0s autopkgtest [16:09:16]: starting date and time: 2025-03-15 16:09:16+0000 0s autopkgtest [16:09:16]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:09:16]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.z_ms2yx_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-24.secgroup --name adt-plucky-arm64-ray-20250315-160916-juju-7f2275-prod-proposed-migration-environment-15-fe550483-345a-4f21-9f94-93fc04805218 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 144s autopkgtest [16:11:40]: testbed dpkg architecture: arm64 144s autopkgtest [16:11:40]: testbed apt version: 2.9.33 145s autopkgtest [16:11:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 145s autopkgtest [16:11:41]: testbed release detected to be: None 146s autopkgtest [16:11:42]: updating testbed package index (apt update) 146s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 146s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 147s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 147s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 147s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 148s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 148s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 148s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 148s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 148s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 149s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 149s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 149s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 149s Fetched 1078 kB in 3s (348 kB/s) 150s Reading package lists... 151s + lsb_release --codename --short 151s + RELEASE=plucky 151s + cat 151s + [ plucky != trusty ] 151s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Calculating upgrade... 152s Calculating upgrade... 153s The following packages will be upgraded: 153s pinentry-curses python3-jinja2 strace 153s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 647 kB of archives. 153s After this operation, 11.3 kB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 154s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 155s Fetched 647 kB in 2s (342 kB/s) 155s (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 ... 117701 files and directories currently installed.) 155s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 155s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 155s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 155s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 156s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 156s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 156s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 156s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 156s Setting up strace (6.13+ds-1ubuntu1) ... 156s Processing triggers for man-db (2.13.0-1) ... 157s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 157s + /usr/lib/apt/apt-helper analyze-pattern ?true 157s + uname -r 157s + sed s/\./\\./g 157s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 157s + tail -n+2 157s + apt list ?obsolete 157s + cut -d/ -f1 157s + grep -v ^linux-.*6\.14\.0-10-generic.* 157s + obsolete_pkgs=linux-headers-6.11.0-8-generic 157s linux-headers-6.11.0-8 157s linux-image-6.11.0-8-generic 157s linux-modules-6.11.0-8-generic 157s linux-tools-6.11.0-8-generic 157s linux-tools-6.11.0-8 157s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 157s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Solving dependencies... 159s The following packages will be REMOVED: 159s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 159s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 159s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 159s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 159s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 159s After this operation, 267 MB disk space will be freed. 159s (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 ... 117701 files and directories currently installed.) 159s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 159s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 159s Removing libpython3.12t64:arm64 (3.12.9-1) ... 159s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 159s Removing libnsl2:arm64 (1.3.0-3build3) ... 159s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 159s Removing libunwind8:arm64 (1.6.2-3.1) ... 159s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 160s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 162s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 162s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 162s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 162s /etc/kernel/postrm.d/initramfs-tools: 162s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 162s /etc/kernel/postrm.d/zz-flash-kernel: 162s flash-kernel: Kernel 6.11.0-8-generic has been removed. 162s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 163s /etc/kernel/postrm.d/zz-update-grub: 163s Sourcing file `/etc/default/grub' 163s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 163s Generating grub configuration file ... 163s Found linux image: /boot/vmlinuz-6.14.0-10-generic 163s Found initrd image: /boot/initrd.img-6.14.0-10-generic 163s Warning: os-prober will not be executed to detect other bootable partitions. 163s Systems on them will not be added to the GRUB boot configuration. 163s Check GRUB_DISABLE_OS_PROBER documentation entry. 163s Adding boot menu entry for UEFI Firmware Settings ... 163s done 164s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 164s Processing triggers for libc-bin (2.41-1ubuntu1) ... 164s (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 ... 81650 files and directories currently installed.) 164s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 164s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 164s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 164s + grep -q trusty /etc/lsb-release 164s + [ ! -d /usr/share/doc/unattended-upgrades ] 164s + [ ! -d /usr/share/doc/lxd ] 164s + [ ! -d /usr/share/doc/lxd-client ] 164s + [ ! -d /usr/share/doc/snapd ] 164s + type iptables 164s + cat 164s + chmod 755 /etc/rc.local 164s + . /etc/rc.local 164s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 164s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 164s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 164s + uname -m 164s + [ aarch64 = ppc64le ] 164s + [ -d /run/systemd/system ] 164s + systemd-detect-virt --quiet --vm 164s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 164s + cat 164s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 164s + echo COMPRESS=lz4 164s autopkgtest [16:12:00]: upgrading testbed (apt dist-upgrade and autopurge) 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s Entering ResolveByKeep 167s 167s Calculating upgrade... 167s The following packages will be upgraded: 167s libc-bin libc-dev-bin libc6 libc6-dev locales 168s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 9530 kB of archives. 168s After this operation, 0 B of additional disk space will be used. 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 170s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 170s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 173s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 180s Preconfiguring packages ... 180s Fetched 9530 kB in 12s (793 kB/s) 180s (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 ... 81647 files and directories currently installed.) 180s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 180s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 180s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 180s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 180s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 180s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 181s Setting up libc6:arm64 (2.41-1ubuntu2) ... 181s (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 ... 81647 files and directories currently installed.) 181s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 181s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 181s Setting up libc-bin (2.41-1ubuntu2) ... 181s (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 ... 81647 files and directories currently installed.) 181s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 181s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 181s Setting up locales (2.41-1ubuntu2) ... 182s Generating locales (this might take a while)... 184s en_US.UTF-8... done 184s Generation complete. 184s Setting up libc-dev-bin (2.41-1ubuntu2) ... 184s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 184s Processing triggers for man-db (2.13.0-1) ... 185s Processing triggers for systemd (257.3-1ubuntu3) ... 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 187s Solving dependencies... 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s autopkgtest [16:12:24]: rebooting testbed after setup commands that affected boot 214s autopkgtest [16:12:50]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 217s autopkgtest [16:12:53]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (dsc) [2123 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (tar) [450 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ray 2.3.1-9 (diff) [213 kB] 222s gpgv: Signature made Mon Dec 2 16:02:51 2024 UTC 222s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 222s gpgv: issuer "tille@debian.org" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-9.dsc: no acceptable signature found 222s autopkgtest [16:12:58]: testing package ray version 2.3.1-9 223s autopkgtest [16:12:59]: build not needed 223s autopkgtest [16:12:59]: test run-unit-test: preparing testbed 223s Reading package lists... 224s Building dependency tree... 224s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 226s The following NEW packages will be installed: 226s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 226s libamd-comgr2 libamdhip64-5 libblas3 libcairo2 libdatrie1 libdeflate0 226s libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 libgfortran5 libgomp1 226s libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 226s libhwloc15 libibmad5 libibumad3 libice6 libjbig0 libjpeg-turbo8 libjpeg8 226s liblapack3 liblerc4 libllvm17t64 libmunge2 libopenmpi40 libpango-1.0-0 226s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 226s libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 libsm6 libtcl8.6 226s libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 libxcb-render0 226s libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6t64 226s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 226s ray ray-doc ray-extra unzip x11-common xdg-utils zip 226s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 93.7 MB of archives. 226s After this operation, 312 MB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 228s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 228s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 228s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 228s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 261s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 281s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 281s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 282s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 294s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 294s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 294s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 294s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 294s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 294s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 295s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 295s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 295s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 295s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB] 296s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 296s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 297s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 297s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 297s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 298s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 298s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 298s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 298s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 298s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 298s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 301s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 302s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 302s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 302s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 302s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 302s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 302s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 303s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB] 303s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB] 303s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 304s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 307s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 308s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 308s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 308s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 308s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 308s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 308s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 308s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 308s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 308s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 309s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 309s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 310s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 310s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 310s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 310s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 311s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 311s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-common all 5.0.7-1 [97.9 kB] 311s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-bin arm64 5.0.7-1 [195 kB] 311s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 311s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 312s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 312s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 347s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 mpi-default-bin arm64 1.18 [2510 B] 347s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 ray arm64 2.3.1-9 [727 kB] 348s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 ray-doc all 2.3.1-9 [35.2 kB] 348s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 ray-extra all 2.3.1-9 [12.3 kB] 349s Preconfiguring packages ... 