0s autopkgtest [11:59:58]: starting date: 2024-03-18 0s autopkgtest [11:59:58]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [11:59:58]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s45i__l3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade ray --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-14.secgroup --name adt-noble-arm64-ray-20240318-115958-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 216s autopkgtest [12:03:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 217s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 217s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 217s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 217s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3727 kB] 217s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 217s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 217s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 217s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 217s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 217s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4127 kB] 218s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 218s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 218s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 219s Fetched 9270 kB in 2s (5468 kB/s) 219s Reading package lists... 222s Reading package lists... 222s Building dependency tree... 222s Reading state information... 223s Calculating upgrade... 223s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 225s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 225s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 225s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 226s Reading package lists... 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 227s Calculating upgrade... 227s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 227s Reading package lists... 227s Building dependency tree... 227s Reading state information... 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s autopkgtest [12:03:46]: testbed dpkg architecture: arm64 230s autopkgtest [12:03:48]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 230s autopkgtest [12:03:48]: @@@@@@@@@@@@@@@@@@@@ apt-source ray 233s Get:1 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (dsc) [2114 B] 233s Get:2 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (tar) [450 kB] 233s Get:3 http://ftpmaster.internal/ubuntu noble/universe ray 2.3.1-8 (diff) [213 kB] 233s gpgv: Signature made Wed Dec 6 21:31:12 2023 UTC 233s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 233s gpgv: issuer "tille@debian.org" 233s gpgv: Can't check signature: No public key 233s dpkg-source: warning: cannot verify inline signature for ./ray_2.3.1-8.dsc: no acceptable signature found 233s autopkgtest [12:03:51]: testing package ray version 2.3.1-8 233s autopkgtest [12:03:51]: build not needed 234s autopkgtest [12:03:52]: test run-unit-test: preparing testbed 249s Reading package lists... 249s Building dependency tree... 249s Reading state information... 249s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 249s Starting 2 pkgProblemResolver with broken count: 0 249s Done 250s Done 250s Starting pkgProblemResolver with broken count: 0 250s Starting 2 pkgProblemResolver with broken count: 0 250s Done 251s The following additional packages will be installed: 251s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 251s libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libcairo2 libdatrie1 251s libdeflate0 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfontconfig1 251s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 251s libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 251s libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3t64 251s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 251s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 251s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 251s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 251s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 251s ray ray-doc ray-extra unzip x11-common xdg-utils zip 251s Suggested packages: 251s tcl8.6 tk8.6 opencl-icd gfortran | fortran-compiler elpa-ess r-doc-info 251s | r-doc-pdf r-mathlib r-base-html 251s Recommended packages: 251s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 251s libx11-protocol-perl x11-utils x11-xserver-utils 251s The following NEW packages will be installed: 251s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 251s libamd-comgr2 libamdhip64-5 libatomic1 libblas3 libcairo2 libdatrie1 251s libdeflate0 libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfontconfig1 251s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhsa-runtime64-1 251s libhsakmt1 libhwloc-plugins libhwloc15 libice6 libjbig0 libjpeg-turbo8 251s libjpeg8 liblapack3 liblerc4 libllvm17 libmunge2 libopenmpi3t64 251s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 251s libpaper1 libpciaccess0 libpixman-1-0 libpmix2t64 librdmacm1t64 libsharpyuv0 251s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libucx0 libwebp7 251s libxcb-render0 libxcb-shm0 libxft2 libxnvctrl0 libxrender1 libxss1 libxt6 251s mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common r-base-core 251s ray ray-doc ray-extra unzip x11-common xdg-utils zip 251s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 251s 1 not fully installed or removed. 251s Need to get 87.4 MB of archives. 251s After this operation, 300 MB of additional disk space will be used. 251s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 251s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 251s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 251s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 251s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 251s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 251s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 251s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 251s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 251s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 251s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix2t64 arm64 5.0.1-4.1 [655 kB] 251s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 252s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 252s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 252s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 252s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 252s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 252s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 253s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi3t64 arm64 4.1.6-7ubuntu1 [2463 kB] 253s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-common all 4.1.6-7ubuntu1 [170 kB] 253s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-bin arm64 4.1.6-7ubuntu1 [113 kB] 253s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-bin arm64 1.15 [2336 B] 253s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 ray arm64 2.3.1-8 [727 kB] 253s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 ray-doc all 2.3.1-8 [35.2 kB] 253s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 253s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 253s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 253s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 253s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 253s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 253s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 253s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 253s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 253s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 253s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 253s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 253s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 253s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 253s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 253s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 253s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 253s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 253s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 253s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 253s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 253s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 253s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 253s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 253s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 253s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 253s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 253s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 253s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 253s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 253s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 253s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 253s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 253s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 253s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 253s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 253s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 253s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 253s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 253s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 253s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 253s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 253s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 253s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 255s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 ray-extra all 2.3.1-8 [12.3 kB] 255s Preconfiguring packages ... 255s Fetched 87.4 MB in 3s (29.2 MB/s) 255s Selecting previously unselected package libevent-pthreads-2.1-7:arm64. 255s (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 ... 74758 files and directories currently installed.) 255s Preparing to unpack .../00-libevent-pthreads-2.1-7_2.1.12-stable-9_arm64.deb ... 255s Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 255s Selecting previously unselected package libatomic1:arm64. 255s Preparing to unpack .../01-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 255s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 255s Selecting previously unselected package librdmacm1t64:arm64. 256s Preparing to unpack .../02-librdmacm1t64_50.0-2_arm64.deb ... 256s Unpacking librdmacm1t64:arm64 (50.0-2) ... 256s Selecting previously unselected package libfabric1:arm64. 256s Preparing to unpack .../03-libfabric1_1.17.0-3_arm64.deb ... 256s Unpacking libfabric1:arm64 (1.17.0-3) ... 256s Selecting previously unselected package libhwloc15:arm64. 256s Preparing to unpack .../04-libhwloc15_2.10.0-1_arm64.deb ... 256s Unpacking libhwloc15:arm64 (2.10.0-1) ... 256s Selecting previously unselected package libmunge2:arm64. 256s Preparing to unpack .../05-libmunge2_0.5.15-3ubuntu1_arm64.deb ... 256s Unpacking libmunge2:arm64 (0.5.15-3ubuntu1) ... 256s Selecting previously unselected package libpciaccess0:arm64. 256s Preparing to unpack .../06-libpciaccess0_0.17-3_arm64.deb ... 256s Unpacking libpciaccess0:arm64 (0.17-3) ... 256s Selecting previously unselected package libxnvctrl0:arm64. 256s Preparing to unpack .../07-libxnvctrl0_510.47.03-0ubuntu1_arm64.deb ... 256s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 256s Selecting previously unselected package ocl-icd-libopencl1:arm64. 256s Preparing to unpack .../08-ocl-icd-libopencl1_2.3.2-1_arm64.deb ... 256s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1) ... 256s Selecting previously unselected package libhwloc-plugins:arm64. 256s Preparing to unpack .../09-libhwloc-plugins_2.10.0-1_arm64.deb ... 256s Unpacking libhwloc-plugins:arm64 (2.10.0-1) ... 256s Selecting previously unselected package libpmix2t64:arm64. 256s Preparing to unpack .../10-libpmix2t64_5.0.1-4.1_arm64.deb ... 256s Unpacking libpmix2t64:arm64 (5.0.1-4.1) ... 256s Selecting previously unselected package libllvm17:arm64. 256s Preparing to unpack .../11-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 256s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 257s Selecting previously unselected package libamd-comgr2:arm64. 257s Preparing to unpack .../12-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 257s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 257s Selecting previously unselected package libdrm-amdgpu1:arm64. 257s Preparing to unpack .../13-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 257s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 257s Selecting previously unselected package libhsakmt1:arm64. 257s Preparing to unpack .../14-libhsakmt1_5.7.0-1_arm64.deb ... 257s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 257s Selecting previously unselected package libhsa-runtime64-1. 257s Preparing to unpack .../15-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 257s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 257s Selecting previously unselected package libamdhip64-5. 257s Preparing to unpack .../16-libamdhip64-5_5.2.3-12_arm64.deb ... 257s Unpacking libamdhip64-5 (5.2.3-12) ... 257s Selecting previously unselected package libucx0:arm64. 258s Preparing to unpack .../17-libucx0_1.16.0+ds-4_arm64.deb ... 258s Unpacking libucx0:arm64 (1.16.0+ds-4) ... 258s Selecting previously unselected package libopenmpi3t64:arm64. 258s Preparing to unpack .../18-libopenmpi3t64_4.1.6-7ubuntu1_arm64.deb ... 258s Unpacking libopenmpi3t64:arm64 (4.1.6-7ubuntu1) ... 258s Selecting previously unselected package openmpi-common. 