0s autopkgtest [16:48:34]: starting date and time: 2025-03-15 16:48:34+0000 0s autopkgtest [16:48:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:48:34]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.etao1j4j/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade ragout --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.28 lxd-armhf-10.145.243.28:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [16:48:55]: testbed dpkg architecture: armhf 23s autopkgtest [16:48:57]: testbed apt version: 2.9.33 26s autopkgtest [16:49:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [16:49:02]: testbed release detected to be: None 35s autopkgtest [16:49:09]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 64s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 66s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 68s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 68s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 68s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 83s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 85s Fetched 41.0 MB in 47s (867 kB/s) 86s Reading package lists... 92s autopkgtest [16:50:06]: upgrading testbed (apt dist-upgrade and autopurge) 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 96s Entering ResolveByKeep 96s 96s Calculating upgrade... 97s The following packages will be upgraded: 97s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 97s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 8683 kB of archives. 97s After this operation, 23.6 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 105s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 105s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 105s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 106s Preconfiguring packages ... 106s Fetched 8683 kB in 9s (973 kB/s) 107s (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 ... 64655 files and directories currently installed.) 107s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 107s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 107s Setting up libc6:armhf (2.41-1ubuntu2) ... 107s (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 ... 64655 files and directories currently installed.) 107s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 107s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 107s Setting up libc-bin (2.41-1ubuntu2) ... 107s (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 ... 64655 files and directories currently installed.) 108s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 108s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 108s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 108s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 108s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 108s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 108s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 108s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 108s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 108s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 108s Setting up sos (4.9.0-5) ... 109s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 109s Setting up locales (2.41-1ubuntu2) ... 110s Generating locales (this might take a while)... 112s en_US.UTF-8... done 112s Generation complete. 112s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 112s Setting up strace (6.13+ds-1ubuntu1) ... 112s Processing triggers for man-db (2.13.0-1) ... 113s Processing triggers for systemd (257.3-1ubuntu3) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s Solving dependencies... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [16:50:34]: rebooting testbed after setup commands that affected boot 166s autopkgtest [16:51:20]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 193s autopkgtest [16:51:47]: @@@@@@@@@@@@@@@@@@@@ apt-source ragout 226s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (dsc) [2117 B] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (tar) [12.3 MB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ragout 2.3-5 (diff) [15.0 kB] 226s gpgv: Signature made Fri Feb 2 10:15:47 2024 UTC 226s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 226s gpgv: issuer "tille@debian.org" 226s gpgv: Can't check signature: No public key 226s dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: no acceptable signature found 227s autopkgtest [16:52:21]: testing package ragout version 2.3-5 229s autopkgtest [16:52:23]: build not needed 245s autopkgtest [16:52:39]: test run-unit-test: preparing testbed 247s Reading package lists... 