0s autopkgtest [13:34:22]: starting date and time: 2025-03-15 13:34:22+0000 0s autopkgtest [13:34:22]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:34:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8s98h_08/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-16.secgroup --name adt-plucky-arm64-progressivemauve-20250315-133421-juju-7f2275-prod-proposed-migration-environment-2-ed8170b6-7882-42b1-950b-1cf197d0299f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 169s autopkgtest [13:37:11]: testbed dpkg architecture: arm64 169s autopkgtest [13:37:11]: testbed apt version: 2.9.33 169s autopkgtest [13:37:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 169s autopkgtest [13:37:11]: testbed release detected to be: None 170s autopkgtest [13:37:12]: updating testbed package index (apt update) 171s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 171s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 171s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 171s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 171s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 171s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 172s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 172s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 172s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 172s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 172s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 172s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 172s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 172s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 173s Fetched 1094 kB in 2s (699 kB/s) 174s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 177s Calculating upgrade... 177s Calculating upgrade... 177s The following packages will be upgraded: 177s python3-jinja2 strace 178s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 608 kB of archives. 178s After this operation, 11.3 kB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 179s Fetched 608 kB in 1s (644 kB/s) 179s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 179s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 179s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 180s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 180s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 180s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 180s Setting up strace (6.13+ds-1ubuntu1) ... 180s Processing triggers for man-db (2.13.0-1) ... 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s Solving dependencies... 182s The following packages will be REMOVED: 182s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 182s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 182s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 182s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 183s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 183s After this operation, 267 MB disk space will be freed. 183s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 183s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 183s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 183s Removing libpython3.12t64:arm64 (3.12.9-1) ... 183s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 183s Removing libnsl2:arm64 (1.3.0-3build3) ... 183s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 183s Removing libunwind8:arm64 (1.6.2-3.1) ... 183s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 184s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 186s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 186s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 186s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 186s /etc/kernel/postrm.d/initramfs-tools: 186s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 186s /etc/kernel/postrm.d/zz-flash-kernel: 186s flash-kernel: Kernel 6.11.0-8-generic has been removed. 186s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 186s /etc/kernel/postrm.d/zz-update-grub: 186s Sourcing file `/etc/default/grub' 186s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 186s Generating grub configuration file ... 187s Found linux image: /boot/vmlinuz-6.14.0-10-generic 187s Found initrd image: /boot/initrd.img-6.14.0-10-generic 187s Warning: os-prober will not be executed to detect other bootable partitions. 187s Systems on them will not be added to the GRUB boot configuration. 187s Check GRUB_DISABLE_OS_PROBER documentation entry. 187s Adding boot menu entry for UEFI Firmware Settings ... 187s done 187s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s Processing triggers for libc-bin (2.41-1ubuntu1) ... 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 188s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 188s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 188s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s autopkgtest [13:37:30]: upgrading testbed (apt dist-upgrade and autopurge) 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s Entering ResolveByKeep 192s 192s Calculating upgrade... 193s The following packages will be upgraded: 193s libc-bin libc-dev-bin libc6 libc6-dev locales 193s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 9530 kB of archives. 193s After this operation, 0 B of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 198s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 203s Preconfiguring packages ... 