000 437s Median: 1000 437s Largest: 1000 437s Scaffolds >= 500 nt 437s Number: 1 437s Total length: 1000 437s Average: 1000 437s N50: 1000 437s Median: 1000 437s Largest: 1000 437s 437s Rank 0 wrote test1/Contigs.fasta 437s Rank 0 wrote test1/Scaffolds.fasta 437s Check for test1/* 437s 437s 438s 438s ************************************************** 438s This program comes with ABSOLUTELY NO WARRANTY. 438s This is free software, and you are welcome to redistribute it 438s under certain conditions; see "LICENSE.txt" for details. 438s ************************************************** 438s 438s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 438s Centre de recherche en infectiologie de l'Université Laval 438s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 438s http://denovoassembler.sf.net/ 438s 438s References to cite: 438s 438s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 438s Ray Meta: scalable de novo metagenome assembly and profiling. 438s Genome Biology (BioMed Central Ltd). 438s 13:R122, Published: 22 December 2012 438s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 438s 438s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 438s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 438s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 438s November 2010, Volume 17, Issue 11, Pages 1519-1533. 438s http://dx.doi.org/doi:10.1089/cmb.2009.0238 438s 438s Ray version 2.3.1 438s License for Ray: GNU General Public License version 3 438s RayPlatform version: 2.0.1 438s License for RayPlatform: GNU Lesser General Public License version 3 438s 438s MAXKMERLENGTH: 32 438s Maximum coverage depth stored by CoverageDepth: 4294967295 438s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 438s FORCE_PACKING = n 438s ASSERT = n 438s HAVE_LIBZ = y 438s HAVE_LIBBZ2 = y 438s PROFILER_COLLECT = n 438s MINIRANKS = y 438s CLOCK_GETTIME = n 438s __linux__ = y 438s _MSC_VER = n 438s __GNUC__ = y 438s RAY_32_BITS = y 438s RAY_64_BITS = n 438s MPI standard version: MPI 3.1 438s MPI library: Open-MPI 4.1.6 438s Compiler: GNU gcc/g++ 13.2.0 438s MPI I/O: n 438s 438s 438s -k (to set the k-mer size) 438s Value: 31 438s 438s 438s Paired library # 0 438s -p (paired-end sequences) 438s Left sequences: SampleDirectory/s_6.first1000_1.fastq 438s Right sequences: SampleDirectory/s_6.first1000_2.fastq 438s Average length: automatic detection 438s Standard deviation: automatic detection 438s 438s Ray command: 438s mpiexec -n 1 Ray \ 438s -k \ 438s 31 \ 438s -detect-sequence-files \ 438s SampleDirectory \ 438s -o \ 438s test2 438s 438s Rank 0 wrote test2/RayCommand.txt 438s 438s k-mer length: 31 438s Rank 0: assembler memory usage: 41168 KiB 438s Rank 0: assembler memory usage: 106900 KiB 438s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2245 438s Rank 0: testing the network, please wait... 438s 438s Rank 0 is testing the network [0/1000] 438s Rank 0 is testing the network [1000/1000] 438s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 438s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 438s 438s Rank 0 wrote test2/NetworkTest.txt 438s 438s 438s *** 438s Step: Network testing 438s Date: Wed Jul 24 11:21:54 2024 438s Elapsed time: 0 seconds 438s Since beginning: 0 seconds 438s *** 438s 438s 438s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 438s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 438s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 438s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 438s Rank 0 wrote test2/NumberOfSequences.txt 438s Rank 0 wrote test2/SequencePartition.txt 438s 438s *** 438s Step: Counting sequences to assemble 438s Date: Wed Jul 24 11:21:54 2024 438s Elapsed time: 0 seconds 438s Since beginning: 0 seconds 438s *** 438s 438s 438s Rank 0 is loading sequence reads 438s Rank 0 : partition is [0;4107], 4108 sequence reads 438s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 438s Rank 0 has 0 sequence reads 438s Rank 0: assembler memory usage: 115608 KiB 438s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 438s Rank 0 has 4108 sequence reads (completed) 438s 438s *** 438s Step: Sequence loading 438s Date: Wed Jul 24 11:21:54 2024 438s Elapsed time: 0 seconds 438s Since beginning: 0 seconds 438s *** 438s 438s 438s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 438s Rank 0 created its Bloom filter 439s Rank 0 is counting k-mers in sequence reads [1/4108] 439s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 439s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 439s 439s 439s *** 439s Step: K-mer counting 439s Date: Wed Jul 24 11:21:54 2024 439s Elapsed time: 0 seconds 439s Since beginning: 0 seconds 439s *** 439s 439s 439s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 439s Rank 0 destroyed its Bloom filter 439s Rank 0 has 1954 k-mers (completed) 439s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 439s Rank 0: assembler memory usage: 114884 KiB 448s 448s 448s Rank 0: the minimum coverage is 3 448s Rank 0: the peak coverage is 3 448s Warning: no peak observed in the k-mer coverage distribution. 448s to deal with the sequencing error rate, try to lower the k-mer length (-k) 448s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 448s 448s *** 448s Step: Coverage distribution analysis 448s Date: Wed Jul 24 11:22:04 2024 448s Elapsed time: 10 seconds 448s Since beginning: 10 seconds 448s *** 448s 448s 448s 449s Rank 0 is adding edges [1/4108] 449s Rank 0 is adding edges [4108/4108] (completed) 449s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 449s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 449s 449s *** 449s Step: Graph construction 449s Date: Wed Jul 24 11:22:05 2024 449s Elapsed time: 1 seconds 449s Since beginning: 11 seconds 449s *** 449s 449s 449s Rank 0 has 1954 vertices (completed) 449s Rank 0: assembler memory usage: 114884 KiB 458s Rank 0 is purging edges [1/1954] 458s Rank 0 is purging edges [1954/1954] (completed) 458s Rank 0: assembler memory usage: 115280 KiB 458s VirtualProcessor: completed jobs: 1954 458s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 467s Rank 0 wrote test2/degreeDistribution.txt 467s 467s *** 467s Step: Null edge purging 467s Date: Wed Jul 24 11:22:23 2024 467s Elapsed time: 18 seconds 467s Since beginning: 29 seconds 467s *** 467s 467s 467s Rank 0 is selecting optimal read markers [1/4108] 467s Rank 0: assembler memory usage: 115280 KiB 468s Rank 0 is selecting optimal read markers [4108/4108] (completed) 468s Rank 0: peak number of workers: 599, maximum: 32768 468s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 468s Rank 0: assembler memory usage: 123480 KiB 468s Rank 0: Freeing unused assembler memory: 4096 KiB freed 468s Rank 0: assembler memory usage: 119380 KiB 468s 468s *** 468s Step: Selection of optimal read markers 468s Date: Wed Jul 24 11:22:24 2024 468s Elapsed time: 1 seconds 468s Since beginning: 30 seconds 468s *** 468s 468s 468s Rank 0: memory usage for optimal read markers= 4096 KiB 468s Rank 0 is creating seeds [1/1954] 468s Rank 0: assembler memory usage: 119380 KiB 477s Rank 0 has 1 seeds 477s Rank 0 is creating seeds [1954/1954] (completed) 477s Rank 0: peak number of workers: 746, maximum: 32768 477s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 477s Rank 0 runtime statistics for seeding algorithm: 477s Rank 0 Skipped paths because of dead end for head: 0 477s Rank 0 Skipped paths because of dead end for tail: 0 477s Rank 0 Skipped paths because of two dead ends: 0 477s Rank 0 Skipped paths because of bubble weak component: 0 477s Rank 0 Skipped paths because of short length: 1952 477s Rank 0 Skipped paths because of bad ownership: 1 477s Rank 0 Skipped paths because of low coverage: 0 477s Rank 0 Eligible paths: 1 477s Rank 0: assembler memory usage: 119512 KiB 477s Rank 0 has 1 seeds to register. 