349s Fetched 93.7 MB in 2min 3s (763 kB/s) 349s Selecting previously unselected package fonts-dejavu-mono. 349s (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 ... 81647 files and directories currently installed.) 349s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 349s Unpacking fonts-dejavu-mono (2.37-8) ... 349s Selecting previously unselected package fonts-dejavu-core. 349s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 349s Unpacking fonts-dejavu-core (2.37-8) ... 349s Selecting previously unselected package fontconfig-config. 349s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 350s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 350s Selecting previously unselected package libfontconfig1:arm64. 350s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 350s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 350s Selecting previously unselected package fontconfig. 350s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 350s Unpacking fontconfig (2.15.0-2ubuntu1) ... 350s Selecting previously unselected package libllvm17t64:arm64. 350s Preparing to unpack .../05-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 350s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 350s Selecting previously unselected package libamd-comgr2:arm64. 350s Preparing to unpack .../06-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 350s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 351s Selecting previously unselected package libhsakmt1:arm64. 351s Preparing to unpack .../07-libhsakmt1_5.7.0-1build1_arm64.deb ... 351s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 351s Selecting previously unselected package libhsa-runtime64-1. 351s Preparing to unpack .../08-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 351s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 351s Selecting previously unselected package libamdhip64-5. 351s Preparing to unpack .../09-libamdhip64-5_5.7.1-5_arm64.deb ... 351s Unpacking libamdhip64-5 (5.7.1-5) ... 351s Selecting previously unselected package libblas3:arm64. 351s Preparing to unpack .../10-libblas3_3.12.1-2_arm64.deb ... 351s Unpacking libblas3:arm64 (3.12.1-2) ... 351s Selecting previously unselected package libpixman-1-0:arm64. 351s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_arm64.deb ... 351s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 351s Selecting previously unselected package libxcb-render0:arm64. 351s Preparing to unpack .../12-libxcb-render0_1.17.0-2_arm64.deb ... 351s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 351s Selecting previously unselected package libxcb-shm0:arm64. 351s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_arm64.deb ... 351s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 351s Selecting previously unselected package libxrender1:arm64. 351s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 351s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 351s Selecting previously unselected package libcairo2:arm64. 351s Preparing to unpack .../15-libcairo2_1.18.2-2_arm64.deb ... 351s Unpacking libcairo2:arm64 (1.18.2-2) ... 351s Selecting previously unselected package libdatrie1:arm64. 351s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_arm64.deb ... 351s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 351s Selecting previously unselected package libdeflate0:arm64. 351s Preparing to unpack .../17-libdeflate0_1.23-1_arm64.deb ... 351s Unpacking libdeflate0:arm64 (1.23-1) ... 351s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 351s Preparing to unpack .../18-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 351s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 351s Selecting previously unselected package librdmacm1t64:arm64. 351s Preparing to unpack .../19-librdmacm1t64_55.0-1ubuntu1_arm64.deb ... 351s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ... 351s Selecting previously unselected package libfabric1:arm64. 351s Preparing to unpack .../20-libfabric1_1.17.0-3.1_arm64.deb ... 351s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 351s Selecting previously unselected package libgfortran5:arm64. 351s Preparing to unpack .../21-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 351s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 351s Selecting previously unselected package libgomp1:arm64. 351s Preparing to unpack .../22-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 351s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 351s Selecting previously unselected package libgraphite2-3:arm64. 351s Preparing to unpack .../23-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 351s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 351s Selecting previously unselected package libharfbuzz0b:arm64. 352s Preparing to unpack .../24-libharfbuzz0b_10.2.0-1_arm64.deb ... 352s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 352s Selecting previously unselected package libhwloc15:arm64. 352s Preparing to unpack .../25-libhwloc15_2.12.0-1_arm64.deb ... 352s Unpacking libhwloc15:arm64 (2.12.0-1) ... 352s Selecting previously unselected package x11-common. 352s Preparing to unpack .../26-x11-common_1%3a7.7+23ubuntu3_all.deb ... 352s Unpacking x11-common (1:7.7+23ubuntu3) ... 352s Selecting previously unselected package libice6:arm64. 352s Preparing to unpack .../27-libice6_2%3a1.1.1-1_arm64.deb ... 352s Unpacking libice6:arm64 (2:1.1.1-1) ... 352s Selecting previously unselected package libjpeg-turbo8:arm64. 352s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 352s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 352s Selecting previously unselected package libjpeg8:arm64. 352s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_arm64.deb ... 352s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 352s Selecting previously unselected package liblapack3:arm64. 352s Preparing to unpack .../30-liblapack3_3.12.1-2_arm64.deb ... 352s Unpacking liblapack3:arm64 (3.12.1-2) ... 352s Selecting previously unselected package liblerc4:arm64. 352s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 352s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 352s Selecting previously unselected package libmunge2:arm64. 352s Preparing to unpack .../32-libmunge2_0.5.16-1_arm64.deb ... 352s Unpacking libmunge2:arm64 (0.5.16-1) ... 352s Selecting previously unselected package libpciaccess0:arm64. 352s Preparing to unpack .../33-libpciaccess0_0.17-3build1_arm64.deb ... 352s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 352s Selecting previously unselected package libxnvctrl0:arm64. 352s Preparing to unpack .../34-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 352s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 352s Selecting previously unselected package ocl-icd-libopencl1:arm64. 352s Preparing to unpack .../35-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 352s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 352s Selecting previously unselected package libhwloc-plugins:arm64. 352s Preparing to unpack .../36-libhwloc-plugins_2.12.0-1_arm64.deb ... 352s Unpacking libhwloc-plugins:arm64 (2.12.0-1) ... 352s Selecting previously unselected package libpmix2t64:arm64. 352s Preparing to unpack .../37-libpmix2t64_5.0.6-5_arm64.deb ... 352s Unpacking libpmix2t64:arm64 (5.0.6-5) ... 352s Selecting previously unselected package libibumad3:arm64. 352s Preparing to unpack .../38-libibumad3_55.0-1ubuntu1_arm64.deb ... 352s Unpacking libibumad3:arm64 (55.0-1ubuntu1) ... 352s Selecting previously unselected package libibmad5:arm64. 352s Preparing to unpack .../39-libibmad5_55.0-1ubuntu1_arm64.deb ... 352s Unpacking libibmad5:arm64 (55.0-1ubuntu1) ... 352s Selecting previously unselected package libucx0:arm64. 352s Preparing to unpack .../40-libucx0_1.18.1+ds-2_arm64.deb ... 352s Unpacking libucx0:arm64 (1.18.1+ds-2) ... 352s Selecting previously unselected package libopenmpi40:arm64. 352s Preparing to unpack .../41-libopenmpi40_5.0.7-1_arm64.deb ... 352s Unpacking libopenmpi40:arm64 (5.0.7-1) ... 352s Selecting previously unselected package libthai-data. 352s Preparing to unpack .../42-libthai-data_0.1.29-2build1_all.deb ... 352s Unpacking libthai-data (0.1.29-2build1) ... 352s Selecting previously unselected package libthai0:arm64. 352s Preparing to unpack .../43-libthai0_0.1.29-2build1_arm64.deb ... 352s Unpacking libthai0:arm64 (0.1.29-2build1) ... 352s Selecting previously unselected package libpango-1.0-0:arm64. 352s Preparing to unpack .../44-libpango-1.0-0_1.56.2-1_arm64.deb ... 352s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 352s Selecting previously unselected package libpangoft2-1.0-0:arm64. 352s Preparing to unpack .../45-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 352s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 352s Selecting previously unselected package libpangocairo-1.0-0:arm64. 352s Preparing to unpack .../46-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 352s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 353s Selecting previously unselected package libpaper2:arm64. 353s Preparing to unpack .../47-libpaper2_2.2.5-0.3_arm64.deb ... 353s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 353s Selecting previously unselected package libpaper-utils. 353s Preparing to unpack .../48-libpaper-utils_2.2.5-0.3_arm64.deb ... 353s Unpacking libpaper-utils (2.2.5-0.3) ... 353s Selecting previously unselected package libsharpyuv0:arm64. 353s Preparing to unpack .../49-libsharpyuv0_1.5.0-0.1_arm64.deb ... 353s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 353s Selecting previously unselected package libsm6:arm64. 353s Preparing to unpack .../50-libsm6_2%3a1.2.4-1_arm64.deb ... 353s Unpacking libsm6:arm64 (2:1.2.4-1) ... 353s Selecting previously unselected package libtcl8.6:arm64. 353s Preparing to unpack .../51-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 353s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 353s Selecting previously unselected package libjbig0:arm64. 353s Preparing to unpack .../52-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 353s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 353s Selecting previously unselected package libwebp7:arm64. 353s Preparing to unpack .../53-libwebp7_1.5.0-0.1_arm64.deb ... 353s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 353s Selecting previously unselected package libtiff6:arm64. 353s Preparing to unpack .../54-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 353s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 353s Selecting previously unselected package libxft2:arm64. 353s Preparing to unpack .../55-libxft2_2.3.6-1build1_arm64.deb ... 353s Unpacking libxft2:arm64 (2.3.6-1build1) ... 353s Selecting previously unselected package libxss1:arm64. 353s Preparing to unpack .../56-libxss1_1%3a1.2.3-1build3_arm64.deb ... 353s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 353s Selecting previously unselected package libtk8.6:arm64. 353s Preparing to unpack .../57-libtk8.6_8.6.16-1_arm64.deb ... 353s Unpacking libtk8.6:arm64 (8.6.16-1) ... 353s Selecting previously unselected package libxt6t64:arm64. 353s Preparing to unpack .../58-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 353s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 353s Selecting previously unselected package openmpi-common. 353s Preparing to unpack .../59-openmpi-common_5.0.7-1_all.deb ... 353s Unpacking openmpi-common (5.0.7-1) ... 353s Selecting previously unselected package openmpi-bin. 353s Preparing to unpack .../60-openmpi-bin_5.0.7-1_arm64.deb ... 353s Unpacking openmpi-bin (5.0.7-1) ... 353s Selecting previously unselected package zip. 353s Preparing to unpack .../61-zip_3.0-14ubuntu2_arm64.deb ... 353s Unpacking zip (3.0-14ubuntu2) ... 353s Selecting previously unselected package unzip. 353s Preparing to unpack .../62-unzip_6.0-28ubuntu6_arm64.deb ... 353s Unpacking unzip (6.0-28ubuntu6) ... 353s Selecting previously unselected package xdg-utils. 353s Preparing to unpack .../63-xdg-utils_1.2.1-2ubuntu1_all.deb ... 353s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 353s Selecting previously unselected package r-base-core. 353s Preparing to unpack .../64-r-base-core_4.4.3-1_arm64.deb ... 353s Unpacking r-base-core (4.4.3-1) ... 354s Selecting previously unselected package mpi-default-bin. 354s Preparing to unpack .../65-mpi-default-bin_1.18_arm64.deb ... 354s Unpacking mpi-default-bin (1.18) ... 354s Selecting previously unselected package ray. 354s Preparing to unpack .../66-ray_2.3.1-9_arm64.deb ... 