0s autopkgtest [21:09:56]: starting date and time: 2024-03-16 21:09:56+0000 0s autopkgtest [21:09:56]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:09:56]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pg0rglqj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-9.secgroup --name adt-noble-arm64-ray-20240316-210955-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 231s autopkgtest [21:13:47]: testbed dpkg architecture: arm64 232s autopkgtest [21:13:48]: testbed apt version: 2.7.12 232s autopkgtest [21:13:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 233s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 234s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 234s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 235s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 235s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3703 kB] 235s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 235s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 235s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 235s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 235s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4017 kB] 236s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 236s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 236s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 250s Fetched 9115 kB in 6s (1410 kB/s) 251s Reading package lists... 258s Reading package lists... 259s Building dependency tree... 259s Reading state information... 262s Calculating upgrade... 263s The following packages will be REMOVED: 263s libglib2.0-0 libssl3 263s The following NEW packages will be installed: 263s libglib2.0-0t64 libssl3t64 xdg-user-dirs 263s The following packages have been kept back: 263s curl 263s The following packages will be upgraded: 263s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 263s 5 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 263s Need to get 4592 kB of archives. 263s After this operation, 211 kB of additional disk space will be used. 263s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 264s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 264s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 264s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 264s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 264s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 264s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 264s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 266s Fetched 4592 kB in 1s (4045 kB/s) 272s (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 ... 75850 files and directories currently installed.) 272s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 272s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 273s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 273s udisks2 depends on libglib2.0-0 (>= 2.77.0). 273s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 273s python3-gi depends on libglib2.0-0 (>= 2.77.0). 273s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 273s netplan.io depends on libglib2.0-0 (>= 2.70.0). 273s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 273s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 273s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 273s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 273s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 273s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 273s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 273s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 273s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 273s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 273s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 273s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 273s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 273s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 273s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 273s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 273s fwupd depends on libglib2.0-0 (>= 2.79.0). 273s bolt depends on libglib2.0-0 (>= 2.56.0). 273s 273s (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 ... 75850 files and directories currently installed.) 274s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 274s Selecting previously unselected package libglib2.0-0t64:arm64. 274s (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 ... 75825 files and directories currently installed.) 274s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 274s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 274s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 274s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 274s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 274s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 276s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 276s wget depends on libssl3 (>= 3.0.0). 276s u-boot-tools depends on libssl3 (>= 3.0.0). 276s tnftp depends on libssl3 (>= 3.0.0). 276s tcpdump depends on libssl3 (>= 3.0.0). 276s systemd-resolved depends on libssl3 (>= 3.0.0). 276s systemd depends on libssl3 (>= 3.0.0). 276s sudo depends on libssl3 (>= 3.0.0). 276s sbsigntool depends on libssl3 (>= 3.0.0). 276s rsync depends on libssl3 (>= 3.0.0). 276s python3-cryptography depends on libssl3 (>= 3.0.0). 276s openssh-server depends on libssl3 (>= 3.0.10). 276s openssh-client depends on libssl3 (>= 3.0.10). 276s mtd-utils depends on libssl3 (>= 3.0.0). 276s mokutil depends on libssl3 (>= 3.0.0). 276s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 276s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 276s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 276s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 276s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 276s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 276s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 276s libnvme1 depends on libssl3 (>= 3.0.0). 276s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 276s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 276s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 276s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 276s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 276s kmod depends on libssl3 (>= 3.0.0). 276s dhcpcd-base depends on libssl3 (>= 3.0.0). 276s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 276s 276s (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 ... 75850 files and directories currently installed.) 276s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 276s Selecting previously unselected package libssl3t64:arm64. 276s (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 ... 75839 files and directories currently installed.) 276s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 276s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 277s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 277s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 277s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 277s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 277s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 277s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 277s Selecting previously unselected package xdg-user-dirs. 278s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 278s Unpacking xdg-user-dirs (0.18-1) ... 278s Setting up xdg-user-dirs (0.18-1) ... 278s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 278s Setting up libtirpc-common (1.3.4+ds-1.1) ... 278s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 278s No schema files found: doing nothing. 278s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 278s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 278s Setting up openssl (3.0.13-0ubuntu1) ... 278s Setting up readline-common (8.2-3.1) ... 278s Processing triggers for man-db (2.12.0-3) ... 281s Processing triggers for install-info (7.1-3) ... 282s Processing triggers for libc-bin (2.39-0ubuntu2) ... 283s Reading package lists... 284s Building dependency tree... 284s Reading state information... 286s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 289s sh: Attempting to set up Debian/Ubuntu apt sources automatically 289s sh: Distribution appears to be Ubuntu 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 295s eatmydata is already the newest version (131-1). 295s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 295s Reading package lists... 296s Building dependency tree... 296s Reading state information... 298s dbus is already the newest version (1.14.10-4ubuntu1). 298s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 302s rng-tools-debian is already the newest version (2.4). 302s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 302s Reading package lists... 302s Building dependency tree... 302s Reading state information... 305s The following packages will be REMOVED: 305s cloud-init* python3-configobj* python3-debconf* 307s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 307s After this operation, 3252 kB disk space will be freed. 308s (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 ... 75866 files and directories currently installed.) 308s Removing cloud-init (24.1.1-0ubuntu1) ... 314s Removing python3-configobj (5.0.8-3) ... 315s Removing python3-debconf (1.5.86) ... 315s Processing triggers for man-db (2.12.0-3) ... 316s (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 ... 75477 files and directories currently installed.) 316s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 321s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 321s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 321s invoke-rc.d: policy-rc.d denied execution of try-restart. 321s Reading package lists... 322s Building dependency tree... 322s Reading state information... 324s linux-generic is already the newest version (6.8.0-11.11+1). 324s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 325s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 325s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 325s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 340s Reading package lists... 340s Reading package lists... 341s Building dependency tree... 341s Reading state information... 343s Calculating upgrade... 344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 344s Reading package lists... 345s Building dependency tree... 345s Reading state information... 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 348s autopkgtest [21:15:44]: rebooting testbed after setup commands that affected boot 515s autopkgtest [21:18:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 519s autopkgtest [21:18:35]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 524s Get:1 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (dsc) [2114 B] 524s Get:2 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (tar) [450 kB] 524s Get:3 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (diff) [213 kB] 526s gpgv: Signature made Wed Dec 6 21:31:12 2023 UTC 526s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 526s gpgv: issuer "tille@debian.org" 526s gpgv: Can't check signature: No public key 526s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8.dsc: no acceptable signature found 527s autopkgtest [21:18:43]: testing package ray version 2.3.1-8 528s autopkgtest [21:18:44]: build not needed 528s autopkgtest [21:18:44]: test run-unit-test: preparing testbed 530s Reading package lists... 531s Building dependency tree... 531s Reading state information... 531s Starting pkgProblemResolver with broken count: 0 532s Starting 2 pkgProblemResolver with broken count: 0 532s Done 533s The following additional packages will be installed: 533s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 533s libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libcairo2 libdatrie1 533s libdeflate0 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfontconfig1 533s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 533s libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 533s libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3 libpango-1.0-0 533s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 533s libpixman-1-0 libpmix2 librdmacm1t64 libsharpyuv0 libsm6 libtcl8.6 533s libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 libxcb-render0 533s libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 mpi-default-bin 533s ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core ray ray-doc 533s ray-extra unzip x11-common xdg-utils zip 534s Suggested packages: 534s tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler elpa-ess r-doc-info 534s | r-doc-pdf r-mathlib r-base-html 534s Recommended packages: 534s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 534s libx11-protocol-perl x11-utils x11-xserver-utils 534s The following NEW packages will be installed: 534s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 534s fonts-dejavu-mono libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libcairo2 534s libdatrie1 libdeflate0 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 534s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 534s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 534s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3 534s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 534s libpaper1 libpciaccess0 libpixman-1-0 libpmix2 librdmacm1t64 libsharpyuv0 534s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 534s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 534s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 534s ray ray-doc ray-extra unzip x11-common xdg-utils zip 534s 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. 534s Need to get 88.0 MB/88.0 MB of archives. 