477s Rank 0 registered 0/1 477s Rank 0 registered 0/1 477s Rank 0 registered its seeds 477s VirtualProcessor: completed jobs: 0 477s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 487s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 497s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 497s Rank 0 merged its seeds: 1 seeds -> 1 seeds 497s 497s *** 497s Step: Detection of assembly seeds 497s Date: Wed Jul 24 11:22:53 2024 497s Elapsed time: 29 seconds 497s Since beginning: 59 seconds 497s *** 497s 497s 497s Rank 0 is calculating library lengths [1/1] 497s Rank 0 detected 1737 library lengths 497s Rank 0 is calculating library lengths [1/1] (completed) 497s Rank 0: peak number of workers: 1, maximum: 32768 497s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 497s Rank 0: assembler memory usage: 152284 KiB 497s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 497s 497s Mode= 2 signalAverage= 9 497s CURRENT IS NOISE, 244 497s GOT HIT 212 497s 497s 497s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 497s 497s *** 497s Step: Estimation of outer distances for paired reads 497s Date: Wed Jul 24 11:22:53 2024 497s Elapsed time: 0 seconds 497s Since beginning: 59 seconds 497s *** 497s 497s 498s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 498s Rank 0 traversed 1000 nucleotide symbols 498s Rank 0: assembler memory usage: 156384 KiB 498s Rank 0 is extending seeds [1/1] (completed) 498s Rank 0 extended 1 seeds out of 1 (100.00%) 498s Rank 0: assembler memory usage: 152284 KiB 498s Rank 0 starting fusions 498s 498s *** 498s Step: Bidirectional extension of seeds 498s Date: Wed Jul 24 11:22:54 2024 498s Elapsed time: 1 seconds 498s Since beginning: 1 minutes, 0 seconds 498s *** 498s 498s 498s Rank 0: starting clear step. cycleNumber= 0 507s Rank 0 adding 0 new fusions 507s Rank 0 cleared, 1 paths 507s Rank 0: starting distribution step 507s Rank 0 is distributing fusions [1/1] 507s Rank 0: assembler memory usage: 152284 KiB 507s Date: Wed Jul 24 11:23:03 2024 507s Rank 0 is distributing fusions [1/1] (completed) 507s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 507s Rank 0: assembler memory usage: 156384 KiB 507s Date: Wed Jul 24 11:23:03 2024 507s Rank 0 tells others to compute fusions. 507s Rank 0 FusionTaskCreator assignNextTask [0/2] 507s Rank 0: assembler memory usage: 156384 KiB 507s Date: Wed Jul 24 11:23:03 2024 507s Rank 0 FusionTaskCreator processWorkerResult [0/2] 507s Rank 0: assembler memory usage: 156384 KiB 507s Date: Wed Jul 24 11:23:03 2024 507s Rank 0 FusionTaskCreator [2/2] 507s Statistics: all paths: 1 eliminated during fusing: 0 507s Rank 0: assembler memory usage: 156384 KiB 507s VirtualProcessor: completed jobs: 2 507s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 507s Rank 0: starting clear step. cycleNumber= 1 516s Rank 0 adding 0 new fusions 516s Rank 0 cleared, 1 paths 516s Rank 0 is distributing fusions [1/1] 516s Rank 0: assembler memory usage: 152284 KiB 516s Date: Wed Jul 24 11:23:12 2024 516s Rank 0 is distributing fusions [1/1] (completed) 516s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 516s Rank 0: assembler memory usage: 156384 KiB 516s Date: Wed Jul 24 11:23:12 2024 516s Rank 0 JoinerTaskCreator assignNextTask [0/2] 516s Rank 0: assembler memory usage: 156384 KiB 516s Date: Wed Jul 24 11:23:12 2024 516s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 516s Rank 0: assembler memory usage: 156384 KiB 516s Date: Wed Jul 24 11:23:12 2024 516s Rank 0 JoinerTaskCreator [2/2] 516s Statistics: all paths: 1 eliminated during joining: 0 516s Rank 0: assembler memory usage: 156384 KiB 516s Date: Wed Jul 24 11:23:12 2024 516s VirtualProcessor: completed jobs: 2 516s 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: 152284 KiB 526s Date: Wed Jul 24 11:23:22 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: 156384 KiB 526s Date: Wed Jul 24 11:23:22 2024 526s Rank 0 tells others to compute fusions. 526s Rank 0 FusionTaskCreator assignNextTask [0/2] 526s Rank 0: assembler memory usage: 156384 KiB 526s Date: Wed Jul 24 11:23:22 2024 526s Rank 0 FusionTaskCreator processWorkerResult [0/2] 526s Rank 0: assembler memory usage: 156384 KiB 526s Date: Wed Jul 24 11:23:22 2024 526s Rank 0 FusionTaskCreator [2/2] 526s Statistics: all paths: 1 eliminated during fusing: 0 526s Rank 0: assembler memory usage: 156384 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 535s Rank 0 adding 0 new fusions 535s Rank 0 cleared, 1 paths 535s Rank 0 is distributing fusions [1/1] 535s Rank 0: assembler memory usage: 152284 KiB 535s Date: Wed Jul 24 11:23:31 2024 535s Rank 0 is distributing fusions [1/1] (completed) 535s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 535s Rank 0: assembler memory usage: 156384 KiB 535s Date: Wed Jul 24 11:23:31 2024 535s Rank 0 JoinerTaskCreator assignNextTask [0/2] 535s Rank 0: assembler memory usage: 156384 KiB 535s Date: Wed Jul 24 11:23:31 2024 535s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 535s Rank 0: assembler memory usage: 156384 KiB 535s Date: Wed Jul 24 11:23:31 2024 535s Rank 0 JoinerTaskCreator [2/2] 535s Statistics: all paths: 1 eliminated during joining: 0 535s Rank 0: assembler memory usage: 156384 KiB 535s Date: Wed Jul 24 11:23:31 2024 535s VirtualProcessor: completed jobs: 2 535s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 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: 152284 KiB 544s Date: Wed Jul 24 11:23:40 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: 156384 KiB 544s Date: Wed Jul 24 11:23:40 2024 544s Rank 0 cycleNumber= 2 544s 544s *** 544s Step: Merging of redundant paths 544s Date: Wed Jul 24 11:23:40 2024 544s Elapsed time: 46 seconds 544s Since beginning: 1 minutes, 46 seconds 544s *** 544s 544s 544s Rank 0 appended 1 elements 544s 544s *** 544s Step: Generation of contigs 544s Date: Wed Jul 24 11:23:40 2024 544s Elapsed time: 0 seconds 544s Since beginning: 1 minutes, 46 seconds 544s *** 544s 544s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 545s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 545s Rank 0 ineligibleObjects: 0/970 (0.00%) 545s Rank 0: assembler memory usage: 156384 KiB 545s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 545s Rank 0 finished gathering scaffold links. 545s Rank 0 will write 1 contig lengths 545s Rank 0 will solve the scaffolding problem. 545s Welcome to GreedySolver v1.0 545s 1 vertices; 0 edges 545s 1 contigs >= 500 545s Edges in solution: 0 545s 545s Conflict statistics: 545s 1 scaffolds, 1 >= 500 545s Total: 1000 nucleotides 545s 545s *** 545s Step: Scaffolding of contigs 545s Date: Wed Jul 24 11:23:41 2024 545s Elapsed time: 1 seconds 545s Since beginning: 1 minutes, 47 seconds 545s *** 545s 545s Rank 0 syncing with master 545s 545s *** 545s Step: Counting sequences to search 545s Date: Wed Jul 24 11:23:41 2024 545s Elapsed time: 0 seconds 545s Since beginning: 1 minutes, 47 seconds 545s *** 545s 545s 545s Rank 0 will add colors, 0 sequences in 0 files to process 545s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 555s 555s *** 555s Step: Graph coloring 555s Date: Wed Jul 24 11:23:51 2024 555s Elapsed time: 10 seconds 555s Since beginning: 1 minutes, 57 seconds 555s *** 555s 555s 555s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 555s Rank 0 shares its counts 555s Rank 0 computing contig abundances [1/1] [1/970] 555s Rank 0 computing contig abundances [1/1] [970/970] 555s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 555s 555s *** 555s Step: Counting contig biological abundances 555s Date: Wed Jul 24 11:23:51 2024 555s Elapsed time: 0 seconds 555s Since beginning: 1 minutes, 57 seconds 555s *** 555s 555s 555s Rank 0 colored the graph with 0 real colors using 1 virtual colors 555s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 555s 555s *** 555s Step: Counting sequence biological abundances 555s Date: Wed Jul 24 11:23:51 2024 555s Elapsed time: 0 seconds 555s Since beginning: 1 minutes, 57 seconds 555s *** 555s 555s 555s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 555s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 564s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 564s 564s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 564s Rank 0 is starting taxon syncing across the compute tribe. 