0s autopkgtest [15:24:07]: starting date and time: 2025-03-15 15:24:07+0000 0s autopkgtest [15:24:07]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:24:07]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vnnn6h6j/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 progressivemauve --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:24:28]: testbed dpkg architecture: armhf 23s autopkgtest [15:24:30]: testbed apt version: 2.9.33 27s autopkgtest [15:24:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [15:24:37]: testbed release detected to be: None 38s autopkgtest [15:24:45]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 41s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 41s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 41s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 42s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 52s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 52s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 53s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 53s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 53s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 60s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 62s Fetched 41.0 MB in 22s (1899 kB/s) 63s Reading package lists... 69s autopkgtest [15:25:16]: upgrading testbed (apt dist-upgrade and autopurge) 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 73s Entering ResolveByKeep 73s 73s Calculating upgrade... 73s The following packages will be upgraded: 73s libc-bin libc6 locales python3-jinja2 sos strace 74s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 8642 kB of archives. 74s After this operation, 23.6 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 78s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 79s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 79s Preconfiguring packages ... 79s Fetched 8642 kB in 5s (1674 kB/s) 79s (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.) 79s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 79s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 80s Setting up libc6:armhf (2.41-1ubuntu2) ... 80s (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.) 80s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 80s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 80s Setting up libc-bin (2.41-1ubuntu2) ... 80s (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.) 80s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 80s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 80s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 80s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 80s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 81s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 81s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 81s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 81s Setting up sos (4.9.0-5) ... 81s Setting up locales (2.41-1ubuntu2) ... 82s Generating locales (this might take a while)... 84s en_US.UTF-8... done 84s Generation complete. 84s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 84s Setting up strace (6.13+ds-1ubuntu1) ... 84s Processing triggers for man-db (2.13.0-1) ... 85s Processing triggers for systemd (257.3-1ubuntu3) ... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 89s Solving dependencies... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s autopkgtest [15:25:38]: rebooting testbed after setup commands that affected boot 133s autopkgtest [15:26:20]: 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 166s autopkgtest [15:26:53]: @@@@@@@@@@@@@@@@@@@@ apt-source progressivemauve 178s Get:1 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (dsc) [2413 B] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (tar) [96.1 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (diff) [18.1 kB] 178s gpgv: Signature made Mon Apr 8 15:02:20 2024 UTC 178s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 178s gpgv: issuer "juliank@ubuntu.com" 178s gpgv: Can't check signature: No public key 178s dpkg-source: warning: cannot verify inline signature for ./progressivemauve_1.2.0+4713+dfsg-5build3.dsc: no acceptable signature found 178s autopkgtest [15:27:05]: testing package progressivemauve version 1.2.0+4713+dfsg-5build3 180s autopkgtest [15:27:07]: build not needed 182s autopkgtest [15:27:09]: test run-unit-test: preparing testbed 184s Reading package lists... 185s Building dependency tree... 185s Reading state information... 186s Starting pkgProblemResolver with broken count: 0 186s Starting 2 pkgProblemResolver with broken count: 0 186s Done 187s The following NEW packages will be installed: 187s libboost-filesystem1.83.0 libboost-iostreams1.83.0 187s libboost-program-options1.83.0 libgenome0 libgomp1 libmems1t64 libmuscle1 187s progressivemauve 188s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 188s Need to get 2768 kB of archives. 