534s After this operation, 300 MB of additional disk space will be used. 534s Get:1 /tmp/autopkgtest.hGUJkb/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 534s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 534s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 535s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 535s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 535s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 535s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 536s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 536s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 536s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 536s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 536s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 536s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 536s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 536s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 536s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 536s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 536s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 536s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 537s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 537s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 537s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 537s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 537s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 537s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 537s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 537s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 537s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 537s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 537s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 537s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 537s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 537s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 537s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 537s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 537s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 537s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 537s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 537s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 537s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 537s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 libpmix2 arm64 5.0.1-4 [659 kB] 537s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 537s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmpi3 arm64 4.1.6-5ubuntu1 [3081 kB] 537s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 537s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 537s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 537s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 537s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 537s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 537s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 537s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 537s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 537s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 537s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 537s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 537s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 537s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 537s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 537s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 537s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 537s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] 537s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 openmpi-bin arm64 4.1.6-5ubuntu1 [123 kB] 537s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 537s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 537s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 537s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 538s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-bin arm64 1.15 [2336 B] 538s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 ray arm64 2.3.1-8 [727 kB] 539s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 ray-doc all 2.3.1-8 [35.2 kB] 539s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 ray-extra all 2.3.1-8 [12.3 kB] 540s Preconfiguring packages ... 540s Fetched 88.0 MB in 5s (18.6 MB/s) 540s Selecting previously unselected package fonts-dejavu-mono. 541s (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 ... 75422 files and directories currently installed.) 541s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 541s Unpacking fonts-dejavu-mono (2.37-8) ... 541s Selecting previously unselected package fonts-dejavu-core. 541s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 541s Unpacking fonts-dejavu-core (2.37-8) ... 541s Selecting previously unselected package fontconfig-config. 541s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 542s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 542s Selecting previously unselected package libfontconfig1:arm64. 542s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 542s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 542s Selecting previously unselected package fontconfig. 542s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 542s Unpacking fontconfig (2.15.0-1ubuntu1) ... 542s Selecting previously unselected package libllvm17:arm64. 542s Preparing to unpack .../05-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 542s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 544s Selecting previously unselected package libamd-comgr2:arm64. 544s Preparing to unpack .../06-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 544s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 546s Selecting previously unselected package libdrm-amdgpu1:arm64. 546s Preparing to unpack .../07-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 546s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 546s Selecting previously unselected package libhsakmt1:arm64. 546s Preparing to unpack .../08-libhsakmt1_5.7.0-1_arm64.deb ... 546s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 546s Selecting previously unselected package libhsa-runtime64-1. 546s Preparing to unpack .../09-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 546s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 546s Selecting previously unselected package libamdhip64-5. 546s Preparing to unpack .../10-libamdhip64-5_5.2.3-12_arm64.deb ... 546s Unpacking libamdhip64-5 (5.2.3-12) ... 547s Selecting previously unselected package libatomic1:arm64. 547s Preparing to unpack .../11-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 547s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 547s Selecting previously unselected package libblas3:arm64. 547s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 547s Unpacking libblas3:arm64 (3.12.0-3) ... 547s Selecting previously unselected package libpixman-1-0:arm64. 547s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_arm64.deb ... 547s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 547s Selecting previously unselected package libxcb-render0:arm64. 547s Preparing to unpack .../14-libxcb-render0_1.15-1_arm64.deb ... 547s Unpacking libxcb-render0:arm64 (1.15-1) ... 547s Selecting previously unselected package libxcb-shm0:arm64. 547s Preparing to unpack .../15-libxcb-shm0_1.15-1_arm64.deb ... 547s Unpacking libxcb-shm0:arm64 (1.15-1) ... 547s Selecting previously unselected package libxrender1:arm64. 547s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 547s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 547s Selecting previously unselected package libcairo2:arm64. 547s Preparing to unpack .../17-libcairo2_1.18.0-1_arm64.deb ... 547s Unpacking libcairo2:arm64 (1.18.0-1) ... 547s Selecting previously unselected package libdatrie1:arm64. 547s Preparing to unpack .../18-libdatrie1_0.2.13-3_arm64.deb ... 547s Unpacking libdatrie1:arm64 (0.2.13-3) ... 548s Selecting previously unselected package libdeflate0:arm64. 548s Preparing to unpack .../19-libdeflate0_1.19-1_arm64.deb ... 548s Unpacking libdeflate0:arm64 (1.19-1) ... 548s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 548s Preparing to unpack .../20-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 548s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 548s Selecting previously unselected package librdmacm1t64:arm64. 548s Preparing to unpack .../21-librdmacm1t64_50.0-2_arm64.deb ... 548s Unpacking librdmacm1t64:arm64 (50.0-2) ... 548s Selecting previously unselected package libfabric1:arm64. 548s Preparing to unpack .../22-libfabric1_1.17.0-3_arm64.deb ... 548s Unpacking libfabric1:arm64 (1.17.0-3) ... 548s Selecting previously unselected package libgfortran5:arm64. 548s Preparing to unpack .../23-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 548s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 548s Selecting previously unselected package libgomp1:arm64. 548s Preparing to unpack .../24-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 548s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 548s Selecting previously unselected package libgraphite2-3:arm64. 548s Preparing to unpack .../25-libgraphite2-3_1.3.14-2_arm64.deb ... 548s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 548s Selecting previously unselected package libharfbuzz0b:arm64. 548s Preparing to unpack .../26-libharfbuzz0b_8.3.0-2_arm64.deb ... 548s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 548s Selecting previously unselected package libhwloc15:arm64. 548s Preparing to unpack .../27-libhwloc15_2.10.0-1_arm64.deb ... 548s Unpacking libhwloc15:arm64 (2.10.0-1) ... 549s Selecting previously unselected package x11-common. 549s Preparing to unpack .../28-x11-common_1%3a7.7+23ubuntu2_all.deb ... 549s Unpacking x11-common (1:7.7+23ubuntu2) ... 549s Selecting previously unselected package libice6:arm64. 549s Preparing to unpack .../29-libice6_2%3a1.0.10-1build2_arm64.deb ... 549s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 549s Selecting previously unselected package libjpeg-turbo8:arm64. 549s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 549s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 549s Selecting previously unselected package libjpeg8:arm64. 549s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_arm64.deb ... 549s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 549s Selecting previously unselected package liblapack3:arm64. 549s Preparing to unpack .../32-liblapack3_3.12.0-3_arm64.deb ... 549s Unpacking liblapack3:arm64 (3.12.0-3) ... 549s Selecting previously unselected package liblerc4:arm64. 549s Preparing to unpack .../33-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 549s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 549s Selecting previously unselected package libmunge2:arm64. 549s Preparing to unpack .../34-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 549s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 549s Selecting previously unselected package libpciaccess0:arm64. 549s Preparing to unpack .../35-libpciaccess0_0.17-3_arm64.deb ... 549s Unpacking libpciaccess0:arm64 (0.17-3) ... 550s Selecting previously unselected package libxnvctrl0:arm64. 550s Preparing to unpack .../36-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 550s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 550s Selecting previously unselected package ocl-icd-libopencl1:arm64. 550s Preparing to unpack .../37-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 550s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 550s Selecting previously unselected package libhwloc-plugins:arm64. 550s Preparing to unpack .../38-libhwloc-plugins_2.10.0-1_arm64.deb ... 550s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 550s Selecting previously unselected package libpmix2:arm64. 550s Preparing to unpack .../39-libpmix2_5.0.1-4_arm64.deb ... 550s Unpacking libpmix2:arm64 (5.0.1-4) ... 550s Selecting previously unselected package libucx0:arm64. 550s Preparing to unpack .../40-libucx0_1.16.0+ds-4_arm64.deb ... 550s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 550s Selecting previously unselected package libopenmpi3:arm64. 550s Preparing to unpack .../41-libopenmpi3_4.1.6-5ubuntu1_arm64.deb ... 550s Unpacking libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 551s Selecting previously unselected package libthai-data. 551s Preparing to unpack .../42-libthai-data_0.1.29-2_all.deb ... 551s Unpacking libthai-data (0.1.29-2) ... 551s Selecting previously unselected package libthai0:arm64. 551s Preparing to unpack .../43-libthai0_0.1.29-2_arm64.deb ... 551s Unpacking libthai0:arm64 (0.1.29-2) ... 551s Selecting previously unselected package libpango-1.0-0:arm64. 551s Preparing to unpack .../44-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 551s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 551s Selecting previously unselected package libpangoft2-1.0-0:arm64. 551s Preparing to unpack .../45-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 551s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 551s Selecting previously unselected package libpangocairo-1.0-0:arm64. 551s Preparing to unpack .../46-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 551s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 551s Selecting previously unselected package libpaper1:arm64. 551s Preparing to unpack .../47-libpaper1_1.1.29_arm64.deb ... 551s Unpacking libpaper1:arm64 (1.1.29) ... 551s Selecting previously unselected package libpaper-utils. 551s Preparing to unpack .../48-libpaper-utils_1.1.29_arm64.deb ... 551s Unpacking libpaper-utils (1.1.29) ... 551s Selecting previously unselected package libsharpyuv0:arm64. 551s Preparing to unpack .../49-libsharpyuv0_1.3.2-0.4_arm64.deb ... 551s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 551s Selecting previously unselected package libsm6:arm64. 551s Preparing to unpack .../50-libsm6_2%3a1.2.3-1build2_arm64.deb ... 551s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 552s Selecting previously unselected package libtcl8.6:arm64. 552s Preparing to unpack .../51-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 552s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 552s Selecting previously unselected package libjbig0:arm64. 552s Preparing to unpack .../52-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 552s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 552s Selecting previously unselected package libwebp7:arm64. 552s Preparing to unpack .../53-libwebp7_1.3.2-0.4_arm64.deb ... 552s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 552s Selecting previously unselected package libtiff6:arm64. 552s Preparing to unpack .../54-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 552s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 552s Selecting previously unselected package libxft2:arm64. 552s Preparing to unpack .../55-libxft2_2.3.6-1_arm64.deb ... 552s Unpacking libxft2:arm64 (2.3.6-1) ... 552s Selecting previously unselected package libxss1:arm64. 552s Preparing to unpack .../56-libxss1_1%3a1.2.3-1build2_arm64.deb ... 552s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 552s Selecting previously unselected package libtk8.6:arm64. 552s Preparing to unpack .../57-libtk8.6_8.6.13-2_arm64.deb ... 552s Unpacking libtk8.6:arm64 (8.6.13-2) ... 553s Selecting previously unselected package libxt6:arm64. 553s Preparing to unpack .../58-libxt6_1%3a1.2.1-1.1_arm64.deb ... 553s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 553s Selecting previously unselected package openmpi-common. 553s Preparing to unpack .../59-openmpi-common_4.1.6-5ubuntu1_all.deb ... 