354s Unpacking ray (2.3.1-9) ... 354s Selecting previously unselected package ray-doc. 354s Preparing to unpack .../67-ray-doc_2.3.1-9_all.deb ... 354s Unpacking ray-doc (2.3.1-9) ... 354s Selecting previously unselected package ray-extra. 354s Preparing to unpack .../68-ray-extra_2.3.1-9_all.deb ... 354s Unpacking ray-extra (2.3.1-9) ... 354s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 354s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 354s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 354s Setting up ray-doc (2.3.1-9) ... 354s Setting up libpciaccess0:arm64 (0.17-3build1) ... 354s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 354s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 354s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 354s Setting up libxcb-render0:arm64 (1.17.0-2) ... 354s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 354s Setting up unzip (6.0-28ubuntu6) ... 354s Setting up x11-common (1:7.7+23ubuntu3) ... 354s Setting up libibumad3:arm64 (55.0-1ubuntu1) ... 354s Setting up libdeflate0:arm64 (1.23-1) ... 354s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 354s Setting up libibmad5:arm64 (55.0-1ubuntu1) ... 354s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 354s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 354s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 354s Setting up zip (3.0-14ubuntu2) ... 354s Setting up libblas3:arm64 (3.12.1-2) ... 354s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 355s Setting up libmunge2:arm64 (0.5.16-1) ... 355s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 355s Setting up fonts-dejavu-mono (2.37-8) ... 355s Setting up libhwloc15:arm64 (2.12.0-1) ... 355s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 355s Setting up fonts-dejavu-core (2.37-8) ... 355s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 355s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 355s Setting up libwebp7:arm64 (1.5.0-0.1) ... 355s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 355s Setting up openmpi-common (5.0.7-1) ... 355s Setting up librdmacm1t64:arm64 (55.0-1ubuntu1) ... 355s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 355s Setting up libthai-data (0.1.29-2build1) ... 355s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 355s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 355s Setting up libpaper2:arm64 (2.2.5-0.3) ... 355s Setting up xdg-utils (1.2.1-2ubuntu1) ... 355s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 355s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 355s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 355s Setting up libfabric1:arm64 (1.17.0-3.1) ... 355s Setting up libice6:arm64 (2:1.1.1-1) ... 355s Setting up liblapack3:arm64 (3.12.1-2) ... 355s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 355s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 355s Setting up libpaper-utils (2.2.5-0.3) ... 355s Setting up libhwloc-plugins:arm64 (2.12.0-1) ... 355s Setting up libthai0:arm64 (0.1.29-2build1) ... 355s Setting up libpmix2t64:arm64 (5.0.6-5) ... 355s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 355s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 355s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 355s Setting up libsm6:arm64 (2:1.2.4-1) ... 355s Setting up fontconfig (2.15.0-2ubuntu1) ... 358s Regenerating fonts cache... done. 358s Setting up libxft2:arm64 (2.3.6-1build1) ... 358s Setting up libtk8.6:arm64 (8.6.16-1) ... 358s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 358s Setting up libcairo2:arm64 (1.18.2-2) ... 358s Setting up libamdhip64-5 (5.7.1-5) ... 358s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 358s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 358s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 358s Setting up libucx0:arm64 (1.18.1+ds-2) ... 358s Setting up r-base-core (4.4.3-1) ... 358s Creating config file /etc/R/Renviron with new version 358s Setting up libopenmpi40:arm64 (5.0.7-1) ... 358s Setting up ray-extra (2.3.1-9) ... 358s Setting up openmpi-bin (5.0.7-1) ... 358s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 358s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 358s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 358s Setting up mpi-default-bin (1.18) ... 358s Setting up ray (2.3.1-9) ... 358s Processing triggers for libc-bin (2.41-1ubuntu2) ... 358s Processing triggers for man-db (2.13.0-1) ... 359s Processing triggers for install-info (7.1.1-1) ... 361s autopkgtest [16:15:17]: test run-unit-test: [----------------------- 361s 361s ************************************************** 361s This program comes with ABSOLUTELY NO WARRANTY. 361s This is free software, and you are welcome to redistribute it 361s under certain conditions; see "LICENSE.txt" for details. 361s ************************************************** 361s 361s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 361s Centre de recherche en infectiologie de l'Université Laval 361s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 361s http://denovoassembler.sf.net/ 361s 361s References to cite: 361s 361s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 361s Ray Meta: scalable de novo metagenome assembly and profiling. 361s Genome Biology (BioMed Central Ltd). 361s 13:R122, Published: 22 December 2012 361s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 361s 361s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 361s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 361s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 361s November 2010, Volume 17, Issue 11, Pages 1519-1533. 361s http://dx.doi.org/doi:10.1089/cmb.2009.0238 361s 361s Ray version 2.3.1 361s License for Ray: GNU General Public License version 3 361s RayPlatform version: 2.0.1 361s License for RayPlatform: GNU Lesser General Public License version 3 361s 361s MAXKMERLENGTH: 32 361s Maximum coverage depth stored by CoverageDepth: 4294967295 361s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 361s FORCE_PACKING = n 361s ASSERT = n 361s HAVE_LIBZ = y 361s HAVE_LIBBZ2 = y 361s PROFILER_COLLECT = n 361s MINIRANKS = y 361s CLOCK_GETTIME = n 361s __linux__ = y 361s _MSC_VER = n 361s __GNUC__ = y 361s RAY_32_BITS = n 361s RAY_64_BITS = y 361s MPI standard version: MPI 3.1 361s MPI library: Open-MPI 5.0.6 361s Compiler: GNU gcc/g++ 14.2.0 361s MPI I/O: n 361s 361s 361s -k (to set the k-mer size) 361s Value: 31 361s 361s 361s Paired library # 0 361s -p (paired-end sequences) 361s Left sequences: ecoli_1K_1.fq 361s Right sequences: ecoli_1K_2.fq 361s Average length: automatic detection 361s Standard deviation: automatic detection 361s 361s Ray command: 361s mpiexec -n 1 Ray \ 361s -k \ 361s 31 \ 361s -p \ 361s ecoli_1K_1.fq \ 361s ecoli_1K_2.fq \ 361s -o \ 361s test1 361s 361s Rank 0 wrote test1/RayCommand.txt 361s 361s k-mer length: 31 361s Rank 0: assembler memory usage: 42240 KiB 361s Rank 0: assembler memory usage: 107912 KiB 361s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2571 361s Rank 0: testing the network, please wait... 361s 361s Rank 0 is testing the network [0/1000] 361s Rank 0 is testing the network [1000/1000] 361s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 361s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 361s 361s Rank 0 wrote test1/NetworkTest.txt 361s 361s 361s *** 361s Step: Network testing 361s Date: Sat Mar 15 16:15:17 2025 361s Elapsed time: 0 seconds 361s Since beginning: 0 seconds 361s *** 361s 361s 361s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 361s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 361s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 361s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 361s Rank 0 wrote test1/NumberOfSequences.txt 361s Rank 0 wrote test1/SequencePartition.txt 361s 361s *** 361s Step: Counting sequences to assemble 361s Date: Sat Mar 15 16:15:17 2025 361s Elapsed time: 0 seconds 361s Since beginning: 0 seconds 361s *** 361s 361s 361s Rank 0 is loading sequence reads 361s Rank 0 : partition is [0;4107], 4108 sequence reads 361s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 361s Rank 0 has 0 sequence reads 361s Rank 0: assembler memory usage: 120888 KiB 361s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 361s Rank 0 has 4108 sequence reads (completed) 361s 361s *** 361s Step: Sequence loading 361s Date: Sat Mar 15 16:15:17 2025 361s Elapsed time: 0 seconds 361s Since beginning: 0 seconds 361s *** 361s 361s 361s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 361s Rank 0 created its Bloom filter 361s Rank 0 is counting k-mers in sequence reads [1/4108] 361s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 361s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 361s 361s 361s *** 361s Step: K-mer counting 361s Date: Sat Mar 15 16:15:17 2025 361s Elapsed time: 0 seconds 361s Since beginning: 0 seconds 361s *** 361s 361s 361s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 361s Rank 0 destroyed its Bloom filter 361s Rank 0 has 1954 k-mers (completed) 361s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 361s Rank 0: assembler memory usage: 117280 KiB 362s 362s 362s Rank 0: the minimum coverage is 3 362s Rank 0: the peak coverage is 3 362s Warning: no peak observed in the k-mer coverage distribution. 362s to deal with the sequencing error rate, try to lower the k-mer length (-k) 362s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 362s 362s *** 362s Step: Coverage distribution analysis 362s Date: Sat Mar 15 16:15:18 2025 362s Elapsed time: 1 seconds 362s Since beginning: 1 seconds 362s *** 362s 362s 362s 362s Rank 0 is adding edges [1/4108] 362s Rank 0 is adding edges [4108/4108] (completed) 362s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 362s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 362s 362s *** 362s Step: Graph construction 362s Date: Sat Mar 15 16:15:18 2025 362s Elapsed time: 0 seconds 362s Since beginning: 1 seconds 362s *** 362s 362s 362s Rank 0 has 1954 vertices (completed) 362s Rank 0: assembler memory usage: 117280 KiB 363s Rank 0 is purging edges [1/1954] 363s Rank 0 is purging edges [1954/1954] (completed) 363s Rank 0: assembler memory usage: 117808 KiB 363s VirtualProcessor: completed jobs: 1954 363s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 364s Rank 0 wrote test1/degreeDistribution.txt 364s 364s *** 364s Step: Null edge purging 364s Date: Sat Mar 15 16:15:20 2025 364s Elapsed time: 2 seconds 364s Since beginning: 3 seconds 364s *** 364s 364s 364s Rank 0 is selecting optimal read markers [1/4108] 364s Rank 0: assembler memory usage: 117808 KiB 364s Rank 0 is selecting optimal read markers [4108/4108] (completed) 364s Rank 0: peak number of workers: 599, maximum: 32768 364s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 364s Rank 0: assembler memory usage: 125976 KiB 364s Rank 0: Freeing unused assembler memory: 4096 KiB freed 364s Rank 0: assembler memory usage: 125976 KiB 364s 364s *** 364s Step: Selection of optimal read markers 364s Date: Sat Mar 15 16:15:20 2025 364s Elapsed time: 0 seconds 364s Since beginning: 3 seconds 364s *** 364s 364s 364s Rank 0: memory usage for optimal read markers= 4096 KiB 364s Rank 0 is creating seeds [1/1954] 364s Rank 0: assembler memory usage: 125976 KiB 365s Rank 0 has 1 seeds 365s Rank 0 is creating seeds [1954/1954] (completed) 365s Rank 0: peak number of workers: 746, maximum: 32768 365s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 365s Rank 0 runtime statistics for seeding algorithm: 365s Rank 0 Skipped paths because of dead end for head: 0 365s Rank 0 Skipped paths because of dead end for tail: 0 365s Rank 0 Skipped paths because of two dead ends: 0 365s Rank 0 Skipped paths because of bubble weak component: 0 365s Rank 0 Skipped paths because of short length: 1952 365s Rank 0 Skipped paths because of bad ownership: 1 365s Rank 0 Skipped paths because of low coverage: 0 365s Rank 0 Eligible paths: 1 365s Rank 0: assembler memory usage: 125976 KiB 365s Rank 0 has 1 seeds to register. 365s Rank 0 registered 0/1 365s Rank 0 registered 0/1 365s Rank 0 registered its seeds 365s VirtualProcessor: completed jobs: 0 365s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 365s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 375s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 375s Rank 0 merged its seeds: 1 seeds -> 1 seeds 375s 375s *** 375s Step: Detection of assembly seeds 375s Date: Sat Mar 15 16:15:31 2025 375s Elapsed time: 11 seconds 375s Since beginning: 14 seconds 375s *** 375s 375s 375s Rank 0 is calculating library lengths [1/1] 375s Rank 0 detected 1737 library lengths 375s Rank 0 is calculating library lengths [1/1] (completed) 375s Rank 0: peak number of workers: 1, maximum: 32768 375s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 375s Rank 0: assembler memory usage: 162844 KiB 375s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 375s 375s Mode= 2 signalAverage= 9 375s CURRENT IS NOISE, 244 375s GOT HIT 212 375s 375s 375s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 375s 375s *** 375s Step: Estimation of outer distances for paired reads 375s Date: Sat Mar 15 16:15:31 2025 375s Elapsed time: 0 seconds 375s Since beginning: 14 seconds 375s *** 375s 375s 375s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 375s Rank 0 traversed 1000 nucleotide symbols 375s Rank 0: assembler memory usage: 166940 KiB 375s Rank 0 is extending seeds [1/1] (completed) 375s Rank 0 extended 1 seeds out of 1 (100.00%) 375s Rank 0: assembler memory usage: 158748 KiB 375s Rank 0 starting fusions 375s 375s *** 375s Step: Bidirectional extension of seeds 375s Date: Sat Mar 15 16:15:31 2025 375s Elapsed time: 0 seconds 375s Since beginning: 14 seconds 375s *** 375s 375s 375s Rank 0: starting clear step. cycleNumber= 0 376s Rank 0 adding 0 new fusions 376s Rank 0 cleared, 1 paths 376s Rank 0: starting distribution step 376s Rank 0 is distributing fusions [1/1] 376s Rank 0: assembler memory usage: 158748 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 is distributing fusions [1/1] (completed) 376s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 tells others to compute fusions. 