188s After this operation, 12.4 MB of additional disk space will be used. 188s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-filesystem1.83.0 armhf 1.83.0-4.1ubuntu2 [281 kB] 188s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-iostreams1.83.0 armhf 1.83.0-4.1ubuntu2 [258 kB] 188s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-program-options1.83.0 armhf 1.83.0-4.1ubuntu2 [345 kB] 188s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libgenome0 armhf 1.3.11+svn20110227.4616-6 [116 kB] 189s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 189s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libmuscle1 armhf 3.7+4565-8 [228 kB] 189s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libmems1t64 armhf 1.6.0+4725-11 [636 kB] 189s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf progressivemauve armhf 1.2.0+4713+dfsg-5build3 [777 kB] 190s Fetched 2768 kB in 2s (1207 kB/s) 190s Selecting previously unselected package libboost-filesystem1.83.0:armhf. 190s (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.) 190s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-4.1ubuntu2_armhf.deb ... 190s Unpacking libboost-filesystem1.83.0:armhf (1.83.0-4.1ubuntu2) ... 190s Selecting previously unselected package libboost-iostreams1.83.0:armhf. 190s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_armhf.deb ... 190s Unpacking libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ... 190s Selecting previously unselected package libboost-program-options1.83.0:armhf. 190s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_armhf.deb ... 190s Unpacking libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ... 190s Selecting previously unselected package libgenome0:armhf. 190s Preparing to unpack .../3-libgenome0_1.3.11+svn20110227.4616-6_armhf.deb ... 190s Unpacking libgenome0:armhf (1.3.11+svn20110227.4616-6) ... 190s Selecting previously unselected package libgomp1:armhf. 190s Preparing to unpack .../4-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 190s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 190s Selecting previously unselected package libmuscle1. 190s Preparing to unpack .../5-libmuscle1_3.7+4565-8_armhf.deb ... 190s Unpacking libmuscle1 (3.7+4565-8) ... 190s Selecting previously unselected package libmems1t64:armhf. 190s Preparing to unpack .../6-libmems1t64_1.6.0+4725-11_armhf.deb ... 190s Unpacking libmems1t64:armhf (1.6.0+4725-11) ... 190s Selecting previously unselected package progressivemauve. 190s Preparing to unpack .../7-progressivemauve_1.2.0+4713+dfsg-5build3_armhf.deb ... 190s Unpacking progressivemauve (1.2.0+4713+dfsg-5build3) ... 191s Setting up libboost-program-options1.83.0:armhf (1.83.0-4.1ubuntu2) ... 191s Setting up libgenome0:armhf (1.3.11+svn20110227.4616-6) ... 191s Setting up libboost-filesystem1.83.0:armhf (1.83.0-4.1ubuntu2) ... 191s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 191s Setting up libboost-iostreams1.83.0:armhf (1.83.0-4.1ubuntu2) ... 191s Setting up libmuscle1 (3.7+4565-8) ... 191s Setting up libmems1t64:armhf (1.6.0+4725-11) ... 191s Setting up progressivemauve (1.2.0+4713+dfsg-5build3) ... 191s Processing triggers for man-db (2.13.0-1) ... 191s Processing triggers for libc-bin (2.41-1ubuntu2) ... 199s autopkgtest [15:27:26]: test run-unit-test: [----------------------- 201s Storing raw sequence at /tmp/rawseq909.000 201s Sequence loaded successfully. 201s genome_1.gbk 2175 base pairs. 201s Storing raw sequence at /tmp/rawseq909.001 201s Sequence loaded successfully. 201s genome_2.gbk 2199 base pairs. 201s Storing raw sequence at /tmp/rawseq909.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s 33%.. 202s 66%.. 202s 99%.. 202s done. 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s Starting with 152 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s Writing guide tree to /tmp/guide_tree909.000 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22995.7 202s Pair (0,1) has 1 well-supported breakpoints 202s Pair 0, 2 has 29 initial LCBs 202s Using scaled bp penalty: 10025.6 202s Pair (0,2) has 1 well-supported breakpoints 202s Pair 1, 2 has 31 initial LCBs 202s Using scaled bp penalty: 13766.1 202s Pair (1,2) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s bp distance matrix: 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 202s Aligning... 202s Aligning node 2 to 3 via 1! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 220 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 175 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 50704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 4 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 60 tracking matches 202s There are 239 / 300 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 89 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 1%..2%..3%..4%..5%..6%..7%..8%.. 202s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 202s 20%..21%..22%..23%..24%..25%..26%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 99201 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 3 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 3 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 3 pairwise matches 202s 1,2 has 1 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 99201, new anchor score: 102789 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 102789, new anchor score: 102789 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 202s Organisms have 52.8% GC 202s Storing raw sequence at /tmp/rawseq910.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq910.