564s 564s *** 564s Step: Loading taxons 564s Date: Wed Jul 24 11:24:00 2024 564s Elapsed time: 9 seconds 564s Since beginning: 2 minutes, 6 seconds 564s *** 564s 564s Rank 0 synced taxons across the grid with 1 poor slaves. 564s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 564s Rank 0 has 0 taxons after syncing with master 574s 574s 574s *** 574s Step: Loading tree 574s Date: Wed Jul 24 11:24:10 2024 574s Elapsed time: 10 seconds 574s Since beginning: 2 minutes, 16 seconds 574s *** 574s 583s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 583s 583s Rank 0: counting ontology terms in the graph... 594s Rank 0: 0 have some biological signal 594s Number of dereferenced alternate handles: 0 594s Number of k-mer observations with gene ontology terms: 0 594s Rank 0: synced ontology term profiles with master 594s Rank 0: synchronization is complete! 594s Rank 0: ontology terms with biological signal: 0 594s Populated recursive values... 594s Gene ontology terms without depth information: 0 594s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 594s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 594s 594s *** 594s Step: Processing gene ontologies 594s Date: Wed Jul 24 11:24:30 2024 594s Elapsed time: 20 seconds 594s Since beginning: 2 minutes, 36 seconds 594s *** 594s 594s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 594s [GenomeNeighbourhood] in final list: 0 594s 594s *** 594s Step: Computing neighbourhoods 594s Date: Wed Jul 24 11:24:30 2024 594s Elapsed time: 0 seconds 594s Since beginning: 2 minutes, 36 seconds 594s *** 594s 594s Contigs >= 100 nt 594s Number: 1 594s Total length: 1000 594s Average: 1000 594s N50: 1000 594s Median: 1000 594s Largest: 1000 594s Contigs >= 500 nt 594s Number: 1 594s Total length: 1000 594s Average: 1000 594s N50: 1000 594s Median: 1000 594s Largest: 1000 594s Scaffolds >= 100 nt 594s Number: 1 594s Total length: 1000 594s Average: 1000 594s N50: 1000 594s Median: 1000 594s Largest: 1000 594s Scaffolds >= 500 nt 594s Number: 1 594s Total length: 1000 594s Average: 1000 594s N50: 1000 594s Median: 1000 594s Largest: 1000 594s 594s Rank 0 wrote test2/Contigs.fasta 594s Rank 0 wrote test2/Scaffolds.fasta 594s Check for test2/* 594s 594s 594s 594s ************************************************** 594s This program comes with ABSOLUTELY NO WARRANTY. 594s This is free software, and you are welcome to redistribute it 594s under certain conditions; see "LICENSE.txt" for details. 594s ************************************************** 594s 594s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 594s Centre de recherche en infectiologie de l'Université Laval 594s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 594s http://denovoassembler.sf.net/ 594s 594s References to cite: 594s 594s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 594s Ray Meta: scalable de novo metagenome assembly and profiling. 594s Genome Biology (BioMed Central Ltd). 594s 13:R122, Published: 22 December 2012 594s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 594s 594s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 594s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 594s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 594s November 2010, Volume 17, Issue 11, Pages 1519-1533. 594s http://dx.doi.org/doi:10.1089/cmb.2009.0238 594s 594s Ray version 2.3.1 594s License for Ray: GNU General Public License version 3 594s RayPlatform version: 2.0.1 594s License for RayPlatform: GNU Lesser General Public License version 3 594s 594s MAXKMERLENGTH: 32 594s Maximum coverage depth stored by CoverageDepth: 4294967295 594s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 594s FORCE_PACKING = n 594s ASSERT = n 594s HAVE_LIBZ = y 594s HAVE_LIBBZ2 = y 594s PROFILER_COLLECT = n 594s MINIRANKS = y 594s CLOCK_GETTIME = n 594s __linux__ = y 594s _MSC_VER = n 594s __GNUC__ = y 594s RAY_32_BITS = y 594s RAY_64_BITS = n 594s MPI standard version: MPI 3.1 594s MPI library: Open-MPI 4.1.6 594s Compiler: GNU gcc/g++ 13.2.0 594s MPI I/O: n 594s 594s 594s -k (to set the k-mer size) 594s Value: 29 594s 594s 594s Paired library # 0 594s -p (paired-end sequences) 594s Left sequences: SampleDirectory/s_6.first1000_1.fastq 594s Right sequences: SampleDirectory/s_6.first1000_2.fastq 594s Average length: automatic detection 594s Standard deviation: automatic detection 594s 594s Ray command: 594s mpiexec -n 1 Ray \ 594s -k \ 594s 29 \ 594s -desable-recycling \ 594s -p \ 594s SampleDirectory/s_6.first1000_1.fastq \ 594s SampleDirectory/s_6.first1000_2.fastq 594s 594s Rank 0 wrote RayOutput/RayCommand.txt 594s 594s k-mer length: 29 594s Rank 0: assembler memory usage: 41156 KiB 594s Rank 0: assembler memory usage: 106828 KiB 594s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2254 594s Rank 0: testing the network, please wait... 594s 594s Rank 0 is testing the network [0/1000] 594s Rank 0 is testing the network [1000/1000] 594s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 594s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 594s 594s Rank 0 wrote RayOutput/NetworkTest.txt 594s 594s 594s *** 594s Step: Network testing 594s Date: Wed Jul 24 11:24:30 2024 594s Elapsed time: 0 seconds 594s Since beginning: 0 seconds 594s *** 594s 594s 594s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 594s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 594s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 594s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 594s Rank 0 wrote RayOutput/NumberOfSequences.txt 594s Rank 0 wrote RayOutput/SequencePartition.txt 594s 594s *** 594s Step: Counting sequences to assemble 594s Date: Wed Jul 24 11:24:30 2024 594s Elapsed time: 0 seconds 594s Since beginning: 0 seconds 594s *** 594s 594s 594s Rank 0 is loading sequence reads 594s Rank 0 : partition is [0;4107], 4108 sequence reads 594s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 594s Rank 0 has 0 sequence reads 594s Rank 0: assembler memory usage: 115660 KiB 594s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 594s Rank 0 has 4108 sequence reads (completed) 594s 594s *** 594s Step: Sequence loading 594s Date: Wed Jul 24 11:24:30 2024 594s Elapsed time: 0 seconds 594s Since beginning: 0 seconds 594s *** 594s 594s 594s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 594s Rank 0 created its Bloom filter 595s Rank 0 is counting k-mers in sequence reads [1/4108] 595s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 595s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 595s 595s 595s *** 595s Step: K-mer counting 595s Date: Wed Jul 24 11:24:31 2024 595s Elapsed time: 1 seconds 595s Since beginning: 1 seconds 595s *** 595s 595s 595s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 595s Rank 0 destroyed its Bloom filter 595s Rank 0 has 1958 k-mers (completed) 595s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 595s Rank 0: assembler memory usage: 114804 KiB 604s 604s 604s Rank 0: the minimum coverage is 3 604s Rank 0: the peak coverage is 3 604s Warning: no peak observed in the k-mer coverage distribution. 