553s Unpacking openmpi-common (4.1.6-5ubuntu1) ... 553s Selecting previously unselected package openmpi-bin. 553s Preparing to unpack .../60-openmpi-bin_4.1.6-5ubuntu1_arm64.deb ... 553s Unpacking openmpi-bin (4.1.6-5ubuntu1) ... 553s Selecting previously unselected package zip. 553s Preparing to unpack .../61-zip_3.0-13_arm64.deb ... 553s Unpacking zip (3.0-13) ... 553s Selecting previously unselected package unzip. 553s Preparing to unpack .../62-unzip_6.0-28ubuntu3_arm64.deb ... 553s Unpacking unzip (6.0-28ubuntu3) ... 553s Selecting previously unselected package xdg-utils. 553s Preparing to unpack .../63-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 553s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 553s Selecting previously unselected package r-base-core. 554s Preparing to unpack .../64-r-base-core_4.3.2-1build1_arm64.deb ... 554s Unpacking r-base-core (4.3.2-1build1) ... 555s Selecting previously unselected package mpi-default-bin. 555s Preparing to unpack .../65-mpi-default-bin_1.15_arm64.deb ... 555s Unpacking mpi-default-bin (1.15) ... 555s Selecting previously unselected package ray. 555s Preparing to unpack .../66-ray_2.3.1-8_arm64.deb ... 555s Unpacking ray (2.3.1-8) ... 555s Selecting previously unselected package ray-doc. 555s Preparing to unpack .../67-ray-doc_2.3.1-8_all.deb ... 555s Unpacking ray-doc (2.3.1-8) ... 556s Selecting previously unselected package ray-extra. 556s Preparing to unpack .../68-ray-extra_2.3.1-8_all.deb ... 556s Unpacking ray-extra (2.3.1-8) ... 556s Selecting previously unselected package autopkgtest-satdep. 556s Preparing to unpack .../69-1-autopkgtest-satdep.deb ... 556s Unpacking autopkgtest-satdep (0) ... 556s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 556s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 556s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 556s Setting up libpaper1:arm64 (1.1.29) ... 556s 556s Creating config file /etc/papersize with new version 557s Setting up ray-doc (2.3.1-8) ... 557s Setting up libpciaccess0:arm64 (0.17-3) ... 557s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 557s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 557s Setting up libdatrie1:arm64 (0.2.13-3) ... 557s Setting up libxcb-render0:arm64 (1.15-1) ... 557s Setting up unzip (6.0-28ubuntu3) ... 557s Setting up x11-common (1:7.7+23ubuntu2) ... 558s Setting up libdeflate0:arm64 (1.19-1) ... 558s Setting up libxcb-shm0:arm64 (1.15-1) ... 558s Setting up libpaper-utils (1.1.29) ... 558s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 558s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 558s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 558s Setting up zip (3.0-13) ... 558s Setting up libblas3:arm64 (3.12.0-3) ... 558s 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 558s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 558s Setting up fonts-dejavu-mono (2.37-8) ... 558s Setting up libhwloc15:arm64 (2.10.0-1) ... 558s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 558s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 558s Setting up fonts-dejavu-core (2.37-8) ... 558s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 558s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 558s Setting up libwebp7:arm64 (1.3.2-0.4) ... 558s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 558s Setting up openmpi-common (4.1.6-5ubuntu1) ... 558s Setting up librdmacm1t64:arm64 (50.0-2) ... 558s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 558s Setting up libthai-data (0.1.29-2) ... 558s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 558s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 558s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 558s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 559s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 559s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 559s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 559s Setting up libfabric1:arm64 (1.17.0-3) ... 559s Setting up libice6:arm64 (2:1.0.10-1build2) ... 559s Setting up liblapack3:arm64 (3.12.0-3) ... 559s 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 559s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 559s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 559s Setting up libthai0:arm64 (0.1.29-2) ... 559s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 559s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 559s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 559s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 559s Setting up libhsakmt1:arm64 (5.7.0-1) ... 559s Setting up fontconfig (2.15.0-1ubuntu1) ... 561s Regenerating fonts cache... done. 561s Setting up libxft2:arm64 (2.3.6-1) ... 561s Setting up libpmix2:arm64 (5.0.1-4) ... 561s Setting up libtk8.6:arm64 (8.6.13-2) ... 561s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 561s Setting up libcairo2:arm64 (1.18.0-1) ... 561s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 561s Setting up libhsa-runtime64-1 (5.7.1-1) ... 561s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 561s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 561s Setting up libamdhip64-5 (5.2.3-12) ... 561s Setting up r-base-core (4.3.2-1build1) ... 562s 562s Creating config file /etc/R/Renviron with new version 563s Setting up libucx0:arm64 (1.16.0+ds-4) ... 563s Setting up libopenmpi3:arm64 (4.1.6-5ubuntu1) ... 563s Setting up ray-extra (2.3.1-8) ... 563s Setting up openmpi-bin (4.1.6-5ubuntu1) ... 563s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 563s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 563s Setting up mpi-default-bin (1.15) ... 563s Setting up ray (2.3.1-8) ... 563s Setting up autopkgtest-satdep (0) ... 563s Processing triggers for man-db (2.12.0-3) ... 568s Processing triggers for install-info (7.1-3) ... 568s Processing triggers for libc-bin (2.39-0ubuntu2) ... 581s (Reading database ... 78069 files and directories currently installed.) 581s Removing autopkgtest-satdep (0) ... 583s autopkgtest [21:19:39]: test run-unit-test: [----------------------- 585s 585s ************************************************** 585s This program comes with ABSOLUTELY NO WARRANTY. 585s This is free software, and you are welcome to redistribute it 585s under certain conditions; see "LICENSE.txt" for details. 585s ************************************************** 585s 585s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 585s Centre de recherche en infectiologie de l'Université Laval 585s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 585s http://denovoassembler.sf.net/ 585s 585s References to cite: 585s 585s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 585s Ray Meta: scalable de novo metagenome assembly and profiling. 585s Genome Biology (BioMed Central Ltd). 585s 13:R122, Published: 22 December 2012 585s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 585s 585s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 585s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 585s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 585s November 2010, Volume 17, Issue 11, Pages 1519-1533. 585s http://dx.doi.org/doi:10.1089/cmb.2009.0238 585s 585s Ray version 2.3.1 585s License for Ray: GNU General Public License version 3 585s RayPlatform version: 2.0.1 585s License for RayPlatform: GNU Lesser General Public License version 3 585s 585s MAXKMERLENGTH: 32 585s Maximum coverage depth stored by CoverageDepth: 4294967295 585s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 585s FORCE_PACKING = n 585s ASSERT = n 585s HAVE_LIBZ = y 585s HAVE_LIBBZ2 = y 585s PROFILER_COLLECT = n 585s MINIRANKS = y 585s CLOCK_GETTIME = n 585s __linux__ = y 585s _MSC_VER = n 585s __GNUC__ = y 585s RAY_32_BITS = n 585s RAY_64_BITS = y 585s MPI standard version: MPI 3.1 585s MPI library: Open-MPI 4.1.6 585s Compiler: GNU gcc/g++ 13.2.0 585s MPI I/O: n 585s 585s 585s -k (to set the k-mer size) 585s Value: 31 585s 585s 585s Paired library # 0 585s -p (paired-end sequences) 585s Left sequences: ecoli_1K_1.fq 585s Right sequences: ecoli_1K_2.fq 585s Average length: automatic detection 585s Standard deviation: automatic detection 585s 585s Ray command: 585s mpiexec -n 1 Ray \ 585s -k \ 585s 31 \ 585s -p \ 585s ecoli_1K_1.fq \ 585s ecoli_1K_2.fq \ 585s -o \ 585s test1 585s 585s Rank 0 wrote test1/RayCommand.txt 585s 585s k-mer length: 31 585s Rank 0: assembler memory usage: 42736 KiB 585s Rank 0: assembler memory usage: 108408 KiB 585s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2513 585s Rank 0: testing the network, please wait... 585s 585s Rank 0 is testing the network [0/1000] 585s Rank 0 is testing the network [1000/1000] 585s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 585s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 7 microseconds (10^-6 seconds) 585s 585s Rank 0 wrote test1/NetworkTest.txt 585s 585s 585s *** 585s Step: Network testing 585s Date: Sat Mar 16 21:19:41 2024 585s Elapsed time: 0 seconds 585s Since beginning: 0 seconds 585s *** 585s 585s 585s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 585s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 585s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 585s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 585s Rank 0 wrote test1/NumberOfSequences.txt 585s Rank 0 wrote test1/SequencePartition.txt 585s 585s *** 585s Step: Counting sequences to assemble 585s Date: Sat Mar 16 21:19:41 2024 585s Elapsed time: 0 seconds 585s Since beginning: 0 seconds 585s *** 585s 585s 585s Rank 0 is loading sequence reads 585s Rank 0 : partition is [0;4107], 4108 sequence reads 585s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 585s Rank 0 has 0 sequence reads 585s Rank 0: assembler memory usage: 121392 KiB 585s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 585s Rank 0 has 4108 sequence reads (completed) 585s 585s *** 585s Step: Sequence loading 585s Date: Sat Mar 16 21:19:41 2024 585s Elapsed time: 0 seconds 585s Since beginning: 0 seconds 585s *** 585s 585s 585s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 585s Rank 0 created its Bloom filter 586s Rank 0 is counting k-mers in sequence reads [1/4108] 586s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 586s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 586s 586s 586s *** 586s Step: K-mer counting 586s Date: Sat Mar 16 21:19:42 2024 586s Elapsed time: 1 seconds 586s Since beginning: 1 seconds 586s *** 586s 586s 586s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 586s Rank 0 destroyed its Bloom filter 586s Rank 0 has 1954 k-mers (completed) 586s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 586s Rank 0: assembler memory usage: 117788 KiB 590s 590s 590s Rank 0: the minimum coverage is 3 590s Rank 0: the peak coverage is 3 590s Warning: no peak observed in the k-mer coverage distribution. 590s to deal with the sequencing error rate, try to lower the k-mer length (-k) 590s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 590s 590s *** 590s Step: Coverage distribution analysis 590s Date: Sat Mar 16 21:19:46 2024 590s Elapsed time: 4 seconds 590s Since beginning: 5 seconds 590s *** 590s 590s 590s 591s Rank 0 is adding edges [1/4108] 591s Rank 0 is adding edges [4108/4108] (completed) 591s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 591s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 591s 591s *** 591s Step: Graph construction 591s Date: Sat Mar 16 21:19:47 2024 591s Elapsed time: 1 seconds 591s Since beginning: 6 seconds 591s *** 591s 591s 591s Rank 0 has 1954 vertices (completed) 591s Rank 0: assembler memory usage: 117788 KiB 596s Rank 0 is purging edges [1/1954] 596s Rank 0 is purging edges [1954/1954] (completed) 596s Rank 0: assembler memory usage: 118316 KiB 596s VirtualProcessor: completed jobs: 1954 596s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 600s Rank 0 wrote test1/degreeDistribution.txt 600s 600s *** 600s Step: Null edge purging 600s Date: Sat Mar 16 21:19:56 2024 600s Elapsed time: 9 seconds 600s Since beginning: 15 seconds 600s *** 600s 600s 600s Rank 0 is selecting optimal read markers [1/4108] 600s Rank 0: assembler memory usage: 118316 KiB 601s Rank 0 is selecting optimal read markers [4108/4108] (completed) 601s Rank 0: peak number of workers: 599, maximum: 32768 601s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 601s Rank 0: assembler memory usage: 126480 KiB 601s Rank 0: Freeing unused assembler memory: 4096 KiB freed 601s Rank 0: assembler memory usage: 126480 KiB 601s 601s *** 601s Step: Selection of optimal read markers 601s Date: Sat Mar 16 21:19:57 2024 601s Elapsed time: 1 seconds 601s Since beginning: 16 seconds 601s *** 601s 601s 601s Rank 0: memory usage for optimal read markers= 4096 KiB 601s Rank 0 is creating seeds [1/1954] 601s Rank 0: assembler memory usage: 126480 KiB 606s Rank 0 has 1 seeds 606s Rank 0 is creating seeds [1954/1954] (completed) 606s Rank 0: peak number of workers: 746, maximum: 32768 606s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 606s Rank 0 runtime statistics for seeding algorithm: 606s Rank 0 Skipped paths because of dead end for head: 0 606s Rank 0 Skipped paths because of dead end for tail: 0 606s Rank 0 Skipped paths because of two dead ends: 0 606s Rank 0 Skipped paths because of bubble weak component: 0 606s Rank 0 Skipped paths because of short length: 1952 606s Rank 0 Skipped paths because of bad ownership: 1 606s Rank 0 Skipped paths because of low coverage: 0 606s Rank 0 Eligible paths: 1 606s Rank 0: assembler memory usage: 126480 KiB 606s Rank 0 has 1 seeds to register. 606s Rank 0 registered 0/1 606s Rank 0 registered 0/1 606s Rank 0 registered its seeds 606s VirtualProcessor: completed jobs: 0 606s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 611s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 620s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 620s Rank 0 merged its seeds: 1 seeds -> 1 seeds 620s 620s *** 620s Step: Detection of assembly seeds 620s Date: Sat Mar 16 21:20:16 2024 620s Elapsed time: 19 seconds 620s Since beginning: 35 seconds 620s *** 620s 620s 620s Rank 0 is calculating library lengths [1/1] 620s Rank 0 detected 1737 library lengths 620s Rank 0 is calculating library lengths [1/1] (completed) 620s Rank 0: peak number of workers: 1, maximum: 32768 620s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 620s Rank 0: assembler memory usage: 163348 KiB 620s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 620s 620s Mode= 2 signalAverage= 9 620s CURRENT IS NOISE, 244 620s GOT HIT 212 620s 620s 620s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 620s 620s *** 620s Step: Estimation of outer distances for paired reads 620s Date: Sat Mar 16 21:20:16 2024 620s Elapsed time: 0 seconds 620s Since beginning: 35 seconds 620s *** 620s 620s 621s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 621s Rank 0 traversed 1000 nucleotide symbols 621s Rank 0: assembler memory usage: 167444 KiB 621s Rank 0 is extending seeds [1/1] (completed) 621s Rank 0 extended 1 seeds out of 1 (100.00%) 621s Rank 0: assembler memory usage: 159252 KiB 621s Rank 0 starting fusions 621s 621s *** 621s Step: Bidirectional extension of seeds 621s Date: Sat Mar 16 21:20:17 2024 621s Elapsed time: 1 seconds 621s Since beginning: 36 seconds 621s *** 621s 621s 621s Rank 0: starting clear step. cycleNumber= 0 626s Rank 0 adding 0 new fusions 626s Rank 0 cleared, 1 paths 626s Rank 0: starting distribution step 626s Rank 0 is distributing fusions [1/1] 626s Rank 0: assembler memory usage: 159252 KiB 626s Date: Sat Mar 16 21:20:22 2024 626s Rank 0 is distributing fusions [1/1] (completed) 626s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 626s Rank 0: assembler memory usage: 163348 KiB 626s Date: Sat Mar 16 21:20:22 2024 626s Rank 0 tells others to compute fusions. 