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Storing raw sequence at /tmp/rawseq910.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s 33%.. 202s 66%.. 202s 99%.. 202s done. 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s Starting with 152 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s Writing guide tree to threeway.tree 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22995.7 202s Pair (0,1) has 1 well-supported breakpoints 202s Pair 0, 2 has 29 initial LCBs 202s Using scaled bp penalty: 10025.6 202s Pair (0,2) has 1 well-supported breakpoints 202s Pair 1, 2 has 31 initial LCBs 202s Using scaled bp penalty: 13766.1 202s Pair (1,2) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s bp distance matrix: 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 202s Aligning... 202s Aligning node 2 to 3 via 1! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 220 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 175 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 50704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 4 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 60 tracking matches 202s There are 239 / 300 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 89 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 1%..2%..3%..4%..5%..6%..7%..8%.. 202s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 202s 20%..21%..22%..23%..24%..25%..26%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 99201 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 3 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 3 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 3 pairwise matches 202s 1,2 has 1 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 99201, new anchor score: 102789 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 102789, new anchor score: 102789 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 202s Organisms have 52.8% GC 202s Storing raw sequence at /tmp/rawseq911.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq911.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Storing raw sequence at /tmp/rawseq911.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s 33%.. 202s 66%.. 202s 99%.. 202s done. 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s Starting with 152 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s Writing guide tree to /tmp/guide_tree911.000 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22995.7 202s Pair (0,1) has 1 well-supported breakpoints 202s Pair 0, 2 has 29 initial LCBs 202s Using scaled bp penalty: 10025.6 202s Pair (0,2) has 1 well-supported breakpoints 202s Pair 1, 2 has 31 initial LCBs 202s Using scaled bp penalty: 13766.1 202s Pair (1,2) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s bp distance matrix: 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 202s Aligning... 202s Aligning node 2 to 3 via 1! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 220 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 175 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 50704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 4 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 60 tracking matches 202s There are 239 / 300 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 89 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 1%..2%..3%..4%..5%..6%..7%..8%.. 202s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 202s 20%..21%..22%..23%..24%..25%..26%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 99201 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 3 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 3 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 3 pairwise matches 202s 1,2 has 1 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 99201, new anchor score: 102789 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 102789, new anchor score: 102789 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Organisms have 52.8% GC 202s Storing raw sequence at /tmp/rawseq913.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq913.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Storing raw sequence at /tmp/rawseq913.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s 33%.. 202s 66%.. 202s 99%.. 202s done. 202s Storing raw sequence at /tmp/rawseq914.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq914.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Storing raw sequence at /tmp/rawseq914.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s Starting with 152 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s Writing guide tree to /tmp/guide_tree914.000 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22995.7 202s Pair (0,1) has 1 well-supported breakpoints 202s Pair 0, 2 has 29 initial LCBs 202s Using scaled bp penalty: 10025.6 202s Pair (0,2) has 1 well-supported breakpoints 202s Pair 1, 2 has 31 initial LCBs 202s Using scaled bp penalty: 13766.1 202s Pair (1,2) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s bp distance matrix: 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 202s Aligning... 202s Aligning node 2 to 3 via 1! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 220 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 175 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 50704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 4 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 60 tracking matches 202s There are 239 / 300 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 89 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 1%..2%..3%..4%..5%..6%..7%..8%.. 202s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 202s 20%..21%..22%..23%..24%..25%..26%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 99201 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 3 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 3 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 3 pairwise matches 202s 1,2 has 1 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 99201, new anchor score: 102789 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 102789, new anchor score: 102789 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 202s Organisms have 52.8% GC 202s Exception FileNotOpened thrown from 202s Unknown() in gnFileSource.cpp 67 202s Called by Unknown() 202s Storing raw sequence at /tmp/rawseq915.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq915.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s 49%.. 202s 99%.. 202s done. 202s using default bp penalty: 50000 202s using default bp estimate min score: 232989 202s Starting with 55 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 202s 0.4396 0 202s 202s Writing guide tree to /tmp/guide_tree915.000 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22978.9 202s Pair (0,1) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 202s 0.4396 0 202s 202s bp distance matrix: 202s 0.9 0.9 202s 0.9 0.9 202s 202s Aligning... 202s Aligning node 1 to 2 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 132 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 105 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 4000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 50704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2249 202s Organisms have 53.2% GC 202s Storing raw sequence at /tmp/rawseq916.000 202s Sequence loaded successfully. 202s genome_1.gbk 2175 base pairs. 202s Storing raw sequence at /tmp/rawseq916.001 202s Sequence loaded successfully. 202s genome_2.gbk 2199 base pairs. 202s Storing raw sequence at /tmp/rawseq916.002 202s Sequence loaded successfully. 202s genome_3.gbk 2224 base pairs. 202s Using weight 9 mers for initial seeds 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s Sorted mer list loaded successfully 202s 33%.. 202s 66%.. 202s 99%.. 202s done. 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s Starting with 152 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s Writing guide tree to /tmp/guide_tree916.000 202s reading tree... 202s initializing alignment tree... 202s Constructing seed occurrence lists for repeat detection 202s Calculating pairwise breakpoint distances 202s Pair 0, 1 has 30 initial LCBs 202s Using scaled bp penalty: 22995.7 202s Pair (0,1) has 1 well-supported breakpoints 202s Pair 0, 2 has 29 initial LCBs 202s Using scaled bp penalty: 10025.6 202s Pair (0,2) has 1 well-supported breakpoints 202s Pair 1, 2 has 31 initial LCBs 202s Using scaled bp penalty: 13766.1 202s Pair (1,2) has 1 well-supported breakpoints 202s genome content distance matrix: 202s 0 0.4396 0.54463 202s 0.4396 0 0.507065 202s 0.54463 0.507065 0 202s 202s bp distance matrix: 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 0.9 0.9 0.9 202s 202s Aligning... 202s Aligning node 2 to 3 via 1! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 44 tracking matches 202s There are 88 / 220 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 27 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 5000 202s 3%..7%.. 202s 11%..14%..18%.. 202s 22%..25%..29%.. 202s 33%..37%.. 202s 40%..44%..48%.. 202s 51%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 57862 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 0,0 has an additional 5 matches 202s Restoring backed up alignment tree... 202s 1,0 has 5 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 35 tracking matches 202s There are 70 / 175 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 7 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.4396 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 5000 202s 202s 14%.. 202s 28%..done 202s Arrived at 3 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 8 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(2) has 1 intervals 202s descendant 1(3) has 1 intervals 202s propagateDescendantBreakpoints yields 3 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 57862, new anchor score: 48704 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 4 via 0! 202s get ancestral matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 60 tracking matches 202s There are 239 / 300 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 89 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 5000 202s 1%..2%..3%..4%..5%..6%..7%..8%.. 