247s Building dependency tree... 247s Reading state information... 248s Starting pkgProblemResolver with broken count: 0 248s Starting 2 pkgProblemResolver with broken count: 0 248s Done 250s The following NEW packages will be installed: 250s lagan libdivsufsort3 python3-networkx ragout ragout-examples sibelia 251s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 251s Need to get 32.6 MB of archives. 251s After this operation, 103 MB of additional disk space will be used. 251s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf lagan armhf 2.0-10 [180 kB] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libdivsufsort3 armhf 2.0.1-6 [45.4 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 263s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf ragout armhf 2.3-5 [2172 kB] 265s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf ragout-examples all 2.3-5 [18.4 MB] 287s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf sibelia armhf 3.0.7+dfsg-3 [298 kB] 288s Fetched 32.6 MB in 37s (883 kB/s) 288s Selecting previously unselected package lagan. 288s (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 ... 64655 files and directories currently installed.) 288s Preparing to unpack .../0-lagan_2.0-10_armhf.deb ... 288s Unpacking lagan (2.0-10) ... 288s Selecting previously unselected package libdivsufsort3:armhf. 288s Preparing to unpack .../1-libdivsufsort3_2.0.1-6_armhf.deb ... 288s Unpacking libdivsufsort3:armhf (2.0.1-6) ... 288s Selecting previously unselected package python3-networkx. 288s Preparing to unpack .../2-python3-networkx_3.2.1-4ubuntu1_all.deb ... 288s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 289s Selecting previously unselected package ragout. 289s Preparing to unpack .../3-ragout_2.3-5_armhf.deb ... 289s Unpacking ragout (2.3-5) ... 289s Selecting previously unselected package ragout-examples. 289s Preparing to unpack .../4-ragout-examples_2.3-5_all.deb ... 289s Unpacking ragout-examples (2.3-5) ... 289s Selecting previously unselected package sibelia. 289s Preparing to unpack .../5-sibelia_3.0.7+dfsg-3_armhf.deb ... 289s Unpacking sibelia (3.0.7+dfsg-3) ... 289s Setting up ragout-examples (2.3-5) ... 289s Setting up python3-networkx (3.2.1-4ubuntu1) ... 291s Setting up ragout (2.3-5) ... 291s Setting up lagan (2.0-10) ... 291s Setting up libdivsufsort3:armhf (2.0.1-6) ... 291s Setting up sibelia (3.0.7+dfsg-3) ... 291s Processing triggers for man-db (2.13.0-1) ... 292s Processing triggers for libc-bin (2.41-1ubuntu2) ... 301s autopkgtest [16:53:35]: test run-unit-test: [----------------------- 304s + ragout E.Coli/ecoli.rcp --outdir E.Coli/out/ --refine 304s [16:53:38] INFO: Starting Ragout v2.3 304s [16:53:38] INFO: Running withs synteny block sizes '[5000, 500, 100]' 304s [16:53:38] INFO: Running Sibelia with block size 5000 357s [16:54:31] INFO: Running Sibelia with block size 500 413s [16:55:27] INFO: Running Sibelia with block size 100 465s [16:56:19] INFO: Inferring phylogeny from synteny blocks data 465s [16:56:19] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 465s [16:56:19] INFO: "dh1" synteny blocks coverage: 99.86% 465s [16:56:19] INFO: "mg1655" synteny blocks coverage: 99.56% 465s [16:56:19] INFO: Inferred tree: ('dh1' : 1.5, 'mg1655' : 1.5) 465s [16:56:19] INFO: 'dh1' is chosen as a naming reference 465s [16:56:19] INFO: Processing permutation files 465s [16:56:19] INFO: Reading E.Coli/out/sibelia-workdir/5000/blocks_coords.txt 465s [16:56:19] INFO: "dh1" synteny blocks coverage: 96.41% 465s [16:56:19] INFO: "mg1655" synteny blocks coverage: 99.45% 465s [16:56:19] INFO: Reading E.Coli/out/sibelia-workdir/500/blocks_coords.txt 465s [16:56:19] INFO: "dh1" synteny blocks coverage: 99.58% 465s [16:56:19] INFO: "mg1655" synteny blocks coverage: 99.66% 465s [16:56:19] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 465s [16:56:19] INFO: "dh1" synteny blocks coverage: 99.86% 465s [16:56:19] INFO: "mg1655" synteny blocks coverage: 99.56% 465s [16:56:19] INFO: Reading E.Coli/out/sibelia-workdir/100/blocks_coords.txt 