258s Preparing to unpack .../19-openmpi-common_4.1.6-7ubuntu1_all.deb ... 258s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 258s Selecting previously unselected package openmpi-bin. 258s Preparing to unpack .../20-openmpi-bin_4.1.6-7ubuntu1_arm64.deb ... 258s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 258s Selecting previously unselected package mpi-default-bin. 258s Preparing to unpack .../21-mpi-default-bin_1.15_arm64.deb ... 258s Unpacking mpi-default-bin (1.15) ... 258s Selecting previously unselected package ray. 258s Preparing to unpack .../22-ray_2.3.1-8_arm64.deb ... 258s Unpacking ray (2.3.1-8) ... 258s Selecting previously unselected package ray-doc. 258s Preparing to unpack .../23-ray-doc_2.3.1-8_all.deb ... 258s Unpacking ray-doc (2.3.1-8) ... 258s Selecting previously unselected package zip. 258s Preparing to unpack .../24-zip_3.0-13_arm64.deb ... 258s Unpacking zip (3.0-13) ... 258s Selecting previously unselected package unzip. 258s Preparing to unpack .../25-unzip_6.0-28ubuntu3_arm64.deb ... 258s Unpacking unzip (6.0-28ubuntu3) ... 258s Selecting previously unselected package libpaper1:arm64. 258s Preparing to unpack .../26-libpaper1_1.1.29_arm64.deb ... 258s Unpacking libpaper1:arm64 (1.1.29) ... 258s Selecting previously unselected package libpaper-utils. 258s Preparing to unpack .../27-libpaper-utils_1.1.29_arm64.deb ... 258s Unpacking libpaper-utils (1.1.29) ... 258s Selecting previously unselected package xdg-utils. 258s Preparing to unpack .../28-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 258s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 258s Selecting previously unselected package libblas3:arm64. 258s Preparing to unpack .../29-libblas3_3.12.0-3_arm64.deb ... 258s Unpacking libblas3:arm64 (3.12.0-3) ... 258s Selecting previously unselected package fonts-dejavu-mono. 258s Preparing to unpack .../30-fonts-dejavu-mono_2.37-8_all.deb ... 258s Unpacking fonts-dejavu-mono (2.37-8) ... 258s Selecting previously unselected package fonts-dejavu-core. 258s Preparing to unpack .../31-fonts-dejavu-core_2.37-8_all.deb ... 258s Unpacking fonts-dejavu-core (2.37-8) ... 258s Selecting previously unselected package fontconfig-config. 258s Preparing to unpack .../32-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 258s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 258s Selecting previously unselected package libfontconfig1:arm64. 258s Preparing to unpack .../33-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 258s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 258s Selecting previously unselected package libpixman-1-0:arm64. 259s Preparing to unpack .../34-libpixman-1-0_0.42.2-1_arm64.deb ... 259s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 259s Selecting previously unselected package libxcb-render0:arm64. 259s Preparing to unpack .../35-libxcb-render0_1.15-1_arm64.deb ... 259s Unpacking libxcb-render0:arm64 (1.15-1) ... 259s Selecting previously unselected package libxcb-shm0:arm64. 259s Preparing to unpack .../36-libxcb-shm0_1.15-1_arm64.deb ... 259s Unpacking libxcb-shm0:arm64 (1.15-1) ... 259s Selecting previously unselected package libxrender1:arm64. 259s Preparing to unpack .../37-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 259s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 259s Selecting previously unselected package libcairo2:arm64. 259s Preparing to unpack .../38-libcairo2_1.18.0-1_arm64.deb ... 259s Unpacking libcairo2:arm64 (1.18.0-1) ... 259s Selecting previously unselected package libgomp1:arm64. 259s Preparing to unpack .../39-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 259s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 259s Selecting previously unselected package libjpeg-turbo8:arm64. 259s Preparing to unpack .../40-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 259s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 259s Selecting previously unselected package libjpeg8:arm64. 259s Preparing to unpack .../41-libjpeg8_8c-2ubuntu11_arm64.deb ... 259s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 259s Selecting previously unselected package libgfortran5:arm64. 259s Preparing to unpack .../42-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 259s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 259s Selecting previously unselected package liblapack3:arm64. 259s Preparing to unpack .../43-liblapack3_3.12.0-3_arm64.deb ... 259s Unpacking liblapack3:arm64 (3.12.0-3) ... 259s Selecting previously unselected package fontconfig. 259s Preparing to unpack .../44-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 259s Unpacking fontconfig (2.15.0-1ubuntu1) ... 259s Selecting previously unselected package libgraphite2-3:arm64. 259s Preparing to unpack .../45-libgraphite2-3_1.3.14-2_arm64.deb ... 259s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 259s Selecting previously unselected package libharfbuzz0b:arm64. 259s Preparing to unpack .../46-libharfbuzz0b_8.3.0-2_arm64.deb ... 259s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 259s Selecting previously unselected package libthai-data. 259s Preparing to unpack .../47-libthai-data_0.1.29-2_all.deb ... 259s Unpacking libthai-data (0.1.29-2) ... 259s Selecting previously unselected package libdatrie1:arm64. 259s Preparing to unpack .../48-libdatrie1_0.2.13-3_arm64.deb ... 259s Unpacking libdatrie1:arm64 (0.2.13-3) ... 259s Selecting previously unselected package libthai0:arm64. 259s Preparing to unpack .../49-libthai0_0.1.29-2_arm64.deb ... 259s Unpacking libthai0:arm64 (0.1.29-2) ... 259s Selecting previously unselected package libpango-1.0-0:arm64. 259s Preparing to unpack .../50-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 259s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 259s Selecting previously unselected package libpangoft2-1.0-0:arm64. 259s Preparing to unpack .../51-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 259s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 259s Selecting previously unselected package libpangocairo-1.0-0:arm64. 259s Preparing to unpack .../52-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 259s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 259s Selecting previously unselected package libtcl8.6:arm64. 259s Preparing to unpack .../53-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 259s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 259s Selecting previously unselected package libdeflate0:arm64. 259s Preparing to unpack .../54-libdeflate0_1.19-1_arm64.deb ... 259s Unpacking libdeflate0:arm64 (1.19-1) ... 259s Selecting previously unselected package libjbig0:arm64. 259s Preparing to unpack .../55-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 259s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 259s Selecting previously unselected package liblerc4:arm64. 259s Preparing to unpack .../56-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 259s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 259s Selecting previously unselected package libsharpyuv0:arm64. 259s Preparing to unpack .../57-libsharpyuv0_1.3.2-0.4_arm64.deb ... 259s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 259s Selecting previously unselected package libwebp7:arm64. 259s Preparing to unpack .../58-libwebp7_1.3.2-0.4_arm64.deb ... 259s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 260s Selecting previously unselected package libtiff6:arm64. 260s Preparing to unpack .../59-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 260s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 260s Selecting previously unselected package libxft2:arm64. 260s Preparing to unpack .../60-libxft2_2.3.6-1_arm64.deb ... 260s Unpacking libxft2:arm64 (2.3.6-1) ... 260s Selecting previously unselected package x11-common. 260s Preparing to unpack .../61-x11-common_1%3a7.7+23ubuntu2_all.deb ... 260s Unpacking x11-common (1:7.7+23ubuntu2) ... 260s Selecting previously unselected package libxss1:arm64. 260s Preparing to unpack .../62-libxss1_1%3a1.2.3-1build2_arm64.deb ... 260s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 260s Selecting previously unselected package libtk8.6:arm64. 260s Preparing to unpack .../63-libtk8.6_8.6.13-2_arm64.deb ... 260s Unpacking libtk8.6:arm64 (8.6.13-2) ... 260s Selecting previously unselected package libice6:arm64. 260s Preparing to unpack .../64-libice6_2%3a1.0.10-1build2_arm64.deb ... 260s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 260s Selecting previously unselected package libsm6:arm64. 260s Preparing to unpack .../65-libsm6_2%3a1.2.3-1build2_arm64.deb ... 260s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 260s Selecting previously unselected package libxt6:arm64. 260s Preparing to unpack .../66-libxt6_1%3a1.2.1-1.1_arm64.deb ... 260s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 260s Selecting previously unselected package r-base-core. 260s Preparing to unpack .../67-r-base-core_4.3.2-1build1_arm64.deb ... 260s Unpacking r-base-core (4.3.2-1build1) ... 260s Selecting previously unselected package ray-extra. 260s Preparing to unpack .../68-ray-extra_2.3.1-8_all.deb ... 260s Unpacking ray-extra (2.3.1-8) ... 260s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 260s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 260s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 260s Setting up libpaper1:arm64 (1.1.29) ... 260s 260s Creating config file /etc/papersize with new version 261s Setting up ray-doc (2.3.1-8) ... 261s Setting up libpciaccess0:arm64 (0.17-3) ... 261s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 261s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 261s Setting up libdatrie1:arm64 (0.2.13-3) ... 261s Setting up libxcb-render0:arm64 (1.15-1) ... 261s Setting up unzip (6.0-28ubuntu3) ... 261s Setting up x11-common (1:7.7+23ubuntu2) ... 261s Setting up libdeflate0:arm64 (1.19-1) ... 261s Setting up libxcb-shm0:arm64 (1.15-1) ... 261s Setting up libpaper-utils (1.1.29) ... 261s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 261s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 261s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 261s Setting up zip (3.0-13) ... 261s Setting up libblas3:arm64 (3.12.0-3) ... 261s 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 261s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 261s Setting up fonts-dejavu-mono (2.37-8) ... 261s Setting up libhwloc15:arm64 (2.10.0-1) ... 261s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 261s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 261s Setting up fonts-dejavu-core (2.37-8) ... 261s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 261s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 261s Setting up libwebp7:arm64 (1.3.2-0.4) ... 261s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 261s Setting up openmpi-common (4.1.6-7ubuntu1) ... 261s Setting up librdmacm1t64:arm64 (50.0-2) ... 261s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 261s Setting up libthai-data (0.1.29-2) ... 261s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 261s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 261s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 261s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 261s Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9) ... 261s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 261s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 261s Setting up libfabric1:arm64 (1.17.0-3) ... 261s Setting up libice6:arm64 (2:1.0.10-1build2) ... 261s Setting up liblapack3:arm64 (3.12.0-3) ... 261s 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 261s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 262s Setting up libhwloc-plugins:arm64 (2.10.0-1) ... 262s Setting up libthai0:arm64 (0.1.29-2) ... 262s Setting up libpmix2t64:arm64 (5.0.1-4.1) ... 262s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 262s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 262s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 262s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 262s Setting up libhsakmt1:arm64 (5.7.0-1) ... 262s Setting up fontconfig (2.15.0-1ubuntu1) ... 263s Regenerating fonts cache... done. 263s Setting up libxft2:arm64 (2.3.6-1) ... 263s Setting up libtk8.6:arm64 (8.6.13-2) ... 263s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 263s Setting up libcairo2:arm64 (1.18.0-1) ... 263s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 263s Setting up libhsa-runtime64-1 (5.7.1-1) ... 263s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 263s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 263s Setting up libamdhip64-5 (5.2.3-12) ... 263s Setting up r-base-core (4.3.2-1build1) ... 264s 264s Creating config file /etc/R/Renviron with new version 264s Setting up libucx0:arm64 (1.16.0+ds-4) ... 264s Setting up ray-extra (2.3.1-8) ... 264s Setting up libopenmpi3t64:arm64 (4.1.6-7ubuntu1) ... 264s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 264s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 264s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 264s Setting up mpi-default-bin (1.15) ... 264s Setting up ray (2.3.1-8) ... 264s Setting up autopkgtest-satdep (0) ... 264s Processing triggers for man-db (2.12.0-3) ... 265s Processing triggers for install-info (7.1-3) ... 265s Processing triggers for libc-bin (2.39-0ubuntu2) ... 271s (Reading database ... 77407 files and directories currently installed.) 271s Removing autopkgtest-satdep (0) ... 272s autopkgtest [12:04:30]: test run-unit-test: [----------------------- 272s 272s ************************************************** 272s This program comes with ABSOLUTELY NO WARRANTY. 