202s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 202s 20%..21%..22%..23%..24%..25%..26%..done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: -1.79769e+308, new anchor score: 99201 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 3 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 3 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 3 pairwise matches 202s 1,2 has 1 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 5000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 99201, new anchor score: 102789 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Performing Sum-of-pairs Greedy Breakpoint Elimination 202s construct LCB tracking matches 202s There are 38 tracking matches 202s There are 152 / 190 components used 202s init tracking match LCB tracking 202s pairwise score tracking matches 202s get pairwise LCBs 202s there are 2 pairwise LCBs 202s scaling bp penalty by conservation weight: 202s 0.54463 202s 0.507065 202s 202s 202s scaling bp penalty by bp weight: 202s 0.9 202s 0.9 202s 202s Greedy BPE 202s Scoring with scaled breakpoint penalty: 5000 202s done 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Previous anchoring score: 102789, new anchor score: 102789 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 202s Organisms have 52.8% GC 202s Sequence loaded successfully. 202s all_virii.fasta 2175 base pairs. 202s Sequence loaded successfully. 202s all_virii.fasta 2199 base pairs. 202s Sequence loaded successfully. 202s all_virii.fasta 2224 base pairs. 202s Using 9-mers for initial seeds 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s 202s Searching with seed pattern 11100100100100111 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s 32%.. 202s 65%.. 202s 99%.. 202s 202s Searching with seed pattern 111001010100111 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s 33%.. 202s 66%.. 202s 99%.. 202s 202s Searching with seed pattern 111010010010111 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s Creating sorted mer list 202s Create time was: 0 seconds. 202s 32%.. 202s 65%.. 202s 99%.. 202s done 202s using default bp penalty: 77720 202s using default bp estimate min score: 233160 202s 202s Assuming collinear genomes... 202s Starting with 291 multi-matches 202s Computing genome content distance matrix... 202s 202s 202s Genome conservation distance matrix: 202s 0 0.220697 0.310296 202s 0.220697 0 0.291861 202s 0.310296 0.291861 0 202s 202s Writing guide tree to /tmp/guide_tree917.000 202s reading tree... 202s initializing alignment tree... 202s Aligning... 202s Aligning node 3 to 4 via 1! 202s get ancestral matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(3) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 18446744073709551615, new alignment length: 3832 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 1,0 has 0 pairwise matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(3) has 1 intervals 202s descendant 1(4) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 3832, new alignment length: 3832 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Aligning node 1 to 2 via 0! 202s get ancestral matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 5 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 18446744073709551615, new alignment length: 4373 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 14 new matches outside LCBs 202s 1,0 have 17 new matches outside LCBs 202s 0,0 has an additional 38 matches 202s 1,0 has an additional 41 matches 202s Restoring backed up alignment tree... 202s 0,2 has 38 pairwise matches 202s 1,2 has 41 pairwise matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 3 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 4373, new alignment length: 3825 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 2 new matches outside LCBs 202s 1,0 have 1 new matches outside LCBs 202s 0,0 has an additional 2 matches 202s 1,0 has an additional 1 matches 202s Restoring backed up alignment tree... 202s 0,2 has 2 pairwise matches 202s 1,2 has 1 pairwise matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 1 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 3825, new alignment length: 3802 202s Backing up alignment tree... 202s propagating ancestral breakpoints 202s recursive anchor search 202s 0,0 have 0 new matches outside LCBs 202s 1,0 have 0 new matches outside LCBs 202s Restoring backed up alignment tree... 202s 0,2 has 0 pairwise matches 202s 1,2 has 0 pairwise matches 202s Arrived at 1 intervals 202s Adding unaligned intervals 202s addUnalignedIntervals yields 1 intervals 202s Merging unaligned intervals 202s Marbling gaps 202s Propagating descendant breakpoints 202s descendant 0(1) has 1 intervals 202s descendant 1(2) has 1 intervals 202s propagateDescendantBreakpoints yields 1 intervals 202s Creating ancestral ordering 202s Prev alignment len: 3802, new alignment length: 3802 202s propagating ancestral breakpoints 202s performing a gapped alignment 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s Performing final pass iterative refinement 202s 202s 0%.. 202s 100%..Fix left ends 202s 202s done. 202s root alignment has 1 superintervals 202s root alignment length: 2328 203s autopkgtest [15:27:30]: test run-unit-test: -----------------------] 206s autopkgtest [15:27:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 206s run-unit-test PASS 210s autopkgtest [15:27:37]: @@@@@@@@@@@@@@@@@@@@ summary 210s run-unit-test PASS