604s to deal with the sequencing error rate, try to lower the k-mer length (-k) 604s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 604s 604s *** 604s Step: Coverage distribution analysis 604s Date: Wed Jul 24 11:24:40 2024 604s Elapsed time: 9 seconds 604s Since beginning: 10 seconds 604s *** 604s 604s 604s 605s Rank 0 is adding edges [1/4108] 605s Rank 0 is adding edges [4108/4108] (completed) 605s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 605s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 605s 605s *** 605s Step: Graph construction 605s Date: Wed Jul 24 11:24:41 2024 605s Elapsed time: 1 seconds 605s Since beginning: 11 seconds 605s *** 605s 605s 605s Rank 0 has 1958 vertices (completed) 605s Rank 0: assembler memory usage: 114804 KiB 615s Rank 0 is purging edges [1/1958] 616s Rank 0 is purging edges [1958/1958] (completed) 616s Rank 0: assembler memory usage: 115344 KiB 616s VirtualProcessor: completed jobs: 1958 616s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 624s Rank 0 wrote RayOutput/degreeDistribution.txt 624s 624s *** 624s Step: Null edge purging 624s Date: Wed Jul 24 11:25:00 2024 624s Elapsed time: 19 seconds 624s Since beginning: 30 seconds 624s *** 624s 624s 624s Rank 0 is selecting optimal read markers [1/4108] 624s Rank 0: assembler memory usage: 115344 KiB 625s Rank 0 is selecting optimal read markers [4108/4108] (completed) 625s Rank 0: peak number of workers: 599, maximum: 32768 625s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 625s Rank 0: assembler memory usage: 123544 KiB 625s Rank 0: Freeing unused assembler memory: 4096 KiB freed 625s Rank 0: assembler memory usage: 119444 KiB 625s 625s *** 625s Step: Selection of optimal read markers 625s Date: Wed Jul 24 11:25:01 2024 625s Elapsed time: 1 seconds 625s Since beginning: 31 seconds 625s *** 625s 625s 625s Rank 0: memory usage for optimal read markers= 4096 KiB 625s Rank 0 is creating seeds [1/1958] 625s Rank 0: assembler memory usage: 119444 KiB 634s Rank 0 has 1 seeds 634s Rank 0 is creating seeds [1958/1958] (completed) 634s Rank 0: peak number of workers: 746, maximum: 32768 634s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 634s Rank 0 runtime statistics for seeding algorithm: 634s Rank 0 Skipped paths because of dead end for head: 0 634s Rank 0 Skipped paths because of dead end for tail: 0 634s Rank 0 Skipped paths because of two dead ends: 0 634s Rank 0 Skipped paths because of bubble weak component: 0 634s Rank 0 Skipped paths because of short length: 1956 634s Rank 0 Skipped paths because of bad ownership: 1 634s Rank 0 Skipped paths because of low coverage: 0 634s Rank 0 Eligible paths: 1 634s Rank 0: assembler memory usage: 119576 KiB 634s Rank 0 has 1 seeds to register. 634s Rank 0 registered 0/1 634s Rank 0 registered 0/1 634s Rank 0 registered its seeds 634s VirtualProcessor: completed jobs: 0 634s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 643s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 653s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 653s Rank 0 merged its seeds: 1 seeds -> 1 seeds 653s 653s *** 653s Step: Detection of assembly seeds 653s Date: Wed Jul 24 11:25:29 2024 653s Elapsed time: 28 seconds 653s Since beginning: 59 seconds 653s *** 653s 653s 653s Rank 0 is calculating library lengths [1/1] 653s Rank 0 detected 1743 library lengths 653s Rank 0 is calculating library lengths [1/1] (completed) 653s Rank 0: peak number of workers: 1, maximum: 32768 653s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 653s Rank 0: assembler memory usage: 152348 KiB 653s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 653s 653s Mode= 2 signalAverage= 10 653s CURRENT IS NOISE, 244 653s GOT HIT 214 653s 653s 653s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 653s 653s *** 653s Step: Estimation of outer distances for paired reads 653s Date: Wed Jul 24 11:25:29 2024 653s Elapsed time: 0 seconds 653s Since beginning: 59 seconds 653s *** 653s 653s 654s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 654s Rank 0 traversed 1000 nucleotide symbols 654s Rank 0: assembler memory usage: 156448 KiB 654s Rank 0 is extending seeds [1/1] (completed) 654s Rank 0 extended 1 seeds out of 1 (100.00%) 654s Rank 0: assembler memory usage: 152348 KiB 654s Rank 0 starting fusions 654s 654s *** 654s Step: Bidirectional extension of seeds 654s Date: Wed Jul 24 11:25:30 2024 654s Elapsed time: 1 seconds 654s Since beginning: 1 minutes, 0 seconds 654s *** 654s 654s 654s Rank 0: starting clear step. cycleNumber= 0 663s Rank 0 adding 0 new fusions 663s Rank 0 cleared, 1 paths 663s Rank 0: starting distribution step 663s Rank 0 is distributing fusions [1/1] 663s Rank 0: assembler memory usage: 152348 KiB 663s Date: Wed Jul 24 11:25:39 2024 663s Rank 0 is distributing fusions [1/1] (completed) 663s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 663s Rank 0: assembler memory usage: 156448 KiB 663s Date: Wed Jul 24 11:25:39 2024 663s Rank 0 tells others to compute fusions. 663s Rank 0 FusionTaskCreator assignNextTask [0/2] 663s Rank 0: assembler memory usage: 156448 KiB 663s Date: Wed Jul 24 11:25:39 2024 663s Rank 0 FusionTaskCreator processWorkerResult [0/2] 663s Rank 0: assembler memory usage: 156448 KiB 663s Date: Wed Jul 24 11:25:39 2024 663s Rank 0 FusionTaskCreator [2/2] 663s Statistics: all paths: 1 eliminated during fusing: 0 663s Rank 0: assembler memory usage: 156448 KiB 663s VirtualProcessor: completed jobs: 2 663s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 663s Rank 0: starting clear step. cycleNumber= 1 672s Rank 0 adding 0 new fusions 672s Rank 0 cleared, 1 paths 672s Rank 0 is distributing fusions [1/1] 672s Rank 0: assembler memory usage: 152348 KiB 672s Date: Wed Jul 24 11:25:48 2024 672s Rank 0 is distributing fusions [1/1] (completed) 672s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 672s Rank 0: assembler memory usage: 156448 KiB 672s Date: Wed Jul 24 11:25:48 2024 672s Rank 0 JoinerTaskCreator assignNextTask [0/2] 672s Rank 0: assembler memory usage: 156448 KiB 672s Date: Wed Jul 24 11:25:48 2024 672s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 672s Rank 0: assembler memory usage: 156448 KiB 672s Date: Wed Jul 24 11:25:48 2024 672s Rank 0 JoinerTaskCreator [2/2] 672s Statistics: all paths: 1 eliminated during joining: 0 672s Rank 0: assembler memory usage: 156448 KiB 672s Date: Wed Jul 24 11:25:48 2024 672s VirtualProcessor: completed jobs: 2 672s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 682s Rank 0 adding 0 new fusions 682s Rank 0 cleared, 1 paths 682s Rank 0: starting distribution step 682s Rank 0 is distributing fusions [1/1] 682s Rank 0: assembler memory usage: 152348 KiB 682s Date: Wed Jul 24 11:25:57 2024 682s Rank 0 is distributing fusions [1/1] (completed) 682s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 682s Rank 0: assembler memory usage: 156448 KiB 682s Date: Wed Jul 24 11:25:57 2024 682s Rank 0 tells others to compute fusions. 682s Rank 0 FusionTaskCreator assignNextTask [0/2] 682s Rank 0: assembler memory usage: 156448 KiB 682s Date: Wed Jul 24 11:25:57 2024 682s Rank 0 FusionTaskCreator processWorkerResult [0/2] 682s Rank 0: assembler memory usage: 156448 KiB 682s Date: Wed Jul 24 11:25:57 2024 682s Rank 0 FusionTaskCreator [2/2] 682s Statistics: all paths: 1 eliminated during fusing: 0 682s Rank 0: assembler memory usage: 156448 KiB 682s VirtualProcessor: completed jobs: 2 682s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 682s Rank 0: starting clear step. cycleNumber= 2 691s Rank 0 adding 0 new fusions 691s Rank 0 cleared, 1 paths 691s Rank 0 is distributing fusions [1/1] 691s Rank 0: assembler memory usage: 152348 KiB 691s Date: Wed Jul 24 11:26:07 2024 691s Rank 0 is distributing fusions [1/1] (completed) 691s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 691s Rank 0: assembler memory usage: 156448 KiB 691s Date: Wed Jul 24 11:26:07 2024 691s Rank 0 JoinerTaskCreator assignNextTask [0/2] 691s Rank 0: assembler memory usage: 156448 KiB 691s Date: Wed Jul 24 11:26:07 2024 691s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 691s Rank 0: assembler memory usage: 156448 KiB 691s Date: Wed Jul 24 11:26:07 2024 691s Rank 0 JoinerTaskCreator [2/2] 691s Statistics: all paths: 1 eliminated during joining: 0 691s Rank 0: assembler memory usage: 156448 KiB 691s Date: Wed Jul 24 11:26:07 2024 691s VirtualProcessor: completed jobs: 2 691s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 700s Rank 0 adding 0 new fusions 700s Rank 0 cleared, 1 paths 700s Rank 0: starting distribution step 700s Rank 0 is distributing fusions [1/1] 700s Rank 0: assembler memory usage: 152348 KiB 700s Date: Wed Jul 24 11:26:16 2024 700s Rank 0 is distributing fusions [1/1] (completed) 700s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 700s Rank 0: assembler memory usage: 156448 KiB 700s Date: Wed Jul 24 11:26:16 2024 700s Rank 0 cycleNumber= 2 700s 700s *** 700s Step: Merging of redundant paths 700s Date: Wed Jul 24 11:26:16 2024 700s Elapsed time: 46 seconds 700s Since beginning: 1 minutes, 46 seconds 700s *** 700s 700s 700s Rank 0 appended 1 elements 700s 700s *** 700s Step: Generation of contigs 700s Date: Wed Jul 24 11:26:16 2024 700s Elapsed time: 0 seconds 700s Since beginning: 1 minutes, 46 seconds 700s *** 700s 700s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 700s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 700s Rank 0 ineligibleObjects: 0/972 (0.00%) 700s Rank 0: assembler memory usage: 156448 KiB 700s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 700s Rank 0 finished gathering scaffold links. 