376s Rank 0 FusionTaskCreator assignNextTask [0/2] 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 FusionTaskCreator processWorkerResult [0/2] 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 FusionTaskCreator [2/2] 376s Statistics: all paths: 1 eliminated during fusing: 0 376s Rank 0: assembler memory usage: 162844 KiB 376s VirtualProcessor: completed jobs: 2 376s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 376s Rank 0: starting clear step. cycleNumber= 1 376s Rank 0 adding 0 new fusions 376s Rank 0 cleared, 1 paths 376s Rank 0 is distributing fusions [1/1] 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 is distributing fusions [1/1] (completed) 376s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 JoinerTaskCreator assignNextTask [0/2] 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s Rank 0 JoinerTaskCreator [2/2] 376s Statistics: all paths: 1 eliminated during joining: 0 376s Rank 0: assembler memory usage: 162844 KiB 376s Date: Sat Mar 15 16:15:32 2025 376s VirtualProcessor: completed jobs: 2 376s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 377s Rank 0 adding 0 new fusions 377s Rank 0 cleared, 1 paths 377s Rank 0: starting distribution step 377s Rank 0 is distributing fusions [1/1] 377s Rank 0: assembler memory usage: 162844 KiB 377s Date: Sat Mar 15 16:15:33 2025 377s Rank 0 is distributing fusions [1/1] (completed) 377s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 377s Rank 0: assembler memory usage: 162844 KiB 377s Date: Sat Mar 15 16:15:33 2025 377s Rank 0 tells others to compute fusions. 377s Rank 0 FusionTaskCreator assignNextTask [0/2] 377s Rank 0: assembler memory usage: 162844 KiB 377s Date: Sat Mar 15 16:15:33 2025 377s Rank 0 FusionTaskCreator processWorkerResult [0/2] 377s Rank 0: assembler memory usage: 162844 KiB 377s Date: Sat Mar 15 16:15:33 2025 377s Rank 0 FusionTaskCreator [2/2] 377s Statistics: all paths: 1 eliminated during fusing: 0 377s Rank 0: assembler memory usage: 162844 KiB 377s VirtualProcessor: completed jobs: 2 377s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 377s Rank 0: starting clear step. cycleNumber= 2 378s Rank 0 adding 0 new fusions 378s Rank 0 cleared, 1 paths 378s Rank 0 is distributing fusions [1/1] 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 is distributing fusions [1/1] (completed) 378s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 JoinerTaskCreator assignNextTask [0/2] 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 JoinerTaskCreator [2/2] 378s Statistics: all paths: 1 eliminated during joining: 0 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s VirtualProcessor: completed jobs: 2 378s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 378s Rank 0 adding 0 new fusions 378s Rank 0 cleared, 1 paths 378s Rank 0: starting distribution step 378s Rank 0 is distributing fusions [1/1] 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 is distributing fusions [1/1] (completed) 378s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 378s Rank 0: assembler memory usage: 162844 KiB 378s Date: Sat Mar 15 16:15:34 2025 378s Rank 0 cycleNumber= 2 378s 378s *** 378s Step: Merging of redundant paths 378s Date: Sat Mar 15 16:15:34 2025 378s Elapsed time: 3 seconds 378s Since beginning: 17 seconds 378s *** 378s 378s 378s Rank 0 appended 1 elements 378s 378s *** 378s Step: Generation of contigs 378s Date: Sat Mar 15 16:15:34 2025 378s Elapsed time: 0 seconds 378s Since beginning: 17 seconds 378s *** 378s 378s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 378s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 378s Rank 0 ineligibleObjects: 0/970 (0.00%) 378s Rank 0: assembler memory usage: 162844 KiB 378s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 378s Rank 0 finished gathering scaffold links. 378s Rank 0 will write 1 contig lengths 378s Rank 0 will solve the scaffolding problem. 378s Welcome to GreedySolver v1.0 378s 1 vertices; 0 edges 378s 1 contigs >= 500 378s Edges in solution: 0 378s 378s Conflict statistics: 378s 1 scaffolds, 1 >= 500 378s Total: 1000 nucleotides 378s 378s *** 378s Step: Scaffolding of contigs 378s Date: Sat Mar 15 16:15:34 2025 378s Elapsed time: 0 seconds 378s Since beginning: 17 seconds 378s *** 378s 378s Rank 0 syncing with master 378s 378s *** 378s Step: Counting sequences to search 378s Date: Sat Mar 15 16:15:34 2025 378s Elapsed time: 0 seconds 378s Since beginning: 17 seconds 378s *** 378s 378s 378s Rank 0 will add colors, 0 sequences in 0 files to process 378s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 379s 379s *** 379s Step: Graph coloring 379s Date: Sat Mar 15 16:15:35 2025 379s Elapsed time: 1 seconds 379s Since beginning: 18 seconds 379s *** 379s 379s 379s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 379s Rank 0 shares its counts 379s Rank 0 computing contig abundances [1/1] [1/970] 379s Rank 0 computing contig abundances [1/1] [970/970] 379s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 379s 379s *** 379s Step: Counting contig biological abundances 379s Date: Sat Mar 15 16:15:35 2025 379s Elapsed time: 0 seconds 379s Since beginning: 18 seconds 379s *** 379s 379s 379s Rank 0 colored the graph with 0 real colors using 1 virtual colors 379s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 379s 379s *** 379s Step: Counting sequence biological abundances 379s Date: Sat Mar 15 16:15:35 2025 379s Elapsed time: 0 seconds 379s Since beginning: 18 seconds 379s *** 379s 379s 379s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 379s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 380s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 380s 380s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 380s Rank 0 is starting taxon syncing across the compute tribe. 380s 380s *** 380s Step: Loading taxons 380s Date: Sat Mar 15 16:15:36 2025 380s Elapsed time: 1 seconds 380s Since beginning: 19 seconds 380s *** 380s 380s Rank 0 synced taxons across the grid with 1 poor slaves. 380s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 380s Rank 0 has 0 taxons after syncing with master 380s 380s 380s *** 380s Step: Loading tree 380s Date: Sat Mar 15 16:15:36 2025 380s Elapsed time: 0 seconds 380s Since beginning: 19 seconds 380s *** 380s 381s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 381s 381s Rank 0: counting ontology terms in the graph... 382s Rank 0: 0 have some biological signal 382s Number of dereferenced alternate handles: 0 382s Number of k-mer observations with gene ontology terms: 0 382s Rank 0: synced ontology term profiles with master 382s Rank 0: synchronization is complete! 382s Rank 0: ontology terms with biological signal: 0 382s Populated recursive values... 382s Gene ontology terms without depth information: 0 382s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 382s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 382s 382s *** 382s Step: Processing gene ontologies 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 2 seconds 382s Since beginning: 21 seconds 382s *** 382s 382s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 382s [GenomeNeighbourhood] in final list: 0 382s 382s *** 382s Step: Computing neighbourhoods 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 0 seconds 382s Since beginning: 21 seconds 382s *** 382s 382s Contigs >= 100 nt 382s Number: 1 382s Total length: 1000 382s Average: 1000 382s N50: 1000 382s Median: 1000 382s Largest: 1000 382s Contigs >= 500 nt 382s Number: 1 382s Total length: 1000 382s Average: 1000 382s N50: 1000 382s Median: 1000 382s Largest: 1000 382s Scaffolds >= 100 nt 382s Number: 1 382s Total length: 1000 382s Average: 1000 382s N50: 1000 382s Median: 1000 382s Largest: 1000 382s Scaffolds >= 500 nt 382s Number: 1 382s Total length: 1000 382s Average: 1000 382s N50: 1000 382s Median: 1000 382s Largest: 1000 382s 382s Rank 0 wrote test1/Contigs.fasta 382s Rank 0 wrote test1/Scaffolds.fasta 382s Check for test1/* 382s 382s 382s 382s ************************************************** 382s This program comes with ABSOLUTELY NO WARRANTY. 382s This is free software, and you are welcome to redistribute it 382s under certain conditions; see "LICENSE.txt" for details. 382s ************************************************** 382s 382s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 382s Centre de recherche en infectiologie de l'Université Laval 382s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 382s http://denovoassembler.sf.net/ 382s 382s References to cite: 382s 382s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 382s Ray Meta: scalable de novo metagenome assembly and profiling. 382s Genome Biology (BioMed Central Ltd). 382s 13:R122, Published: 22 December 2012 382s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 382s 382s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 382s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 382s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 382s November 2010, Volume 17, Issue 11, Pages 1519-1533. 382s http://dx.doi.org/doi:10.1089/cmb.2009.0238 382s 382s Ray version 2.3.1 382s License for Ray: GNU General Public License version 3 382s RayPlatform version: 2.0.1 382s License for RayPlatform: GNU Lesser General Public License version 3 382s 382s MAXKMERLENGTH: 32 382s Maximum coverage depth stored by CoverageDepth: 4294967295 382s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 382s FORCE_PACKING = n 382s ASSERT = n 382s HAVE_LIBZ = y 382s HAVE_LIBBZ2 = y 382s PROFILER_COLLECT = n 382s MINIRANKS = y 382s CLOCK_GETTIME = n 382s __linux__ = y 382s _MSC_VER = n 382s __GNUC__ = y 382s RAY_32_BITS = n 382s RAY_64_BITS = y 382s MPI standard version: MPI 3.1 382s MPI library: Open-MPI 5.0.6 382s Compiler: GNU gcc/g++ 14.2.0 382s MPI I/O: n 382s 382s 382s -k (to set the k-mer size) 382s Value: 31 382s 382s 382s Paired library # 0 382s -p (paired-end sequences) 382s Left sequences: SampleDirectory/s_6.first1000_1.fastq 382s Right sequences: SampleDirectory/s_6.first1000_2.fastq 382s Average length: automatic detection 382s Standard deviation: automatic detection 382s 382s Ray command: 382s mpiexec -n 1 Ray \ 382s -k \ 382s 31 \ 382s -detect-sequence-files \ 382s SampleDirectory \ 382s -o \ 382s test2 382s 382s Rank 0 wrote test2/RayCommand.txt 382s 382s k-mer length: 31 382s Rank 0: assembler memory usage: 42240 KiB 382s Rank 0: assembler memory usage: 107912 KiB 382s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2574 382s Rank 0: testing the network, please wait... 382s 382s Rank 0 is testing the network [0/1000] 382s Rank 0 is testing the network [1000/1000] 382s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 382s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 382s 382s Rank 0 wrote test2/NetworkTest.txt 382s 382s 382s *** 382s Step: Network testing 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 0 seconds 382s Since beginning: 0 seconds 382s *** 382s 382s 382s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 382s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 382s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 382s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 382s Rank 0 wrote test2/NumberOfSequences.txt 382s Rank 0 wrote test2/SequencePartition.txt 382s 382s *** 382s Step: Counting sequences to assemble 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 0 seconds 382s Since beginning: 0 seconds 382s *** 382s 382s 382s Rank 0 is loading sequence reads 382s Rank 0 : partition is [0;4107], 4108 sequence reads 382s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 382s Rank 0 has 0 sequence reads 382s Rank 0: assembler memory usage: 120888 KiB 382s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 382s Rank 0 has 4108 sequence reads (completed) 382s 382s *** 382s Step: Sequence loading 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 0 seconds 382s Since beginning: 0 seconds 382s *** 382s 382s 382s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 382s Rank 0 created its Bloom filter 382s Rank 0 is counting k-mers in sequence reads [1/4108] 382s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 382s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 382s 382s 382s *** 382s Step: K-mer counting 382s Date: Sat Mar 15 16:15:38 2025 382s Elapsed time: 0 seconds 382s Since beginning: 0 seconds 382s *** 382s 382s 382s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 382s Rank 0 destroyed its Bloom filter 382s Rank 0 has 1954 k-mers (completed) 382s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 382s Rank 0: assembler memory usage: 117284 KiB 383s 383s 383s Rank 0: the minimum coverage is 3 383s Rank 0: the peak coverage is 3 383s Warning: no peak observed in the k-mer coverage distribution. 