272s This is free software, and you are welcome to redistribute it 272s under certain conditions; see "LICENSE.txt" for details. 272s ************************************************** 272s 272s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 272s Centre de recherche en infectiologie de l'Université Laval 272s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 272s http://denovoassembler.sf.net/ 272s 272s References to cite: 272s 272s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 272s Ray Meta: scalable de novo metagenome assembly and profiling. 272s Genome Biology (BioMed Central Ltd). 272s 13:R122, Published: 22 December 2012 272s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 272s 272s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 272s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 272s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 272s November 2010, Volume 17, Issue 11, Pages 1519-1533. 272s http://dx.doi.org/doi:10.1089/cmb.2009.0238 272s 272s Ray version 2.3.1 272s License for Ray: GNU General Public License version 3 272s RayPlatform version: 2.0.1 272s License for RayPlatform: GNU Lesser General Public License version 3 272s 272s MAXKMERLENGTH: 32 272s Maximum coverage depth stored by CoverageDepth: 4294967295 272s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 272s FORCE_PACKING = n 272s ASSERT = n 272s HAVE_LIBZ = y 272s HAVE_LIBBZ2 = y 272s PROFILER_COLLECT = n 272s MINIRANKS = y 272s CLOCK_GETTIME = n 272s __linux__ = y 272s _MSC_VER = n 272s __GNUC__ = y 272s RAY_32_BITS = n 272s RAY_64_BITS = y 272s MPI standard version: MPI 3.1 272s MPI library: Open-MPI 4.1.6 272s Compiler: GNU gcc/g++ 13.2.0 272s MPI I/O: n 272s 272s 272s -k (to set the k-mer size) 272s Value: 31 272s 272s 272s Paired library # 0 272s -p (paired-end sequences) 272s Left sequences: ecoli_1K_1.fq 272s Right sequences: ecoli_1K_2.fq 272s Average length: automatic detection 272s Standard deviation: automatic detection 272s 272s Ray command: 272s mpiexec -n 1 Ray \ 272s -k \ 272s 31 \ 272s -p \ 272s ecoli_1K_1.fq \ 272s ecoli_1K_2.fq \ 272s -o \ 272s test1 272s 272s Rank 0 wrote test1/RayCommand.txt 272s 272s k-mer length: 31 272s Rank 0: assembler memory usage: 41928 KiB 272s Rank 0: assembler memory usage: 107760 KiB 272s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3303 272s Rank 0: testing the network, please wait... 272s 272s Rank 0 is testing the network [0/1000] 272s Rank 0 is testing the network [1000/1000] 272s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 272s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 272s 272s Rank 0 wrote test1/NetworkTest.txt 272s 272s 272s *** 272s Step: Network testing 272s Date: Mon Mar 18 12:04:30 2024 272s Elapsed time: 0 seconds 272s Since beginning: 0 seconds 272s *** 272s 272s 272s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 272s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 272s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 272s Rank 0: File ecoli_1K_2.fq (Number 1) has 2054 sequences 272s Rank 0 wrote test1/NumberOfSequences.txt 272s Rank 0 wrote test1/SequencePartition.txt 272s 272s *** 272s Step: Counting sequences to assemble 272s Date: Mon Mar 18 12:04:30 2024 272s Elapsed time: 0 seconds 272s Since beginning: 0 seconds 272s *** 272s 272s 272s Rank 0 is loading sequence reads 272s Rank 0 : partition is [0;4107], 4108 sequence reads 272s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 272s Rank 0 has 0 sequence reads 272s Rank 0: assembler memory usage: 120636 KiB 272s Rank 0 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 272s Rank 0 has 4108 sequence reads (completed) 272s 272s *** 272s Step: Sequence loading 272s Date: Mon Mar 18 12:04:30 2024 272s Elapsed time: 0 seconds 272s Since beginning: 0 seconds 272s *** 272s 272s 272s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 272s Rank 0 created its Bloom filter 273s Rank 0 is counting k-mers in sequence reads [1/4108] 273s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 273s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 273s 273s 273s *** 273s Step: K-mer counting 273s Date: Mon Mar 18 12:04:30 2024 273s Elapsed time: 0 seconds 273s Since beginning: 0 seconds 273s *** 273s 273s 273s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 273s Rank 0 destroyed its Bloom filter 273s Rank 0 has 1954 k-mers (completed) 273s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 273s Rank 0: assembler memory usage: 117028 KiB 273s 273s 273s Rank 0: the minimum coverage is 3 273s Rank 0: the peak coverage is 3 273s Warning: no peak observed in the k-mer coverage distribution. 273s to deal with the sequencing error rate, try to lower the k-mer length (-k) 273s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 273s 273s *** 273s Step: Coverage distribution analysis 273s Date: Mon Mar 18 12:04:31 2024 273s Elapsed time: 1 seconds 273s Since beginning: 1 seconds 273s *** 273s 273s 273s 273s Rank 0 is adding edges [1/4108] 273s Rank 0 is adding edges [4108/4108] (completed) 273s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 273s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 273s 273s *** 273s Step: Graph construction 273s Date: Mon Mar 18 12:04:31 2024 273s Elapsed time: 0 seconds 273s Since beginning: 1 seconds 273s *** 273s 273s 273s Rank 0 has 1954 vertices (completed) 273s Rank 0: assembler memory usage: 117028 KiB 274s Rank 0 is purging edges [1/1954] 274s Rank 0 is purging edges [1954/1954] (completed) 274s Rank 0: assembler memory usage: 117556 KiB 274s VirtualProcessor: completed jobs: 1954 274s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 275s Rank 0 wrote test1/degreeDistribution.txt 275s 275s *** 275s Step: Null edge purging 275s Date: Mon Mar 18 12:04:33 2024 275s Elapsed time: 2 seconds 275s Since beginning: 3 seconds 275s *** 275s 275s 275s Rank 0 is selecting optimal read markers [1/4108] 275s Rank 0: assembler memory usage: 117556 KiB 275s Rank 0 is selecting optimal read markers [4108/4108] (completed) 275s Rank 0: peak number of workers: 599, maximum: 32768 275s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 275s Rank 0: assembler memory usage: 125728 KiB 275s Rank 0: Freeing unused assembler memory: 4096 KiB freed 275s Rank 0: assembler memory usage: 125728 KiB 275s 275s *** 275s Step: Selection of optimal read markers 275s Date: Mon Mar 18 12:04:33 2024 275s Elapsed time: 0 seconds 275s Since beginning: 3 seconds 275s *** 275s 275s 275s Rank 0: memory usage for optimal read markers= 4096 KiB 275s Rank 0 is creating seeds [1/1954] 275s Rank 0: assembler memory usage: 125728 KiB 276s Rank 0 has 1 seeds 276s Rank 0 is creating seeds [1954/1954] (completed) 276s Rank 0: peak number of workers: 746, maximum: 32768 276s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 276s Rank 0 runtime statistics for seeding algorithm: 276s Rank 0 Skipped paths because of dead end for head: 0 276s Rank 0 Skipped paths because of dead end for tail: 0 276s Rank 0 Skipped paths because of two dead ends: 0 276s Rank 0 Skipped paths because of bubble weak component: 0 276s Rank 0 Skipped paths because of short length: 1952 276s Rank 0 Skipped paths because of bad ownership: 1 276s Rank 0 Skipped paths because of low coverage: 0 276s Rank 0 Eligible paths: 1 276s Rank 0: assembler memory usage: 125728 KiB 276s Rank 0 has 1 seeds to register. 276s Rank 0 registered 0/1 276s Rank 0 registered 0/1 276s Rank 0 registered its seeds 276s VirtualProcessor: completed jobs: 0 276s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 276s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 286s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 286s Rank 0 merged its seeds: 1 seeds -> 1 seeds 286s 286s *** 286s Step: Detection of assembly seeds 286s Date: Mon Mar 18 12:04:44 2024 286s Elapsed time: 11 seconds 286s Since beginning: 14 seconds 286s *** 286s 286s 286s Rank 0 is calculating library lengths [1/1] 286s Rank 0 detected 1737 library lengths 286s Rank 0 is calculating library lengths [1/1] (completed) 286s Rank 0: peak number of workers: 1, maximum: 32768 286s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 286s Rank 0: assembler memory usage: 162596 KiB 286s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 286s 286s Mode= 2 signalAverage= 9 286s CURRENT IS NOISE, 244 286s GOT HIT 212 286s 286s 286s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 286s 286s *** 286s Step: Estimation of outer distances for paired reads 286s Date: Mon Mar 18 12:04:44 2024 286s Elapsed time: 0 seconds 286s Since beginning: 14 seconds 286s *** 286s 286s 286s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 286s Rank 0 traversed 1000 nucleotide symbols 286s Rank 0: assembler memory usage: 166692 KiB 286s Rank 0 is extending seeds [1/1] (completed) 286s Rank 0 extended 1 seeds out of 1 (100.00%) 286s Rank 0: assembler memory usage: 158500 KiB 286s Rank 0 starting fusions 286s 286s *** 286s Step: Bidirectional extension of seeds 286s Date: Mon Mar 18 12:04:44 2024 286s Elapsed time: 0 seconds 286s Since beginning: 14 seconds 286s *** 286s 286s 286s Rank 0: starting clear step. cycleNumber= 0 287s Rank 0 adding 0 new fusions 287s Rank 0 cleared, 1 paths 287s Rank 0: starting distribution step 287s Rank 0 is distributing fusions [1/1] 287s Rank 0: assembler memory usage: 158500 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 is distributing fusions [1/1] (completed) 287s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 tells others to compute fusions. 287s Rank 0 FusionTaskCreator assignNextTask [0/2] 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 FusionTaskCreator processWorkerResult [0/2] 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 FusionTaskCreator [2/2] 287s Statistics: all paths: 1 eliminated during fusing: 0 287s Rank 0: assembler memory usage: 162596 KiB 287s VirtualProcessor: completed jobs: 2 287s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 287s Rank 0: starting clear step. cycleNumber= 1 287s Rank 0 adding 0 new fusions 287s Rank 0 cleared, 1 paths 287s Rank 0 is distributing fusions [1/1] 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 is distributing fusions [1/1] (completed) 287s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 JoinerTaskCreator assignNextTask [0/2] 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s Rank 0 JoinerTaskCreator [2/2] 287s Statistics: all paths: 1 eliminated during joining: 0 287s Rank 0: assembler memory usage: 162596 KiB 287s Date: Mon Mar 18 12:04:45 2024 287s VirtualProcessor: completed jobs: 2 287s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 288s Rank 0 adding 0 new fusions 288s Rank 0 cleared, 1 paths 288s Rank 0: starting distribution step 288s Rank 0 is distributing fusions [1/1] 288s Rank 0: assembler memory usage: 162596 KiB 288s Date: Mon Mar 18 12:04:46 2024 288s Rank 0 is distributing fusions [1/1] (completed) 288s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 288s Rank 0: assembler memory usage: 162596 KiB 288s Date: Mon Mar 18 12:04:46 2024 288s Rank 0 tells others to compute fusions. 288s Rank 0 FusionTaskCreator assignNextTask [0/2] 288s Rank 0: assembler memory usage: 162596 KiB 288s Date: Mon Mar 18 12:04:46 2024 288s Rank 0 FusionTaskCreator processWorkerResult [0/2] 288s Rank 0: assembler memory usage: 162596 KiB 288s Date: Mon Mar 18 12:04:46 2024 288s Rank 0 FusionTaskCreator [2/2] 288s Statistics: all paths: 1 eliminated during fusing: 0 288s Rank 0: assembler memory usage: 162596 KiB 288s VirtualProcessor: completed jobs: 2 288s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 288s Rank 0: starting clear step. cycleNumber= 2 289s Rank 0 adding 0 new fusions 289s Rank 0 cleared, 1 paths 289s Rank 0 is distributing fusions [1/1] 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 is distributing fusions [1/1] (completed) 289s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 JoinerTaskCreator assignNextTask [0/2] 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 JoinerTaskCreator [2/2] 289s Statistics: all paths: 1 eliminated during joining: 0 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s VirtualProcessor: completed jobs: 2 289s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 289s Rank 0 adding 0 new fusions 289s Rank 0 cleared, 1 paths 289s Rank 0: starting distribution step 289s Rank 0 is distributing fusions [1/1] 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 is distributing fusions [1/1] (completed) 289s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 289s Rank 0: assembler memory usage: 162596 KiB 289s Date: Mon Mar 18 12:04:47 2024 289s Rank 0 cycleNumber= 2 289s 289s *** 289s Step: Merging of redundant paths 289s Date: Mon Mar 18 12:04:47 2024 289s Elapsed time: 3 seconds 289s Since beginning: 17 seconds 289s *** 289s 289s 289s Rank 0 appended 1 elements 289s 289s *** 289s Step: Generation of contigs 289s Date: Mon Mar 18 12:04:47 2024 289s Elapsed time: 0 seconds 289s Since beginning: 17 seconds 289s *** 289s 289s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 289s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 289s Rank 0 ineligibleObjects: 0/970 (0.00%) 289s Rank 0: assembler memory usage: 162596 KiB 289s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 289s Rank 0 finished gathering scaffold links. 289s Rank 0 will write 1 contig lengths 289s Rank 0 will solve the scaffolding problem. 