626s Rank 0 FusionTaskCreator assignNextTask [0/2] 626s Rank 0: assembler memory usage: 163348 KiB 626s Date: Sat Mar 16 21:20:22 2024 626s Rank 0 FusionTaskCreator processWorkerResult [0/2] 626s Rank 0: assembler memory usage: 163348 KiB 626s Date: Sat Mar 16 21:20:22 2024 626s Rank 0 FusionTaskCreator [2/2] 626s Statistics: all paths: 1 eliminated during fusing: 0 626s Rank 0: assembler memory usage: 163348 KiB 626s VirtualProcessor: completed jobs: 2 626s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 626s Rank 0: starting clear step. cycleNumber= 1 630s Rank 0 adding 0 new fusions 630s Rank 0 cleared, 1 paths 630s Rank 0 is distributing fusions [1/1] 630s Rank 0: assembler memory usage: 163348 KiB 630s Date: Sat Mar 16 21:20:26 2024 630s Rank 0 is distributing fusions [1/1] (completed) 630s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 630s Rank 0: assembler memory usage: 163348 KiB 630s Date: Sat Mar 16 21:20:26 2024 630s Rank 0 JoinerTaskCreator assignNextTask [0/2] 630s Rank 0: assembler memory usage: 163348 KiB 630s Date: Sat Mar 16 21:20:26 2024 630s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 630s Rank 0: assembler memory usage: 163348 KiB 630s Date: Sat Mar 16 21:20:26 2024 630s Rank 0 JoinerTaskCreator [2/2] 630s Statistics: all paths: 1 eliminated during joining: 0 630s Rank 0: assembler memory usage: 163348 KiB 630s Date: Sat Mar 16 21:20:26 2024 630s VirtualProcessor: completed jobs: 2 630s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 635s Rank 0 adding 0 new fusions 635s Rank 0 cleared, 1 paths 635s Rank 0: starting distribution step 635s Rank 0 is distributing fusions [1/1] 635s Rank 0: assembler memory usage: 163348 KiB 635s Date: Sat Mar 16 21:20:31 2024 635s Rank 0 is distributing fusions [1/1] (completed) 635s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 635s Rank 0: assembler memory usage: 163348 KiB 635s Date: Sat Mar 16 21:20:31 2024 635s Rank 0 tells others to compute fusions. 635s Rank 0 FusionTaskCreator assignNextTask [0/2] 635s Rank 0: assembler memory usage: 163348 KiB 635s Date: Sat Mar 16 21:20:31 2024 635s Rank 0 FusionTaskCreator processWorkerResult [0/2] 635s Rank 0: assembler memory usage: 163348 KiB 635s Date: Sat Mar 16 21:20:31 2024 635s Rank 0 FusionTaskCreator [2/2] 635s Statistics: all paths: 1 eliminated during fusing: 0 635s Rank 0: assembler memory usage: 163348 KiB 635s VirtualProcessor: completed jobs: 2 635s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 635s Rank 0: starting clear step. cycleNumber= 2 639s Rank 0 adding 0 new fusions 639s Rank 0 cleared, 1 paths 639s Rank 0 is distributing fusions [1/1] 639s Rank 0: assembler memory usage: 163348 KiB 639s Date: Sat Mar 16 21:20:35 2024 639s Rank 0 is distributing fusions [1/1] (completed) 639s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 639s Rank 0: assembler memory usage: 163348 KiB 639s Date: Sat Mar 16 21:20:35 2024 639s Rank 0 JoinerTaskCreator assignNextTask [0/2] 639s Rank 0: assembler memory usage: 163348 KiB 639s Date: Sat Mar 16 21:20:35 2024 639s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 639s Rank 0: assembler memory usage: 163348 KiB 639s Date: Sat Mar 16 21:20:35 2024 639s Rank 0 JoinerTaskCreator [2/2] 639s Statistics: all paths: 1 eliminated during joining: 0 639s Rank 0: assembler memory usage: 163348 KiB 639s Date: Sat Mar 16 21:20:35 2024 639s VirtualProcessor: completed jobs: 2 639s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 644s Rank 0 adding 0 new fusions 644s Rank 0 cleared, 1 paths 644s Rank 0: starting distribution step 644s Rank 0 is distributing fusions [1/1] 644s Rank 0: assembler memory usage: 163348 KiB 644s Date: Sat Mar 16 21:20:40 2024 644s Rank 0 is distributing fusions [1/1] (completed) 644s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 644s Rank 0: assembler memory usage: 163348 KiB 644s Date: Sat Mar 16 21:20:40 2024 644s Rank 0 cycleNumber= 2 644s 644s *** 644s Step: Merging of redundant paths 644s Date: Sat Mar 16 21:20:40 2024 644s Elapsed time: 23 seconds 644s Since beginning: 59 seconds 644s *** 644s 644s 644s Rank 0 appended 1 elements 644s 644s *** 644s Step: Generation of contigs 644s Date: Sat Mar 16 21:20:40 2024 644s Elapsed time: 0 seconds 644s Since beginning: 59 seconds 644s *** 644s 644s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 644s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 644s Rank 0 ineligibleObjects: 0/970 (0.00%) 644s Rank 0: assembler memory usage: 163348 KiB 644s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 644s Rank 0 finished gathering scaffold links. 644s Rank 0 will write 1 contig lengths 644s Rank 0 will solve the scaffolding problem. 644s Welcome to GreedySolver v1.0 644s 1 vertices; 0 edges 644s 1 contigs >= 500 644s Edges in solution: 0 644s 644s Conflict statistics: 644s 1 scaffolds, 1 >= 500 644s Total: 1000 nucleotides 644s 644s *** 644s Step: Scaffolding of contigs 644s Date: Sat Mar 16 21:20:40 2024 644s Elapsed time: 0 seconds 644s Since beginning: 59 seconds 644s *** 644s 644s Rank 0 syncing with master 644s 644s *** 644s Step: Counting sequences to search 644s Date: Sat Mar 16 21:20:40 2024 644s Elapsed time: 0 seconds 644s Since beginning: 59 seconds 644s *** 644s 644s 644s Rank 0 will add colors, 0 sequences in 0 files to process 644s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 649s 649s *** 649s Step: Graph coloring 649s Date: Sat Mar 16 21:20:45 2024 649s Elapsed time: 5 seconds 649s Since beginning: 1 minutes, 4 seconds 649s *** 649s 649s 649s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 649s Rank 0 shares its counts 649s Rank 0 computing contig abundances [1/1] [1/970] 649s Rank 0 computing contig abundances [1/1] [970/970] 649s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 649s 649s *** 649s Step: Counting contig biological abundances 649s Date: Sat Mar 16 21:20:45 2024 649s Elapsed time: 0 seconds 649s Since beginning: 1 minutes, 4 seconds 649s *** 649s 649s 649s Rank 0 colored the graph with 0 real colors using 1 virtual colors 649s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 649s 649s *** 649s Step: Counting sequence biological abundances 649s Date: Sat Mar 16 21:20:45 2024 649s Elapsed time: 0 seconds 649s Since beginning: 1 minutes, 4 seconds 649s *** 649s 649s 649s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 649s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 653s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 653s 653s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 653s Rank 0 is starting taxon syncing across the compute tribe. 653s 653s *** 653s Step: Loading taxons 653s Date: Sat Mar 16 21:20:49 2024 653s Elapsed time: 4 seconds 653s Since beginning: 1 minutes, 8 seconds 653s *** 653s 653s Rank 0 synced taxons across the grid with 1 poor slaves. 653s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 653s Rank 0 has 0 taxons after syncing with master 657s 657s 657s *** 657s Step: Loading tree 657s Date: Sat Mar 16 21:20:53 2024 657s Elapsed time: 4 seconds 657s Since beginning: 1 minutes, 12 seconds 657s *** 657s 662s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 662s 662s Rank 0: counting ontology terms in the graph... 666s Rank 0: 0 have some biological signal 666s Number of dereferenced alternate handles: 0 666s Number of k-mer observations with gene ontology terms: 0 666s Rank 0: synced ontology term profiles with master 666s Rank 0: synchronization is complete! 666s Rank 0: ontology terms with biological signal: 0 666s Populated recursive values... 666s Gene ontology terms without depth information: 0 666s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 666s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 666s 666s *** 666s Step: Processing gene ontologies 666s Date: Sat Mar 16 21:21:02 2024 666s Elapsed time: 9 seconds 666s Since beginning: 1 minutes, 21 seconds 666s *** 666s 666s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 666s [GenomeNeighbourhood] in final list: 0 666s 666s *** 666s Step: Computing neighbourhoods 666s Date: Sat Mar 16 21:21:02 2024 666s Elapsed time: 0 seconds 666s Since beginning: 1 minutes, 21 seconds 666s *** 666s 666s Contigs >= 100 nt 666s Number: 1 666s Total length: 1000 666s Average: 1000 666s N50: 1000 666s Median: 1000 666s Largest: 1000 666s Contigs >= 500 nt 666s Number: 1 666s Total length: 1000 666s Average: 1000 666s N50: 1000 666s Median: 1000 666s Largest: 1000 666s Scaffolds >= 100 nt 666s Number: 1 666s Total length: 1000 666s Average: 1000 666s N50: 1000 666s Median: 1000 666s Largest: 1000 666s Scaffolds >= 500 nt 666s Number: 1 666s Total length: 1000 666s Average: 1000 666s N50: 1000 666s Median: 1000 666s Largest: 1000 666s 666s Rank 0 wrote test1/Contigs.fasta 666s Rank 0 wrote test1/Scaffolds.fasta 666s Check for test1/* 666s 666s 667s 667s ************************************************** 667s This program comes with ABSOLUTELY NO WARRANTY. 667s This is free software, and you are welcome to redistribute it 667s under certain conditions; see "LICENSE.txt" for details. 667s ************************************************** 667s 667s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 667s Centre de recherche en infectiologie de l'Université Laval 667s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 667s http://denovoassembler.sf.net/ 667s 667s References to cite: 667s 667s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 667s Ray Meta: scalable de novo metagenome assembly and profiling. 667s Genome Biology (BioMed Central Ltd). 667s 13:R122, Published: 22 December 2012 667s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 667s 667s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 667s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 667s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 667s November 2010, Volume 17, Issue 11, Pages 1519-1533. 667s http://dx.doi.org/doi:10.1089/cmb.2009.0238 667s 667s Ray version 2.3.1 667s License for Ray: GNU General Public License version 3 667s RayPlatform version: 2.0.1 667s License for RayPlatform: GNU Lesser General Public License version 3 667s 667s MAXKMERLENGTH: 32 667s Maximum coverage depth stored by CoverageDepth: 4294967295 667s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 667s FORCE_PACKING = n 667s ASSERT = n 667s HAVE_LIBZ = y 667s HAVE_LIBBZ2 = y 667s PROFILER_COLLECT = n 667s MINIRANKS = y 667s CLOCK_GETTIME = n 667s __linux__ = y 667s _MSC_VER = n 667s __GNUC__ = y 667s RAY_32_BITS = n 667s RAY_64_BITS = y 667s MPI standard version: MPI 3.1 667s MPI library: Open-MPI 4.1.6 667s Compiler: GNU gcc/g++ 13.2.0 667s MPI I/O: n 667s 667s 667s -k (to set the k-mer size) 667s Value: 31 667s 667s 667s Paired library # 0 667s -p (paired-end sequences) 667s Left sequences: SampleDirectory/s_6.first1000_1.fastq 667s Right sequences: SampleDirectory/s_6.first1000_2.fastq 667s Average length: automatic detection 667s Standard deviation: automatic detection 667s 667s Ray command: 667s mpiexec -n 1 Ray \ 667s -k \ 667s 31 \ 667s -detect-sequence-files \ 667s SampleDirectory \ 667s -o \ 667s test2 667s 667s Rank 0 wrote test2/RayCommand.txt 667s 667s k-mer length: 31 667s Rank 0: assembler memory usage: 42736 KiB 667s Rank 0: assembler memory usage: 108408 KiB 667s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2521 667s Rank 0: testing the network, please wait... 667s 667s Rank 0 is testing the network [0/1000] 667s Rank 0 is testing the network [1000/1000] 667s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 667s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 6 microseconds (10^-6 seconds) 667s 667s Rank 0 wrote test2/NetworkTest.txt 667s 667s 667s *** 667s Step: Network testing 667s Date: Sat Mar 16 21:21:03 2024 667s Elapsed time: 0 seconds 667s Since beginning: 0 seconds 667s *** 667s 667s 667s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 667s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 667s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 667s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 667s Rank 0 wrote test2/NumberOfSequences.txt 667s Rank 0 wrote test2/SequencePartition.txt 667s 667s *** 667s Step: Counting sequences to assemble 667s Date: Sat Mar 16 21:21:03 2024 667s Elapsed time: 0 seconds 667s Since beginning: 0 seconds 667s *** 667s 667s 667s Rank 0 is loading sequence reads 667s Rank 0 : partition is [0;4107], 4108 sequence reads 667s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 667s Rank 0 has 0 sequence reads 667s Rank 0: assembler memory usage: 121396 KiB 667s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 667s Rank 0 has 4108 sequence reads (completed) 667s 667s *** 667s Step: Sequence loading 667s Date: Sat Mar 16 21:21:03 2024 667s Elapsed time: 0 seconds 667s Since beginning: 0 seconds 667s *** 667s 667s 667s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 667s Rank 0 created its Bloom filter 667s Rank 0 is counting k-mers in sequence reads [1/4108] 667s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 667s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 667s 667s 667s *** 667s Step: K-mer counting 667s Date: Sat Mar 16 21:21:03 2024 667s Elapsed time: 0 seconds 667s Since beginning: 0 seconds 667s *** 667s 667s 667s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 667s Rank 0 destroyed its Bloom filter 667s Rank 0 has 1954 k-mers (completed) 667s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 667s Rank 0: assembler memory usage: 117788 KiB 672s 672s 672s Rank 0: the minimum coverage is 3 672s Rank 0: the peak coverage is 3 672s Warning: no peak observed in the k-mer coverage distribution. 