204s Fetched 9530 kB in 10s (945 kB/s) 204s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 204s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up libc6:arm64 (2.41-1ubuntu2) ... 205s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 205s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 205s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up libc-bin (2.41-1ubuntu2) ... 205s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 205s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 205s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up locales (2.41-1ubuntu2) ... 207s Generating locales (this might take a while)... 209s en_US.UTF-8... done 209s Generation complete. 209s Setting up libc-dev-bin (2.41-1ubuntu2) ... 209s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 209s Processing triggers for man-db (2.13.0-1) ... 210s Processing triggers for systemd (257.3-1ubuntu3) ... 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Starting pkgProblemResolver with broken count: 0 213s Starting 2 pkgProblemResolver with broken count: 0 213s Done 213s Solving dependencies... 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 215s autopkgtest [13:37:57]: rebooting testbed after setup commands that affected boot 238s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 245s autopkgtest [13:38:27]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 248s autopkgtest [13:38:30]: @@@@@@@@@@@@@@@@@@@@ apt-source progressivemauve 251s Get:1 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (dsc) [2413 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (tar) [96.1 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (diff) [18.1 kB] 251s gpgv: Signature made Mon Apr 8 15:02:20 2024 UTC 251s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 251s gpgv: issuer "juliank@ubuntu.com" 251s gpgv: Can't check signature: No public key 251s dpkg-source: warning: cannot verify inline signature for ./progressivemauve_1.2.0+4713+dfsg-5build3.dsc: no acceptable signature found 251s autopkgtest [13:38:33]: testing package progressivemauve version 1.2.0+4713+dfsg-5build3 252s autopkgtest [13:38:34]: build not needed 253s autopkgtest [13:38:35]: test run-unit-test: preparing testbed 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s Starting pkgProblemResolver with broken count: 0 254s Starting 2 pkgProblemResolver with broken count: 0 254s Done 255s The following NEW packages will be installed: 255s libboost-filesystem1.83.0 libboost-iostreams1.83.0 255s libboost-program-options1.83.0 libgenome0 libgomp1 libmems1t64 libmuscle1 255s progressivemauve 255s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 255s Need to get 3000 kB of archives. 255s After this operation, 15.6 MB of additional disk space will be used. 255s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-4.1ubuntu2 [283 kB] 255s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-4.1ubuntu2 [259 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4.1ubuntu2 [319 kB] 256s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgenome0 arm64 1.3.11+svn20110227.4616-6 [112 kB] 256s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 256s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmuscle1 arm64 3.7+4565-8 [273 kB] 257s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmems1t64 arm64 1.6.0+4725-11 [642 kB] 257s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 progressivemauve arm64 1.2.0+4713+dfsg-5build3 [966 kB] 259s Fetched 3000 kB in 4s (809 kB/s) 259s Selecting previously unselected package libboost-filesystem1.83.0:arm64. 259s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 259s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 259s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 259s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 259s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 259s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 260s Selecting previously unselected package libboost-program-options1.83.0:arm64. 260s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_arm64.deb ... 260s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 260s Selecting previously unselected package libgenome0:arm64. 260s Preparing to unpack .../3-libgenome0_1.3.11+svn20110227.4616-6_arm64.deb ... 260s Unpacking libgenome0:arm64 (1.3.11+svn20110227.4616-6) ... 260s Selecting previously unselected package libgomp1:arm64. 260s Preparing to unpack .../4-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 260s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 260s Selecting previously unselected package libmuscle1. 260s Preparing to unpack .../5-libmuscle1_3.7+4565-8_arm64.deb ... 260s Unpacking libmuscle1 (3.7+4565-8) ... 260s Selecting previously unselected package libmems1t64:arm64. 260s Preparing to unpack .../6-libmems1t64_1.6.0+4725-11_arm64.deb ... 260s Unpacking libmems1t64:arm64 (1.6.0+4725-11) ... 260s Selecting previously unselected package progressivemauve. 260s Preparing to unpack .../7-progressivemauve_1.2.0+4713+dfsg-5build3_arm64.deb ... 260s Unpacking progressivemauve (1.2.0+4713+dfsg-5build3) ... 260s Setting up libboost-program-options1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 260s Setting up libgenome0:arm64 (1.3.11+svn20110227.4616-6) ... 260s Setting up libboost-filesystem1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 260s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 260s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-4.1ubuntu2) ... 