700s Rank 0 will write 1 contig lengths 700s Rank 0 will solve the scaffolding problem. 700s Welcome to GreedySolver v1.0 700s 1 vertices; 0 edges 700s 1 contigs >= 500 700s Edges in solution: 0 700s 700s Conflict statistics: 700s 1 scaffolds, 1 >= 500 700s Total: 1000 nucleotides 700s 700s *** 700s Step: Scaffolding of contigs 700s Date: Wed Jul 24 11:26:16 2024 700s Elapsed time: 0 seconds 700s Since beginning: 1 minutes, 46 seconds 700s *** 700s 700s Rank 0 syncing with master 700s 700s *** 700s Step: Counting sequences to search 700s Date: Wed Jul 24 11:26:16 2024 700s Elapsed time: 0 seconds 700s Since beginning: 1 minutes, 46 seconds 700s *** 700s 700s 700s Rank 0 will add colors, 0 sequences in 0 files to process 700s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 710s 710s *** 710s Step: Graph coloring 710s Date: Wed Jul 24 11:26:26 2024 710s Elapsed time: 10 seconds 710s Since beginning: 1 minutes, 56 seconds 710s *** 710s 710s 710s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 710s Rank 0 shares its counts 710s Rank 0 computing contig abundances [1/1] [1/972] 710s Rank 0 computing contig abundances [1/1] [972/972] 710s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 710s 710s *** 710s Step: Counting contig biological abundances 710s Date: Wed Jul 24 11:26:26 2024 710s Elapsed time: 0 seconds 710s Since beginning: 1 minutes, 56 seconds 710s *** 710s 710s 710s Rank 0 colored the graph with 0 real colors using 1 virtual colors 710s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 710s 710s *** 710s Step: Counting sequence biological abundances 710s Date: Wed Jul 24 11:26:26 2024 710s Elapsed time: 0 seconds 710s Since beginning: 1 minutes, 56 seconds 710s *** 710s 710s 710s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 710s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 719s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 719s 719s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 719s Rank 0 is starting taxon syncing across the compute tribe. 719s 719s *** 719s Step: Loading taxons 719s Date: Wed Jul 24 11:26:35 2024 719s Elapsed time: 9 seconds 719s Since beginning: 2 minutes, 5 seconds 719s *** 719s 719s Rank 0 synced taxons across the grid with 1 poor slaves. 719s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 719s Rank 0 has 0 taxons after syncing with master 729s 729s 729s *** 729s Step: Loading tree 729s Date: Wed Jul 24 11:26:45 2024 729s Elapsed time: 10 seconds 729s Since beginning: 2 minutes, 15 seconds 729s *** 729s 738s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 739s 739s Rank 0: counting ontology terms in the graph... 748s Rank 0: 0 have some biological signal 748s Number of dereferenced alternate handles: 0 748s Number of k-mer observations with gene ontology terms: 0 748s Rank 0: synced ontology term profiles with master 748s Rank 0: synchronization is complete! 748s Rank 0: ontology terms with biological signal: 0 748s Populated recursive values... 748s Gene ontology terms without depth information: 0 748s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 748s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 748s 748s *** 748s Step: Processing gene ontologies 748s Date: Wed Jul 24 11:27:04 2024 748s Elapsed time: 19 seconds 748s Since beginning: 2 minutes, 34 seconds 748s *** 748s 748s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 748s [GenomeNeighbourhood] in final list: 0 748s 748s *** 748s Step: Computing neighbourhoods 748s Date: Wed Jul 24 11:27:04 2024 748s Elapsed time: 0 seconds 748s Since beginning: 2 minutes, 34 seconds 748s *** 748s 748s Contigs >= 100 nt 748s Number: 1 748s Total length: 1000 748s Average: 1000 748s N50: 1000 748s Median: 1000 748s Largest: 1000 748s Contigs >= 500 nt 748s Number: 1 748s Total length: 1000 748s Average: 1000 748s N50: 1000 748s Median: 1000 748s Largest: 1000 748s Scaffolds >= 100 nt 748s Number: 1 748s Total length: 1000 748s Average: 1000 748s N50: 1000 748s Median: 1000 748s Largest: 1000 748s Scaffolds >= 500 nt 748s Number: 1 748s Total length: 1000 748s Average: 1000 748s N50: 1000 748s Median: 1000 748s Largest: 1000 748s 748s Rank 0 wrote RayOutput/Contigs.fasta 748s Rank 0 wrote RayOutput/Scaffolds.fasta 748s Check for RayOutput/* 748s 748s 748s 748s ************************************************** 748s This program comes with ABSOLUTELY NO WARRANTY. 748s This is free software, and you are welcome to redistribute it 748s under certain conditions; see "LICENSE.txt" for details. 748s ************************************************** 748s 748s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 748s Centre de recherche en infectiologie de l'Université Laval 748s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 748s http://denovoassembler.sf.net/ 748s 748s References to cite: 748s 748s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 748s Ray Meta: scalable de novo metagenome assembly and profiling. 748s Genome Biology (BioMed Central Ltd). 748s 13:R122, Published: 22 December 2012 748s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 748s 748s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 748s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 748s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 748s November 2010, Volume 17, Issue 11, Pages 1519-1533. 748s http://dx.doi.org/doi:10.1089/cmb.2009.0238 748s 748s Ray version 2.3.1 748s License for Ray: GNU General Public License version 3 748s RayPlatform version: 2.0.1 748s License for RayPlatform: GNU Lesser General Public License version 3 748s 748s MAXKMERLENGTH: 32 748s Maximum coverage depth stored by CoverageDepth: 4294967295 748s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 748s FORCE_PACKING = n 748s ASSERT = n 748s HAVE_LIBZ = y 748s HAVE_LIBBZ2 = y 748s PROFILER_COLLECT = n 748s MINIRANKS = y 748s CLOCK_GETTIME = n 748s __linux__ = y 748s _MSC_VER = n 748s __GNUC__ = y 748s RAY_32_BITS = y 748s RAY_64_BITS = n 748s MPI standard version: MPI 3.1 748s MPI library: Open-MPI 4.1.6 748s Compiler: GNU gcc/g++ 13.2.0 748s MPI I/O: n 748s 748s 748s -k (to set the k-mer size) 748s Value: 31 748s 748s 748s Paired library # 0 748s -p (paired-end sequences) 748s Left sequences: ecoli_1K_1.fq 748s Right sequences: ecoli_1K_2.fq 748s Average length: automatic detection 748s Standard deviation: automatic detection 748s 748s Ray command: 748s mpiexec -n 2 Ray \ 748s -k \ 748s 31 \ 748s -p \ 748s ecoli_1K_1.fq \ 748s ecoli_1K_2.fq \ 748s -o \ 748s test3 748s 748s Rank 0 wrote test3/RayCommand.txt 748s 748s k-mer length: 31 748s Rank 1: assembler memory usage: 41160 KiB 748s Rank 0: assembler memory usage: 41164 KiB 748s Rank 1: assembler memory usage: 106832 KiB 748s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 2269 748s Rank 0: assembler memory usage: 106836 KiB 748s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 2268 748s Rank 0: testing the network, please wait... 748s 748s Rank 1 is testing the network [0/1000] 