672s to deal with the sequencing error rate, try to lower the k-mer length (-k) 672s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 672s 672s *** 672s Step: Coverage distribution analysis 672s Date: Sat Mar 16 21:21:08 2024 672s Elapsed time: 5 seconds 672s Since beginning: 5 seconds 672s *** 672s 672s 672s 673s Rank 0 is adding edges [1/4108] 673s Rank 0 is adding edges [4108/4108] (completed) 673s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 673s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 673s 673s *** 673s Step: Graph construction 673s Date: Sat Mar 16 21:21:09 2024 673s Elapsed time: 1 seconds 673s Since beginning: 6 seconds 673s *** 673s 673s 673s Rank 0 has 1954 vertices (completed) 673s Rank 0: assembler memory usage: 117788 KiB 677s Rank 0 is purging edges [1/1954] 677s Rank 0 is purging edges [1954/1954] (completed) 677s Rank 0: assembler memory usage: 118316 KiB 677s VirtualProcessor: completed jobs: 1954 677s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 682s Rank 0 wrote test2/degreeDistribution.txt 682s 682s *** 682s Step: Null edge purging 682s Date: Sat Mar 16 21:21:18 2024 682s Elapsed time: 9 seconds 682s Since beginning: 15 seconds 682s *** 682s 682s 682s Rank 0 is selecting optimal read markers [1/4108] 682s Rank 0: assembler memory usage: 118316 KiB 683s Rank 0 is selecting optimal read markers [4108/4108] (completed) 683s Rank 0: peak number of workers: 599, maximum: 32768 683s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 683s Rank 0: assembler memory usage: 126444 KiB 683s Rank 0: Freeing unused assembler memory: 4096 KiB freed 683s Rank 0: assembler memory usage: 126444 KiB 683s 683s *** 683s Step: Selection of optimal read markers 683s Date: Sat Mar 16 21:21:19 2024 683s Elapsed time: 1 seconds 683s Since beginning: 16 seconds 683s *** 683s 683s 683s Rank 0: memory usage for optimal read markers= 4096 KiB 683s Rank 0 is creating seeds [1/1954] 683s Rank 0: assembler memory usage: 126444 KiB 688s Rank 0 has 1 seeds 688s Rank 0 is creating seeds [1954/1954] (completed) 688s Rank 0: peak number of workers: 746, maximum: 32768 688s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 688s Rank 0 runtime statistics for seeding algorithm: 688s Rank 0 Skipped paths because of dead end for head: 0 688s Rank 0 Skipped paths because of dead end for tail: 0 688s Rank 0 Skipped paths because of two dead ends: 0 688s Rank 0 Skipped paths because of bubble weak component: 0 688s Rank 0 Skipped paths because of short length: 1952 688s Rank 0 Skipped paths because of bad ownership: 1 688s Rank 0 Skipped paths because of low coverage: 0 688s Rank 0 Eligible paths: 1 688s Rank 0: assembler memory usage: 126444 KiB 688s Rank 0 has 1 seeds to register. 688s Rank 0 registered 0/1 688s Rank 0 registered 0/1 688s Rank 0 registered its seeds 688s VirtualProcessor: completed jobs: 0 688s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 692s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 702s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 702s Rank 0 merged its seeds: 1 seeds -> 1 seeds 702s 702s *** 702s Step: Detection of assembly seeds 702s Date: Sat Mar 16 21:21:38 2024 702s Elapsed time: 19 seconds 702s Since beginning: 35 seconds 702s *** 702s 702s 702s Rank 0 is calculating library lengths [1/1] 702s Rank 0 detected 1737 library lengths 702s Rank 0 is calculating library lengths [1/1] (completed) 702s Rank 0: peak number of workers: 1, maximum: 32768 702s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 702s Rank 0: assembler memory usage: 163312 KiB 702s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 702s 702s Mode= 2 signalAverage= 9 702s CURRENT IS NOISE, 244 702s GOT HIT 212 702s 702s 702s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 702s 702s *** 702s Step: Estimation of outer distances for paired reads 702s Date: Sat Mar 16 21:21:38 2024 702s Elapsed time: 0 seconds 702s Since beginning: 35 seconds 702s *** 702s 702s 703s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 703s Rank 0 traversed 1000 nucleotide symbols 703s Rank 0: assembler memory usage: 167408 KiB 703s Rank 0 is extending seeds [1/1] (completed) 703s Rank 0 extended 1 seeds out of 1 (100.00%) 703s Rank 0: assembler memory usage: 159216 KiB 703s Rank 0 starting fusions 703s 703s *** 703s Step: Bidirectional extension of seeds 703s Date: Sat Mar 16 21:21:39 2024 703s Elapsed time: 1 seconds 703s Since beginning: 36 seconds 703s *** 703s 703s 703s Rank 0: starting clear step. cycleNumber= 0 708s Rank 0 adding 0 new fusions 708s Rank 0 cleared, 1 paths 708s Rank 0: starting distribution step 708s Rank 0 is distributing fusions [1/1] 708s Rank 0: assembler memory usage: 159216 KiB 708s Date: Sat Mar 16 21:21:44 2024 708s Rank 0 is distributing fusions [1/1] (completed) 708s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 708s Rank 0: assembler memory usage: 163312 KiB 708s Date: Sat Mar 16 21:21:44 2024 708s Rank 0 tells others to compute fusions. 708s Rank 0 FusionTaskCreator assignNextTask [0/2] 708s Rank 0: assembler memory usage: 163312 KiB 708s Date: Sat Mar 16 21:21:44 2024 708s Rank 0 FusionTaskCreator processWorkerResult [0/2] 708s Rank 0: assembler memory usage: 163312 KiB 708s Date: Sat Mar 16 21:21:44 2024 708s Rank 0 FusionTaskCreator [2/2] 708s Statistics: all paths: 1 eliminated during fusing: 0 708s Rank 0: assembler memory usage: 163312 KiB 708s VirtualProcessor: completed jobs: 2 708s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 708s Rank 0: starting clear step. cycleNumber= 1 712s Rank 0 adding 0 new fusions 712s Rank 0 cleared, 1 paths 712s Rank 0 is distributing fusions [1/1] 712s Rank 0: assembler memory usage: 163312 KiB 712s Date: Sat Mar 16 21:21:48 2024 712s Rank 0 is distributing fusions [1/1] (completed) 712s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 712s Rank 0: assembler memory usage: 163312 KiB 712s Date: Sat Mar 16 21:21:48 2024 712s Rank 0 JoinerTaskCreator assignNextTask [0/2] 712s Rank 0: assembler memory usage: 163312 KiB 712s Date: Sat Mar 16 21:21:48 2024 712s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 712s Rank 0: assembler memory usage: 163312 KiB 712s Date: Sat Mar 16 21:21:48 2024 712s Rank 0 JoinerTaskCreator [2/2] 712s Statistics: all paths: 1 eliminated during joining: 0 712s Rank 0: assembler memory usage: 163312 KiB 712s Date: Sat Mar 16 21:21:48 2024 712s VirtualProcessor: completed jobs: 2 712s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 717s Rank 0 adding 0 new fusions 717s Rank 0 cleared, 1 paths 717s Rank 0: starting distribution step 717s Rank 0 is distributing fusions [1/1] 717s Rank 0: assembler memory usage: 163312 KiB 717s Date: Sat Mar 16 21:21:53 2024 717s Rank 0 is distributing fusions [1/1] (completed) 717s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 717s Rank 0: assembler memory usage: 163312 KiB 717s Date: Sat Mar 16 21:21:53 2024 717s Rank 0 tells others to compute fusions. 717s Rank 0 FusionTaskCreator assignNextTask [0/2] 717s Rank 0: assembler memory usage: 163312 KiB 717s Date: Sat Mar 16 21:21:53 2024 717s Rank 0 FusionTaskCreator processWorkerResult [0/2] 717s Rank 0: assembler memory usage: 163312 KiB 717s Date: Sat Mar 16 21:21:53 2024 717s Rank 0 FusionTaskCreator [2/2] 717s Statistics: all paths: 1 eliminated during fusing: 0 717s Rank 0: assembler memory usage: 163312 KiB 717s VirtualProcessor: completed jobs: 2 717s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 717s Rank 0: starting clear step. cycleNumber= 2 721s Rank 0 adding 0 new fusions 721s Rank 0 cleared, 1 paths 721s Rank 0 is distributing fusions [1/1] 721s Rank 0: assembler memory usage: 163312 KiB 721s Date: Sat Mar 16 21:21:57 2024 721s Rank 0 is distributing fusions [1/1] (completed) 721s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 721s Rank 0: assembler memory usage: 163312 KiB 721s Date: Sat Mar 16 21:21:57 2024 721s Rank 0 JoinerTaskCreator assignNextTask [0/2] 721s Rank 0: assembler memory usage: 163312 KiB 721s Date: Sat Mar 16 21:21:57 2024 721s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 721s Rank 0: assembler memory usage: 163312 KiB 721s Date: Sat Mar 16 21:21:57 2024 721s Rank 0 JoinerTaskCreator [2/2] 721s Statistics: all paths: 1 eliminated during joining: 0 721s Rank 0: assembler memory usage: 163312 KiB 721s Date: Sat Mar 16 21:21:57 2024 721s VirtualProcessor: completed jobs: 2 721s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 726s Rank 0 adding 0 new fusions 726s Rank 0 cleared, 1 paths 726s Rank 0: starting distribution step 726s Rank 0 is distributing fusions [1/1] 726s Rank 0: assembler memory usage: 163312 KiB 726s Date: Sat Mar 16 21:22:02 2024 726s Rank 0 is distributing fusions [1/1] (completed) 726s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 726s Rank 0: assembler memory usage: 163312 KiB 726s Date: Sat Mar 16 21:22:02 2024 726s Rank 0 cycleNumber= 2 726s 726s *** 726s Step: Merging of redundant paths 726s Date: Sat Mar 16 21:22:02 2024 726s Elapsed time: 23 seconds 726s Since beginning: 59 seconds 726s *** 726s 726s 726s Rank 0 appended 1 elements 726s 726s *** 726s Step: Generation of contigs 726s Date: Sat Mar 16 21:22:02 2024 726s Elapsed time: 0 seconds 726s Since beginning: 59 seconds 726s *** 726s 726s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 726s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 726s Rank 0 ineligibleObjects: 0/970 (0.00%) 726s Rank 0: assembler memory usage: 163312 KiB 726s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 726s Rank 0 finished gathering scaffold links. 726s Rank 0 will write 1 contig lengths 726s Rank 0 will solve the scaffolding problem. 726s Welcome to GreedySolver v1.0 726s 1 vertices; 0 edges 726s 1 contigs >= 500 726s Edges in solution: 0 726s 726s Conflict statistics: 726s 1 scaffolds, 1 >= 500 726s Total: 1000 nucleotides 726s 726s *** 726s Step: Scaffolding of contigs 726s Date: Sat Mar 16 21:22:02 2024 726s Elapsed time: 0 seconds 726s Since beginning: 59 seconds 726s *** 726s 726s Rank 0 syncing with master 726s 726s *** 726s Step: Counting sequences to search 726s Date: Sat Mar 16 21:22:02 2024 726s Elapsed time: 0 seconds 726s Since beginning: 59 seconds 726s *** 726s 726s 726s Rank 0 will add colors, 0 sequences in 0 files to process 726s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 730s 730s *** 730s Step: Graph coloring 730s Date: Sat Mar 16 21:22:06 2024 730s Elapsed time: 4 seconds 730s Since beginning: 1 minutes, 3 seconds 730s *** 730s 730s 730s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 730s Rank 0 shares its counts 730s Rank 0 computing contig abundances [1/1] [1/970] 730s Rank 0 computing contig abundances [1/1] [970/970] 730s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 730s 730s *** 730s Step: Counting contig biological abundances 730s Date: Sat Mar 16 21:22:06 2024 730s Elapsed time: 0 seconds 730s Since beginning: 1 minutes, 3 seconds 731s *** 731s 731s 731s Rank 0 colored the graph with 0 real colors using 1 virtual colors 731s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 731s 731s *** 731s Step: Counting sequence biological abundances 731s Date: Sat Mar 16 21:22:06 2024 731s Elapsed time: 0 seconds 731s Since beginning: 1 minutes, 3 seconds 731s *** 731s 731s 731s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 731s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 735s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 735s 735s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 735s Rank 0 is starting taxon syncing across the compute tribe. 735s 735s *** 735s Step: Loading taxons 735s Date: Sat Mar 16 21:22:11 2024 735s Elapsed time: 5 seconds 735s Since beginning: 1 minutes, 8 seconds 735s *** 735s 735s Rank 0 synced taxons across the grid with 1 poor slaves. 735s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 735s Rank 0 has 0 taxons after syncing with master 739s 739s 739s *** 739s Step: Loading tree 739s Date: Sat Mar 16 21:22:15 2024 739s Elapsed time: 4 seconds 739s Since beginning: 1 minutes, 12 seconds 739s *** 739s 745s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 745s 745s Rank 0: counting ontology terms in the graph... 749s Rank 0: 0 have some biological signal 749s Number of dereferenced alternate handles: 0 749s Number of k-mer observations with gene ontology terms: 0 749s Rank 0: synced ontology term profiles with master 749s Rank 0: synchronization is complete! 749s Rank 0: ontology terms with biological signal: 0 749s Populated recursive values... 749s Gene ontology terms without depth information: 0 749s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 749s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 749s 749s *** 749s Step: Processing gene ontologies 749s Date: Sat Mar 16 21:22:25 2024 749s Elapsed time: 10 seconds 749s Since beginning: 1 minutes, 22 seconds 749s *** 749s 749s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 749s [GenomeNeighbourhood] in final list: 0 749s 749s *** 749s Step: Computing neighbourhoods 749s Date: Sat Mar 16 21:22:25 2024 749s Elapsed time: 0 seconds 749s Since beginning: 1 minutes, 22 seconds 749s *** 749s 749s Contigs >= 100 nt 749s Number: 1 749s Total length: 1000 749s Average: 1000 749s N50: 1000 749s Median: 1000 749s Largest: 1000 749s Contigs >= 500 nt 749s Number: 1 749s Total length: 1000 749s Average: 1000 749s N50: 1000 749s Median: 1000 749s Largest: 1000 749s Scaffolds >= 100 nt 749s Number: 1 749s Total length: 1000 749s Average: 1000 749s N50: 1000 749s Median: 1000 749s Largest: 1000 749s Scaffolds >= 500 nt 749s Number: 1 749s Total length: 1000 749s Average: 1000 749s N50: 1000 749s Median: 1000 749s Largest: 1000 749s 749s Rank 0 wrote test2/Contigs.fasta 749s Rank 0 wrote test2/Scaffolds.fasta 749s Check for test2/* 749s 749s 750s 750s ************************************************** 750s This program comes with ABSOLUTELY NO WARRANTY. 750s This is free software, and you are welcome to redistribute it 750s under certain conditions; see "LICENSE.txt" for details. 750s ************************************************** 750s 750s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 750s Centre de recherche en infectiologie de l'Université Laval 750s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 750s http://denovoassembler.sf.net/ 750s 750s References to cite: 750s 750s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 750s Ray Meta: scalable de novo metagenome assembly and profiling. 750s Genome Biology (BioMed Central Ltd). 750s 13:R122, Published: 22 December 2012 750s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 750s 750s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 750s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 750s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 750s November 2010, Volume 17, Issue 11, Pages 1519-1533. 