289s Welcome to GreedySolver v1.0 289s 1 vertices; 0 edges 289s 1 contigs >= 500 289s Edges in solution: 0 289s 289s Conflict statistics: 289s 1 scaffolds, 1 >= 500 289s Total: 1000 nucleotides 289s 289s *** 289s Step: Scaffolding of contigs 289s Date: Mon Mar 18 12:04:47 2024 289s Elapsed time: 0 seconds 289s Since beginning: 17 seconds 289s *** 289s 289s Rank 0 syncing with master 289s 289s *** 289s Step: Counting sequences to search 289s Date: Mon Mar 18 12:04:47 2024 289s Elapsed time: 0 seconds 289s Since beginning: 17 seconds 290s *** 290s 290s 290s Rank 0 will add colors, 0 sequences in 0 files to process 290s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 290s 290s *** 290s Step: Graph coloring 290s Date: Mon Mar 18 12:04:48 2024 290s Elapsed time: 1 seconds 290s Since beginning: 18 seconds 290s *** 290s 290s 290s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 290s Rank 0 shares its counts 290s Rank 0 computing contig abundances [1/1] [1/970] 290s Rank 0 computing contig abundances [1/1] [970/970] 290s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 290s 290s *** 290s Step: Counting contig biological abundances 290s Date: Mon Mar 18 12:04:48 2024 290s Elapsed time: 0 seconds 290s Since beginning: 18 seconds 290s *** 290s 290s 290s Rank 0 colored the graph with 0 real colors using 1 virtual colors 290s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 290s 290s *** 290s Step: Counting sequence biological abundances 290s Date: Mon Mar 18 12:04:48 2024 290s Elapsed time: 0 seconds 290s Since beginning: 18 seconds 290s *** 290s 290s 290s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 290s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 291s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 291s 291s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 291s Rank 0 is starting taxon syncing across the compute tribe. 291s 291s *** 291s Step: Loading taxons 291s Date: Mon Mar 18 12:04:49 2024 291s Elapsed time: 1 seconds 291s Since beginning: 19 seconds 291s *** 291s 291s Rank 0 synced taxons across the grid with 1 poor slaves. 291s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 291s Rank 0 has 0 taxons after syncing with master 291s 291s 291s *** 291s Step: Loading tree 291s Date: Mon Mar 18 12:04:49 2024 291s Elapsed time: 0 seconds 291s Since beginning: 19 seconds 291s *** 291s 292s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 292s 292s Rank 0: counting ontology terms in the graph... 293s Rank 0: 0 have some biological signal 293s Number of dereferenced alternate handles: 0 293s Number of k-mer observations with gene ontology terms: 0 293s Rank 0: synced ontology term profiles with master 293s Rank 0: synchronization is complete! 293s Rank 0: ontology terms with biological signal: 0 293s Populated recursive values... 293s Gene ontology terms without depth information: 0 293s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 293s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 293s 293s *** 293s Step: Processing gene ontologies 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 2 seconds 293s Since beginning: 21 seconds 293s *** 293s 293s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 293s [GenomeNeighbourhood] in final list: 0 293s 293s *** 293s Step: Computing neighbourhoods 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 0 seconds 293s Since beginning: 21 seconds 293s *** 293s 293s Contigs >= 100 nt 293s Number: 1 293s Total length: 1000 293s Average: 1000 293s N50: 1000 293s Median: 1000 293s Largest: 1000 293s Contigs >= 500 nt 293s Number: 1 293s Total length: 1000 293s Average: 1000 293s N50: 1000 293s Median: 1000 293s Largest: 1000 293s Scaffolds >= 100 nt 293s Number: 1 293s Total length: 1000 293s Average: 1000 293s N50: 1000 293s Median: 1000 293s Largest: 1000 293s Scaffolds >= 500 nt 293s Number: 1 293s Total length: 1000 293s Average: 1000 293s N50: 1000 293s Median: 1000 293s Largest: 1000 293s 293s Rank 0 wrote test1/Contigs.fasta 293s Rank 0 wrote test1/Scaffolds.fasta 293s Check for test1/* 293s 293s 293s 293s ************************************************** 293s This program comes with ABSOLUTELY NO WARRANTY. 293s This is free software, and you are welcome to redistribute it 293s under certain conditions; see "LICENSE.txt" for details. 293s ************************************************** 293s 293s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 293s Centre de recherche en infectiologie de l'Université Laval 293s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 293s http://denovoassembler.sf.net/ 293s 293s References to cite: 293s 293s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 293s Ray Meta: scalable de novo metagenome assembly and profiling. 293s Genome Biology (BioMed Central Ltd). 293s 13:R122, Published: 22 December 2012 293s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 293s 293s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 293s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 293s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 293s November 2010, Volume 17, Issue 11, Pages 1519-1533. 293s http://dx.doi.org/doi:10.1089/cmb.2009.0238 293s 293s Ray version 2.3.1 293s License for Ray: GNU General Public License version 3 293s RayPlatform version: 2.0.1 293s License for RayPlatform: GNU Lesser General Public License version 3 293s 293s MAXKMERLENGTH: 32 293s Maximum coverage depth stored by CoverageDepth: 4294967295 293s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 293s FORCE_PACKING = n 293s ASSERT = n 293s HAVE_LIBZ = y 293s HAVE_LIBBZ2 = y 293s PROFILER_COLLECT = n 293s MINIRANKS = y 293s CLOCK_GETTIME = n 293s __linux__ = y 293s _MSC_VER = n 293s __GNUC__ = y 293s RAY_32_BITS = n 293s RAY_64_BITS = y 293s MPI standard version: MPI 3.1 293s MPI library: Open-MPI 4.1.6 293s Compiler: GNU gcc/g++ 13.2.0 293s MPI I/O: n 293s 293s 293s -k (to set the k-mer size) 293s Value: 31 293s 293s 293s Paired library # 0 293s -p (paired-end sequences) 293s Left sequences: SampleDirectory/s_6.first1000_1.fastq 293s Right sequences: SampleDirectory/s_6.first1000_2.fastq 293s Average length: automatic detection 293s Standard deviation: automatic detection 293s 293s Ray command: 293s mpiexec -n 1 Ray \ 293s -k \ 293s 31 \ 293s -detect-sequence-files \ 293s SampleDirectory \ 293s -o \ 293s test2 293s 293s Rank 0 wrote test2/RayCommand.txt 293s 293s k-mer length: 31 293s Rank 0: assembler memory usage: 41944 KiB 293s Rank 0: assembler memory usage: 107764 KiB 293s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3309 293s Rank 0: testing the network, please wait... 293s 293s Rank 0 is testing the network [0/1000] 293s Rank 0 is testing the network [1000/1000] 293s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 293s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 293s 293s Rank 0 wrote test2/NetworkTest.txt 293s 293s 293s *** 293s Step: Network testing 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 0 seconds 293s Since beginning: 0 seconds 293s *** 293s 293s 293s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 293s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 293s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 293s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 293s Rank 0 wrote test2/NumberOfSequences.txt 293s Rank 0 wrote test2/SequencePartition.txt 293s 293s *** 293s Step: Counting sequences to assemble 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 0 seconds 293s Since beginning: 0 seconds 293s *** 293s 293s 293s Rank 0 is loading sequence reads 293s Rank 0 : partition is [0;4107], 4108 sequence reads 293s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 293s Rank 0 has 0 sequence reads 293s Rank 0: assembler memory usage: 120644 KiB 293s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 293s Rank 0 has 4108 sequence reads (completed) 293s 293s *** 293s Step: Sequence loading 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 0 seconds 293s Since beginning: 0 seconds 293s *** 293s 293s 293s [BloomFilter] allocated 254696 bytes for table with 2037568 bits 293s Rank 0 created its Bloom filter 293s Rank 0 is counting k-mers in sequence reads [1/4108] 293s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 293s Rank 0 : VirtualCommunicator (service provided by BufferedData): 230710 virtual messages generated 462 real messages (0.200251%) 293s 293s 293s *** 293s Step: K-mer counting 293s Date: Mon Mar 18 12:04:51 2024 293s Elapsed time: 0 seconds 293s Since beginning: 0 seconds 293s *** 293s 293s 293s Rank 0 number of set bits in the Bloom filter: [ 7801 / 2037568 ] (0.382858%) 293s Rank 0 destroyed its Bloom filter 293s Rank 0 has 1954 k-mers (completed) 293s [BloomFilter] Rank 0: k-mers sampled -> 1954, k-mers dropped -> 0 (0%), k-mers accepted -> 1954 (100%) 293s Rank 0: assembler memory usage: 117036 KiB 294s 294s 294s Rank 0: the minimum coverage is 3 294s Rank 0: the peak coverage is 3 294s Warning: no peak observed in the k-mer coverage distribution. 294s to deal with the sequencing error rate, try to lower the k-mer length (-k) 294s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 294s 294s *** 294s Step: Coverage distribution analysis 294s Date: Mon Mar 18 12:04:52 2024 294s Elapsed time: 1 seconds 294s Since beginning: 1 seconds 294s *** 294s 294s 294s 294s Rank 0 is adding edges [1/4108] 294s Rank 0 is adding edges [4108/4108] (completed) 294s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 294s Rank 0 : VirtualCommunicator (service provided by BufferedData): 453238 virtual messages generated 1813 real messages (0.400011%) 294s 294s *** 294s Step: Graph construction 294s Date: Mon Mar 18 12:04:52 2024 294s Elapsed time: 0 seconds 294s Since beginning: 1 seconds 294s *** 294s 294s 294s Rank 0 has 1954 vertices (completed) 294s Rank 0: assembler memory usage: 117036 KiB 295s Rank 0 is purging edges [1/1954] 295s Rank 0 is purging edges [1954/1954] (completed) 295s Rank 0: assembler memory usage: 117564 KiB 295s VirtualProcessor: completed jobs: 1954 295s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3904 virtual messages generated 11 real messages (0.281762%) 296s Rank 0 wrote test2/degreeDistribution.txt 296s 296s *** 296s Step: Null edge purging 296s Date: Mon Mar 18 12:04:53 2024 296s Elapsed time: 1 seconds 296s Since beginning: 2 seconds 296s *** 296s 296s 296s Rank 0 is selecting optimal read markers [1/4108] 296s Rank 0: assembler memory usage: 117564 KiB 296s Rank 0 is selecting optimal read markers [4108/4108] (completed) 296s Rank 0: peak number of workers: 599, maximum: 32768 296s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 238890 virtual messages generated 609 real messages (0.254929%) 296s Rank 0: assembler memory usage: 125692 KiB 296s Rank 0: Freeing unused assembler memory: 4096 KiB freed 296s Rank 0: assembler memory usage: 125692 KiB 296s 296s *** 296s Step: Selection of optimal read markers 296s Date: Mon Mar 18 12:04:54 2024 296s Elapsed time: 1 seconds 296s Since beginning: 3 seconds 296s *** 296s 296s 296s Rank 0: memory usage for optimal read markers= 4096 KiB 296s Rank 0 is creating seeds [1/1954] 296s Rank 0: assembler memory usage: 125692 KiB 297s Rank 0 has 1 seeds 297s Rank 0 is creating seeds [1954/1954] (completed) 297s Rank 0: peak number of workers: 746, maximum: 32768 297s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13612 virtual messages generated 1720 real messages (12.6359%) 297s Rank 0 runtime statistics for seeding algorithm: 297s Rank 0 Skipped paths because of dead end for head: 0 297s Rank 0 Skipped paths because of dead end for tail: 0 297s Rank 0 Skipped paths because of two dead ends: 0 297s Rank 0 Skipped paths because of bubble weak component: 0 297s Rank 0 Skipped paths because of short length: 1952 297s Rank 0 Skipped paths because of bad ownership: 1 297s Rank 0 Skipped paths because of low coverage: 0 297s Rank 0 Eligible paths: 1 297s Rank 0: assembler memory usage: 125692 KiB 297s Rank 0 has 1 seeds to register. 297s Rank 0 registered 0/1 297s Rank 0 registered 0/1 297s Rank 0 registered its seeds 297s VirtualProcessor: completed jobs: 0 297s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 297s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 307s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 307s Rank 0 merged its seeds: 1 seeds -> 1 seeds 307s 307s *** 307s Step: Detection of assembly seeds 307s Date: Mon Mar 18 12:05:05 2024 307s Elapsed time: 11 seconds 307s Since beginning: 14 seconds 307s *** 307s 307s 307s Rank 0 is calculating library lengths [1/1] 307s Rank 0 detected 1737 library lengths 307s Rank 0 is calculating library lengths [1/1] (completed) 307s Rank 0: peak number of workers: 1, maximum: 32768 307s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7997 virtual messages generated 7997 real messages (100%) 307s Rank 0: assembler memory usage: 162560 KiB 307s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 307s 307s Mode= 2 signalAverage= 9 307s CURRENT IS NOISE, 244 307s GOT HIT 212 307s 307s 307s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 307s 307s *** 307s Step: Estimation of outer distances for paired reads 307s Date: Mon Mar 18 12:05:05 2024 307s Elapsed time: 0 seconds 307s Since beginning: 14 seconds 307s *** 307s 307s 307s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 307s Rank 0 traversed 1000 nucleotide symbols 307s Rank 0: assembler memory usage: 166656 KiB 307s Rank 0 is extending seeds [1/1] (completed) 307s Rank 0 extended 1 seeds out of 1 (100.00%) 307s Rank 0: assembler memory usage: 158464 KiB 307s Rank 0 starting fusions 307s 307s *** 307s Step: Bidirectional extension of seeds 307s Date: Mon Mar 18 12:05:05 2024 307s Elapsed time: 0 seconds 307s Since beginning: 14 seconds 307s *** 307s 307s 307s Rank 0: starting clear step. cycleNumber= 0 308s Rank 0 adding 0 new fusions 308s Rank 0 cleared, 1 paths 308s Rank 0: starting distribution step 308s Rank 0 is distributing fusions [1/1] 308s Rank 0: assembler memory usage: 158464 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 is distributing fusions [1/1] (completed) 308s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 tells others to compute fusions. 