383s to deal with the sequencing error rate, try to lower the k-mer length (-k) 383s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 383s 383s *** 383s Step: Coverage distribution analysis 383s Date: Sat Mar 15 16:15:39 2025 383s Elapsed time: 1 seconds 383s Since beginning: 1 seconds 383s *** 383s 383s 383s 383s Rank 0 is adding edges [1/4108] 383s Rank 0 is adding edges [4108/4108] (completed) 383s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 383s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 383s 383s *** 383s Step: Graph construction 383s Date: Sat Mar 15 16:15:39 2025 383s Elapsed time: 0 seconds 383s Since beginning: 1 seconds 383s *** 383s 383s 383s Rank 0 has 1954 vertices (completed) 383s Rank 0: assembler memory usage: 117284 KiB 384s Rank 0 is purging edges [1/1954] 384s Rank 0 is purging edges [1954/1954] (completed) 384s Rank 0: assembler memory usage: 117812 KiB 384s VirtualProcessor: completed jobs: 1954 384s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 384s Rank 0 wrote test2/degreeDistribution.txt 384s 384s *** 384s Step: Null edge purging 384s Date: Sat Mar 15 16:15:40 2025 384s Elapsed time: 1 seconds 384s Since beginning: 2 seconds 384s *** 384s 384s 384s Rank 0 is selecting optimal read markers [1/4108] 384s Rank 0: assembler memory usage: 117812 KiB 385s Rank 0 is selecting optimal read markers [4108/4108] (completed) 385s Rank 0: peak number of workers: 599, maximum: 32768 385s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 385s Rank 0: assembler memory usage: 125940 KiB 385s Rank 0: Freeing unused assembler memory: 4096 KiB freed 385s Rank 0: assembler memory usage: 125940 KiB 385s 385s *** 385s Step: Selection of optimal read markers 385s Date: Sat Mar 15 16:15:41 2025 385s Elapsed time: 1 seconds 385s Since beginning: 3 seconds 385s *** 385s 385s 385s Rank 0: memory usage for optimal read markers= 4096 KiB 385s Rank 0 is creating seeds [1/1954] 385s Rank 0: assembler memory usage: 125940 KiB 385s Rank 0 has 1 seeds 385s Rank 0 is creating seeds [1954/1954] (completed) 385s Rank 0: peak number of workers: 746, maximum: 32768 385s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 385s Rank 0 runtime statistics for seeding algorithm: 385s Rank 0 Skipped paths because of dead end for head: 0 385s Rank 0 Skipped paths because of dead end for tail: 0 385s Rank 0 Skipped paths because of two dead ends: 0 385s Rank 0 Skipped paths because of bubble weak component: 0 385s Rank 0 Skipped paths because of short length: 1952 385s Rank 0 Skipped paths because of bad ownership: 1 385s Rank 0 Skipped paths because of low coverage: 0 385s Rank 0 Eligible paths: 1 385s Rank 0: assembler memory usage: 125940 KiB 385s Rank 0 has 1 seeds to register. 385s Rank 0 registered 0/1 385s Rank 0 registered 0/1 385s Rank 0 registered its seeds 385s VirtualProcessor: completed jobs: 0 385s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 386s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 396s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 396s Rank 0 merged its seeds: 1 seeds -> 1 seeds 396s 396s *** 396s Step: Detection of assembly seeds 396s Date: Sat Mar 15 16:15:52 2025 396s Elapsed time: 11 seconds 396s Since beginning: 14 seconds 396s *** 396s 396s 396s Rank 0 is calculating library lengths [1/1] 396s Rank 0 detected 1737 library lengths 396s Rank 0 is calculating library lengths [1/1] (completed) 396s Rank 0: peak number of workers: 1, maximum: 32768 396s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 396s Rank 0: assembler memory usage: 162808 KiB 396s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 396s 396s Mode= 2 signalAverage= 9 396s CURRENT IS NOISE, 244 396s GOT HIT 212 396s 396s 396s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 396s 396s *** 396s Step: Estimation of outer distances for paired reads 396s Date: Sat Mar 15 16:15:52 2025 396s Elapsed time: 0 seconds 396s Since beginning: 14 seconds 396s *** 396s 396s 396s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 396s Rank 0 traversed 1000 nucleotide symbols 396s Rank 0: assembler memory usage: 166904 KiB 396s Rank 0 is extending seeds [1/1] (completed) 396s Rank 0 extended 1 seeds out of 1 (100.00%) 396s Rank 0: assembler memory usage: 158712 KiB 396s Rank 0 starting fusions 396s 396s *** 396s Step: Bidirectional extension of seeds 396s Date: Sat Mar 15 16:15:52 2025 396s Elapsed time: 0 seconds 396s Since beginning: 14 seconds 396s *** 396s 396s 396s Rank 0: starting clear step. cycleNumber= 0 397s Rank 0 adding 0 new fusions 397s Rank 0 cleared, 1 paths 397s Rank 0: starting distribution step 397s Rank 0 is distributing fusions [1/1] 397s Rank 0: assembler memory usage: 158712 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 is distributing fusions [1/1] (completed) 397s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 tells others to compute fusions. 397s Rank 0 FusionTaskCreator assignNextTask [0/2] 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 FusionTaskCreator processWorkerResult [0/2] 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 FusionTaskCreator [2/2] 397s Statistics: all paths: 1 eliminated during fusing: 0 397s Rank 0: assembler memory usage: 162808 KiB 397s VirtualProcessor: completed jobs: 2 397s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 397s Rank 0: starting clear step. cycleNumber= 1 397s Rank 0 adding 0 new fusions 397s Rank 0 cleared, 1 paths 397s Rank 0 is distributing fusions [1/1] 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 is distributing fusions [1/1] (completed) 397s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 JoinerTaskCreator assignNextTask [0/2] 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s Rank 0 JoinerTaskCreator [2/2] 397s Statistics: all paths: 1 eliminated during joining: 0 397s Rank 0: assembler memory usage: 162808 KiB 397s Date: Sat Mar 15 16:15:53 2025 397s VirtualProcessor: completed jobs: 2 397s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 398s Rank 0 adding 0 new fusions 398s Rank 0 cleared, 1 paths 398s Rank 0: starting distribution step 398s Rank 0 is distributing fusions [1/1] 398s Rank 0: assembler memory usage: 162808 KiB 398s Date: Sat Mar 15 16:15:54 2025 398s Rank 0 is distributing fusions [1/1] (completed) 398s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 398s Rank 0: assembler memory usage: 162808 KiB 398s Date: Sat Mar 15 16:15:54 2025 398s Rank 0 tells others to compute fusions. 398s Rank 0 FusionTaskCreator assignNextTask [0/2] 398s Rank 0: assembler memory usage: 162808 KiB 398s Date: Sat Mar 15 16:15:54 2025 398s Rank 0 FusionTaskCreator processWorkerResult [0/2] 398s Rank 0: assembler memory usage: 162808 KiB 398s Date: Sat Mar 15 16:15:54 2025 398s Rank 0 FusionTaskCreator [2/2] 398s Statistics: all paths: 1 eliminated during fusing: 0 398s Rank 0: assembler memory usage: 162808 KiB 398s VirtualProcessor: completed jobs: 2 398s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 398s Rank 0: starting clear step. cycleNumber= 2 399s Rank 0 adding 0 new fusions 399s Rank 0 cleared, 1 paths 399s Rank 0 is distributing fusions [1/1] 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 is distributing fusions [1/1] (completed) 399s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 JoinerTaskCreator assignNextTask [0/2] 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 JoinerTaskCreator [2/2] 399s Statistics: all paths: 1 eliminated during joining: 0 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s VirtualProcessor: completed jobs: 2 399s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 399s Rank 0 adding 0 new fusions 399s Rank 0 cleared, 1 paths 399s Rank 0: starting distribution step 399s Rank 0 is distributing fusions [1/1] 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 is distributing fusions [1/1] (completed) 399s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 399s Rank 0: assembler memory usage: 162808 KiB 399s Date: Sat Mar 15 16:15:55 2025 399s Rank 0 cycleNumber= 2 399s 399s *** 399s Step: Merging of redundant paths 399s Date: Sat Mar 15 16:15:55 2025 399s Elapsed time: 3 seconds 399s Since beginning: 17 seconds 399s *** 399s 399s 399s Rank 0 appended 1 elements 399s 400s *** 400s Step: Generation of contigs 400s Date: Sat Mar 15 16:15:55 2025 400s Elapsed time: 0 seconds 400s Since beginning: 17 seconds 400s *** 400s 400s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 400s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 400s Rank 0 ineligibleObjects: 0/970 (0.00%) 400s Rank 0: assembler memory usage: 162808 KiB 400s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 400s Rank 0 finished gathering scaffold links. 400s Rank 0 will write 1 contig lengths 400s Rank 0 will solve the scaffolding problem. 400s Welcome to GreedySolver v1.0 400s 1 vertices; 0 edges 400s 1 contigs >= 500 400s Edges in solution: 0 400s 400s Conflict statistics: 400s 1 scaffolds, 1 >= 500 400s Total: 1000 nucleotides 400s 400s *** 400s Step: Scaffolding of contigs 400s Date: Sat Mar 15 16:15:55 2025 400s Elapsed time: 0 seconds 400s Since beginning: 17 seconds 400s *** 400s 400s Rank 0 syncing with master 400s 400s *** 400s Step: Counting sequences to search 400s Date: Sat Mar 15 16:15:55 2025 400s Elapsed time: 0 seconds 400s Since beginning: 17 seconds 400s *** 400s 400s 400s Rank 0 will add colors, 0 sequences in 0 files to process 400s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 400s 400s *** 400s Step: Graph coloring 400s Date: Sat Mar 15 16:15:56 2025 400s Elapsed time: 1 seconds 400s Since beginning: 18 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: Sat Mar 15 16:15:56 2025 400s Elapsed time: 0 seconds 400s Since beginning: 18 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: Sat Mar 15 16:15:56 2025 400s Elapsed time: 0 seconds 400s Since beginning: 18 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 401s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 401s 401s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 401s Rank 0 is starting taxon syncing across the compute tribe. 401s 401s *** 401s Step: Loading taxons 401s Date: Sat Mar 15 16:15:57 2025 401s Elapsed time: 1 seconds 401s Since beginning: 19 seconds 401s *** 401s 401s Rank 0 synced taxons across the grid with 1 poor slaves. 401s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 401s Rank 0 has 0 taxons after syncing with master 401s 401s 401s *** 401s Step: Loading tree 401s Date: Sat Mar 15 16:15:57 2025 401s Elapsed time: 0 seconds 401s Since beginning: 19 seconds 401s *** 401s 402s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 402s 402s Rank 0: counting ontology terms in the graph... 403s Rank 0: 0 have some biological signal 403s Number of dereferenced alternate handles: 0 403s Number of k-mer observations with gene ontology terms: 0 403s Rank 0: synced ontology term profiles with master 403s Rank 0: synchronization is complete! 403s Rank 0: ontology terms with biological signal: 0 403s Populated recursive values... 403s Gene ontology terms without depth information: 0 403s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 403s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 403s 403s *** 403s Step: Processing gene ontologies 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 2 seconds 403s Since beginning: 21 seconds 403s *** 403s 403s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 403s [GenomeNeighbourhood] in final list: 0 403s 403s *** 403s Step: Computing neighbourhoods 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 0 seconds 403s Since beginning: 21 seconds 403s *** 403s 403s Contigs >= 100 nt 403s Number: 1 403s Total length: 1000 403s Average: 1000 403s N50: 1000 403s Median: 1000 403s Largest: 1000 403s Contigs >= 500 nt 403s Number: 1 403s Total length: 1000 403s Average: 1000 403s N50: 1000 403s Median: 1000 403s Largest: 1000 403s Scaffolds >= 100 nt 403s Number: 1 403s Total length: 1000 403s Average: 1000 403s N50: 1000 403s Median: 1000 403s Largest: 1000 403s Scaffolds >= 500 nt 403s Number: 1 403s Total length: 1000 403s Average: 1000 403s N50: 1000 403s Median: 1000 403s Largest: 1000 403s 403s Rank 0 wrote test2/Contigs.fasta 403s Rank 0 wrote test2/Scaffolds.fasta 403s Check for test2/* 403s 403s 403s 403s ************************************************** 403s This program comes with ABSOLUTELY NO WARRANTY. 403s This is free software, and you are welcome to redistribute it 403s under certain conditions; see "LICENSE.txt" for details. 403s ************************************************** 403s 403s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 403s Centre de recherche en infectiologie de l'Université Laval 403s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 403s http://denovoassembler.sf.net/ 403s 403s References to cite: 403s 403s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 403s Ray Meta: scalable de novo metagenome assembly and profiling. 403s Genome Biology (BioMed Central Ltd). 403s 13:R122, Published: 22 December 2012 403s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 403s 403s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 403s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 403s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 403s November 2010, Volume 17, Issue 11, Pages 1519-1533. 