750s http://dx.doi.org/doi:10.1089/cmb.2009.0238 750s 750s Ray version 2.3.1 750s License for Ray: GNU General Public License version 3 750s RayPlatform version: 2.0.1 750s License for RayPlatform: GNU Lesser General Public License version 3 750s 750s MAXKMERLENGTH: 32 750s Maximum coverage depth stored by CoverageDepth: 4294967295 750s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 750s FORCE_PACKING = n 750s ASSERT = n 750s HAVE_LIBZ = y 750s HAVE_LIBBZ2 = y 750s PROFILER_COLLECT = n 750s MINIRANKS = y 750s CLOCK_GETTIME = n 750s __linux__ = y 750s _MSC_VER = n 750s __GNUC__ = y 750s RAY_32_BITS = n 750s RAY_64_BITS = y 750s MPI standard version: MPI 3.1 750s MPI library: Open-MPI 4.1.6 750s Compiler: GNU gcc/g++ 13.2.0 750s MPI I/O: n 750s 750s 750s -k (to set the k-mer size) 750s Value: 29 750s 750s 750s Paired library # 0 750s -p (paired-end sequences) 750s Left sequences: SampleDirectory/s_6.first1000_1.fastq 750s Right sequences: SampleDirectory/s_6.first1000_2.fastq 750s Average length: automatic detection 750s Standard deviation: automatic detection 750s 750s Ray command: 750s mpiexec -n 1 Ray \ 750s -k \ 750s 29 \ 750s -desable-recycling \ 750s -p \ 750s SampleDirectory/s_6.first1000_1.fastq \ 750s SampleDirectory/s_6.first1000_2.fastq 750s 750s Rank 0 wrote RayOutput/RayCommand.txt 750s 750s k-mer length: 29 750s Rank 0: assembler memory usage: 42736 KiB 750s Rank 0: assembler memory usage: 108408 KiB 750s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 2527 750s Rank 0: testing the network, please wait... 750s 750s Rank 0 is testing the network [0/1000] 750s Rank 0 is testing the network [1000/1000] 750s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 5 microseconds (10^-6 seconds) 750s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 7 microseconds (10^-6 seconds) 750s 750s Rank 0 wrote RayOutput/NetworkTest.txt 750s 750s 750s *** 750s Step: Network testing 750s Date: Sat Mar 16 21:22:26 2024 750s Elapsed time: 0 seconds 750s Since beginning: 0 seconds 750s *** 750s 750s 750s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 750s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 750s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 750s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 750s Rank 0 wrote RayOutput/NumberOfSequences.txt 750s Rank 0 wrote RayOutput/SequencePartition.txt 750s 750s *** 750s Step: Counting sequences to assemble 750s Date: Sat Mar 16 21:22:26 2024 750s Elapsed time: 0 seconds 750s Since beginning: 0 seconds 750s *** 750s 750s 750s Rank 0 is loading sequence reads 750s Rank 0 : partition is [0;4107], 4108 sequence reads 750s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 750s Rank 0 has 0 sequence reads 750s Rank 0: assembler memory usage: 121396 KiB 750s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 750s Rank 0 has 4108 sequence reads (completed) 750s 750s *** 750s Step: Sequence loading 750s Date: Sat Mar 16 21:22:26 2024 750s Elapsed time: 0 seconds 750s Since beginning: 0 seconds 750s *** 750s 750s 750s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 750s Rank 0 created its Bloom filter 750s Rank 0 is counting k-mers in sequence reads [1/4108] 750s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 750s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 750s 750s 750s *** 750s Step: K-mer counting 750s Date: Sat Mar 16 21:22:26 2024 750s Elapsed time: 0 seconds 750s Since beginning: 0 seconds 750s *** 750s 750s 750s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 750s Rank 0 destroyed its Bloom filter 750s Rank 0 has 1958 k-mers (completed) 750s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 750s Rank 0: assembler memory usage: 117772 KiB 755s 755s 755s Rank 0: the minimum coverage is 3 755s Rank 0: the peak coverage is 3 755s Warning: no peak observed in the k-mer coverage distribution. 755s to deal with the sequencing error rate, try to lower the k-mer length (-k) 755s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 755s 755s *** 755s Step: Coverage distribution analysis 755s Date: Sat Mar 16 21:22:31 2024 755s Elapsed time: 5 seconds 755s Since beginning: 5 seconds 755s *** 755s 755s 755s 756s Rank 0 is adding edges [1/4108] 756s Rank 0 is adding edges [4108/4108] (completed) 756s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 756s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 756s 756s *** 756s Step: Graph construction 756s Date: Sat Mar 16 21:22:32 2024 756s Elapsed time: 1 seconds 756s Since beginning: 6 seconds 756s *** 756s 756s 756s Rank 0 has 1958 vertices (completed) 756s Rank 0: assembler memory usage: 117772 KiB 760s Rank 0 is purging edges [1/1958] 760s Rank 0 is purging edges [1958/1958] (completed) 760s Rank 0: assembler memory usage: 118304 KiB 760s VirtualProcessor: completed jobs: 1958 760s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 764s Rank 0 wrote RayOutput/degreeDistribution.txt 764s 764s *** 764s Step: Null edge purging 765s Date: Sat Mar 16 21:22:40 2024 765s Elapsed time: 8 seconds 765s Since beginning: 14 seconds 765s *** 765s 765s 765s Rank 0 is selecting optimal read markers [1/4108] 765s Rank 0: assembler memory usage: 118304 KiB 766s Rank 0 is selecting optimal read markers [4108/4108] (completed) 766s Rank 0: peak number of workers: 599, maximum: 32768 766s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 766s Rank 0: assembler memory usage: 126516 KiB 766s Rank 0: Freeing unused assembler memory: 4096 KiB freed 766s Rank 0: assembler memory usage: 126516 KiB 766s 766s *** 766s Step: Selection of optimal read markers 766s Date: Sat Mar 16 21:22:42 2024 766s Elapsed time: 2 seconds 766s Since beginning: 16 seconds 766s *** 766s 766s 766s Rank 0: memory usage for optimal read markers= 4096 KiB 766s Rank 0 is creating seeds [1/1958] 766s Rank 0: assembler memory usage: 126516 KiB 770s Rank 0 has 1 seeds 770s Rank 0 is creating seeds [1958/1958] (completed) 770s Rank 0: peak number of workers: 746, maximum: 32768 770s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 770s Rank 0 runtime statistics for seeding algorithm: 770s Rank 0 Skipped paths because of dead end for head: 0 770s Rank 0 Skipped paths because of dead end for tail: 0 770s Rank 0 Skipped paths because of two dead ends: 0 770s Rank 0 Skipped paths because of bubble weak component: 0 770s Rank 0 Skipped paths because of short length: 1956 770s Rank 0 Skipped paths because of bad ownership: 1 770s Rank 0 Skipped paths because of low coverage: 0 770s Rank 0 Eligible paths: 1 770s Rank 0: assembler memory usage: 126516 KiB 770s Rank 0 has 1 seeds to register. 770s Rank 0 registered 0/1 770s Rank 0 registered 0/1 770s Rank 0 registered its seeds 770s VirtualProcessor: completed jobs: 0 770s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 775s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 785s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 785s Rank 0 merged its seeds: 1 seeds -> 1 seeds 785s 785s *** 785s Step: Detection of assembly seeds 785s Date: Sat Mar 16 21:23:01 2024 785s Elapsed time: 19 seconds 785s Since beginning: 35 seconds 785s *** 785s 785s 785s Rank 0 is calculating library lengths [1/1] 785s Rank 0 detected 1743 library lengths 785s Rank 0 is calculating library lengths [1/1] (completed) 785s Rank 0: peak number of workers: 1, maximum: 32768 785s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 785s Rank 0: assembler memory usage: 163384 KiB 785s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 785s 785s Mode= 2 signalAverage= 10 785s CURRENT IS NOISE, 244 785s GOT HIT 214 785s 785s 785s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 785s 785s *** 785s Step: Estimation of outer distances for paired reads 785s Date: Sat Mar 16 21:23:01 2024 785s Elapsed time: 0 seconds 785s Since beginning: 35 seconds 785s *** 785s 785s 786s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 786s Rank 0 traversed 1000 nucleotide symbols 786s Rank 0: assembler memory usage: 167480 KiB 786s Rank 0 is extending seeds [1/1] (completed) 786s Rank 0 extended 1 seeds out of 1 (100.00%) 786s Rank 0: assembler memory usage: 159288 KiB 786s Rank 0 starting fusions 786s 786s *** 786s Step: Bidirectional extension of seeds 786s Date: Sat Mar 16 21:23:02 2024 786s Elapsed time: 1 seconds 786s Since beginning: 36 seconds 786s *** 786s 786s 786s Rank 0: starting clear step. cycleNumber= 0 791s Rank 0 adding 0 new fusions 791s Rank 0 cleared, 1 paths 791s Rank 0: starting distribution step 791s Rank 0 is distributing fusions [1/1] 791s Rank 0: assembler memory usage: 159288 KiB 791s Date: Sat Mar 16 21:23:07 2024 791s Rank 0 is distributing fusions [1/1] (completed) 791s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 791s Rank 0: assembler memory usage: 163384 KiB 791s Date: Sat Mar 16 21:23:07 2024 791s Rank 0 tells others to compute fusions. 791s Rank 0 FusionTaskCreator assignNextTask [0/2] 791s Rank 0: assembler memory usage: 163384 KiB 791s Date: Sat Mar 16 21:23:07 2024 791s Rank 0 FusionTaskCreator processWorkerResult [0/2] 791s Rank 0: assembler memory usage: 163384 KiB 791s Date: Sat Mar 16 21:23:07 2024 791s Rank 0 FusionTaskCreator [2/2] 791s Statistics: all paths: 1 eliminated during fusing: 0 791s Rank 0: assembler memory usage: 163384 KiB 791s VirtualProcessor: completed jobs: 2 791s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 791s Rank 0: starting clear step. cycleNumber= 1 795s Rank 0 adding 0 new fusions 795s Rank 0 cleared, 1 paths 795s Rank 0 is distributing fusions [1/1] 795s Rank 0: assembler memory usage: 163384 KiB 795s Date: Sat Mar 16 21:23:11 2024 795s Rank 0 is distributing fusions [1/1] (completed) 795s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 795s Rank 0: assembler memory usage: 163384 KiB 795s Date: Sat Mar 16 21:23:11 2024 795s Rank 0 JoinerTaskCreator assignNextTask [0/2] 795s Rank 0: assembler memory usage: 163384 KiB 795s Date: Sat Mar 16 21:23:11 2024 795s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 795s Rank 0: assembler memory usage: 163384 KiB 795s Date: Sat Mar 16 21:23:11 2024 795s Rank 0 JoinerTaskCreator [2/2] 795s Statistics: all paths: 1 eliminated during joining: 0 795s Rank 0: assembler memory usage: 163384 KiB 795s Date: Sat Mar 16 21:23:11 2024 795s VirtualProcessor: completed jobs: 2 795s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 800s Rank 0 adding 0 new fusions 800s Rank 0 cleared, 1 paths 800s Rank 0: starting distribution step 800s Rank 0 is distributing fusions [1/1] 800s Rank 0: assembler memory usage: 163384 KiB 800s Date: Sat Mar 16 21:23:16 2024 800s Rank 0 is distributing fusions [1/1] (completed) 800s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 800s Rank 0: assembler memory usage: 163384 KiB 800s Date: Sat Mar 16 21:23:16 2024 800s Rank 0 tells others to compute fusions. 800s Rank 0 FusionTaskCreator assignNextTask [0/2] 800s Rank 0: assembler memory usage: 163384 KiB 800s Date: Sat Mar 16 21:23:16 2024 800s Rank 0 FusionTaskCreator processWorkerResult [0/2] 800s Rank 0: assembler memory usage: 163384 KiB 800s Date: Sat Mar 16 21:23:16 2024 800s Rank 0 FusionTaskCreator [2/2] 800s Statistics: all paths: 1 eliminated during fusing: 0 800s Rank 0: assembler memory usage: 163384 KiB 800s VirtualProcessor: completed jobs: 2 800s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 800s Rank 0: starting clear step. cycleNumber= 2 804s Rank 0 adding 0 new fusions 804s Rank 0 cleared, 1 paths 804s Rank 0 is distributing fusions [1/1] 804s Rank 0: assembler memory usage: 163384 KiB 804s Date: Sat Mar 16 21:23:20 2024 804s Rank 0 is distributing fusions [1/1] (completed) 804s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 804s Rank 0: assembler memory usage: 163384 KiB 804s Date: Sat Mar 16 21:23:20 2024 804s Rank 0 JoinerTaskCreator assignNextTask [0/2] 804s Rank 0: assembler memory usage: 163384 KiB 804s Date: Sat Mar 16 21:23:20 2024 804s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 804s Rank 0: assembler memory usage: 163384 KiB 804s Date: Sat Mar 16 21:23:20 2024 804s Rank 0 JoinerTaskCreator [2/2] 804s Statistics: all paths: 1 eliminated during joining: 0 804s Rank 0: assembler memory usage: 163384 KiB 804s Date: Sat Mar 16 21:23:20 2024 804s VirtualProcessor: completed jobs: 2 804s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 809s Rank 0 adding 0 new fusions 809s Rank 0 cleared, 1 paths 809s Rank 0: starting distribution step 809s Rank 0 is distributing fusions [1/1] 809s Rank 0: assembler memory usage: 163384 KiB 809s Date: Sat Mar 16 21:23:25 2024 809s Rank 0 is distributing fusions [1/1] (completed) 809s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 809s Rank 0: assembler memory usage: 163384 KiB 809s Date: Sat Mar 16 21:23:25 2024 809s Rank 0 cycleNumber= 2 809s 809s *** 809s Step: Merging of redundant paths 809s Date: Sat Mar 16 21:23:25 2024 809s Elapsed time: 23 seconds 809s Since beginning: 59 seconds 809s *** 809s 809s 809s Rank 0 appended 1 elements 809s 809s *** 809s Step: Generation of contigs 809s Date: Sat Mar 16 21:23:25 2024 809s Elapsed time: 0 seconds 809s Since beginning: 59 seconds 809s *** 809s 809s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 809s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 809s Rank 0 ineligibleObjects: 0/972 (0.00%) 809s Rank 0: assembler memory usage: 163384 KiB 809s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 809s Rank 0 finished gathering scaffold links. 809s Rank 0 will write 1 contig lengths 809s Rank 0 will solve the scaffolding problem. 809s Welcome to GreedySolver v1.0 809s 1 vertices; 0 edges 809s 1 contigs >= 500 809s Edges in solution: 0 809s 809s Conflict statistics: 809s 1 scaffolds, 1 >= 500 809s Total: 1000 nucleotides 809s 809s *** 809s Step: Scaffolding of contigs 809s Date: Sat Mar 16 21:23:25 2024 809s Elapsed time: 0 seconds 809s Since beginning: 59 seconds 809s *** 809s 809s Rank 0 syncing with master 809s 809s *** 809s Step: Counting sequences to search 809s Date: Sat Mar 16 21:23:25 2024 809s Elapsed time: 0 seconds 809s Since beginning: 59 seconds 809s *** 809s 809s 809s Rank 0 will add colors, 0 sequences in 0 files to process 809s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 814s 814s *** 814s Step: Graph coloring 814s Date: Sat Mar 16 21:23:30 2024 814s Elapsed time: 5 seconds 814s Since beginning: 1 minutes, 4 seconds 814s *** 814s 814s 814s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 814s Rank 0 shares its counts 814s Rank 0 computing contig abundances [1/1] [1/972] 814s Rank 0 computing contig abundances [1/1] [972/972] 814s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 814s 814s *** 814s Step: Counting contig biological abundances 814s Date: Sat Mar 16 21:23:30 2024 814s Elapsed time: 0 seconds 814s Since beginning: 1 minutes, 4 seconds 814s *** 814s 814s 814s Rank 0 colored the graph with 0 real colors using 1 virtual colors 814s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 814s 814s *** 814s Step: Counting sequence biological abundances 814s Date: Sat Mar 16 21:23:30 2024 814s Elapsed time: 0 seconds 814s Since beginning: 1 minutes, 4 seconds 814s *** 814s 814s 814s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 814s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 818s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 818s 818s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 818s Rank 0 is starting taxon syncing across the compute tribe. 