748s Rank 0 is testing the network [0/1000] 748s Rank 1 is testing the network [1000/1000] 748s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 748s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 7 microseconds (10^-6 seconds) 748s Rank 0 is testing the network [1000/1000] 748s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 748s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 7 microseconds (10^-6 seconds) 748s 748s Rank 0 wrote test3/NetworkTest.txt 748s 748s 748s *** 748s Step: Network testing 748s Date: Wed Jul 24 11:27:04 2024 748s Elapsed time: 0 seconds 748s Since beginning: 0 seconds 748s *** 748s 748s 748s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 748s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 748s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 748s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 748s Rank 0 wrote test3/NumberOfSequences.txt 748s Rank 0 wrote test3/SequencePartition.txt 748s 748s *** 748s Step: Counting sequences to assemble 748s Date: Wed Jul 24 11:27:04 2024 748s Elapsed time: 0 seconds 748s Since beginning: 0 seconds 748s *** 748s 748s 748s Rank 1 is loading sequence reads 748s Rank 1 : partition is [2054;4107], 2054 sequence reads 748s Rank 0 is loading sequence reads 748s Rank 0 : partition is [0;2053], 2054 sequence reads 748s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 748s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 748s Rank 1 has 0 sequence reads 748s Rank 0 has 0 sequence reads 748s Rank 0: assembler memory usage: 111568 KiB 748s Rank 1: assembler memory usage: 111440 KiB 748s Rank 1 has 2054 sequence reads (completed) 748s Rank 0 has 2054 sequence reads (completed) 748s 748s *** 748s Step: Sequence loading 748s Date: Wed Jul 24 11:27:04 2024 748s Elapsed time: 0 seconds 748s Since beginning: 0 seconds 748s *** 748s 748s 748s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 748s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 748s Rank 0 created its Bloom filter 748s Rank 0 is counting k-mers in sequence reads [1/2054] 748s Rank 1 created its Bloom filter 748s Rank 1 is counting k-mers in sequence reads [1/2054] 749s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 749s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 749s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 749s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 749s 749s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 749s Rank 1 destroyed its Bloom filter 749s Rank 1 has 922 k-mers (completed) 749s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 749s 749s *** 749s Step: K-mer counting 749s Date: Wed Jul 24 11:27:05 2024 749s Elapsed time: 1 seconds 749s Since beginning: 1 seconds 749s *** 749s 749s 749s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 749s Rank 0 destroyed its Bloom filter 749s Rank 0 has 1032 k-mers (completed) 749s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 749s Rank 0: assembler memory usage: 110844 KiB 749s Rank 1: assembler memory usage: 110828 KiB 758s 758s 758s Rank 0: the minimum coverage is 3 758s Rank 0: the peak coverage is 3 758s Warning: no peak observed in the k-mer coverage distribution. 758s to deal with the sequencing error rate, try to lower the k-mer length (-k) 758s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 758s 758s *** 758s Step: Coverage distribution analysis 758s Date: Wed Jul 24 11:27:14 2024 758s Elapsed time: 9 seconds 758s Since beginning: 10 seconds 758s *** 758s 758s 758s 758s Rank 0 is adding edges [1/2054] 758s Rank 1 is adding edges [1/2054] 759s Rank 1 is adding edges [2054/2054] (completed) 759s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 759s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 759s Rank 0 is adding edges [2054/2054] (completed) 759s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 759s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 759s 759s *** 759s Step: Graph construction 759s Date: Wed Jul 24 11:27:15 2024 759s Elapsed time: 1 seconds 759s Since beginning: 11 seconds 759s *** 759s 759s 759s Rank 1 has 922 vertices (completed) 759s Rank 0 has 1032 vertices (completed) 759s Rank 0: assembler memory usage: 110844 KiB 759s Rank 1: assembler memory usage: 110828 KiB 768s Rank 1 is purging edges [1/922] 768s Rank 0 is purging edges [1/1032] 768s Rank 1 is purging edges [922/922] (completed) 768s Rank 1: assembler memory usage: 110960 KiB 768s VirtualProcessor: completed jobs: 922 768s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 768s Rank 0 is purging edges [1032/1032] (completed) 768s Rank 0: assembler memory usage: 110976 KiB 768s VirtualProcessor: completed jobs: 1032 768s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 777s Rank 0 wrote test3/degreeDistribution.txt 777s 777s *** 777s Step: Null edge purging 777s Rank 1 is selecting optimal read markers [1/2054] 777s Date: Wed Jul 24 11:27:33 2024 777s Elapsed time: 18 seconds 777s Since beginning: 29 seconds 777s *** 777s 777s 777s Rank 0 is selecting optimal read markers [1/2054] 777s Rank 0: assembler memory usage: 110976 KiB 777s Rank 1: assembler memory usage: 110960 KiB 778s Rank 1 is selecting optimal read markers [2054/2054] (completed) 778s Rank 1: peak number of workers: 1121, maximum: 32768 778s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 778s Rank 1: assembler memory usage: 119160 KiB 778s Rank 1: Freeing unused assembler memory: 4096 KiB freed 778s Rank 1: assembler memory usage: 115060 KiB 778s Rank 0 is selecting optimal read markers [2054/2054] (completed) 778s Rank 0: peak number of workers: 1135, maximum: 32768 778s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 778s Rank 0: assembler memory usage: 119176 KiB 778s Rank 0: Freeing unused assembler memory: 4096 KiB freed 778s Rank 0: assembler memory usage: 115076 KiB 778s Rank 1: memory usage for optimal read markers= 4096 KiB 778s 778s *** 778s Step: Selection of optimal read markers 778s Date: Wed Jul 24 11:27:34 2024 778s Elapsed time: 1 seconds 778s Since beginning: 30 seconds 778s *** 778s 778s 778s Rank 0: memory usage for optimal read markers= 4096 KiB 778s Rank 1 is creating seeds [1/922] 778s Rank 1: assembler memory usage: 115060 KiB 778s Rank 0 is creating seeds [1/1032] 778s Rank 0: assembler memory usage: 115076 KiB 787s Rank 1 has 1 seeds 787s Rank 1 is creating seeds [922/922] (completed) 787s Rank 1: peak number of workers: 916, maximum: 32768 787s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 787s Rank 1 runtime statistics for seeding algorithm: 787s Rank 1 Skipped paths because of dead end for head: 0 787s Rank 1 Skipped paths because of dead end for tail: 0 787s Rank 1 Skipped paths because of two dead ends: 0 787s Rank 1 Skipped paths because of bubble weak component: 0 787s Rank 1 Skipped paths because of short length: 921 787s Rank 1 Skipped paths because of bad ownership: 0 787s Rank 1 Skipped paths because of low coverage: 0 787s Rank 1 Eligible paths: 1 787s Rank 1: assembler memory usage: 115456 KiB 787s Rank 0 has 0 seeds 787s Rank 0 is creating seeds [1032/1032] (completed) 787s Rank 0: peak number of workers: 998, maximum: 32768 787s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 787s Rank 0 runtime statistics for seeding algorithm: 787s Rank 0 Skipped paths because of dead end for head: 0 787s Rank 0 Skipped paths because of dead end for tail: 0 787s Rank 0 Skipped paths because of two dead ends: 0 787s Rank 0 Skipped paths because of bubble weak component: 0 787s Rank 0 Skipped paths because of short length: 1031 787s Rank 0 Skipped paths because of bad ownership: 1 787s Rank 0 Skipped paths because of low coverage: 0 787s Rank 0 Eligible paths: 0 787s Rank 1 has 1 seeds to register. 