403s http://dx.doi.org/doi:10.1089/cmb.2009.0238 403s 403s Ray version 2.3.1 403s License for Ray: GNU General Public License version 3 403s RayPlatform version: 2.0.1 403s License for RayPlatform: GNU Lesser General Public License version 3 403s 403s MAXKMERLENGTH: 32 403s Maximum coverage depth stored by CoverageDepth: 4294967295 403s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 403s FORCE_PACKING = n 403s ASSERT = n 403s HAVE_LIBZ = y 403s HAVE_LIBBZ2 = y 403s PROFILER_COLLECT = n 403s MINIRANKS = y 403s CLOCK_GETTIME = n 403s __linux__ = y 403s _MSC_VER = n 403s __GNUC__ = y 403s RAY_32_BITS = n 403s RAY_64_BITS = y 403s MPI standard version: MPI 3.1 403s MPI library: Open-MPI 5.0.6 403s Compiler: GNU gcc/g++ 14.2.0 403s MPI I/O: n 403s 403s 403s -k (to set the k-mer size) 403s Value: 29 403s 403s 403s Paired library # 0 403s -p (paired-end sequences) 403s Left sequences: SampleDirectory/s_6.first1000_1.fastq 403s Right sequences: SampleDirectory/s_6.first1000_2.fastq 403s Average length: automatic detection 403s Standard deviation: automatic detection 403s 403s Ray command: 403s mpiexec -n 1 Ray \ 403s -k \ 403s 29 \ 403s -desable-recycling \ 403s -p \ 403s SampleDirectory/s_6.first1000_1.fastq \ 403s SampleDirectory/s_6.first1000_2.fastq 403s 403s Rank 0 wrote RayOutput/RayCommand.txt 403s 403s k-mer length: 29 403s Rank 0: assembler memory usage: 42240 KiB 403s Rank 0: assembler memory usage: 107912 KiB 403s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2577 403s Rank 0: testing the network, please wait... 403s 403s Rank 0 is testing the network [0/1000] 403s Rank 0 is testing the network [1000/1000] 403s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 403s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 403s 403s Rank 0 wrote RayOutput/NetworkTest.txt 403s 403s 403s *** 403s Step: Network testing 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 0 seconds 403s Since beginning: 0 seconds 403s *** 403s 403s 403s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 403s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 403s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 403s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 403s Rank 0 wrote RayOutput/NumberOfSequences.txt 403s Rank 0 wrote RayOutput/SequencePartition.txt 403s 403s *** 403s Step: Counting sequences to assemble 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 0 seconds 403s Since beginning: 0 seconds 403s *** 403s 403s 403s Rank 0 is loading sequence reads 403s Rank 0 : partition is [0;4107], 4108 sequence reads 403s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 403s Rank 0 has 0 sequence reads 403s Rank 0: assembler memory usage: 120888 KiB 403s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 403s Rank 0 has 4108 sequence reads (completed) 403s 403s *** 403s Step: Sequence loading 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 0 seconds 403s Since beginning: 0 seconds 403s *** 403s 403s 403s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 403s Rank 0 created its Bloom filter 403s Rank 0 is counting k-mers in sequence reads [1/4108] 403s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 403s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 403s 403s 403s *** 403s Step: K-mer counting 403s Date: Sat Mar 15 16:15:59 2025 403s Elapsed time: 0 seconds 403s Since beginning: 0 seconds 403s *** 403s 403s 403s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 403s Rank 0 destroyed its Bloom filter 403s Rank 0 has 1958 k-mers (completed) 403s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 403s Rank 0: assembler memory usage: 117268 KiB 404s 404s 404s Rank 0: the minimum coverage is 3 404s Rank 0: the peak coverage is 3 404s Warning: no peak observed in the k-mer coverage distribution. 404s to deal with the sequencing error rate, try to lower the k-mer length (-k) 404s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 404s 404s *** 404s Step: Coverage distribution analysis 404s Date: Sat Mar 15 16:16:00 2025 404s Elapsed time: 1 seconds 404s Since beginning: 1 seconds 404s *** 404s 404s 404s 404s Rank 0 is adding edges [1/4108] 404s Rank 0 is adding edges [4108/4108] (completed) 404s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 404s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 404s 404s *** 404s Step: Graph construction 404s Date: Sat Mar 15 16:16:00 2025 404s Elapsed time: 0 seconds 404s Since beginning: 1 seconds 404s *** 404s 404s 404s Rank 0 has 1958 vertices (completed) 404s Rank 0: assembler memory usage: 117268 KiB 405s Rank 0 is purging edges [1/1958] 405s Rank 0 is purging edges [1958/1958] (completed) 405s Rank 0: assembler memory usage: 117800 KiB 405s VirtualProcessor: completed jobs: 1958 405s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 405s Rank 0 wrote RayOutput/degreeDistribution.txt 405s 405s *** 405s Step: Null edge purging 405s Date: Sat Mar 15 16:16:01 2025 405s Elapsed time: 1 seconds 405s Since beginning: 2 seconds 405s *** 405s 405s 405s Rank 0 is selecting optimal read markers [1/4108] 405s Rank 0: assembler memory usage: 117800 KiB 406s Rank 0 is selecting optimal read markers [4108/4108] (completed) 406s Rank 0: peak number of workers: 599, maximum: 32768 406s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 406s Rank 0: assembler memory usage: 126012 KiB 406s Rank 0: Freeing unused assembler memory: 4096 KiB freed 406s Rank 0: assembler memory usage: 126012 KiB 406s 406s *** 406s Step: Selection of optimal read markers 406s Date: Sat Mar 15 16:16:02 2025 406s Elapsed time: 1 seconds 406s Since beginning: 3 seconds 406s *** 406s 406s 406s Rank 0: memory usage for optimal read markers= 4096 KiB 406s Rank 0 is creating seeds [1/1958] 406s Rank 0: assembler memory usage: 126012 KiB 406s Rank 0 has 1 seeds 406s Rank 0 is creating seeds [1958/1958] (completed) 406s Rank 0: peak number of workers: 746, maximum: 32768 406s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 406s Rank 0 runtime statistics for seeding algorithm: 406s Rank 0 Skipped paths because of dead end for head: 0 406s Rank 0 Skipped paths because of dead end for tail: 0 406s Rank 0 Skipped paths because of two dead ends: 0 406s Rank 0 Skipped paths because of bubble weak component: 0 406s Rank 0 Skipped paths because of short length: 1956 406s Rank 0 Skipped paths because of bad ownership: 1 406s Rank 0 Skipped paths because of low coverage: 0 406s Rank 0 Eligible paths: 1 406s Rank 0: assembler memory usage: 126012 KiB 406s Rank 0 has 1 seeds to register. 406s Rank 0 registered 0/1 406s Rank 0 registered 0/1 406s Rank 0 registered its seeds 406s VirtualProcessor: completed jobs: 0 406s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 407s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 417s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 417s Rank 0 merged its seeds: 1 seeds -> 1 seeds 417s 417s *** 417s Step: Detection of assembly seeds 417s Date: Sat Mar 15 16:16:13 2025 417s Elapsed time: 11 seconds 417s Since beginning: 14 seconds 417s *** 417s 417s 417s Rank 0 is calculating library lengths [1/1] 417s Rank 0 detected 1743 library lengths 417s Rank 0 is calculating library lengths [1/1] (completed) 417s Rank 0: peak number of workers: 1, maximum: 32768 417s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 417s Rank 0: assembler memory usage: 162880 KiB 417s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 417s 417s Mode= 2 signalAverage= 10 417s CURRENT IS NOISE, 244 417s GOT HIT 214 417s 417s 417s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 417s 417s *** 417s Step: Estimation of outer distances for paired reads 417s Date: Sat Mar 15 16:16:13 2025 417s Elapsed time: 0 seconds 417s Since beginning: 14 seconds 417s *** 417s 417s 417s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 417s Rank 0 traversed 1000 nucleotide symbols 417s Rank 0: assembler memory usage: 166976 KiB 417s Rank 0 is extending seeds [1/1] (completed) 417s Rank 0 extended 1 seeds out of 1 (100.00%) 417s Rank 0: assembler memory usage: 158784 KiB 417s Rank 0 starting fusions 417s 417s *** 417s Step: Bidirectional extension of seeds 417s Date: Sat Mar 15 16:16:13 2025 417s Elapsed time: 0 seconds 417s Since beginning: 14 seconds 417s *** 417s 417s 417s Rank 0: starting clear step. cycleNumber= 0 418s Rank 0 adding 0 new fusions 418s Rank 0 cleared, 1 paths 418s Rank 0: starting distribution step 418s Rank 0 is distributing fusions [1/1] 418s Rank 0: assembler memory usage: 158784 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 is distributing fusions [1/1] (completed) 418s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 tells others to compute fusions. 418s Rank 0 FusionTaskCreator assignNextTask [0/2] 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 FusionTaskCreator processWorkerResult [0/2] 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 FusionTaskCreator [2/2] 418s Statistics: all paths: 1 eliminated during fusing: 0 418s Rank 0: assembler memory usage: 162880 KiB 418s VirtualProcessor: completed jobs: 2 418s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 418s Rank 0: starting clear step. cycleNumber= 1 418s Rank 0 adding 0 new fusions 418s Rank 0 cleared, 1 paths 418s Rank 0 is distributing fusions [1/1] 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 is distributing fusions [1/1] (completed) 418s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 JoinerTaskCreator assignNextTask [0/2] 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s Rank 0 JoinerTaskCreator [2/2] 418s Statistics: all paths: 1 eliminated during joining: 0 418s Rank 0: assembler memory usage: 162880 KiB 418s Date: Sat Mar 15 16:16:14 2025 418s VirtualProcessor: completed jobs: 2 418s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 419s Rank 0 adding 0 new fusions 419s Rank 0 cleared, 1 paths 419s Rank 0: starting distribution step 419s Rank 0 is distributing fusions [1/1] 419s Rank 0: assembler memory usage: 162880 KiB 419s Date: Sat Mar 15 16:16:15 2025 419s Rank 0 is distributing fusions [1/1] (completed) 419s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 419s Rank 0: assembler memory usage: 162880 KiB 419s Date: Sat Mar 15 16:16:15 2025 419s Rank 0 tells others to compute fusions. 419s Rank 0 FusionTaskCreator assignNextTask [0/2] 419s Rank 0: assembler memory usage: 162880 KiB 419s Date: Sat Mar 15 16:16:15 2025 419s Rank 0 FusionTaskCreator processWorkerResult [0/2] 419s Rank 0: assembler memory usage: 162880 KiB 419s Date: Sat Mar 15 16:16:15 2025 419s Rank 0 FusionTaskCreator [2/2] 419s Statistics: all paths: 1 eliminated during fusing: 0 419s Rank 0: assembler memory usage: 162880 KiB 419s VirtualProcessor: completed jobs: 2 419s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 419s Rank 0: starting clear step. cycleNumber= 2 420s Rank 0 adding 0 new fusions 420s Rank 0 cleared, 1 paths 420s Rank 0 is distributing fusions [1/1] 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 is distributing fusions [1/1] (completed) 420s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 JoinerTaskCreator assignNextTask [0/2] 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 JoinerTaskCreator [2/2] 420s Statistics: all paths: 1 eliminated during joining: 0 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s VirtualProcessor: completed jobs: 2 420s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 420s Rank 0 adding 0 new fusions 420s Rank 0 cleared, 1 paths 420s Rank 0: starting distribution step 420s Rank 0 is distributing fusions [1/1] 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 is distributing fusions [1/1] (completed) 420s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 420s Rank 0: assembler memory usage: 162880 KiB 420s Date: Sat Mar 15 16:16:16 2025 420s Rank 0 cycleNumber= 2 420s 420s *** 420s Step: Merging of redundant paths 420s Date: Sat Mar 15 16:16:16 2025 420s Elapsed time: 3 seconds 420s Since beginning: 17 seconds 420s *** 420s 420s 420s Rank 0 appended 1 elements 420s 420s *** 420s Step: Generation of contigs 420s Date: Sat Mar 15 16:16:16 2025 420s Elapsed time: 0 seconds 420s Since beginning: 17 seconds 420s *** 420s 420s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 420s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 420s Rank 0 ineligibleObjects: 0/972 (0.00%) 420s Rank 0: assembler memory usage: 162880 KiB 420s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 420s Rank 0 finished gathering scaffold links. 420s Rank 0 will write 1 contig lengths 420s Rank 0 will solve the scaffolding problem. 420s Welcome to GreedySolver v1.0 420s 1 vertices; 0 edges 420s 1 contigs >= 500 420s Edges in solution: 0 420s 420s Conflict statistics: 420s 1 scaffolds, 1 >= 500 420s Total: 1000 nucleotides 420s 420s *** 420s Step: Scaffolding of contigs 420s Date: Sat Mar 15 16:16:16 2025 420s Elapsed time: 0 seconds 420s Since beginning: 17 seconds 420s *** 420s 420s Rank 0 syncing with master 420s 420s *** 420s Step: Counting sequences to search 420s Date: Sat Mar 15 16:16:16 2025 420s Elapsed time: 0 seconds 420s Since beginning: 17 seconds 420s *** 420s 420s 420s Rank 0 will add colors, 0 sequences in 0 files to process 420s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 421s 421s *** 421s Step: Graph coloring 421s Date: Sat Mar 15 16:16:17 2025 421s Elapsed time: 1 seconds 421s Since beginning: 18 seconds 421s *** 421s 421s 421s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 421s Rank 0 shares its counts 421s Rank 0 computing contig abundances [1/1] [1/972] 421s Rank 0 computing contig abundances [1/1] [972/972] 421s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 421s 421s *** 421s Step: Counting contig biological abundances 421s Date: Sat Mar 15 16:16:17 2025 421s Elapsed time: 0 seconds 421s Since beginning: 18 seconds 421s *** 421s 421s 421s Rank 0 colored the graph with 0 real colors using 1 virtual colors 421s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 421s 421s *** 421s Step: Counting sequence biological abundances 421s Date: Sat Mar 15 16:16:17 2025 421s Elapsed time: 0 seconds 421s Since beginning: 18 seconds 421s *** 421s 421s 421s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 421s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 422s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 422s 422s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 422s Rank 0 is starting taxon syncing across the compute tribe. 422s 422s *** 422s Step: Loading taxons 422s Date: Sat Mar 15 16:16:18 2025 422s Elapsed time: 1 seconds 422s Since beginning: 19 seconds 422s *** 422s 422s Rank 0 synced taxons across the grid with 1 poor slaves. 