308s Rank 0 FusionTaskCreator assignNextTask [0/2] 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 FusionTaskCreator processWorkerResult [0/2] 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 FusionTaskCreator [2/2] 308s Statistics: all paths: 1 eliminated during fusing: 0 308s Rank 0: assembler memory usage: 162560 KiB 308s VirtualProcessor: completed jobs: 2 308s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10907 virtual messages generated 10907 real messages (100%) 308s Rank 0: starting clear step. cycleNumber= 1 308s Rank 0 adding 0 new fusions 308s Rank 0 cleared, 1 paths 308s Rank 0 is distributing fusions [1/1] 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 is distributing fusions [1/1] (completed) 308s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 JoinerTaskCreator assignNextTask [0/2] 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s Rank 0 JoinerTaskCreator [2/2] 308s Statistics: all paths: 1 eliminated during joining: 0 308s Rank 0: assembler memory usage: 162560 KiB 308s Date: Mon Mar 18 12:05:06 2024 308s VirtualProcessor: completed jobs: 2 308s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13817 virtual messages generated 13817 real messages (100%) 309s Rank 0 adding 0 new fusions 309s Rank 0 cleared, 1 paths 309s Rank 0: starting distribution step 309s Rank 0 is distributing fusions [1/1] 309s Rank 0: assembler memory usage: 162560 KiB 309s Date: Mon Mar 18 12:05:07 2024 309s Rank 0 is distributing fusions [1/1] (completed) 309s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 309s Rank 0: assembler memory usage: 162560 KiB 309s Date: Mon Mar 18 12:05:07 2024 309s Rank 0 tells others to compute fusions. 309s Rank 0 FusionTaskCreator assignNextTask [0/2] 309s Rank 0: assembler memory usage: 162560 KiB 309s Date: Mon Mar 18 12:05:07 2024 309s Rank 0 FusionTaskCreator processWorkerResult [0/2] 309s Rank 0: assembler memory usage: 162560 KiB 309s Date: Mon Mar 18 12:05:07 2024 309s Rank 0 FusionTaskCreator [2/2] 309s Statistics: all paths: 1 eliminated during fusing: 0 309s Rank 0: assembler memory usage: 162560 KiB 309s VirtualProcessor: completed jobs: 2 309s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16727 virtual messages generated 16727 real messages (100%) 309s Rank 0: starting clear step. cycleNumber= 2 310s Rank 0 adding 0 new fusions 310s Rank 0 cleared, 1 paths 310s Rank 0 is distributing fusions [1/1] 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 is distributing fusions [1/1] (completed) 310s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 JoinerTaskCreator assignNextTask [0/2] 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 JoinerTaskCreator [2/2] 310s Statistics: all paths: 1 eliminated during joining: 0 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s VirtualProcessor: completed jobs: 2 310s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19637 virtual messages generated 19637 real messages (100%) 310s Rank 0 adding 0 new fusions 310s Rank 0 cleared, 1 paths 310s Rank 0: starting distribution step 310s Rank 0 is distributing fusions [1/1] 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 is distributing fusions [1/1] (completed) 310s Rank 0 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 6 real messages (0.618557%) 310s Rank 0: assembler memory usage: 162560 KiB 310s Date: Mon Mar 18 12:05:08 2024 310s Rank 0 cycleNumber= 2 310s 310s *** 310s Step: Merging of redundant paths 310s Date: Mon Mar 18 12:05:08 2024 310s Elapsed time: 3 seconds 310s Since beginning: 17 seconds 310s *** 310s 310s 310s Rank 0 appended 1 elements 310s 310s *** 310s Step: Generation of contigs 310s Date: Mon Mar 18 12:05:08 2024 310s Elapsed time: 0 seconds 310s Since beginning: 17 seconds 310s *** 310s 310s Rank 0 objectName: 0 => peakCoverage: 237 blockSize: 970 310s Rank 0: gathering scaffold links [1/1] [970/970] (completed) 310s Rank 0 ineligibleObjects: 0/970 (0.00%) 310s Rank 0: assembler memory usage: 162560 KiB 310s contig: 0 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 310s Rank 0 finished gathering scaffold links. 310s Rank 0 will write 1 contig lengths 310s Rank 0 will solve the scaffolding problem. 310s Welcome to GreedySolver v1.0 310s 1 vertices; 0 edges 310s 1 contigs >= 500 310s Edges in solution: 0 310s 310s Conflict statistics: 310s 1 scaffolds, 1 >= 500 310s Total: 1000 nucleotides 310s 310s *** 310s Step: Scaffolding of contigs 310s Date: Mon Mar 18 12:05:08 2024 310s Elapsed time: 0 seconds 310s Since beginning: 17 seconds 310s *** 310s 310s Rank 0 syncing with master 310s 310s *** 310s Step: Counting sequences to search 310s Date: Mon Mar 18 12:05:08 2024 310s Elapsed time: 0 seconds 310s Since beginning: 17 seconds 310s *** 310s 310s 310s Rank 0 will add colors, 0 sequences in 0 files to process 310s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 311s 311s *** 311s Step: Graph coloring 311s Date: Mon Mar 18 12:05:09 2024 311s Elapsed time: 1 seconds 311s Since beginning: 18 seconds 311s *** 311s 311s 311s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 311s Rank 0 shares its counts 311s Rank 0 computing contig abundances [1/1] [1/970] 311s Rank 0 computing contig abundances [1/1] [970/970] 311s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 311s 311s *** 311s Step: Counting contig biological abundances 311s Date: Mon Mar 18 12:05:09 2024 311s Elapsed time: 0 seconds 311s Since beginning: 18 seconds 311s *** 311s 311s 311s Rank 0 colored the graph with 0 real colors using 1 virtual colors 311s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 8 real messages (0.21%) 311s 311s *** 311s Step: Counting sequence biological abundances 311s Date: Mon Mar 18 12:05:09 2024 311s Elapsed time: 0 seconds 311s Since beginning: 18 seconds 311s *** 311s 311s 311s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 311s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 312s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 312s 312s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 312s Rank 0 is starting taxon syncing across the compute tribe. 312s 312s *** 312s Step: Loading taxons 312s Date: Mon Mar 18 12:05:10 2024 312s Elapsed time: 1 seconds 312s Since beginning: 19 seconds 312s *** 312s 312s Rank 0 synced taxons across the grid with 1 poor slaves. 312s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 312s Rank 0 has 0 taxons after syncing with master 312s 312s 312s *** 312s Step: Loading tree 312s Date: Mon Mar 18 12:05:10 2024 312s Elapsed time: 0 seconds 312s Since beginning: 19 seconds 312s *** 312s 313s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 313s 313s Rank 0: counting ontology terms in the graph... 314s Rank 0: 0 have some biological signal 314s Number of dereferenced alternate handles: 0 314s Number of k-mer observations with gene ontology terms: 0 314s Rank 0: synced ontology term profiles with master 314s Rank 0: synchronization is complete! 314s Rank 0: ontology terms with biological signal: 0 314s Populated recursive values... 314s Gene ontology terms without depth information: 0 314s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 314s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 314s 314s *** 314s Step: Processing gene ontologies 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 2 seconds 314s Since beginning: 21 seconds 314s *** 314s 314s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 314s [GenomeNeighbourhood] in final list: 0 314s 314s *** 314s Step: Computing neighbourhoods 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 0 seconds 314s Since beginning: 21 seconds 314s *** 314s 314s Contigs >= 100 nt 314s Number: 1 314s Total length: 1000 314s Average: 1000 314s N50: 1000 314s Median: 1000 314s Largest: 1000 314s Contigs >= 500 nt 314s Number: 1 314s Total length: 1000 314s Average: 1000 314s N50: 1000 314s Median: 1000 314s Largest: 1000 314s Scaffolds >= 100 nt 314s Number: 1 314s Total length: 1000 314s Average: 1000 314s N50: 1000 314s Median: 1000 314s Largest: 1000 314s Scaffolds >= 500 nt 314s Number: 1 314s Total length: 1000 314s Average: 1000 314s N50: 1000 314s Median: 1000 314s Largest: 1000 314s 314s Rank 0 wrote test2/Contigs.fasta 314s Rank 0 wrote test2/Scaffolds.fasta 314s Check for test2/* 314s 314s 314s 314s ************************************************** 314s This program comes with ABSOLUTELY NO WARRANTY. 314s This is free software, and you are welcome to redistribute it 314s under certain conditions; see "LICENSE.txt" for details. 314s ************************************************** 314s 314s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 314s Centre de recherche en infectiologie de l'Université Laval 314s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 314s http://denovoassembler.sf.net/ 314s 314s References to cite: 314s 314s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 314s Ray Meta: scalable de novo metagenome assembly and profiling. 314s Genome Biology (BioMed Central Ltd). 314s 13:R122, Published: 22 December 2012 314s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 314s 314s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 314s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 314s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 314s November 2010, Volume 17, Issue 11, Pages 1519-1533. 314s http://dx.doi.org/doi:10.1089/cmb.2009.0238 314s 314s Ray version 2.3.1 314s License for Ray: GNU General Public License version 3 314s RayPlatform version: 2.0.1 314s License for RayPlatform: GNU Lesser General Public License version 3 314s 314s MAXKMERLENGTH: 32 314s Maximum coverage depth stored by CoverageDepth: 4294967295 314s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 314s FORCE_PACKING = n 314s ASSERT = n 314s HAVE_LIBZ = y 314s HAVE_LIBBZ2 = y 314s PROFILER_COLLECT = n 314s MINIRANKS = y 314s CLOCK_GETTIME = n 314s __linux__ = y 314s _MSC_VER = n 314s __GNUC__ = y 314s RAY_32_BITS = n 314s RAY_64_BITS = y 314s MPI standard version: MPI 3.1 314s MPI library: Open-MPI 4.1.6 314s Compiler: GNU gcc/g++ 13.2.0 314s MPI I/O: n 314s 314s 314s -k (to set the k-mer size) 314s Value: 29 314s 314s 314s Paired library # 0 314s -p (paired-end sequences) 314s Left sequences: SampleDirectory/s_6.first1000_1.fastq 314s Right sequences: SampleDirectory/s_6.first1000_2.fastq 314s Average length: automatic detection 314s Standard deviation: automatic detection 314s 314s Ray command: 314s mpiexec -n 1 Ray \ 314s -k \ 314s 29 \ 314s -desable-recycling \ 314s -p \ 314s SampleDirectory/s_6.first1000_1.fastq \ 314s SampleDirectory/s_6.first1000_2.fastq 314s 314s Rank 0 wrote RayOutput/RayCommand.txt 314s 314s k-mer length: 29 314s Rank 0: assembler memory usage: 41928 KiB 314s Rank 0: assembler memory usage: 107764 KiB 314s Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 3318 314s Rank 0: testing the network, please wait... 314s 314s Rank 0 is testing the network [0/1000] 314s Rank 0 is testing the network [1000/1000] 314s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 314s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 1 microseconds (10^-6 seconds) 314s 314s Rank 0 wrote RayOutput/NetworkTest.txt 314s 314s 314s *** 314s Step: Network testing 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 0 seconds 314s Since beginning: 0 seconds 314s *** 314s 314s 314s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 314s Rank 0: File SampleDirectory/s_6.first1000_1.fastq (Number 0) has 2054 sequences 314s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 314s Rank 0: File SampleDirectory/s_6.first1000_2.fastq (Number 1) has 2054 sequences 314s Rank 0 wrote RayOutput/NumberOfSequences.txt 314s Rank 0 wrote RayOutput/SequencePartition.txt 314s 314s *** 314s Step: Counting sequences to assemble 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 0 seconds 314s Since beginning: 0 seconds 314s *** 314s 314s 314s Rank 0 is loading sequence reads 314s Rank 0 : partition is [0;4107], 4108 sequence reads 314s Rank 0 is fetching file SampleDirectory/s_6.first1000_1.fastq with lazy loading (please wait...) 314s Rank 0 has 0 sequence reads 314s Rank 0: assembler memory usage: 120636 KiB 314s Rank 0 is fetching file SampleDirectory/s_6.first1000_2.fastq with lazy loading (please wait...) 314s Rank 0 has 4108 sequence reads (completed) 314s 314s *** 314s Step: Sequence loading 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 0 seconds 314s Since beginning: 0 seconds 314s *** 314s 314s 314s [BloomFilter] allocated 238264 bytes for table with 1906112 bits 314s Rank 0 created its Bloom filter 314s Rank 0 is counting k-mers in sequence reads [1/4108] 314s Rank 0 is counting k-mers in sequence reads [4108/4108] (completed) 314s Rank 0 : VirtualCommunicator (service provided by BufferedData): 238926 virtual messages generated 478 real messages (0.200062%) 314s 314s 314s *** 314s Step: K-mer counting 314s Date: Mon Mar 18 12:05:12 2024 314s Elapsed time: 0 seconds 314s Since beginning: 0 seconds 314s *** 314s 314s 314s Rank 0 number of set bits in the Bloom filter: [ 7820 / 1906112 ] (0.410259%) 314s Rank 0 destroyed its Bloom filter 314s Rank 0 has 1958 k-mers (completed) 314s [BloomFilter] Rank 0: k-mers sampled -> 1958, k-mers dropped -> 0 (0%), k-mers accepted -> 1958 (100%) 314s Rank 0: assembler memory usage: 117012 KiB 315s 315s 315s Rank 0: the minimum coverage is 3 315s Rank 0: the peak coverage is 3 315s Warning: no peak observed in the k-mer coverage distribution. 