465s [16:56:19] INFO: "dh1" synteny blocks coverage: 99.86% 465s [16:56:19] INFO: "mg1655" synteny blocks coverage: 99.56% 465s [16:56:19] INFO: Reading contigs file 465s [16:56:19] INFO: Detecting chimeric adjacencies 465s [16:56:19] INFO: Stage "5000" 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Inferring missing adjacencies 465s [16:56:19] INFO: Stage "500" 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Inferring missing adjacencies 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Merging two iterations 465s [16:56:19] INFO: Stage "100" 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Inferring missing adjacencies 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Merging two iterations 465s [16:56:19] INFO: Stage "refine" 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Inferring missing adjacencies 465s [16:56:19] INFO: Removing chimeric adjacencies 465s [16:56:19] INFO: Merging two iterations 466s [16:56:19] INFO: Building assembly graph 466s Reading FASTA 466s Building FM-index 466s Overapping 466s Kmer size is set to 55 466s [16:56:20] INFO: Refining with assembly graph 466s [16:56:20] INFO: Generating FASTA output 466s [16:56:20] INFO: Assembly statistics: 466s 466s Scaffolds: 1 466s Used fragments: 145 466s Scaffolds length: 4635053 466s 466s Unplaced fragments: 37 466s Unplaced length: 13411 (0.29%) 466s Introduced Ns length: 69544 (1.50%) 466s 466s Fragments N50: 125773 466s Assembly N50: 4635053 466s 466s [16:56:20] INFO: Done! 466s + ragout H.Pylori/helicobacter.rcp --outdir H.Pylori/out/ --refine 466s [16:56:20] INFO: Starting Ragout v2.3 466s [16:56:20] INFO: Running withs synteny block sizes '[5000, 500, 100]' 466s [16:56:20] INFO: Running Sibelia with block size 5000 566s [16:58:00] INFO: Running Sibelia with block size 500 664s [16:59:38] INFO: Running Sibelia with block size 100 766s [17:01:20] INFO: Phylogeny is taken from the recipe 766s [17:01:20] INFO: 'els' is chosen as a naming reference 766s [17:01:20] INFO: Processing permutation files 766s [17:01:20] INFO: Reading H.Pylori/out/sibelia-workdir/5000/blocks_coords.txt 766s [17:01:20] INFO: "els" synteny blocks coverage: 80.53% 766s [17:01:20] INFO: "g27" synteny blocks coverage: 81.02% 766s [17:01:20] INFO: "gambia" synteny blocks coverage: 80.04% 766s [17:01:20] INFO: "puno" synteny blocks coverage: 80.58% 766s [17:01:20] INFO: "sjm180" synteny blocks coverage: 83.86% 766s [17:01:20] INFO: Reading H.Pylori/out/sibelia-workdir/500/blocks_coords.txt 766s [17:01:20] INFO: "els" synteny blocks coverage: 96.82% 766s [17:01:20] INFO: "g27" synteny blocks coverage: 94.8% 766s [17:01:20] INFO: "gambia" synteny blocks coverage: 94.9% 766s [17:01:20] INFO: "puno" synteny blocks coverage: 92.43% 766s [17:01:20] INFO: "sjm180" synteny blocks coverage: 96.75% 766s [17:01:20] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 766s [17:01:20] INFO: "els" synteny blocks coverage: 97.08% 766s [17:01:20] INFO: "g27" synteny blocks coverage: 95.16% 766s [17:01:20] INFO: "gambia" synteny blocks coverage: 95.13% 766s [17:01:20] INFO: "puno" synteny blocks coverage: 92.78% 766s [17:01:20] INFO: "sjm180" synteny blocks coverage: 96.5% 766s [17:01:20] INFO: Reading H.Pylori/out/sibelia-workdir/100/blocks_coords.txt 766s [17:01:20] INFO: "els" synteny blocks coverage: 97.08% 766s [17:01:20] INFO: "g27" synteny blocks coverage: 95.16% 766s [17:01:20] INFO: "gambia" synteny blocks coverage: 95.13% 766s [17:01:20] INFO: "puno" synteny blocks coverage: 92.78% 766s [17:01:20] INFO: "sjm180" synteny blocks coverage: 96.5% 766s [17:01:20] INFO: Reading contigs file 766s [17:01:20] INFO: Detecting chimeric adjacencies 766s [17:01:20] INFO: Stage "5000" 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Inferring missing adjacencies 766s [17:01:20] INFO: Stage "500" 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Inferring missing adjacencies 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Merging two iterations 766s [17:01:20] INFO: Stage "100" 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Inferring missing adjacencies 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Merging two iterations 766s [17:01:20] INFO: Stage "refine" 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Inferring missing adjacencies 766s [17:01:20] INFO: Removing chimeric