422s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 422s Rank 0 has 0 taxons after syncing with master 422s 422s 422s *** 422s Step: Loading tree 422s Date: Sat Mar 15 16:16:18 2025 422s Elapsed time: 0 seconds 422s Since beginning: 19 seconds 422s *** 422s 423s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 423s 423s Rank 0: counting ontology terms in the graph... 424s Rank 0: 0 have some biological signal 424s Number of dereferenced alternate handles: 0 424s Number of k-mer observations with gene ontology terms: 0 424s Rank 0: synced ontology term profiles with master 424s Rank 0: synchronization is complete! 424s Rank 0: ontology terms with biological signal: 0 424s Populated recursive values... 424s Gene ontology terms without depth information: 0 424s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 424s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 424s 424s *** 424s Step: Processing gene ontologies 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 2 seconds 424s Since beginning: 21 seconds 424s *** 424s 424s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 424s [GenomeNeighbourhood] in final list: 0 424s 424s *** 424s Step: Computing neighbourhoods 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 0 seconds 424s Since beginning: 21 seconds 424s *** 424s 424s Contigs >= 100 nt 424s Number: 1 424s Total length: 1000 424s Average: 1000 424s N50: 1000 424s Median: 1000 424s Largest: 1000 424s Contigs >= 500 nt 424s Number: 1 424s Total length: 1000 424s Average: 1000 424s N50: 1000 424s Median: 1000 424s Largest: 1000 424s Scaffolds >= 100 nt 424s Number: 1 424s Total length: 1000 424s Average: 1000 424s N50: 1000 424s Median: 1000 424s Largest: 1000 424s Scaffolds >= 500 nt 424s Number: 1 424s Total length: 1000 424s Average: 1000 424s N50: 1000 424s Median: 1000 424s Largest: 1000 424s 424s Rank 0 wrote RayOutput/Contigs.fasta 424s Rank 0 wrote RayOutput/Scaffolds.fasta 424s Check for RayOutput/* 424s 424s 424s 424s ************************************************** 424s This program comes with ABSOLUTELY NO WARRANTY. 424s This is free software, and you are welcome to redistribute it 424s under certain conditions; see "LICENSE.txt" for details. 424s ************************************************** 424s 424s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 424s Centre de recherche en infectiologie de l'Université Laval 424s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 424s http://denovoassembler.sf.net/ 424s 424s References to cite: 424s 424s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 424s Ray Meta: scalable de novo metagenome assembly and profiling. 424s Genome Biology (BioMed Central Ltd). 424s 13:R122, Published: 22 December 2012 424s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 424s 424s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 424s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 424s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 424s November 2010, Volume 17, Issue 11, Pages 1519-1533. 424s http://dx.doi.org/doi:10.1089/cmb.2009.0238 424s 424s Ray version 2.3.1 424s License for Ray: GNU General Public License version 3 424s RayPlatform version: 2.0.1 424s License for RayPlatform: GNU Lesser General Public License version 3 424s 424s MAXKMERLENGTH: 32 424s Maximum coverage depth stored by CoverageDepth: 4294967295 424s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 424s FORCE_PACKING = n 424s ASSERT = n 424s HAVE_LIBZ = y 424s HAVE_LIBBZ2 = y 424s PROFILER_COLLECT = n 424s MINIRANKS = y 424s CLOCK_GETTIME = n 424s __linux__ = y 424s _MSC_VER = n 424s __GNUC__ = y 424s RAY_32_BITS = n 424s RAY_64_BITS = y 424s MPI standard version: MPI 3.1 424s MPI library: Open-MPI 5.0.6 424s Compiler: GNU gcc/g++ 14.2.0 424s MPI I/O: n 424s Rank 1: assembler memory usage: 42292 KiB 424s 424s 424s -k (to set the k-mer size) 424s Value: 31 424s 424s 424s Paired library # 0 424s -p (paired-end sequences) 424s Left sequences: ecoli_1K_1.fq 424s Right sequences: ecoli_1K_2.fq 424s Average length: automatic detection 424s Standard deviation: automatic detection 424s 424s Ray command: 424s mpiexec -n 2 Ray \ 424s -k \ 424s 31 \ 424s -p \ 424s ecoli_1K_1.fq \ 424s ecoli_1K_2.fq \ 424s -o \ 424s test3 424s 424s Rank 0 wrote test3/RayCommand.txt 424s 424s k-mer length: 31 424s Rank 0: assembler memory usage: 42296 KiB 424s Rank 1: assembler memory usage: 107976 KiB 424s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 2584 424s Rank 0: assembler memory usage: 107984 KiB 424s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 2583 424s Rank 0: testing the network, please wait... 424s 424s Rank 0 is testing the network [0/1000] 424s Rank 1 is testing the network [0/1000] 424s Rank 0 is testing the network [1000/1000] 424s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 424s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 424s Rank 1 is testing the network [1000/1000] 424s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 424s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 424s 424s Rank 0 wrote test3/NetworkTest.txt 424s 424s 424s *** 424s Step: Network testing 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 0 seconds 424s Since beginning: 0 seconds 424s *** 424s 424s 424s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 424s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 424s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 424s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 424s Rank 0 wrote test3/NumberOfSequences.txt 424s Rank 0 wrote test3/SequencePartition.txt 424s 424s *** 424s Step: Counting sequences to assemble 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 0 seconds 424s Since beginning: 0 seconds 424s *** 424s 424s 424s Rank 0 is loading sequence reads 424s Rank 0 : partition is [0;2053], 2054 sequence reads 424s Rank 1 is loading sequence reads 424s Rank 1 : partition is [2054;4107], 2054 sequence reads 424s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 424s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 424s Rank 0 has 0 sequence reads 424s Rank 0: assembler memory usage: 116824 KiB 424s Rank 1 has 0 sequence reads 424s Rank 1: assembler memory usage: 116816 KiB 424s Rank 0 has 2054 sequence reads (completed) 424s Rank 1 has 2054 sequence reads (completed) 424s 424s *** 424s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 424s Step: Sequence loading 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 0 seconds 424s Since beginning: 0 seconds 424s *** 424s 424s 424s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 424s Rank 0 created its Bloom filter 424s Rank 0 is counting k-mers in sequence reads [1/2054] 424s Rank 1 created its Bloom filter 424s Rank 1 is counting k-mers in sequence reads [1/2054] 424s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 424s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 424s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 424s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 424s 424s 424s *** 424s Step: K-mer counting 424s Date: Sat Mar 15 16:16:20 2025 424s Elapsed time: 0 seconds 424s Since beginning: 0 seconds 424s *** 424s 424s 424s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 424s Rank 0 destroyed its Bloom filter 424s Rank 0 has 1032 k-mers (completed) 424s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 424s Rank 0: assembler memory usage: 113096 KiB 424s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 424s Rank 1 destroyed its Bloom filter 424s Rank 1 has 922 k-mers (completed) 424s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 424s Rank 1: assembler memory usage: 113084 KiB 425s 425s 425s Rank 0: the minimum coverage is 3 425s Rank 0: the peak coverage is 3 425s Warning: no peak observed in the k-mer coverage distribution. 425s to deal with the sequencing error rate, try to lower the k-mer length (-k) 425s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 425s 425s *** 425s Step: Coverage distribution analysis 425s Date: Sat Mar 15 16:16:21 2025 425s Elapsed time: 1 seconds 425s Since beginning: 1 seconds 425s *** 425s 425s 425s 425s Rank 0 is adding edges [1/2054] 425s Rank 1 is adding edges [1/2054] 425s Rank 1 is adding edges [2054/2054] (completed) 425s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 425s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 425s Rank 0 is adding edges [2054/2054] (completed) 425s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 425s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 425s 425s *** 425s Step: Graph construction 425s Date: Sat Mar 15 16:16:21 2025 425s Elapsed time: 0 seconds 425s Since beginning: 1 seconds 425s *** 425s 425s 425s Rank 0 has 1032 vertices (completed) 425s Rank 0: assembler memory usage: 113096 KiB 425s Rank 1 has 922 vertices (completed) 425s Rank 1: assembler memory usage: 113084 KiB 425s Rank 1 is purging edges [1/922] 425s Rank 0 is purging edges [1/1032] 425s Rank 1 is purging edges [922/922] (completed) 425s Rank 1: assembler memory usage: 113348 KiB 425s VirtualProcessor: completed jobs: 922 425s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 425s Rank 0 is purging edges [1032/1032] (completed) 425s Rank 0: assembler memory usage: 113360 KiB 425s VirtualProcessor: completed jobs: 1032 425s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 426s Rank 0 wrote test3/degreeDistribution.txt 426s 426s *** 426s Step: Null edge purging 426s Date: Sat Mar 15 16:16:22 2025 426s Elapsed time: 1 seconds 426s Since beginning: 2 seconds 426s *** 426s 426s 426s Rank 0 is selecting optimal read markers [1/2054] 426s Rank 0: assembler memory usage: 113360 KiB 426s Rank 1 is selecting optimal read markers [1/2054] 426s Rank 1: assembler memory usage: 113348 KiB 426s Rank 1 is selecting optimal read markers [2054/2054] (completed) 426s Rank 1: peak number of workers: 1121, maximum: 32768 426s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 426s Rank 1: assembler memory usage: 121536 KiB 426s Rank 1: Freeing unused assembler memory: 4096 KiB freed 426s Rank 1: assembler memory usage: 121536 KiB 426s Rank 0 is selecting optimal read markers [2054/2054] (completed) 426s Rank 0: peak number of workers: 1135, maximum: 32768 426s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 426s Rank 0: assembler memory usage: 121616 KiB 426s Rank 0: Freeing unused assembler memory: 4096 KiB freed 426s Rank 0: assembler memory usage: 121616 KiB 426s 426s *** 426s Step: Selection of optimal read markers 426s Date: Sat Mar 15 16:16:22 2025 426s Elapsed time: 0 seconds 426s Since beginning: 2 seconds 426s *** 426s 426s 426s Rank 0: memory usage for optimal read markers= 4096 KiB 426s Rank 1: memory usage for optimal read markers= 4096 KiB 426s Rank 1 is creating seeds [1/922] 426s Rank 1: assembler memory usage: 121536 KiB 426s Rank 0 is creating seeds [1/1032] 426s Rank 0: assembler memory usage: 121616 KiB 427s Rank 1 has 1 seeds 427s Rank 1 is creating seeds [922/922] (completed) 427s Rank 1: peak number of workers: 916, maximum: 32768 427s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 427s Rank 1 runtime statistics for seeding algorithm: 427s Rank 1 Skipped paths because of dead end for head: 0 427s Rank 1 Skipped paths because of dead end for tail: 0 427s Rank 1 Skipped paths because of two dead ends: 0 427s Rank 1 Skipped paths because of bubble weak component: 0 427s Rank 1 Skipped paths because of short length: 921 427s Rank 1 Skipped paths because of bad ownership: 0 427s Rank 1 Skipped paths because of low coverage: 0 427s Rank 1 Eligible paths: 1 427s Rank 1: assembler memory usage: 121536 KiB 427s Rank 0 has 0 seeds 427s Rank 0 is creating seeds [1032/1032] (completed) 427s Rank 0: peak number of workers: 998, maximum: 32768 427s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 427s Rank 0 runtime statistics for seeding algorithm: 427s Rank 0 Skipped paths because of dead end for head: 0 427s Rank 0 Skipped paths because of dead end for tail: 0 427s Rank 0 Skipped paths because of two dead ends: 0 427s Rank 0 Skipped paths because of bubble weak component: 0 427s Rank 0 Skipped paths because of short length: 1031 427s Rank 0 Skipped paths because of bad ownership: 1 427s Rank 0 Skipped paths because of low coverage: 0 427s Rank 0 Eligible paths: 0 427s Rank 0: assembler memory usage: 121616 KiB 427s Rank 0 registered -1/0 427s Rank 1 has 1 seeds to register. 