818s 818s *** 818s Step: Loading taxons 818s Date: Sat Mar 16 21:23:34 2024 818s Elapsed time: 4 seconds 818s Since beginning: 1 minutes, 8 seconds 818s *** 818s 818s Rank 0 synced taxons across the grid with 1 poor slaves. 818s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 818s Rank 0 has 0 taxons after syncing with master 823s 823s 823s *** 823s Step: Loading tree 823s Date: Sat Mar 16 21:23:38 2024 823s Elapsed time: 4 seconds 823s Since beginning: 1 minutes, 12 seconds 823s *** 823s 827s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 827s 827s Rank 0: counting ontology terms in the graph... 831s Rank 0: 0 have some biological signal 831s Number of dereferenced alternate handles: 0 831s Number of k-mer observations with gene ontology terms: 0 831s Rank 0: synced ontology term profiles with master 831s Rank 0: synchronization is complete! 831s Rank 0: ontology terms with biological signal: 0 831s Populated recursive values... 831s Gene ontology terms without depth information: 0 831s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 831s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 831s 831s *** 831s Step: Processing gene ontologies 831s Date: Sat Mar 16 21:23:47 2024 831s Elapsed time: 9 seconds 831s Since beginning: 1 minutes, 21 seconds 831s *** 831s 831s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 831s [GenomeNeighbourhood] in final list: 0 831s 831s *** 831s Step: Computing neighbourhoods 831s Date: Sat Mar 16 21:23:47 2024 831s Elapsed time: 0 seconds 831s Since beginning: 1 minutes, 21 seconds 831s *** 831s 831s Contigs >= 100 nt 831s Number: 1 831s Total length: 1000 831s Average: 1000 831s N50: 1000 831s Median: 1000 831s Largest: 1000 831s Contigs >= 500 nt 831s Number: 1 831s Total length: 1000 831s Average: 1000 831s N50: 1000 831s Median: 1000 831s Largest: 1000 831s Scaffolds >= 100 nt 831s Number: 1 831s Total length: 1000 831s Average: 1000 831s N50: 1000 831s Median: 1000 831s Largest: 1000 831s Scaffolds >= 500 nt 831s Number: 1 831s Total length: 1000 831s Average: 1000 831s N50: 1000 831s Median: 1000 831s Largest: 1000 831s 831s Rank 0 wrote RayOutput/Contigs.fasta 831s Rank 0 wrote RayOutput/Scaffolds.fasta 831s Check for RayOutput/* 831s 831s 832s 832s ************************************************** 832s This program comes with ABSOLUTELY NO WARRANTY. 832s This is free software, and you are welcome to redistribute it 832s under certain conditions; see "LICENSE.txt" for details. 832s ************************************************** 832s 832s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 832s Centre de recherche en infectiologie de l'Université Laval 832s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 832s http://denovoassembler.sf.net/ 832s 832s References to cite: 832s 832s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 832s Ray Meta: scalable de novo metagenome assembly and profiling. 832s Genome Biology (BioMed Central Ltd). 832s 13:R122, Published: 22 December 2012 832s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 832s 832s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 832s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 832s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 832s November 2010, Volume 17, Issue 11, Pages 1519-1533. 832s http://dx.doi.org/doi:10.1089/cmb.2009.0238 832s 832s Ray version 2.3.1 832s License for Ray: GNU General Public License version 3 832s RayPlatform version: 2.0.1 832s License for RayPlatform: GNU Lesser General Public License version 3 832s 832s MAXKMERLENGTH: 32 832s Maximum coverage depth stored by CoverageDepth: 4294967295 832s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 832s FORCE_PACKING = n 832s ASSERT = n 832s HAVE_LIBZ = y 832s HAVE_LIBBZ2 = y 832s PROFILER_COLLECT = n 832s MINIRANKS = y 832s CLOCK_GETTIME = n 832s __linux__ = y 832s _MSC_VER = n 832s __GNUC__ = y 832s RAY_32_BITS = n 832s RAY_64_BITS = y 832s MPI standard version: MPI 3.1 832s MPI library: Open-MPI 4.1.6 832s Compiler: GNU gcc/g++ 13.2.0 832s MPI I/O: n 832s 832s 832s -k (to set the k-mer size) 832s Value: 31 832s 832s 832s Paired library # 0 832s -p (paired-end sequences) 832s Left sequences: ecoli_1K_1.fq 832s Right sequences: ecoli_1K_2.fq 832s Average length: automatic detection 832s Standard deviation: automatic detection 832s 832s Ray command: 832s mpiexec -n 2 Ray \ 832s -k \ 832s 31 \ 832s -p \ 832s ecoli_1K_1.fq \ 832s ecoli_1K_2.fq \ 832s -o \ 832s test3 832s 832s Rank 0 wrote test3/RayCommand.txt 832s 832s k-mer length: 31 832s Rank 1: assembler memory usage: 42736 KiB 832s Rank 0: assembler memory usage: 42736 KiB 832s Rank 1: assembler memory usage: 108544 KiB 832s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 2539 832s Rank 0: assembler memory usage: 108544 KiB 832s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 2538 832s Rank 0: testing the network, please wait... 832s 832s Rank 0 is testing the network [0/1000] 832s Rank 1 is testing the network [0/1000] 832s Rank 1 is testing the network [1000/1000] 832s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 8 microseconds (10^-6 seconds) 832s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 38 microseconds (10^-6 seconds) 832s Rank 0 is testing the network [1000/1000] 832s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 8 microseconds (10^-6 seconds) 832s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 40 microseconds (10^-6 seconds) 832s 832s Rank 0 wrote test3/NetworkTest.txt 832s 832s 832s *** 832s Step: Network testing 832s Date: Sat Mar 16 21:23:48 2024 832s Elapsed time: 0 seconds 832s Since beginning: 0 seconds 832s *** 832s 832s 832s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 832s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 832s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 832s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 832s Rank 0 wrote test3/NumberOfSequences.txt 832s Rank 0 wrote test3/SequencePartition.txt 832s 832s *** 832s Step: Counting sequences to assemble 832s Date: Sat Mar 16 21:23:48 2024 832s Elapsed time: 0 seconds 832s Since beginning: 0 seconds 832s *** 832s 832s 832s Rank 1 is loading sequence reads 832s Rank 0 is loading sequence reads 832s Rank 0 : partition is [0;2053], 2054 sequence reads 832s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 832s Rank 1 : partition is [2054;4107], 2054 sequence reads 832s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 832s Rank 0 has 0 sequence reads 832s Rank 1 has 0 sequence reads 832s Rank 0: assembler memory usage: 117328 KiB 832s Rank 1: assembler memory usage: 117320 KiB 832s Rank 0 has 2054 sequence reads (completed) 832s Rank 1 has 2054 sequence reads (completed) 832s 832s *** 832s Step: Sequence loading 832s Date: Sat Mar 16 21:23:48 2024 832s Elapsed time: 0 seconds 832s Since beginning: 0 seconds 832s *** 832s 832s 832s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 832s Rank 1 created its Bloom filter 832s Rank 1 is counting k-mers in sequence reads [1/2054] 832s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 832s Rank 0 created its Bloom filter 832s Rank 0 is counting k-mers in sequence reads [1/2054] 835s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 835s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 835s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 835s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 835s 835s 835s *** 835s Step: K-mer counting 835s Date: Sat Mar 16 21:23:51 2024 835s Elapsed time: 3 seconds 835s Since beginning: 3 seconds 835s *** 835s 835s 835s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 835s Rank 1 destroyed its Bloom filter 835s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 835s Rank 1 has 922 k-mers (completed) 835s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 835s Rank 0 destroyed its Bloom filter 835s Rank 0 has 1032 k-mers (completed) 835s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 835s Rank 0: assembler memory usage: 113596 KiB 835s Rank 1: assembler memory usage: 113588 KiB 843s 843s 843s Rank 0: the minimum coverage is 3 843s Rank 0: the peak coverage is 3 843s Warning: no peak observed in the k-mer coverage distribution. 843s to deal with the sequencing error rate, try to lower the k-mer length (-k) 843s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 843s Rank 1 is adding edges [1/2054] 843s 843s *** 843s Step: Coverage distribution analysis 843s Date: Sat Mar 16 21:23:59 2024 843s Elapsed time: 8 seconds 843s Since beginning: 11 seconds 843s *** 843s 843s 843s 843s Rank 0 is adding edges [1/2054] 846s Rank 1 is adding edges [2054/2054] (completed) 846s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 846s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 846s Rank 0 is adding edges [2054/2054] (completed) 846s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 846s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 846s 846s *** 846s Step: Graph construction 846s Date: Sat Mar 16 21:24:02 2024 846s Elapsed time: 3 seconds 846s Since beginning: 14 seconds 846s *** 846s 846s 846s Rank 0 has 1032 vertices (completed) 846s Rank 0: assembler memory usage: 113596 KiB 846s Rank 1 has 922 vertices (completed) 846s Rank 1: assembler memory usage: 113588 KiB 855s Rank 1 is purging edges [1/922] 855s Rank 0 is purging edges [1/1032] 855s Rank 1 is purging edges [922/922] (completed) 855s Rank 1: assembler memory usage: 113720 KiB 855s VirtualProcessor: completed jobs: 922 855s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 855s Rank 0 is purging edges [1032/1032] (completed) 855s Rank 0: assembler memory usage: 113868 KiB 855s VirtualProcessor: completed jobs: 1032 855s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 864s Rank 0 wrote test3/degreeDistribution.txt 864s 864s *** 864s Step: Null edge purging 864s Date: Sat Mar 16 21:24:20 2024 864s Elapsed time: 18 seconds 864s Since beginning: 32 seconds 864s *** 864s 864s 864s Rank 0 is selecting optimal read markers [1/2054] 864s Rank 0: assembler memory usage: 113868 KiB 864s Rank 1 is selecting optimal read markers [1/2054] 864s Rank 1: assembler memory usage: 113720 KiB 868s Rank 1 is selecting optimal read markers [2054/2054] (completed) 868s Rank 1: peak number of workers: 1121, maximum: 32768 868s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 868s Rank 1: assembler memory usage: 122028 KiB 868s Rank 1: Freeing unused assembler memory: 4096 KiB freed 868s Rank 1: assembler memory usage: 122028 KiB 868s Rank 0 is selecting optimal read markers [2054/2054] (completed) 868s Rank 0: peak number of workers: 1135, maximum: 32768 868s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 868s Rank 0: assembler memory usage: 122072 KiB 868s Rank 0: Freeing unused assembler memory: 4096 KiB freed 868s Rank 0: assembler memory usage: 122072 KiB 868s 868s *** 868s Step: Selection of optimal read markers 868s Date: Sat Mar 16 21:24:24 2024 868s Elapsed time: 4 seconds 868s Since beginning: 36 seconds 868s *** 868s 868s 868s Rank 0: memory usage for optimal read markers= 4096 KiB 868s Rank 1: memory usage for optimal read markers= 4096 KiB 868s Rank 1 is creating seeds [1/922] 868s Rank 0 is creating seeds [1/1032] 868s Rank 1: assembler memory usage: 122028 KiB 868s Rank 0: assembler memory usage: 122072 KiB 877s Rank 1 has 1 seeds 877s Rank 1 is creating seeds [922/922] (completed) 877s Rank 1: peak number of workers: 916, maximum: 32768 877s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 877s Rank 1 runtime statistics for seeding algorithm: 877s Rank 1 Skipped paths because of dead end for head: 0 877s Rank 1 Skipped paths because of dead end for tail: 0 877s Rank 1 Skipped paths because of two dead ends: 0 877s Rank 1 Skipped paths because of bubble weak component: 0 877s Rank 1 Skipped paths because of short length: 921 877s Rank 1 Skipped paths because of bad ownership: 0 877s Rank 1 Skipped paths because of low coverage: 0 877s Rank 1 Eligible paths: 1 877s Rank 1: assembler memory usage: 122028 KiB 877s Rank 0 has 0 seeds 877s Rank 0 is creating seeds [1032/1032] (completed) 877s Rank 0: peak number of workers: 998, maximum: 32768 877s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 877s Rank 0 runtime statistics for seeding algorithm: 877s Rank 0 Skipped paths because of dead end for head: 0 877s Rank 0 Skipped paths because of dead end for tail: 0 877s Rank 0 Skipped paths because of two dead ends: 0 877s Rank 0 Skipped paths because of bubble weak component: 0 877s Rank 0 Skipped paths because of short length: 1031 877s Rank 0 Skipped paths because of bad ownership: 1 877s Rank 0 Skipped paths because of low coverage: 0 877s Rank 0 Eligible paths: 0 877s Rank 0: assembler memory usage: 122072 KiB 877s Rank 1 has 1 seeds to register. 