787s Rank 0: assembler memory usage: 115604 KiB 787s Rank 0 registered -1/0 787s Rank 0 registered its seeds 787s Rank 1 registered 0/1 787s VirtualProcessor: completed jobs: 0 787s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 787s Rank 1 registered 0/1 787s Rank 1 registered its seeds 787s VirtualProcessor: completed jobs: 0 787s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 797s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 797s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 807s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 807s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 807s Rank 0 merged its seeds: 0 seeds -> 0 seeds 807s Rank 1 merged its seeds: 1 seeds -> 1 seeds 807s 807s *** 807s Step: Detection of assembly seeds 807s Date: Wed Jul 24 11:28:03 2024 807s Elapsed time: 29 seconds 807s Since beginning: 59 seconds 807s *** 807s 807s 807s Rank 0 detected 0 library lengths 807s Rank 0 is calculating library lengths [0/0] (completed) 807s Rank 0: peak number of workers: 0, maximum: 32768 807s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 807s Rank 0: assembler memory usage: 115604 KiB 807s Rank 1 is calculating library lengths [1/1] 807s Rank 1 detected 1737 library lengths 807s Rank 1 is calculating library lengths [1/1] (completed) 807s Rank 1: peak number of workers: 1, maximum: 32768 807s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7983 virtual messages generated 7983 real messages (100%) 807s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 807s Rank 1: assembler memory usage: 148228 KiB 807s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 807s 807s Mode= 2 signalAverage= 9 807s CURRENT IS NOISE, 244 807s GOT HIT 212 807s 807s 807s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 807s 807s *** 807s Step: Estimation of outer distances for paired reads 807s Date: Wed Jul 24 11:28:03 2024 807s Elapsed time: 0 seconds 807s Since beginning: 59 seconds 807s *** 807s 807s 807s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 807s Rank 0 is extending seeds [0/0] (completed) 807s Rank 0 extended 0 seeds out of 0 (0.00%) 807s Rank 0: assembler memory usage: 115604 KiB 808s Rank 1 traversed 1000 nucleotide symbols 808s Rank 1: assembler memory usage: 152328 KiB 808s Rank 1 is extending seeds [1/1] (completed) 808s Rank 1 extended 1 seeds out of 1 (100.00%) 808s Rank 1: assembler memory usage: 148228 KiB 808s Rank 0 starting fusions 808s 808s *** 808s Step: Bidirectional extension of seeds 808s Date: Wed Jul 24 11:28:04 2024 808s Elapsed time: 1 seconds 808s Since beginning: 1 minutes, 0 seconds 808s *** 808s 808s 808s Rank 0: starting clear step. cycleNumber= 0 817s Rank 0 adding 0 new fusions 817s Rank 0 cleared, 0 paths 817s Rank 1 adding 0 new fusions 817s Rank 1 cleared, 1 paths 817s Rank 1 is distributing fusions [1/1] 817s Rank 0: starting distribution step 817s Rank 0 is distributing fusions [0/0] (completed) 817s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 817s Rank 1: assembler memory usage: 148228 KiB 817s Date: Wed Jul 24 11:28:13 2024 817s Rank 0: assembler memory usage: 115604 KiB 817s Date: Wed Jul 24 11:28:13 2024 817s Rank 1 is distributing fusions [1/1] (completed) 817s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 817s Rank 1: assembler memory usage: 152328 KiB 817s Date: Wed Jul 24 11:28:13 2024 817s Rank 0 tells others to compute fusions. 817s Rank 0 FusionTaskCreator [0/0] 817s Statistics: all paths: 0 eliminated during fusing: 0 817s Rank 1 FusionTaskCreator assignNextTask [0/2] 817s Rank 1: assembler memory usage: 152328 KiB 817s Date: Wed Jul 24 11:28:13 2024 817s Rank 0: assembler memory usage: 119704 KiB 817s VirtualProcessor: completed jobs: 0 817s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 817s Rank 1 FusionTaskCreator processWorkerResult [0/2] 817s Rank 1: assembler memory usage: 152328 KiB 817s Date: Wed Jul 24 11:28:13 2024 817s Rank 1 FusionTaskCreator [2/2] 817s Statistics: all paths: 1 eliminated during fusing: 0 817s Rank 1: assembler memory usage: 152328 KiB 817s VirtualProcessor: completed jobs: 2 817s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10893 virtual messages generated 10893 real messages (100%) 817s Rank 0: starting clear step. cycleNumber= 1 826s Rank 1 adding 0 new fusions 826s Rank 1 cleared, 1 paths 826s Rank 0 adding 0 new fusions 826s Rank 0 cleared, 0 paths 826s Rank 0 is distributing fusions [0/0] (completed) 826s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 826s Rank 1 is distributing fusions [1/1] 826s Rank 0: assembler memory usage: 115604 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s Rank 1: assembler memory usage: 148228 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s Rank 1 is distributing fusions [1/1] (completed) 826s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 826s Rank 1: assembler memory usage: 152328 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s Rank 0 JoinerTaskCreator [0/0] 826s Statistics: all paths: 0 eliminated during joining: 0 826s Rank 1 JoinerTaskCreator assignNextTask [0/2] 826s Rank 0: assembler memory usage: 119704 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s VirtualProcessor: completed jobs: 0 826s Rank 1: assembler memory usage: 152328 KiB 826s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 826s Date: Wed Jul 24 11:28:22 2024 826s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 826s Rank 1: assembler memory usage: 152328 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s Rank 1 JoinerTaskCreator [2/2] 826s Statistics: all paths: 1 eliminated during joining: 0 826s Rank 1: assembler memory usage: 152328 KiB 826s Date: Wed Jul 24 11:28:22 2024 826s VirtualProcessor: completed jobs: 2 826s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13803 virtual messages generated 13803 real messages (100%) 836s Rank 0 adding 0 new fusions 836s Rank 0 cleared, 0 paths 836s Rank 0: starting distribution step 836s Rank 0 is distributing fusions [0/0] (completed) 836s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 836s Rank 1 adding 0 new fusions 836s Rank 1 cleared, 1 paths 836s Rank 1 is distributing fusions [1/1] 836s Rank 0: assembler memory usage: 115604 KiB 836s Date: Wed Jul 24 11:28:32 2024 836s Rank 1: assembler memory usage: 148228 KiB 836s Date: Wed Jul 24 11:28:32 2024 836s Rank 1 is distributing fusions [1/1] (completed) 836s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 836s Rank 1: assembler memory usage: 152328 KiB 836s Date: Wed Jul 24 11:28:32 2024 836s Rank 1 FusionTaskCreator assignNextTask [0/2] 836s Rank 0 tells others to compute fusions. 836s Rank 0 FusionTaskCreator [0/0] 836s Statistics: all paths: 0 eliminated during fusing: 0 836s Rank 1: assembler memory usage: 152328 KiB 836s Date: Wed Jul 24 11:28:32 2024 836s Rank 0: assembler memory usage: 119704 KiB 836s VirtualProcessor: completed jobs: 0 836s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 836s Rank 1 FusionTaskCreator processWorkerResult [0/2] 836s Rank 1: assembler memory usage: 152328 KiB 836s Date: Wed Jul 24 11:28:32 2024 836s Rank 1 FusionTaskCreator [2/2] 836s Statistics: all paths: 1 eliminated during fusing: 0 836s Rank 1: assembler memory usage: 152328 KiB 836s VirtualProcessor: completed jobs: 2 836s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16713 virtual messages generated 16713 real messages (100%) 836s Rank 0: starting clear step. cycleNumber= 2 845s Rank 0 adding 0 new fusions 845s Rank 0 cleared, 0 paths 845s Rank 1 adding 0 new fusions 845s Rank 1 cleared, 1 paths 845s Rank 1 is distributing fusions [1/1] 845s Rank 0 is distributing fusions [0/0] (completed) 845s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 845s Rank 1: assembler memory usage: 148228 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s Rank 0: assembler memory usage: 115604 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s Rank 1 is distributing fusions [1/1] (completed) 845s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 845s Rank 1: assembler memory usage: 152328 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s Rank 1 JoinerTaskCreator assignNextTask [0/2] 845s Rank 0 JoinerTaskCreator [0/0] 845s Statistics: all paths: 0 eliminated during joining: 0 845s Rank 1: assembler memory usage: 152328 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s Rank 0: assembler memory usage: 119704 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s VirtualProcessor: completed jobs: 0 845s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 845s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 845s Rank 1: assembler memory usage: 152328 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s Rank 1 JoinerTaskCreator [2/2] 845s Statistics: all paths: 1 eliminated during joining: 0 845s Rank 1: assembler memory usage: 152328 KiB 845s Date: Wed Jul 24 11:28:41 2024 845s VirtualProcessor: completed jobs: 2 845s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19623 virtual messages generated 19623 real messages (100%) 854s Rank 0 adding 0 new fusions 854s Rank 0 cleared, 0 paths 854s Rank 1 adding 0 new fusions 854s Rank 1 cleared, 1 paths 854s Rank 1 is distributing fusions [1/1] 854s Rank 0: starting distribution step 854s Rank 0 is distributing fusions [0/0] (completed) 854s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 854s Rank 1: assembler memory usage: 148228 KiB 854s Date: Wed Jul 24 11:28:50 2024 854s Rank 0: assembler memory usage: 115604 KiB 854s Date: Wed Jul 24 11:28:50 2024 854s Rank 1 is distributing fusions [1/1] (completed) 854s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 854s Rank 0 cycleNumber= 2 854s 854s *** 854s Step: Merging of redundant paths 854s Date: Wed Jul 24 11:28:50 2024 854s Elapsed time: 46 seconds 854s Since beginning: 1 minutes, 46 seconds 854s *** 854s Rank 1: assembler memory usage: 152328 KiB 854s Date: Wed Jul 24 11:28:50 2024 854s 854s 854s Rank 0 appended 0 elements 854s Rank 1 appended 1 elements 854s 854s *** 854s Step: Generation of contigs 854s Date: Wed Jul 24 11:28:50 2024 854s Elapsed time: 0 seconds 854s Since beginning: 1 minutes, 46 seconds 854s *** 854s 854s Rank 0 finished gathering scaffold links. 854s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 854s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 854s Rank 0 ineligibleObjects: 0/970 (0.00%) 854s Rank 1: assembler memory usage: 152328 KiB 854s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 854s Rank 1 finished gathering scaffold links. 854s Rank 0 will write 1 contig lengths 854s Rank 0 will solve the scaffolding problem. 854s Welcome to GreedySolver v1.0 854s 1 vertices; 0 edges 854s 1 contigs >= 500 854s Edges in solution: 0 854s 854s Conflict statistics: 854s 1 scaffolds, 1 >= 500 854s Total: 1000 nucleotides 854s 854s *** 854s Step: Scaffolding of contigs 854s Date: Wed Jul 24 11:28:50 2024 854s Elapsed time: 0 seconds 854s Since beginning: 1 minutes, 46 seconds 854s *** 854s 854s Rank 1 syncing with master 854s Rank 1 will add colors, 0 sequences in 0 files to process 854s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 854s Rank 0 syncing with master 854s 854s *** 854s Step: Counting sequences to search 854s Date: Wed Jul 24 11:28:50 2024 854s Elapsed time: 0 seconds 854s Since beginning: 1 minutes, 46 seconds 854s *** 854s 854s 854s Rank 0 will add colors, 0 sequences in 0 files to process 854s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 865s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 865s 865s *** 865s Step: Graph coloring 865s Date: Wed Jul 24 11:29:01 2024 865s Elapsed time: 11 seconds 865s Since beginning: 1 minutes, 57 seconds 865s *** 865s 865s 865s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 865s Rank 0 shares its counts 865s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 865s Rank 1 computing contig abundances [1/1] [1/970] 865s Rank 1 computing contig abundances [1/1] [970/970] 865s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 865s 865s *** 865s Step: Counting contig biological abundances 865s Date: Wed Jul 24 11:29:01 2024 865s Elapsed time: 0 seconds 865s Since beginning: 1 minutes, 57 seconds 865s *** 865s 865s 865s Rank 0 colored the graph with 0 real colors using 1 virtual colors 865s Rank 1 colored the graph with 0 real colors using 1 virtual colors 865s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 865s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 865s 865s *** 865s Step: Counting sequence biological abundances 865s Date: Wed Jul 24 11:29:01 2024 865s Elapsed time: 0 seconds 865s Since beginning: 1 minutes, 57 seconds 865s *** 865s 865s 865s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 865s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 865s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 865s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 874s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 874s 874s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 874s 874s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 874s Rank 0 is starting taxon syncing across the compute tribe. 874s 874s *** 874s Step: Loading taxons 874s Date: Wed Jul 24 11:29:10 2024 874s Elapsed time: 9 seconds 874s Since beginning: 2 minutes, 6 seconds 874s *** 874s 874s Rank 0 synced taxons across the grid with 2 poor slaves. 874s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 874s Rank 0 has 0 taxons after syncing with master 874s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 874s Rank 1 has 0 taxons after syncing with master 884s 885s 885s 885s *** 885s Step: Loading tree 885s Date: Wed Jul 24 11:29:21 2024 885s Elapsed time: 11 seconds 885s Since beginning: 2 minutes, 17 seconds 885s *** 885s 894s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 894s 894s Rank 0: counting ontology terms in the graph... 894s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 894s 894s Rank 1: counting ontology terms in the graph... 904s Rank 1: 0 have some biological signal 904s Number of dereferenced alternate handles: 0 904s Number of k-mer observations with gene ontology terms: 0 904s Rank 0: 0 have some biological signal 904s Number of dereferenced alternate handles: 0 904s Number of k-mer observations with gene ontology terms: 0 904s Rank 0: synced ontology term profiles with master 904s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 904s Rank 1: synced ontology term profiles with master 904s Rank 0: synchronization is complete! 904s Rank 0: ontology terms with biological signal: 0 904s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 904s Populated recursive values... 904s Gene ontology terms without depth information: 0 904s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 904s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 904s 904s *** 904s Step: Processing gene ontologies 904s Date: Wed Jul 24 11:29:40 2024 904s Elapsed time: 19 seconds 904s Since beginning: 2 minutes, 36 seconds 904s *** 904s 904s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 904s [GenomeNeighbourhood] in final list: 0 904s 904s *** 904s Step: Computing neighbourhoods 904s Date: Wed Jul 24 11:29:40 2024 904s Elapsed time: 0 seconds 904s Since beginning: 2 minutes, 36 seconds 904s *** 904s 904s Contigs >= 100 nt 904s Number: 1 904s Total length: 1000 904s Average: 1000 904s N50: 1000 904s Median: 1000 904s Largest: 1000 904s Contigs >= 500 nt 904s Number: 1 904s Total length: 1000 904s Average: 1000 904s N50: 1000 904s Median: 1000 904s Largest: 1000 904s Scaffolds >= 100 nt 904s Number: 1 904s Total length: 1000 904s Average: 1000 904s N50: 1000 904s Median: 1000 904s Largest: 1000 904s Scaffolds >= 500 nt 904s Number: 1 904s Total length: 1000 904s Average: 1000 904s N50: 1000 904s Median: 1000 904s Largest: 1000 904s 904s Rank 0 wrote test3/Contigs.fasta 904s Rank 0 wrote test3/Scaffolds.fasta 904s Check for test3/* 904s 904s 905s autopkgtest [11:29:41]: test run-unit-test: -----------------------] 909s autopkgtest [11:29:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 909s run-unit-test PASS 913s autopkgtest [11:29:49]: @@@@@@@@@@@@@@@@@@@@ summary 913s run-unit-test PASS