315s to deal with the sequencing error rate, try to lower the k-mer length (-k) 315s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 315s 315s *** 315s Step: Coverage distribution analysis 315s Date: Mon Mar 18 12:05:13 2024 315s Elapsed time: 1 seconds 315s Since beginning: 1 seconds 315s *** 315s 315s 315s 315s Rank 0 is adding edges [1/4108] 315s Rank 0 is adding edges [4108/4108] (completed) 315s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 315s Rank 0 : VirtualCommunicator (service provided by BufferedData): 469636 virtual messages generated 1879 real messages (0.400097%) 315s 315s *** 315s Step: Graph construction 315s Date: Mon Mar 18 12:05:13 2024 315s Elapsed time: 0 seconds 315s Since beginning: 1 seconds 315s *** 315s 315s 315s Rank 0 has 1958 vertices (completed) 315s Rank 0: assembler memory usage: 117012 KiB 316s Rank 0 is purging edges [1/1958] 316s Rank 0 is purging edges [1958/1958] (completed) 316s Rank 0: assembler memory usage: 117544 KiB 316s VirtualProcessor: completed jobs: 1958 316s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 3912 virtual messages generated 12 real messages (0.306748%) 316s Rank 0 wrote RayOutput/degreeDistribution.txt 316s 316s *** 316s Step: Null edge purging 316s Date: Mon Mar 18 12:05:14 2024 316s Elapsed time: 1 seconds 316s Since beginning: 2 seconds 316s *** 316s 316s 316s Rank 0 is selecting optimal read markers [1/4108] 316s Rank 0: assembler memory usage: 117544 KiB 317s Rank 0 is selecting optimal read markers [4108/4108] (completed) 317s Rank 0: peak number of workers: 599, maximum: 32768 317s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 247142 virtual messages generated 624 real messages (0.252486%) 317s Rank 0: assembler memory usage: 125768 KiB 317s Rank 0: Freeing unused assembler memory: 4096 KiB freed 317s Rank 0: assembler memory usage: 125768 KiB 317s 317s *** 317s Step: Selection of optimal read markers 317s Date: Mon Mar 18 12:05:15 2024 317s Elapsed time: 1 seconds 317s Since beginning: 3 seconds 317s *** 317s 317s 317s Rank 0: memory usage for optimal read markers= 4096 KiB 317s Rank 0 is creating seeds [1/1958] 317s Rank 0: assembler memory usage: 125768 KiB 317s Rank 0 has 1 seeds 317s Rank 0 is creating seeds [1958/1958] (completed) 317s Rank 0: peak number of workers: 746, maximum: 32768 317s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13640 virtual messages generated 1708 real messages (12.522%) 317s Rank 0 runtime statistics for seeding algorithm: 317s Rank 0 Skipped paths because of dead end for head: 0 317s Rank 0 Skipped paths because of dead end for tail: 0 317s Rank 0 Skipped paths because of two dead ends: 0 317s Rank 0 Skipped paths because of bubble weak component: 0 317s Rank 0 Skipped paths because of short length: 1956 317s Rank 0 Skipped paths because of bad ownership: 1 317s Rank 0 Skipped paths because of low coverage: 0 317s Rank 0 Eligible paths: 1 317s Rank 0: assembler memory usage: 125768 KiB 317s Rank 0 has 1 seeds to register. 317s Rank 0 registered 0/1 317s Rank 0 registered 0/1 317s Rank 0 registered its seeds 317s VirtualProcessor: completed jobs: 0 317s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 318s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 328s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 328s Rank 0 merged its seeds: 1 seeds -> 1 seeds 328s 328s *** 328s Step: Detection of assembly seeds 328s Date: Mon Mar 18 12:05:26 2024 328s Elapsed time: 11 seconds 328s Since beginning: 14 seconds 328s *** 328s 328s 328s Rank 0 is calculating library lengths [1/1] 328s Rank 0 detected 1743 library lengths 328s Rank 0 is calculating library lengths [1/1] (completed) 328s Rank 0: peak number of workers: 1, maximum: 32768 328s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 8005 virtual messages generated 8005 real messages (100%) 328s Rank 0: assembler memory usage: 162636 KiB 328s Rank 0 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 328s 328s Mode= 2 signalAverage= 10 328s CURRENT IS NOISE, 244 328s GOT HIT 214 328s 328s 328s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 328s 328s *** 328s Step: Estimation of outer distances for paired reads 328s Date: Mon Mar 18 12:05:26 2024 328s Elapsed time: 0 seconds 328s Since beginning: 14 seconds 328s *** 328s 328s 328s Rank 0 starts on seed 0, length is 845, flow 0 [0/1] 328s Rank 0 traversed 1000 nucleotide symbols 328s Rank 0: assembler memory usage: 166732 KiB 328s Rank 0 is extending seeds [1/1] (completed) 328s Rank 0 extended 1 seeds out of 1 (100.00%) 328s Rank 0: assembler memory usage: 158540 KiB 328s Rank 0 starting fusions 328s 328s *** 328s Step: Bidirectional extension of seeds 328s Date: Mon Mar 18 12:05:26 2024 328s Elapsed time: 0 seconds 328s Since beginning: 14 seconds 328s *** 328s 328s 328s Rank 0: starting clear step. cycleNumber= 0 329s Rank 0 adding 0 new fusions 329s Rank 0 cleared, 1 paths 329s Rank 0: starting distribution step 329s Rank 0 is distributing fusions [1/1] 329s Rank 0: assembler memory usage: 158540 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 is distributing fusions [1/1] (completed) 329s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 tells others to compute fusions. 329s Rank 0 FusionTaskCreator assignNextTask [0/2] 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 FusionTaskCreator processWorkerResult [0/2] 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 FusionTaskCreator [2/2] 329s Statistics: all paths: 1 eliminated during fusing: 0 329s Rank 0: assembler memory usage: 162636 KiB 329s VirtualProcessor: completed jobs: 2 329s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 10921 virtual messages generated 10921 real messages (100%) 329s Rank 0: starting clear step. cycleNumber= 1 329s Rank 0 adding 0 new fusions 329s Rank 0 cleared, 1 paths 329s Rank 0 is distributing fusions [1/1] 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 is distributing fusions [1/1] (completed) 329s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 JoinerTaskCreator assignNextTask [0/2] 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s Rank 0 JoinerTaskCreator [2/2] 329s Statistics: all paths: 1 eliminated during joining: 0 329s Rank 0: assembler memory usage: 162636 KiB 329s Date: Mon Mar 18 12:05:27 2024 329s VirtualProcessor: completed jobs: 2 329s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 13837 virtual messages generated 13837 real messages (100%) 330s Rank 0 adding 0 new fusions 330s Rank 0 cleared, 1 paths 330s Rank 0: starting distribution step 330s Rank 0 is distributing fusions [1/1] 330s Rank 0: assembler memory usage: 162636 KiB 330s Date: Mon Mar 18 12:05:28 2024 330s Rank 0 is distributing fusions [1/1] (completed) 330s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 330s Rank 0: assembler memory usage: 162636 KiB 330s Date: Mon Mar 18 12:05:28 2024 330s Rank 0 tells others to compute fusions. 330s Rank 0 FusionTaskCreator assignNextTask [0/2] 330s Rank 0: assembler memory usage: 162636 KiB 330s Date: Mon Mar 18 12:05:28 2024 330s Rank 0 FusionTaskCreator processWorkerResult [0/2] 330s Rank 0: assembler memory usage: 162636 KiB 330s Date: Mon Mar 18 12:05:28 2024 330s Rank 0 FusionTaskCreator [2/2] 330s Statistics: all paths: 1 eliminated during fusing: 0 330s Rank 0: assembler memory usage: 162636 KiB 330s VirtualProcessor: completed jobs: 2 330s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 16753 virtual messages generated 16753 real messages (100%) 330s Rank 0: starting clear step. cycleNumber= 2 331s Rank 0 adding 0 new fusions 331s Rank 0 cleared, 1 paths 331s Rank 0 is distributing fusions [1/1] 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 is distributing fusions [1/1] (completed) 331s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 JoinerTaskCreator assignNextTask [0/2] 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 JoinerTaskCreator processWorkerResult [0/2] 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 JoinerTaskCreator [2/2] 331s Statistics: all paths: 1 eliminated during joining: 0 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s VirtualProcessor: completed jobs: 2 331s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 19669 virtual messages generated 19669 real messages (100%) 331s Rank 0 adding 0 new fusions 331s Rank 0 cleared, 1 paths 331s Rank 0: starting distribution step 331s Rank 0 is distributing fusions [1/1] 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 is distributing fusions [1/1] (completed) 331s Rank 0 : VirtualCommunicator (service provided by BufferedData): 972 virtual messages generated 6 real messages (0.617284%) 331s Rank 0: assembler memory usage: 162636 KiB 331s Date: Mon Mar 18 12:05:29 2024 331s Rank 0 cycleNumber= 2 331s 331s *** 331s Step: Merging of redundant paths 331s Date: Mon Mar 18 12:05:29 2024 331s Elapsed time: 3 seconds 331s Since beginning: 17 seconds 331s *** 331s 331s 331s Rank 0 appended 1 elements 331s 331s *** 331s Step: Generation of contigs 331s Date: Mon Mar 18 12:05:29 2024 331s Elapsed time: 0 seconds 331s Since beginning: 17 seconds 331s *** 331s 331s Rank 0 objectName: 0 => peakCoverage: 245 blockSize: 972 331s Rank 0: gathering scaffold links [1/1] [972/972] (completed) 331s Rank 0 ineligibleObjects: 0/972 (0.00%) 331s Rank 0: assembler memory usage: 162636 KiB 331s contig: 0 vertices: 972 averageCoverage: 245 standardDeviation: 117 peakCoverage: 245 repeatCoverage: 490 331s Rank 0 finished gathering scaffold links. 331s Rank 0 will write 1 contig lengths 331s Rank 0 will solve the scaffolding problem. 331s Welcome to GreedySolver v1.0 331s 1 vertices; 0 edges 331s 1 contigs >= 500 331s Edges in solution: 0 331s 331s Conflict statistics: 331s 1 scaffolds, 1 >= 500 331s Total: 1000 nucleotides 331s 331s *** 331s Step: Scaffolding of contigs 331s Date: Mon Mar 18 12:05:29 2024 331s Elapsed time: 0 seconds 331s Since beginning: 17 seconds 331s *** 331s 331s Rank 0 syncing with master 331s 331s *** 331s Step: Counting sequences to search 331s Date: Mon Mar 18 12:05:29 2024 331s Elapsed time: 0 seconds 331s Since beginning: 17 seconds 331s *** 331s 331s 331s Rank 0 will add colors, 0 sequences in 0 files to process 331s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 332s 332s *** 332s Step: Graph coloring 332s Date: Mon Mar 18 12:05:30 2024 332s Elapsed time: 1 seconds 332s Since beginning: 18 seconds 332s *** 332s 332s 332s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 332s Rank 0 shares its counts 332s Rank 0 computing contig abundances [1/1] [1/972] 332s Rank 0 computing contig abundances [1/1] [972/972] 332s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 332s 332s *** 332s Step: Counting contig biological abundances 332s Date: Mon Mar 18 12:05:30 2024 332s Elapsed time: 0 seconds 332s Since beginning: 18 seconds 332s *** 332s 332s 332s Rank 0 colored the graph with 0 real colors using 1 virtual colors 332s Rank 0 : VirtualCommunicator (service provided by BufferedData): 3888 virtual messages generated 8 real messages (0.21%) 332s 332s *** 332s Step: Counting sequence biological abundances 332s Date: Mon Mar 18 12:05:30 2024 332s Elapsed time: 0 seconds 332s Since beginning: 18 seconds 332s *** 332s 332s 332s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 332s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 333s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 333s 333s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 333s Rank 0 is starting taxon syncing across the compute tribe. 333s 333s *** 333s Step: Loading taxons 333s Date: Mon Mar 18 12:05:31 2024 333s Elapsed time: 1 seconds 333s Since beginning: 19 seconds 333s *** 333s 333s Rank 0 synced taxons across the grid with 1 poor slaves. 333s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 333s Rank 0 has 0 taxons after syncing with master 333s 333s 333s *** 333s Step: Loading tree 333s Date: Mon Mar 18 12:05:31 2024 333s Elapsed time: 0 seconds 333s Since beginning: 19 seconds 333s *** 333s 334s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 334s 334s Rank 0: counting ontology terms in the graph... 335s Rank 0: 0 have some biological signal 335s Number of dereferenced alternate handles: 0 335s Number of k-mer observations with gene ontology terms: 0 335s Rank 0: synced ontology term profiles with master 335s Rank 0: synchronization is complete! 335s Rank 0: ontology terms with biological signal: 0 335s Populated recursive values... 335s Gene ontology terms without depth information: 0 335s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 335s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 335s 335s *** 335s Step: Processing gene ontologies 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 2 seconds 335s Since beginning: 21 seconds 335s *** 335s 335s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 335s [GenomeNeighbourhood] in final list: 0 335s 335s *** 335s Step: Computing neighbourhoods 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 21 seconds 335s *** 335s 335s Contigs >= 100 nt 335s Number: 1 335s Total length: 1000 335s Average: 1000 335s N50: 1000 335s Median: 1000 335s Largest: 1000 335s Contigs >= 500 nt 335s Number: 1 335s Total length: 1000 335s Average: 1000 335s N50: 1000 335s Median: 1000 335s Largest: 1000 335s Scaffolds >= 100 nt 335s Number: 1 335s Total length: 1000 335s Average: 1000 335s N50: 1000 335s Median: 1000 335s Largest: 1000 335s Scaffolds >= 500 nt 335s Number: 1 335s Total length: 1000 335s Average: 1000 335s N50: 1000 335s Median: 1000 335s Largest: 1000 335s 335s Rank 0 wrote RayOutput/Contigs.fasta 335s Rank 0 wrote RayOutput/Scaffolds.fasta 335s Check for RayOutput/* 335s 335s 335s 335s ************************************************** 335s This program comes with ABSOLUTELY NO WARRANTY. 