427s Rank 0 registered its seeds 427s Rank 1 registered 0/1 427s Rank 1 registered 0/1 427s Rank 1 registered its seeds 427s VirtualProcessor: completed jobs: 0 427s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 427s VirtualProcessor: completed jobs: 0 427s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 428s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 428s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 438s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 438s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 438s Rank 0 merged its seeds: 0 seeds -> 0 seeds 438s Rank 1 merged its seeds: 1 seeds -> 1 seeds 438s 438s *** 438s Step: Detection of assembly seeds 438s Date: Sat Mar 15 16:16:34 2025 438s Elapsed time: 12 seconds 438s Since beginning: 14 seconds 438s *** 438s 438s 438s Rank 0 detected 0 library lengths 438s Rank 0 is calculating library lengths [0/0] (completed) 438s Rank 0: peak number of workers: 0, maximum: 32768 438s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 438s Rank 0: assembler memory usage: 125712 KiB 438s Rank 1 is calculating library lengths [1/1] 438s Rank 1 detected 1737 library lengths 438s Rank 1 is calculating library lengths [1/1] (completed) 438s Rank 1: peak number of workers: 1, maximum: 32768 438s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7984 virtual messages generated 7984 real messages (100%) 438s Rank 1: assembler memory usage: 158404 KiB 438s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 438s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 438s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 438s 438s Mode= 2 signalAverage= 9 438s CURRENT IS NOISE, 244 438s GOT HIT 212 438s 438s 438s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 438s 438s *** 438s Step: Estimation of outer distances for paired reads 438s Date: Sat Mar 15 16:16:34 2025 438s Elapsed time: 0 seconds 438s Since beginning: 14 seconds 438s *** 438s 438s 438s Rank 0 is extending seeds [0/0] (completed) 438s Rank 0 extended 0 seeds out of 0 (0.00%) 438s Rank 0: assembler memory usage: 125712 KiB 438s Rank 1 traversed 1000 nucleotide symbols 438s Rank 1: assembler memory usage: 162500 KiB 438s Rank 1 is extending seeds [1/1] (completed) 438s Rank 1 extended 1 seeds out of 1 (100.00%) 438s Rank 1: assembler memory usage: 154308 KiB 438s Rank 0 starting fusions 438s 438s *** 438s Step: Bidirectional extension of seeds 438s Date: Sat Mar 15 16:16:34 2025 438s Elapsed time: 0 seconds 438s Since beginning: 14 seconds 438s *** 438s 438s 438s Rank 0: starting clear step. cycleNumber= 0 439s Rank 1 adding 0 new fusions 439s Rank 1 cleared, 1 paths 439s Rank 0 adding 0 new fusions 439s Rank 0 cleared, 0 paths 439s Rank 0: starting distribution step 439s Rank 0 is distributing fusions [0/0] (completed) 439s Rank 1 is distributing fusions [1/1] 439s Rank 1: assembler memory usage: 154308 KiB 439s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 439s Rank 0: assembler memory usage: 125712 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 is distributing fusions [1/1] (completed) 439s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 0 tells others to compute fusions. 439s Rank 0 FusionTaskCreator [0/0] 439s Statistics: all paths: 0 eliminated during fusing: 0 439s Rank 1 FusionTaskCreator assignNextTask [0/2] 439s Rank 1: assembler memory usage: 158404 KiB 439s Rank 0: assembler memory usage: 125712 KiB 439s VirtualProcessor: completed jobs: 0 439s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 FusionTaskCreator processWorkerResult [0/2] 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 FusionTaskCreator [2/2] 439s Statistics: all paths: 1 eliminated during fusing: 0 439s Rank 1: assembler memory usage: 158404 KiB 439s VirtualProcessor: completed jobs: 2 439s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10894 virtual messages generated 10894 real messages (100%) 439s Rank 0: starting clear step. cycleNumber= 1 439s Rank 1 adding 0 new fusions 439s Rank 1 cleared, 1 paths 439s Rank 0 adding 0 new fusions 439s Rank 0 cleared, 0 paths 439s Rank 1 is distributing fusions [1/1] 439s Rank 0 is distributing fusions [0/0] (completed) 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 439s Rank 0: assembler memory usage: 125712 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 is distributing fusions [1/1] (completed) 439s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 JoinerTaskCreator assignNextTask [0/2] 439s Rank 1: assembler memory usage: 158404 KiB 439s Rank 0 JoinerTaskCreator [0/0] 439s Date: Sat Mar 15 16:16:35 2025 439s Statistics: all paths: 0 eliminated during joining: 0 439s Rank 0: assembler memory usage: 125712 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s VirtualProcessor: completed jobs: 0 439s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 439s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s Rank 1 JoinerTaskCreator [2/2] 439s Statistics: all paths: 1 eliminated during joining: 0 439s Rank 1: assembler memory usage: 158404 KiB 439s Date: Sat Mar 15 16:16:35 2025 439s VirtualProcessor: completed jobs: 2 439s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13804 virtual messages generated 13804 real messages (100%) 440s Rank 1 adding 0 new fusions 440s Rank 1 cleared, 1 paths 440s Rank 0 adding 0 new fusions 440s Rank 0 cleared, 0 paths 440s Rank 0: starting distribution step 440s Rank 0 is distributing fusions [0/0] (completed) 440s Rank 1 is distributing fusions [1/1] 440s Rank 1: assembler memory usage: 158404 KiB 440s Date: Sat Mar 15 16:16:36 2025 440s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 440s Rank 0: assembler memory usage: 125712 KiB 440s Date: Sat Mar 15 16:16:36 2025 440s Rank 1 is distributing fusions [1/1] (completed) 440s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 440s Rank 1: assembler memory usage: 158404 KiB 440s Date: Sat Mar 15 16:16:36 2025 440s Rank 1 FusionTaskCreator assignNextTask [0/2] 440s Rank 0 tells others to compute fusions. 440s Rank 0 FusionTaskCreator [0/0] 440s Statistics: all paths: 0 eliminated during fusing: 0 440s Rank 0: assembler memory usage: 125712 KiB 440s VirtualProcessor: completed jobs: 0 440s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 440s Rank 1: assembler memory usage: 158404 KiB 440s Date: Sat Mar 15 16:16:36 2025 440s Rank 1 FusionTaskCreator processWorkerResult [0/2] 440s Rank 1: assembler memory usage: 158404 KiB 440s Date: Sat Mar 15 16:16:36 2025 440s Rank 1 FusionTaskCreator [2/2] 440s Statistics: all paths: 1 eliminated during fusing: 0 440s Rank 1: assembler memory usage: 158404 KiB 440s VirtualProcessor: completed jobs: 2 440s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16714 virtual messages generated 16714 real messages (100%) 440s Rank 0: starting clear step. cycleNumber= 2 441s Rank 1 adding 0 new fusions 441s Rank 1 cleared, 1 paths 441s Rank 0 adding 0 new fusions 441s Rank 0 cleared, 0 paths 441s Rank 0 is distributing fusions [0/0] (completed) 441s Rank 1 is distributing fusions [1/1] 441s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 0: assembler memory usage: 125712 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 1 is distributing fusions [1/1] (completed) 441s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 0 JoinerTaskCreator [0/0] 441s Rank 1 JoinerTaskCreator assignNextTask [0/2] 441s Statistics: all paths: 0 eliminated during joining: 0 441s Rank 0: assembler memory usage: 125712 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s VirtualProcessor: completed jobs: 0 441s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 1 JoinerTaskCreator [2/2] 441s Statistics: all paths: 1 eliminated during joining: 0 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s VirtualProcessor: completed jobs: 2 441s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19624 virtual messages generated 19624 real messages (100%) 441s Rank 1 adding 0 new fusions 441s Rank 1 cleared, 1 paths 441s Rank 0 adding 0 new fusions 441s Rank 0 cleared, 0 paths 441s Rank 0: starting distribution step 441s Rank 0 is distributing fusions [0/0] (completed) 441s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 441s Rank 1 is distributing fusions [1/1] 441s Rank 1: assembler memory usage: 158404 KiB 441s Rank 0: assembler memory usage: 125712 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s Date: Sat Mar 15 16:16:37 2025 441s Rank 0 cycleNumber= 2 441s Rank 1 is distributing fusions [1/1] (completed) 441s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 441s Rank 1: assembler memory usage: 158404 KiB 441s Date: Sat Mar 15 16:16:37 2025 441s 441s *** 441s Step: Merging of redundant paths 441s Date: Sat Mar 15 16:16:37 2025 441s Elapsed time: 3 seconds 441s Since beginning: 17 seconds 441s *** 441s 441s 441s Rank 0 appended 0 elements 441s 441s Rank 1 appended 1 elements 441s *** 441s Step: Generation of contigs 441s Date: Sat Mar 15 16:16:37 2025 441s Elapsed time: 0 seconds 441s Since beginning: 17 seconds 441s *** 441s 441s Rank 0 finished gathering scaffold links. 441s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 442s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 442s Rank 0 ineligibleObjects: 0/970 (0.00%) 442s Rank 1: assembler memory usage: 158404 KiB 442s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 442s Rank 1 finished gathering scaffold links. 442s Rank 0 will write 1 contig lengths 442s Rank 0 will solve the scaffolding problem. 442s Welcome to GreedySolver v1.0 442s 1 vertices; 0 edges 442s 1 contigs >= 500 442s Edges in solution: 0 442s 442s Conflict statistics: 442s 1 scaffolds, 1 >= 500 442s Total: 1000 nucleotides 442s 442s *** 442s Step: Scaffolding of contigs 442s Date: Sat Mar 15 16:16:37 2025 442s Elapsed time: 0 seconds 442s Since beginning: 17 seconds 442s *** 442s Rank 1 syncing with master 442s 442s Rank 0 syncing with master 442s 442s *** 442s Step: Counting sequences to search 442s Date: Sat Mar 15 16:16:37 2025 442s Elapsed time: 0 seconds 442s Since beginning: 17 seconds 442s *** 442s 442s 442s Rank 1 will add colors, 0 sequences in 0 files to process 442s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 442s Rank 0 will add colors, 0 sequences in 0 files to process 442s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 442s 442s *** 442s Step: Graph coloring 442s Date: Sat Mar 15 16:16:38 2025 442s Elapsed time: 1 seconds 442s Since beginning: 18 seconds 442s *** 442s 442s 442s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 442s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 442s Rank 0 shares its counts 442s Rank 1 computing contig abundances [1/1] [1/970] 442s Rank 1 computing contig abundances [1/1] [970/970] 442s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 442s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 442s 442s *** 442s Step: Counting contig biological abundances 442s Date: Sat Mar 15 16:16:38 2025 442s Elapsed time: 0 seconds 442s Since beginning: 18 seconds 442s *** 442s 442s 442s Rank 0 colored the graph with 0 real colors using 1 virtual colors 442s Rank 1 colored the graph with 0 real colors using 1 virtual colors 442s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 442s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 442s 442s *** 442s Step: Counting sequence biological abundances 442s Date: Sat Mar 15 16:16:38 2025 442s Elapsed time: 0 seconds 442s Since beginning: 18 seconds 442s *** 442s 442s 442s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 442s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 442s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 442s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 443s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 443s 443s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 443s 443s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 443s Rank 0 is starting taxon syncing across the compute tribe. 443s 443s *** 443s Step: Loading taxons 443s Date: Sat Mar 15 16:16:39 2025 443s Elapsed time: 1 seconds 443s Since beginning: 19 seconds 443s *** 443s 443s Rank 0 synced taxons across the grid with 2 poor slaves. 443s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 443s Rank 0 has 0 taxons after syncing with master 443s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 443s Rank 1 has 0 taxons after syncing with master 443s 443s 443s 443s *** 443s Step: Loading tree 443s Date: Sat Mar 15 16:16:39 2025 443s Elapsed time: 0 seconds 443s Since beginning: 19 seconds 443s *** 443s 444s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 444s 444s Rank 1: counting ontology terms in the graph... 444s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 444s 444s Rank 0: counting ontology terms in the graph... 445s Rank 1: 0 have some biological signal 445s Number of dereferenced alternate handles: 0 445s Number of k-mer observations with gene ontology terms: 0 445s Rank 0: 0 have some biological signal 445s Number of dereferenced alternate handles: 0 445s Number of k-mer observations with gene ontology terms: 0 445s Rank 0: synced ontology term profiles with master 445s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 445s Rank 1: synced ontology term profiles with master 445s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 445s Rank 0: synchronization is complete! 445s Rank 0: ontology terms with biological signal: 0 445s Populated recursive values... 445s Gene ontology terms without depth information: 0 445s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 445s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 445s 445s *** 445s Step: Processing gene ontologies 445s Date: Sat Mar 15 16:16:41 2025 445s Elapsed time: 2 seconds 445s Since beginning: 21 seconds 445s *** 445s 445s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 445s [GenomeNeighbourhood] in final list: 0 445s 445s *** 445s Step: Computing neighbourhoods 445s Date: Sat Mar 15 16:16:41 2025 445s Elapsed time: 0 seconds 445s Since beginning: 21 seconds 445s *** 445s 445s Contigs >= 100 nt 445s Number: 1 445s Total length: 1000 445s Average: 1000 445s N50: 1000 445s Median: 1000 445s Largest: 1000 445s Contigs >= 500 nt 445s Number: 1 445s Total length: 1000 445s Average: 1000 445s N50: 1000 445s Median: 1000 445s Largest: 1000 445s Scaffolds >= 100 nt 445s Number: 1 445s Total length: 1000 445s Average: 1000 445s N50: 1000 445s Median: 1000 445s Largest: 1000 445s Scaffolds >= 500 nt 445s Number: 1 445s Total length: 1000 445s Average: 1000 445s N50: 1000 445s Median: 1000 445s Largest: 1000 445s 445s Rank 0 wrote test3/Contigs.fasta 445s Rank 0 wrote test3/Scaffolds.fasta 445s Check for test3/* 445s 445s 445s autopkgtest [16:16:41]: test run-unit-test: -----------------------] 446s run-unit-test PASS 446s autopkgtest [16:16:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 446s autopkgtest [16:16:42]: @@@@@@@@@@@@@@@@@@@@ summary 446s run-unit-test PASS 466s nova [W] Using flock in prodstack6-arm64 466s Creating nova instance adt-plucky-arm64-ray-20250315-160916-juju-7f2275-prod-proposed-migration-environment-15-fe550483-345a-4f21-9f94-93fc04805218 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 466s nova [W] Timed out waiting for 5be6b484-6f9e-4093-a8cd-1d3d3d273a45 to get deleted.