adjacencies 766s [17:01:20] INFO: Merging two iterations 766s [17:01:20] INFO: Building assembly graph 766s Reading FASTA 766s Building FM-index 766s Overapping 766s Kmer size is set to 54 766s [17:01:20] INFO: Refining with assembly graph 766s [17:01:20] INFO: Generating FASTA output 766s [17:01:20] INFO: Assembly statistics: 766s 766s Scaffolds: 1 766s Used fragments: 133 766s Scaffolds length: 1654315 766s 766s Unplaced fragments: 78 766s Unplaced length: 18234 (1.10%) 766s Introduced Ns length: 11306 (0.68%) 766s 766s Fragments N50: 75870 766s Assembly N50: 1654315 766s 766s [17:01:20] INFO: Done! 767s + ragout S.Aureus/aureus.rcp --outdir S.Aureus/out/ --refine 767s [17:01:21] INFO: Starting Ragout v2.3 767s [17:01:21] INFO: Running withs synteny block sizes '[5000, 500, 100]' 767s [17:01:21] INFO: Running Sibelia with block size 5000 878s [17:03:12] INFO: Running Sibelia with block size 500 989s [17:05:03] INFO: Running Sibelia with block size 100 1104s [17:06:58] INFO: Inferring phylogeny from synteny blocks data 1104s [17:06:58] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1104s [17:06:58] INFO: "col" synteny blocks coverage: 98.34% 1104s [17:06:58] INFO: "jkd" synteny blocks coverage: 94.31% 1104s [17:06:58] INFO: "rf122" synteny blocks coverage: 93.71% 1104s [17:06:58] INFO: "n315" synteny blocks coverage: 97.19% 1104s [17:06:58] INFO: "usa" synteny blocks coverage: 96.35% 1104s [17:06:58] INFO: Inferred tree: (('jkd' : 47.625, ('col' : 5.375, 'usa' : 40.625) : 14.375) : 11.4375, ('n315' : 35.333333333333336, 'rf122' : 61.666666666666664) : 11.4375) 1104s [17:06:58] INFO: 'col' is chosen as a naming reference 1104s [17:06:58] INFO: Processing permutation files 1104s [17:06:58] INFO: Reading S.Aureus/out/sibelia-workdir/5000/blocks_coords.txt 1104s [17:06:58] INFO: "col" synteny blocks coverage: 84.15% 1104s [17:06:58] INFO: "jkd" synteny blocks coverage: 80.65% 1104s [17:06:58] INFO: "rf122" synteny blocks coverage: 83.55% 1104s [17:06:58] INFO: "n315" synteny blocks coverage: 83.81% 1104s [17:06:58] INFO: "usa" synteny blocks coverage: 89.64% 1104s [17:06:58] INFO: Reading S.Aureus/out/sibelia-workdir/500/blocks_coords.txt 1104s [17:06:58] INFO: "col" synteny blocks coverage: 97.78% 1104s [17:06:58] INFO: "jkd" synteny blocks coverage: 93.69% 1104s [17:06:58] INFO: "rf122" synteny blocks coverage: 93.63% 1104s [17:06:58] INFO: "n315" synteny blocks coverage: 96.93% 1104s [17:06:58] INFO: "usa" synteny blocks coverage: 97.32% 1104s [17:06:58] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1104s [17:06:58] INFO: "col" synteny blocks coverage: 98.34% 1104s [17:06:58] INFO: "jkd" synteny blocks coverage: 94.31% 1104s [17:06:58] INFO: "rf122" synteny blocks coverage: 93.71% 1104s [17:06:58] INFO: "n315" synteny blocks coverage: 97.19% 1104s [17:06:58] INFO: "usa" synteny blocks coverage: 96.35% 1104s [17:06:58] INFO: Reading S.Aureus/out/sibelia-workdir/100/blocks_coords.txt 1104s [17:06:58] INFO: "col" synteny blocks coverage: 98.34% 1104s [17:06:58] INFO: "jkd" synteny blocks coverage: 94.31% 1104s [17:06:58] INFO: "rf122" synteny blocks coverage: 93.71% 1104s [17:06:58] INFO: "n315" synteny blocks coverage: 97.19% 1104s [17:06:58] INFO: "usa" synteny blocks coverage: 96.35% 1104s [17:06:58] INFO: Reading contigs file 1104s [17:06:58] INFO: Detecting chimeric adjacencies 1104s [17:06:58] INFO: Stage "5000" 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Inferring missing adjacencies 1104s [17:06:58] INFO: Stage "500" 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Inferring missing adjacencies 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Merging two iterations 1104s [17:06:58] INFO: Stage "100" 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Inferring missing adjacencies 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Merging two iterations 1104s [17:06:58] INFO: Stage "refine" 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Inferring missing adjacencies 1104s [17:06:58] INFO: Removing chimeric adjacencies 1104s [17:06:58] INFO: Merging two iterations 1104s [17:06:58] INFO: Building assembly graph 1104s Reading FASTA 1105s Building FM-index 1105s Overapping 1105s Kmer size is set to 55 1105s [17:06:59] INFO: Refining with assembly graph 1105s [17:06:59] INFO: Generating FASTA output 1105s [17:06:59] INFO: Assembly statistics: 1105s 1105s Scaffolds: 1 1105s Used fragments: 169 1105s Scaffolds length: 2828340 1105s 1105s Unplaced fragments: 633 1105s Unplaced length: 441368 (13.88%) 1105s Introduced Ns length: 83415 (2.95%) 1105s 1105s Fragments N50: 45930 1105s Assembly N50: 2828340 1105s 1105s [17:06:59] INFO: Done! 1105s + ragout V.Cholerae/cholerae.rcp --outdir V.Cholerae/out/ --refine 1105s [17:06:59] INFO: Starting Ragout v2.3 1105s [17:06:59] INFO: Running withs synteny block sizes '[5000, 500, 100]' 1105s [17:06:59] INFO: Running Sibelia with block size 5000 1208s [17:08:42] INFO: Running Sibelia with block size 500 1310s [17:10:24] INFO: Running Sibelia with block size 100 1415s [17:12:09] INFO: Inferring phylogeny from synteny blocks data 1415s [17:12:09] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1415s [17:12:09] INFO: "biovar" synteny blocks coverage: 99.26% 1415s [17:12:09] INFO: "inaba" synteny blocks coverage: 97.98% 1415s [17:12:09] INFO: "o395" synteny blocks coverage: 97.85% 1415s [17:12:09] INFO: "h1" synteny blocks coverage: 99.19% 1415s [17:12:09] INFO: Inferred tree: (('biovar' : 4.75, 'o395' : 13.25) : 4.625, ('h1' : 1e-06, 'inaba' : 6.75) : 4.625) 1415s [17:12:09] INFO: 'inaba' is chosen as a naming reference 1415s [17:12:09] INFO: Processing permutation files 1415s [17:12:09] INFO: Reading V.Cholerae/out/sibelia-workdir/5000/blocks_coords.txt 1415s [17:12:09] INFO: "biovar" synteny blocks coverage: 92.08% 1415s [17:12:09] INFO: "inaba" synteny blocks coverage: 91.94% 1415s [17:12:09] INFO: "o395" synteny blocks coverage: 91.08% 1415s [17:12:09] INFO: "h1" synteny blocks coverage: 98.87% 1415s [17:12:09] INFO: Reading V.Cholerae/out/sibelia-workdir/500/blocks_coords.txt 1415s [17:12:09] INFO: "biovar" synteny blocks coverage: 99.0% 1415s [17:12:09] INFO: "inaba" synteny blocks coverage: 97.68% 1415s [17:12:09] INFO: "o395" synteny blocks coverage: 97.52% 1415s [17:12:09] INFO: "h1" synteny blocks coverage: 99.3% 1415s [17:12:09] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1415s [17:12:09] INFO: "biovar" synteny blocks coverage: 99.26% 1415s [17:12:09] INFO: "inaba" synteny blocks coverage: 97.98% 1415s [17:12:09] INFO: "o395" synteny blocks coverage: 97.85% 1415s [17:12:09] INFO: "h1" synteny blocks coverage: 99.19% 1415s [17:12:09] INFO: Reading V.Cholerae/out/sibelia-workdir/100/blocks_coords.txt 1415s [17:12:09] INFO: "biovar" synteny blocks coverage: 99.26% 1415s [17:12:09] INFO: "inaba" synteny blocks coverage: 97.98% 1415s [17:12:09] INFO: "o395" synteny blocks coverage: 97.85% 1415s [17:12:09] INFO: "h1" synteny blocks coverage: 99.19% 1415s [17:12:09] INFO: Reading contigs file 1416s [17:12:09] INFO: Detecting chimeric adjacencies 1416s [17:12:09] INFO: Stage "5000" 1416s [17:12:09] INFO: Removing chimeric adjacencies 1416s [17:12:09] INFO: Inferring missing adjacencies 1416s [17:12:10] INFO: Stage "500" 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Inferring missing adjacencies 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Merging two iterations 1416s [17:12:10] INFO: Stage "100" 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Inferring missing adjacencies 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Merging two iterations 1416s [17:12:10] INFO: Stage "refine" 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Inferring missing adjacencies 1416s [17:12:10] INFO: Removing chimeric adjacencies 1416s [17:12:10] INFO: Merging two iterations 1416s [17:12:10] INFO: Building assembly graph 1416s Reading FASTA 1416s Building FM-index 1416s Overapping 1416s Kmer size is set to 33 1416s [17:12:10] INFO: Refining with assembly graph 1417s [17:12:11] INFO: Generating FASTA output 1417s [17:12:11] INFO: Assembly statistics: 1417s 1417s Scaffolds: 4 1417s Used fragments: 824 1417s Scaffolds length: 4018165 1417s 1417s Unplaced fragments: 885 1417s Unplaced length: 76332 (1.89%) 1417s Introduced Ns length: 32445 (0.81%) 1417s 1417s Fragments N50: 38091 1417s Assembly N50: 2150683 1417s 1417s [17:12:11] INFO: Done! 1417s autopkgtest [17:12:11]: test run-unit-test: -----------------------] 1422s autopkgtest [17:12:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1422s run-unit-test PASS 1426s autopkgtest [17:12:20]: @@@@@@@@@@@@@@@@@@@@ summary 1426s run-unit-test PASS