335s This is free software, and you are welcome to redistribute it 335s under certain conditions; see "LICENSE.txt" for details. 335s ************************************************** 335s 335s Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert 335s Centre de recherche en infectiologie de l'Université Laval 335s Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) 335s http://denovoassembler.sf.net/ 335s 335s References to cite: 335s 335s Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. 335s Ray Meta: scalable de novo metagenome assembly and profiling. 335s Genome Biology (BioMed Central Ltd). 335s 13:R122, Published: 22 December 2012 335s http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122 335s 335s Sébastien Boisvert, François Laviolette & Jacques Corbeil. 335s Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. 335s Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). 335s November 2010, Volume 17, Issue 11, Pages 1519-1533. 335s http://dx.doi.org/doi:10.1089/cmb.2009.0238 335s 335s Ray version 2.3.1 335s License for Ray: GNU General Public License version 3 335s RayPlatform version: 2.0.1 335s License for RayPlatform: GNU Lesser General Public License version 3 335s 335s MAXKMERLENGTH: 32 335s Maximum coverage depth stored by CoverageDepth: 4294967295 335s MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes 335s FORCE_PACKING = n 335s ASSERT = n 335s HAVE_LIBZ = y 335s HAVE_LIBBZ2 = y 335s PROFILER_COLLECT = n 335s MINIRANKS = y 335s CLOCK_GETTIME = n 335s __linux__ = y 335s _MSC_VER = n 335s __GNUC__ = y 335s RAY_32_BITS = n 335s RAY_64_BITS = y 335s MPI standard version: MPI 3.1 335s MPI library: Open-MPI 4.1.6 335s Compiler: GNU gcc/g++ 13.2.0 335s MPI I/O: n 335s 335s 335s -k (to set the k-mer size) 335s Value: 31 335s 335s 335s Paired library # 0 335s -p (paired-end sequences) 335s Left sequences: ecoli_1K_1.fq 335s Right sequences: ecoli_1K_2.fq 335s Average length: automatic detection 335s Standard deviation: automatic detection 335s 335s Ray command: 335s mpiexec -n 2 Ray \ 335s -k \ 335s 31 \ 335s -p \ 335s ecoli_1K_1.fq \ 335s ecoli_1K_2.fq \ 335s -o \ 335s test3 335s 335s Rank 0 wrote test3/RayCommand.txt 335s 335s k-mer length: 31 335s Rank 0: assembler memory usage: 41920 KiB 335s Rank 1: assembler memory usage: 41924 KiB 335s Rank 0: assembler memory usage: 107772 KiB 335s Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 3327 335s Rank 0: testing the network, please wait... 335s 335s Rank 0 is testing the network [0/1000] 335s Rank 1: assembler memory usage: 107760 KiB 335s Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 3328 335s Rank 1 is testing the network [0/1000] 335s Rank 0 is testing the network [1000/1000] 335s Rank 0: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 335s Rank 0: average round trip latency when requesting a reply for a message of 4000 bytes is 4 microseconds (10^-6 seconds) 335s Rank 1 is testing the network [1000/1000] 335s Rank 1: mode round trip latency when requesting a reply for a message of 4000 bytes is 2 microseconds (10^-6 seconds) 335s 335s Rank 0 wrote test3/NetworkTest.txt 335s 335s 335s *** 335s Step: Network testing 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 0 seconds 335s *** 335s 335s 335s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 335s Rank 1: average round trip latency when requesting a reply for a message of 4000 bytes is 3 microseconds (10^-6 seconds) 335s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 335s Rank 0: File ecoli_1K_1.fq (Number 0) has 2054 sequences 335s Rank 1: File ecoli_1K_2.fq (Number 1) has 2054 sequences 335s Rank 0 wrote test3/NumberOfSequences.txt 335s Rank 1 is loading sequence reads 335s Rank 0 wrote test3/SequencePartition.txt 335s 335s *** 335s Step: Counting sequences to assemble 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 0 seconds 335s *** 335s 335s 335s Rank 0 is loading sequence reads 335s Rank 0 : partition is [0;2053], 2054 sequence reads 335s Rank 1 : partition is [2054;4107], 2054 sequence reads 335s Rank 0 is fetching file ecoli_1K_1.fq with lazy loading (please wait...) 335s Rank 1 is fetching file ecoli_1K_2.fq with lazy loading (please wait...) 335s Rank 0 has 0 sequence reads 335s Rank 0: assembler memory usage: 116560 KiB 335s Rank 1 has 0 sequence reads 335s Rank 1: assembler memory usage: 116540 KiB 335s Rank 0 has 2054 sequence reads (completed) 335s Rank 1 has 2054 sequence reads (completed) 335s 335s *** 335s Step: Sequence loading 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 0 seconds 335s *** 335s 335s 335s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 335s Rank 0 created its Bloom filter 335s Rank 0 is counting k-mers in sequence reads [1/2054] 335s [BloomFilter] allocated 127352 bytes for table with 1018784 bits 335s Rank 1 created its Bloom filter 335s Rank 1 is counting k-mers in sequence reads [1/2054] 335s Rank 1 is counting k-mers in sequence reads [2054/2054] (completed) 335s Rank 1 : VirtualCommunicator (service provided by BufferedData): 114119 virtual messages generated 229 real messages (0.200668%) 335s Rank 0 is counting k-mers in sequence reads [2054/2054] (completed) 335s Rank 0 : VirtualCommunicator (service provided by BufferedData): 116591 virtual messages generated 234 real messages (0.200702%) 335s 335s Rank 1 number of set bits in the Bloom filter: [ 3683 / 1018784 ] (0.361509%) 335s 335s *** 335s Step: K-mer counting 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 0 seconds 335s *** 335s 335s 335s Rank 0 number of set bits in the Bloom filter: [ 4119 / 1018784 ] (0.404306%) 335s Rank 0 destroyed its Bloom filter 335s Rank 0 has 1032 k-mers (completed) 335s [BloomFilter] Rank 0: k-mers sampled -> 1032, k-mers dropped -> 0 (0%), k-mers accepted -> 1032 (100%) 335s Rank 0: assembler memory usage: 112828 KiB 335s Rank 1 destroyed its Bloom filter 335s Rank 1 has 922 k-mers (completed) 335s [BloomFilter] Rank 1: k-mers sampled -> 922, k-mers dropped -> 0 (0%), k-mers accepted -> 922 (100%) 335s Rank 1: assembler memory usage: 116540 KiB 335s 335s 335s Rank 0: the minimum coverage is 3 335s Rank 0: the peak coverage is 3 335s Rank 1 is adding edges [1/2054] 335s Warning: no peak observed in the k-mer coverage distribution. 335s to deal with the sequencing error rate, try to lower the k-mer length (-k) 335s If you are using RNA-Seq or metagenomic data, then you can ignore this warning. 335s 335s *** 335s Step: Coverage distribution analysis 335s Date: Mon Mar 18 12:05:33 2024 335s Elapsed time: 0 seconds 335s Since beginning: 0 seconds 335s *** 335s 335s 335s 335s Rank 0 is adding edges [1/2054] 336s Rank 1 is adding edges [2054/2054] (completed) 336s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 336s Rank 1 : VirtualCommunicator (service provided by BufferedData): 224144 virtual messages generated 897 real messages (0.400189%) 336s Rank 0 is adding edges [2054/2054] (completed) 336s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 336s Rank 0 : VirtualCommunicator (service provided by BufferedData): 229094 virtual messages generated 917 real messages (0.400272%) 336s 336s *** 336s Step: Graph construction 336s Date: Mon Mar 18 12:05:34 2024 336s Elapsed time: 1 seconds 336s Since beginning: 1 seconds 336s *** 336s 336s 336s Rank 0 has 1032 vertices (completed) 336s Rank 0: assembler memory usage: 112828 KiB 336s Rank 1 has 922 vertices (completed) 336s Rank 1: assembler memory usage: 116540 KiB 336s Rank 1 is purging edges [1/922] 336s Rank 1 is purging edges [922/922] (completed) 336s Rank 1: assembler memory usage: 116540 KiB 336s VirtualProcessor: completed jobs: 922 336s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 1842 virtual messages generated 11 real messages (0.597177%) 336s Rank 0 is purging edges [1/1032] 336s Rank 0 is purging edges [1032/1032] (completed) 336s Rank 0: assembler memory usage: 113100 KiB 336s VirtualProcessor: completed jobs: 1032 336s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2062 virtual messages generated 9 real messages (0.436469%) 337s Rank 0 wrote test3/degreeDistribution.txt 337s 337s *** 337s Step: Null edge purging 337s Date: Mon Mar 18 12:05:35 2024 337s Rank 1 is selecting optimal read markers [1/2054] 337s Rank 1: assembler memory usage: 116540 KiB 337s Elapsed time: 1 seconds 337s Since beginning: 2 seconds 337s *** 337s 337s 337s Rank 0 is selecting optimal read markers [1/2054] 337s Rank 0: assembler memory usage: 113100 KiB 337s Rank 1 is selecting optimal read markers [2054/2054] (completed) 337s Rank 1: peak number of workers: 1121, maximum: 32768 337s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 118211 virtual messages generated 360 real messages (0.30454%) 337s Rank 1: assembler memory usage: 124220 KiB 337s Rank 1: Freeing unused assembler memory: 4096 KiB freed 337s Rank 1: assembler memory usage: 124220 KiB 337s Rank 0 is selecting optimal read markers [2054/2054] (completed) 337s Rank 0: peak number of workers: 1135, maximum: 32768 337s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 120679 virtual messages generated 369 real messages (0.30577%) 337s Rank 0: assembler memory usage: 121308 KiB 337s Rank 0: Freeing unused assembler memory: 4096 KiB freed 337s Rank 0: assembler memory usage: 121308 KiB 337s 337s *** 337s Step: Selection of optimal read markers 337s Date: Mon Mar 18 12:05:35 2024 337s Elapsed time: 0 seconds 337s Since beginning: 2 seconds 337s *** 337s 337s 337s Rank 0: memory usage for optimal read markers= 4096 KiB 337s Rank 1: memory usage for optimal read markers= 4096 KiB 337s Rank 1 is creating seeds [1/922] 337s Rank 1: assembler memory usage: 124220 KiB 337s Rank 0 is creating seeds [1/1032] 337s Rank 0: assembler memory usage: 121308 KiB 338s Rank 1 has 1 seeds 338s Rank 1 is creating seeds [922/922] (completed) 338s Rank 1: peak number of workers: 916, maximum: 32768 338s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 6519 virtual messages generated 1755 real messages (26.9213%) 338s Rank 1 runtime statistics for seeding algorithm: 338s Rank 1 Skipped paths because of dead end for head: 0 338s Rank 1 Skipped paths because of dead end for tail: 0 338s Rank 1 Skipped paths because of two dead ends: 0 338s Rank 1 Skipped paths because of bubble weak component: 0 338s Rank 1 Skipped paths because of short length: 921 338s Rank 1 Skipped paths because of bad ownership: 0 338s Rank 1 Skipped paths because of low coverage: 0 338s Rank 1 Eligible paths: 1 338s Rank 1: assembler memory usage: 124220 KiB 338s Rank 0 has 0 seeds 338s Rank 0 is creating seeds [1032/1032] (completed) 338s Rank 0: peak number of workers: 998, maximum: 32768 338s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 7093 virtual messages generated 1744 real messages (24.5876%) 338s Rank 0 runtime statistics for seeding algorithm: 338s Rank 0 Skipped paths because of dead end for head: 0 338s Rank 0 Skipped paths because of dead end for tail: 0 338s Rank 0 Skipped paths because of two dead ends: 0 338s Rank 0 Skipped paths because of bubble weak component: 0 338s Rank 0 Skipped paths because of short length: 1031 338s Rank 0 Skipped paths because of bad ownership: 1 338s Rank 0 Skipped paths because of low coverage: 0 338s Rank 0 Eligible paths: 0 338s Rank 0: assembler memory usage: 121308 KiB 338s Rank 1 has 1 seeds to register. 338s Rank 0 registered -1/0 338s Rank 0 registered its seeds 338s Rank 1 registered 0/1 338s Rank 1 registered 0/1 338s Rank 1 registered its seeds 338s VirtualProcessor: completed jobs: 0 338s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 338s VirtualProcessor: completed jobs: 0 338s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 339s Rank 0 freed 4194304 bytes from the path memory pool (chunks: 1) 339s Rank 1 freed 4194304 bytes from the path memory pool (chunks: 1) 349s Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0) 349s Rank 1: gossiping generated 0 messages (gossips: 0 ---> 0) 349s Rank 1 merged its seeds: 1 seeds -> 1 seeds 349s Rank 0 merged its seeds: 0 seeds -> 0 seeds 349s 349s *** 349s Step: Detection of assembly seeds 349s Date: Mon Mar 18 12:05:47 2024 349s Elapsed time: 12 seconds 349s Since beginning: 14 seconds 349s *** 349s 349s 349s Rank 0 detected 0 library lengths 349s Rank 0 is calculating library lengths [0/0] (completed) 349s Rank 0: peak number of workers: 0, maximum: 32768 349s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 349s Rank 0: assembler memory usage: 125404 KiB 349s Rank 1 is calculating library lengths [1/1] 349s Rank 1 detected 1737 library lengths 349s Rank 1 is calculating library lengths [1/1] (completed) 349s Rank 1: peak number of workers: 1, maximum: 32768 349s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 7984 virtual messages generated 7984 real messages (100%) 349s Rank 1: assembler memory usage: 156992 KiB 349s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 349s 349s Mode= 2 signalAverage= 9 349s CURRENT IS NOISE, 244 349s GOT HIT 212 349s 349s 349s Library # 0 (Automatic) -> average length: 214 and standard deviation: 10 349s 349s *** 349s Step: Estimation of outer distances for paired reads 349s Date: Mon Mar 18 12:05:47 2024 349s Elapsed time: 0 seconds 349s Since beginning: 14 seconds 349s *** 349s 349s 349s Rank 0 is extending seeds [0/0] (completed) 349s Rank 0 extended 0 seeds out of 0 (0.00%) 349s Rank 0: assembler memory usage: 125404 KiB 349s Rank 1 : VirtualCommunicator (service provided by BufferedData): 67 virtual messages generated 1 real messages (1.49254%) 349s Rank 1 starts on seed 0, length is 845, flow 0 [0/1] 349s Rank 1 traversed 1000 nucleotide symbols 349s Rank 1: assembler memory usage: 161088 KiB 349s Rank 1 is extending seeds [1/1] (completed) 349s Rank 1 extended 1 seeds out of 1 (100.00%) 349s Rank 1: assembler memory usage: 161088 KiB 349s Rank 0 starting fusions 349s 349s *** 349s Step: Bidirectional extension of seeds 349s Date: Mon Mar 18 12:05:47 2024 349s Elapsed time: 0 seconds 349s Since beginning: 14 seconds 349s *** 349s 349s 349s Rank 0: starting clear step. cycleNumber= 0 350s Rank 0 adding 0 new fusions 350s Rank 0 cleared, 0 paths 350s Rank 1 adding 0 new fusions 350s Rank 1 cleared, 1 paths 350s Rank 0: starting distribution step 350s Rank 0 is distributing fusions [0/0] (completed) 350s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 350s Rank 1 is distributing fusions [1/1] 350s Rank 0: assembler memory usage: 125404 KiB 350s Rank 1: assembler memory usage: 161088 KiB 350s Date: Mon Mar 18 12:05:48 2024 350s Date: Mon Mar 18 12:05:48 2024 350s Rank 1 is distributing fusions [1/1] (completed) 350s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 350s Rank 1: assembler memory usage: 161088 KiB 350s Date: Mon Mar 18 12:05:48 2024 350s Rank 1 FusionTaskCreator assignNextTask [0/2] 350s Rank 0 tells others to compute fusions. 