877s Rank 0 registered -1/0 877s Rank 0 registered its seeds 877s Rank 1 registered 0/1 877s Rank 1 registered 0/1 877s Rank 1 registered its seeds 877s VirtualProcessor: completed jobs: 0 878s VirtualProcessor: completed jobs: 0 878s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 878s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 886s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 886s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 896s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 896s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 896s Rank 0 merged its seeds: 0 seeds -> 0 seeds 896s Rank 1 merged its seeds: 1 seeds -> 1 seeds 896s 896s *** 896s Step: Detection of assembly seeds 896s Date: Sat Mar 16 21:24:52 2024 896s Elapsed time: 28 seconds 896s Since beginning: 1 minutes, 4 seconds 896s *** 896s 896s 896s Rank 0 detected 0 library lengths 896s Rank 0 is calculating library lengths [0/0] (completed) 896s Rank 0: peak number of workers: 0, maximum: 32768 896s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 896s Rank 0: assembler memory usage: 126168 KiB 896s Rank 1 is calculating library lengths [1/1] 896s Rank 1 detected 1737 library lengths 896s Rank 1 is calculating library lengths [1/1] (completed) 896s Rank 1: peak number of workers: 1, maximum: 32768 896s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7985 virtual messages generated 7985 real messages (100%) 896s Rank 1: assembler memory usage: 158896 KiB 896s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 896s 896s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 896s Mode= 2 signalAverage= 9 896s CURRENT IS NOISE, 244 896s GOT HIT 212 896s 896s 896s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 896s 896s *** 896s Step: Estimation of outer distances for paired reads 896s Date: Sat Mar 16 21:24:52 2024 896s Elapsed time: 0 seconds 896s Since beginning: 1 minutes, 4 seconds 896s *** 896s 896s 896s Rank 0 is extending seeds [0/0] (completed) 896s Rank 0 extended 0 seeds out of 0 (0.00%) 896s Rank 0: assembler memory usage: 126168 KiB 896s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 912s Rank 1 traversed 1000 nucleotide symbols 912s Rank 1: assembler memory usage: 162992 KiB 912s Rank 1 is extending seeds [1/1] (completed) 912s Rank 1 extended 1 seeds out of 1 (100.00%) 912s Rank 1: assembler memory usage: 154800 KiB 912s Rank 0 starting fusions 912s 912s *** 912s Step: Bidirectional extension of seeds 912s Date: Sat Mar 16 21:25:08 2024 912s Elapsed time: 16 seconds 912s Since beginning: 1 minutes, 20 seconds 912s *** 912s 912s 912s Rank 0: starting clear step. cycleNumber= 0 921s Rank 1 adding 0 new fusions 921s Rank 1 cleared, 1 paths 921s Rank 0 adding 0 new fusions 921s Rank 0 cleared, 0 paths 921s Rank 0: starting distribution step 921s Rank 1 is distributing fusions [1/1] 921s Rank 1: assembler memory usage: 154800 KiB 921s Rank 0 is distributing fusions [0/0] (completed) 921s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 921s Rank 0: assembler memory usage: 126168 KiB 921s Date: Sat Mar 16 21:25:17 2024 921s Date: Sat Mar 16 21:25:17 2024 921s Rank 1 is distributing fusions [1/1] (completed) 921s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 921s Rank 1: assembler memory usage: 158896 KiB 921s Rank 0 tells others to compute fusions. 921s Rank 0 FusionTaskCreator [0/0] 921s Statistics: all paths: 0 eliminated during fusing: 0 921s Date: Sat Mar 16 21:25:17 2024 921s Rank 1 FusionTaskCreator assignNextTask [0/2] 921s Rank 0: assembler memory usage: 126168 KiB 921s Rank 1: assembler memory usage: 158896 KiB 921s VirtualProcessor: completed jobs: 0 921s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 921s Date: Sat Mar 16 21:25:17 2024 921s Rank 1 FusionTaskCreator processWorkerResult [0/2] 921s Rank 1: assembler memory usage: 158896 KiB 921s Date: Sat Mar 16 21:25:17 2024 921s Rank 1 FusionTaskCreator [2/2] 921s Statistics: all paths: 1 eliminated during fusing: 0 921s Rank 1: assembler memory usage: 158896 KiB 922s VirtualProcessor: completed jobs: 2 922s Rank 0: starting clear step. cycleNumber= 1 922s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10895 virtual messages generated 10895 real messages (100%) 930s Rank 0 adding 0 new fusions 930s Rank 1 adding 0 new fusions 930s Rank 1 cleared, 1 paths 930s Rank 0 cleared, 0 paths 930s Rank 0 is distributing fusions [0/0] (completed) 930s Rank 1 is distributing fusions [1/1] 930s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 930s Rank 1: assembler memory usage: 158896 KiB 930s Rank 0: assembler memory usage: 126168 KiB 930s Date: Sat Mar 16 21:25:26 2024 930s Date: Sat Mar 16 21:25:26 2024 930s Rank 1 is distributing fusions [1/1] (completed) 930s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 930s Rank 1: assembler memory usage: 158896 KiB 930s Rank 0 JoinerTaskCreator [0/0] 930s Statistics: all paths: 0 eliminated during joining: 0 930s Rank 0: assembler memory usage: 126168 KiB 930s Date: Sat Mar 16 21:25:26 2024 930s Rank 1 JoinerTaskCreator assignNextTask [0/2] 930s Date: Sat Mar 16 21:25:26 2024 930s Rank 1: assembler memory usage: 158896 KiB 930s Date: Sat Mar 16 21:25:26 2024 930s VirtualProcessor: completed jobs: 0 930s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 931s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 931s Rank 1: assembler memory usage: 158896 KiB 931s Date: Sat Mar 16 21:25:26 2024 931s Rank 1 JoinerTaskCreator [2/2] 931s Statistics: all paths: 1 eliminated during joining: 0 931s Rank 1: assembler memory usage: 158896 KiB 931s Date: Sat Mar 16 21:25:27 2024 931s VirtualProcessor: completed jobs: 2 931s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13805 virtual messages generated 13805 real messages (100%) 939s Rank 0 adding 0 new fusions 939s Rank 1 adding 0 new fusions 939s Rank 1 cleared, 1 paths 939s Rank 0 cleared, 0 paths 939s Rank 0: starting distribution step 939s Rank 0 is distributing fusions [0/0] (completed) 939s Rank 1 is distributing fusions [1/1] 939s Rank 1: assembler memory usage: 158896 KiB 939s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 939s Rank 0: assembler memory usage: 126168 KiB 939s Date: Sat Mar 16 21:25:35 2024 939s Date: Sat Mar 16 21:25:35 2024 939s Rank 1 is distributing fusions [1/1] (completed) 939s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 939s Rank 1: assembler memory usage: 158896 KiB 939s Date: Sat Mar 16 21:25:35 2024 939s Rank 1 FusionTaskCreator assignNextTask [0/2] 939s Rank 0 tells others to compute fusions. 939s Rank 0 FusionTaskCreator [0/0] 939s Statistics: all paths: 0 eliminated during fusing: 0 939s Rank 1: assembler memory usage: 158896 KiB 939s Date: Sat Mar 16 21:25:35 2024 939s Rank 0: assembler memory usage: 126168 KiB 939s VirtualProcessor: completed jobs: 0 939s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 940s Rank 1 FusionTaskCreator processWorkerResult [0/2] 940s Rank 1: assembler memory usage: 158896 KiB 940s Date: Sat Mar 16 21:25:36 2024 940s Rank 1 FusionTaskCreator [2/2] 940s Statistics: all paths: 1 eliminated during fusing: 0 940s Rank 1: assembler memory usage: 158896 KiB 940s VirtualProcessor: completed jobs: 2 940s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16715 virtual messages generated 16715 real messages (100%) 940s Rank 0: starting clear step. cycleNumber= 2 948s Rank 0 adding 0 new fusions 949s Rank 1 adding 0 new fusions 949s Rank 0 cleared, 0 paths 949s Rank 1 cleared, 1 paths 949s Rank 0 is distributing fusions [0/0] (completed) 949s Rank 1 is distributing fusions [1/1] 949s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 949s Rank 1: assembler memory usage: 158896 KiB 949s Rank 0: assembler memory usage: 126168 KiB 949s Date: Sat Mar 16 21:25:45 2024 949s Date: Sat Mar 16 21:25:45 2024 949s Rank 1 is distributing fusions [1/1] (completed) 949s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 949s Rank 1: assembler memory usage: 158896 KiB 949s Rank 0 JoinerTaskCreator [0/0] 949s Date: Sat Mar 16 21:25:45 2024 949s Rank 1 JoinerTaskCreator assignNextTask [0/2] 949s Rank 1: assembler memory usage: 158896 KiB 949s Statistics: all paths: 0 eliminated during joining: 0 949s Rank 0: assembler memory usage: 126168 KiB 949s Date: Sat Mar 16 21:25:45 2024 949s Date: Sat Mar 16 21:25:45 2024 949s VirtualProcessor: completed jobs: 0 949s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 949s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 949s Rank 1: assembler memory usage: 158896 KiB 949s Date: Sat Mar 16 21:25:45 2024 949s Rank 1 JoinerTaskCreator [2/2] 949s Statistics: all paths: 1 eliminated during joining: 0 949s Rank 1: assembler memory usage: 158896 KiB 949s Date: Sat Mar 16 21:25:45 2024 949s VirtualProcessor: completed jobs: 2 949s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19625 virtual messages generated 19625 real messages (100%) 958s Rank 1 adding 0 new fusions 958s Rank 0 adding 0 new fusions 958s Rank 1 cleared, 1 paths 958s Rank 0 cleared, 0 paths 958s Rank 0: starting distribution step 958s Rank 0 is distributing fusions [0/0] (completed) 958s Rank 1 is distributing fusions [1/1] 958s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 958s Rank 0: assembler memory usage: 126168 KiB 958s Rank 1: assembler memory usage: 158896 KiB 958s Date: Sat Mar 16 21:25:54 2024 958s Date: Sat Mar 16 21:25:54 2024 958s Rank 1 is distributing fusions [1/1] (completed) 958s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 958s Rank 1: assembler memory usage: 158896 KiB 958s Date: Sat Mar 16 21:25:54 2024 958s Rank 0 cycleNumber= 2 958s 958s *** 958s Step: Merging of redundant paths 958s Date: Sat Mar 16 21:25:54 2024 958s Elapsed time: 46 seconds 958s Since beginning: 2 minutes, 6 seconds 958s *** 958s 958s 958s Rank 0 appended 0 elements 958s Rank 1 appended 1 elements 958s 958s *** 958s Step: Generation of contigs 958s Date: Sat Mar 16 21:25:54 2024 958s Elapsed time: 0 seconds 958s Since beginning: 2 minutes, 6 seconds 958s *** 958s 958s Rank 0 finished gathering scaffold links. 958s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 960s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 960s Rank 0 ineligibleObjects: 0/970 (0.00%) 960s Rank 1: assembler memory usage: 158896 KiB 960s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 960s Rank 0 will write 1 contig lengths 960s Rank 1 finished gathering scaffold links. 960s Rank 0 will solve the scaffolding problem. 960s Welcome to GreedySolver v1.0 960s 1 vertices; 0 edges 960s 1 contigs >= 500 960s Edges in solution: 0 960s 960s Conflict statistics: 960s 1 scaffolds, 1 >= 500 960s Total: 1000 nucleotides 960s 960s *** 960s Step: Scaffolding of contigs 960s Date: Sat Mar 16 21:25:56 2024 960s Elapsed time: 2 seconds 960s Since beginning: 2 minutes, 8 seconds 960s *** 960s 960s Rank 0 syncing with master 960s Rank 1 syncing with master 960s 960s *** 960s Step: Counting sequences to search 960s Date: Sat Mar 16 21:25:56 2024 960s Elapsed time: 0 seconds 960s Since beginning: 2 minutes, 8 seconds 960s *** 960s 960s 960s Rank 1 will add colors, 0 sequences in 0 files to process 960s Rank 0 will add colors, 0 sequences in 0 files to process 960s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 960s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 969s 969s *** 969s Step: Graph coloring 969s Date: Sat Mar 16 21:26:05 2024 969s Elapsed time: 9 seconds 969s Since beginning: 2 minutes, 17 seconds 969s *** 969s 969s 969s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 969s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 969s Rank 0 shares its counts 969s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 969s Rank 1 computing contig abundances [1/1] [1/970] 969s Rank 1 computing contig abundances [1/1] [970/970] 969s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 969s 969s *** 969s Step: Counting contig biological abundances 969s Date: Sat Mar 16 21:26:05 2024 969s Elapsed time: 0 seconds 969s Since beginning: 2 minutes, 17 seconds 969s *** 969s 969s 969s Rank 1 colored the graph with 0 real colors using 1 virtual colors 969s Rank 0 colored the graph with 0 real colors using 1 virtual colors 969s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 969s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 969s 969s *** 969s Step: Counting sequence biological abundances 969s Date: Sat Mar 16 21:26:05 2024 969s Elapsed time: 0 seconds 969s Since beginning: 2 minutes, 17 seconds 969s *** 969s 969s 969s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 969s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 969s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 969s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 978s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 978s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 978s 978s 978s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 978s Rank 0 is starting taxon syncing across the compute tribe. 978s 978s *** 978s Step: Loading taxons 978s Date: Sat Mar 16 21:26:14 2024 978s Elapsed time: 9 seconds 978s Since beginning: 2 minutes, 26 seconds 978s *** 978s 978s Rank 0 synced taxons across the grid with 2 poor slaves. 978s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 978s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 978s Rank 0 has 0 taxons after syncing with master 978s Rank 1 has 0 taxons after syncing with master 987s 987s 987s 987s *** 987s Step: Loading tree 987s Date: Sat Mar 16 21:26:23 2024 987s Elapsed time: 9 seconds 987s Since beginning: 2 minutes, 35 seconds 987s *** 987s 996s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 996s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 996s 996s Rank 1: counting ontology terms in the graph... 996s 996s Rank 0: counting ontology terms in the graph... 1005s Rank 1: 0 have some biological signal 1005s Rank 0: 0 have some biological signal 1005s Number of dereferenced alternate handles: 0 1005s Number of k-mer observations with gene ontology terms: 0 1005s Number of dereferenced alternate handles: 0 1005s Number of k-mer observations with gene ontology terms: 0 1005s Rank 0: synced ontology term profiles with master 1005s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 1005s Rank 1: synced ontology term profiles with master 1005s Rank 0: synchronization is complete! 1005s Rank 0: ontology terms with biological signal: 0 1005s Populated recursive values... 1005s Gene ontology terms without depth information: 0 1005s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 1005s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 1005s 1005s *** 1005s Step: Processing gene ontologies 1005s Date: Sat Mar 16 21:26:41 2024 1005s Elapsed time: 18 seconds 1005s Since beginning: 2 minutes, 53 seconds 1005s *** 1005s 1005s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 1005s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 1005s [GenomeNeighbourhood] in final list: 0 1005s 1005s *** 1005s Step: Computing neighbourhoods 1005s Date: Sat Mar 16 21:26:41 2024 1005s Elapsed time: 0 seconds 1005s Since beginning: 2 minutes, 53 seconds 1005s *** 1005s 1005s Contigs >= 100 nt 1005s Number: 1 1005s Total length: 1000 1005s Average: 1000 1005s N50: 1000 1005s Median: 1000 1005s Largest: 1000 1005s Contigs >= 500 nt 1005s Number: 1 1005s Total length: 1000 1005s Average: 1000 1005s N50: 1000 1005s Median: 1000 1005s Largest: 1000 1005s Scaffolds >= 100 nt 1005s Number: 1 1005s Total length: 1000 1005s Average: 1000 1005s N50: 1000 1005s Median: 1000 1005s Largest: 1000 1005s Scaffolds >= 500 nt 1005s Number: 1 1005s Total length: 1000 1005s Average: 1000 1005s N50: 1000 1005s Median: 1000 1005s Largest: 1000 1005s 1005s Rank 0 wrote test3/Contigs.fasta 1005s Rank 0 wrote test3/Scaffolds.fasta 1005s Check for test3/* 1005s 1005s 1005s autopkgtest [21:26:41]: test run-unit-test: -----------------------] 1006s run-unit-test PASS 1006s autopkgtest [21:26:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1007s autopkgtest [21:26:43]: @@@@@@@@@@@@@@@@@@@@ summary 1007s run-unit-test PASS 1024s Creating nova instance adt-noble-arm64-ray-20240316-210955-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...