350s Rank 0 FusionTaskCreator [0/0] 350s Statistics: all paths: 0 eliminated during fusing: 0 350s Rank 0: assembler memory usage: 125404 KiB 350s VirtualProcessor: completed jobs: 0 350s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 350s Rank 1: assembler memory usage: 161088 KiB 350s Date: Mon Mar 18 12:05:48 2024 350s Rank 1 FusionTaskCreator processWorkerResult [0/2] 350s Rank 1: assembler memory usage: 161088 KiB 350s Date: Mon Mar 18 12:05:48 2024 350s Rank 1 FusionTaskCreator [2/2] 350s Statistics: all paths: 1 eliminated during fusing: 0 350s Rank 1: assembler memory usage: 161088 KiB 350s VirtualProcessor: completed jobs: 2 350s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 10894 virtual messages generated 10894 real messages (100%) 350s Rank 0: starting clear step. cycleNumber= 1 351s Rank 0 adding 0 new fusions 351s Rank 0 cleared, 0 paths 351s Rank 1 adding 0 new fusions 351s Rank 1 cleared, 1 paths 351s Rank 0 is distributing fusions [0/0] (completed) 351s Rank 1 is distributing fusions [1/1] 351s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 0: assembler memory usage: 125404 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 is distributing fusions [1/1] (completed) 351s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 JoinerTaskCreator assignNextTask [0/2] 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 0 JoinerTaskCreator [0/0] 351s Statistics: all paths: 0 eliminated during joining: 0 351s Rank 0: assembler memory usage: 125404 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s VirtualProcessor: completed jobs: 0 351s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 351s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 JoinerTaskCreator [2/2] 351s Statistics: all paths: 1 eliminated during joining: 0 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s VirtualProcessor: completed jobs: 2 351s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 13804 virtual messages generated 13804 real messages (100%) 351s Rank 0 adding 0 new fusions 351s Rank 0 cleared, 0 paths 351s Rank 1 adding 0 new fusions 351s Rank 1 cleared, 1 paths 351s Rank 0: starting distribution step 351s Rank 0 is distributing fusions [0/0] (completed) 351s Rank 1 is distributing fusions [1/1] 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 is distributing fusions [1/1] (completed) 351s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 FusionTaskCreator assignNextTask [0/2] 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 351s Rank 0: assembler memory usage: 125404 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 0 tells others to compute fusions. 351s Rank 0 FusionTaskCreator [0/0] 351s Statistics: all paths: 0 eliminated during fusing: 0 351s Rank 0: assembler memory usage: 125404 KiB 351s VirtualProcessor: completed jobs: 0 351s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 351s Rank 1 FusionTaskCreator processWorkerResult [0/2] 351s Rank 1: assembler memory usage: 161088 KiB 351s Date: Mon Mar 18 12:05:49 2024 351s Rank 1 FusionTaskCreator [2/2] 351s Statistics: all paths: 1 eliminated during fusing: 0 351s Rank 1: assembler memory usage: 161088 KiB 351s VirtualProcessor: completed jobs: 2 351s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 16714 virtual messages generated 16714 real messages (100%) 351s Rank 0: starting clear step. cycleNumber= 2 352s Rank 1 adding 0 new fusions 352s Rank 1 cleared, 1 paths 352s Rank 0 adding 0 new fusions 352s Rank 0 cleared, 0 paths 352s Rank 1 is distributing fusions [1/1] 352s Rank 0 is distributing fusions [0/0] (completed) 352s Rank 1: assembler memory usage: 161088 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 352s Rank 0: assembler memory usage: 125404 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s Rank 1 is distributing fusions [1/1] (completed) 352s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 352s Rank 1: assembler memory usage: 161088 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s Rank 1 JoinerTaskCreator assignNextTask [0/2] 352s Rank 0 JoinerTaskCreator [0/0] 352s Rank 1: assembler memory usage: 161088 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s Statistics: all paths: 0 eliminated during joining: 0 352s Rank 0: assembler memory usage: 125404 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s VirtualProcessor: completed jobs: 0 352s Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 0 virtual messages generated 0 real messages (0%) 352s Rank 1 JoinerTaskCreator processWorkerResult [0/2] 352s Rank 1: assembler memory usage: 161088 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s Rank 1 JoinerTaskCreator [2/2] 352s Statistics: all paths: 1 eliminated during joining: 0 352s Rank 1: assembler memory usage: 161088 KiB 352s Date: Mon Mar 18 12:05:50 2024 352s VirtualProcessor: completed jobs: 2 352s Rank 1 : VirtualCommunicator (service provided by VirtualCommunicator): 19624 virtual messages generated 19624 real messages (100%) 353s Rank 0 adding 0 new fusions 353s Rank 0 cleared, 0 paths 353s Rank 1 adding 0 new fusions 353s Rank 1 cleared, 1 paths 353s Rank 1 is distributing fusions [1/1] 353s Rank 1: assembler memory usage: 161088 KiB 353s Date: Mon Mar 18 12:05:51 2024 353s Rank 1 is distributing fusions [1/1] (completed) 353s Rank 1 : VirtualCommunicator (service provided by BufferedData): 970 virtual messages generated 7 real messages (0.721649%) 353s Rank 1: assembler memory usage: 161088 KiB 353s Date: Mon Mar 18 12:05:51 2024 353s Rank 1 appended 1 elements 353s Rank 0: starting distribution step 353s Rank 0 is distributing fusions [0/0] (completed) 353s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 353s Rank 0: assembler memory usage: 125404 KiB 353s Date: Mon Mar 18 12:05:51 2024 353s Rank 0 cycleNumber= 2 353s 353s *** 353s Step: Merging of redundant paths 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 4 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s 353s Rank 0 appended 0 elements 353s 353s *** 353s Step: Generation of contigs 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s Rank 0 finished gathering scaffold links. 353s Rank 0 objectName: 1 => peakCoverage: 237 blockSize: 970 353s Rank 1: gathering scaffold links [1/1] [970/970] (completed) 353s Rank 0 ineligibleObjects: 0/970 (0.00%) 353s Rank 1: assembler memory usage: 161088 KiB 353s contig: 1 vertices: 970 averageCoverage: 237 standardDeviation: 115 peakCoverage: 237 repeatCoverage: 474 353s Rank 1 finished gathering scaffold links. 353s Rank 0 will write 1 contig lengths 353s Rank 0 will solve the scaffolding problem. 353s Welcome to GreedySolver v1.0 353s 1 vertices; 0 edges 353s 1 contigs >= 500 353s Edges in solution: 0 353s 353s Conflict statistics: 353s 1 scaffolds, 1 >= 500 353s Total: 1000 nucleotides 353s 353s *** 353s Step: Scaffolding of contigs 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s Rank 0 syncing with master 353s 353s *** 353s Step: Counting sequences to search 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s 353s Rank 0 will add colors, 0 sequences in 0 files to process 353s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 353s Rank 1 syncing with master 353s Rank 1 will add colors, 0 sequences in 0 files to process 353s Rank 1 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0.00%) 353s 353s *** 353s Step: Graph coloring 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s 353s Rank 1: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 353s Rank 1 computing contig abundances [1/1] [1/970] 353s Rank 1 computing contig abundances [1/1] [970/970] 353s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 353s Rank 1 colored the graph with 0 real colors using 1 virtual colors 353s Rank 1 : VirtualCommunicator (service provided by BufferedData): 3880 virtual messages generated 9 real messages (0.23%) 353s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 353s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 353s Rank 0: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES 353s Rank 0 shares its counts 353s [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes 353s 353s *** 353s Step: Counting contig biological abundances 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s 353s Rank 0 colored the graph with 0 real colors using 1 virtual colors 353s Rank 0 : VirtualCommunicator (service provided by BufferedData): 0 virtual messages generated 0 real messages (0%) 353s 353s *** 353s Step: Counting sequence biological abundances 353s Date: Mon Mar 18 12:05:51 2024 353s Elapsed time: 0 seconds 353s Since beginning: 18 seconds 353s *** 353s 353s 353s [IO] Input/output operations for sequence XML objects: 0 / bufferSize: 16777216 bytes 353s [IO] Input/output operations for identification TSV objects: 0 / bufferSize: 16777216 bytes 354s Rank 1 has exactly 0 k-mer physical colors for the phylogeny. 354s 354s Rank 0 has exactly 0 k-mer physical colors for the phylogeny. 354s 354s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 354s Rank 0 is starting taxon syncing across the compute tribe. 354s 354s *** 354s Step: Loading taxons 354s Date: Mon Mar 18 12:05:52 2024 354s Elapsed time: 1 seconds 354s Since beginning: 19 seconds 354s *** 354s 354s Rank 0 synced taxons across the grid with 2 poor slaves. 354s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 354s [TaxonomyViewer::copyTaxonsFromSecondaryTable] 0 -> 0 354s Rank 0 has 0 taxons after syncing with master 354s Rank 1 has 0 taxons after syncing with master 355s 355s 355s 355s *** 355s Step: Loading tree 355s Date: Mon Mar 18 12:05:53 2024 355s Elapsed time: 1 seconds 355s Since beginning: 20 seconds 355s *** 355s 356s Rank 0 has exactly 0 k-mer physical colors related to EMBL CDS objects. 356s 356s Rank 0: counting ontology terms in the graph... 356s Rank 1 has exactly 0 k-mer physical colors related to EMBL CDS objects. 356s 356s Rank 1: counting ontology terms in the graph... 356s Rank 1: 0 have some biological signal 356s Number of dereferenced alternate handles: 0 356s Number of k-mer observations with gene ontology terms: 0 356s Rank 0: 0 have some biological signal 356s Number of dereferenced alternate handles: 0 356s Number of k-mer observations with gene ontology terms: 0 356s Rank 0: synced ontology term profiles with master 356s Rank 0 Synchronizing kmer observations with gene ontology terms: 0 (from 1) 356s Rank 1: synced ontology term profiles with master 356s Rank 0: synchronization is complete! 356s Rank 0: ontology terms with biological signal: 0 356s Populated recursive values... 356s Gene ontology terms without depth information: 0 356s [GeneOntology] maximum depth for GeneOntologyDomain  is 0 356s [GeneOntology] maximum depth for GeneOntologyDomain [GeneOntology] maximum depth for GeneOntologyDomain  is 0 356s 356s *** 356s Step: Processing gene ontologies 356s Date: Mon Mar 18 12:05:54 2024 356s Elapsed time: 1 seconds 356s Since beginning: 21 seconds 356s *** 356s 356s Rank 0: the CorePlugin GenomeNeighbourhood is disabled... 356s Rank 1: the CorePlugin GenomeNeighbourhood is disabled... 356s [GenomeNeighbourhood] in final list: 0 356s 356s *** 356s Step: Computing neighbourhoods 356s Date: Mon Mar 18 12:05:54 2024 356s Elapsed time: 0 seconds 356s Since beginning: 21 seconds 356s *** 356s 356s Contigs >= 100 nt 356s Number: 1 356s Total length: 1000 356s Average: 1000 356s N50: 1000 356s Median: 1000 356s Largest: 1000 356s Contigs >= 500 nt 356s Number: 1 356s Total length: 1000 356s Average: 1000 356s N50: 1000 356s Median: 1000 356s Largest: 1000 356s Scaffolds >= 100 nt 356s Number: 1 356s Total length: 1000 356s Average: 1000 356s N50: 1000 356s Median: 1000 356s Largest: 1000 356s Scaffolds >= 500 nt 356s Number: 1 356s Total length: 1000 356s Average: 1000 356s N50: 1000 356s Median: 1000 356s Largest: 1000 356s 356s Rank 0 wrote test3/Contigs.fasta 356s Rank 0 wrote test3/Scaffolds.fasta 356s Check for test3/* 356s 356s 358s autopkgtest [12:05:55]: test run-unit-test: -----------------------] 359s autopkgtest [12:05:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 359s run-unit-test PASS 359s autopkgtest [12:05:57]: @@@@@@@@@@@@@@@@@@@@ summary 359s run-unit-test PASS 365s Creating nova instance adt-noble-arm64-ray-20240318-115958-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...