260s Setting up libmuscle1 (3.7+4565-8) ... 260s Setting up libmems1t64:arm64 (1.6.0+4725-11) ... 260s Setting up progressivemauve (1.2.0+4713+dfsg-5build3) ... 260s Processing triggers for man-db (2.13.0-1) ... 261s Processing triggers for libc-bin (2.41-1ubuntu2) ... 262s autopkgtest [13:38:44]: test run-unit-test: [----------------------- 262s Storing raw sequence at /tmp/rawseq1386.000 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Storing raw sequence at /tmp/rawseq1386.001 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Storing raw sequence at /tmp/rawseq1386.002 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Using weight 9 mers for initial seeds 262s Creating sorted mer list 262s Create time was: 0 seconds. 262s Creating sorted mer list 262s Create time was: 0 seconds. 262s Creating sorted mer list 262s Create time was: 0 seconds. 262s 33%.. 262s 66%.. 262s 99%.. 262s done. 262s using default bp penalty: 77720 262s using default bp estimate min score: 233160 262s Starting with 152 multi-matches 262s Computing genome content distance matrix... 262s 262s 262s Genome conservation distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s Writing guide tree to /tmp/guide_tree1386.000 262s reading tree... 262s initializing alignment tree... 262s Constructing seed occurrence lists for repeat detection 262s Calculating pairwise breakpoint distances 262s Pair 0, 1 has 30 initial LCBs 262s Using scaled bp penalty: 22995.7 262s Pair (0,1) has 1 well-supported breakpoints 262s Pair 0, 2 has 29 initial LCBs 262s Using scaled bp penalty: 10025.6 262s Pair (0,2) has 1 well-supported breakpoints 262s Pair 1, 2 has 31 initial LCBs 262s Using scaled bp penalty: 13766.1 262s Pair (1,2) has 1 well-supported breakpoints 262s genome content distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s bp distance matrix: 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 262s Aligning... 262s Aligning node 2 to 3 via 1! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 44 tracking matches 262s There are 88 / 220 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 27 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 3%..7%.. 262s 11%..14%..18%.. 262s 22%..25%..29%.. 262s 33%..37%.. 262s 40%..44%..48%.. 262s 51%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 57862 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 0,0 has an additional 5 matches 262s Restoring backed up alignment tree... 262s 1,0 has 5 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 35 tracking matches 262s There are 70 / 175 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 7 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 262s 14%.. 262s 28%..done 262s Arrived at 3 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 8 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 3 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 57862, new anchor score: 50704 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Aligning node 1 to 4 via 0! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 60 tracking matches 262s There are 239 / 300 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 89 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 1%..2%..3%..4%..5%..6%..7%..8%.. 262s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 262s 20%..21%..22%..23%..24%..25%..26%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 5 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 99201 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 3 new matches outside LCBs 262s 1,0 have 1 new matches outside LCBs 262s 0,0 has an additional 3 matches 262s 1,0 has an additional 1 matches 262s Restoring backed up alignment tree... 262s 0,2 has 3 pairwise matches 262s 1,2 has 1 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 99201, new anchor score: 102789 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 1,0 have 0 new matches outside LCBs 262s Restoring backed up alignment tree... 262s 0,2 has 0 pairwise matches 262s 1,2 has 0 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 102789, new anchor score: 102789 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Performing final pass iterative refinement 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s root alignment has 1 superintervals 262s root alignment length: 2328 262s Organisms have 52.8% GC 262s Storing raw sequence at /tmp/rawseq1387.000 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Storing raw sequence at /tmp/rawseq1387.001 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Storing raw sequence at /tmp/rawseq1387.002 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Using weight 9 mers for initial seeds 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s 33%.. 262s 66%.. 262s 99%.. 262s done. 262s using default bp penalty: 77720 262s using default bp estimate min score: 233160 262s Starting with 152 multi-matches 262s Computing genome content distance matrix... 262s 262s 262s Genome conservation distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s Writing guide tree to threeway.tree 262s reading tree... 262s initializing alignment tree... 262s Constructing seed occurrence lists for repeat detection 262s Calculating pairwise breakpoint distances 262s Pair 0, 1 has 30 initial LCBs 262s Using scaled bp penalty: 22995.7 262s Pair (0,1) has 1 well-supported breakpoints 262s Pair 0, 2 has 29 initial LCBs 262s Using scaled bp penalty: 10025.6 262s Pair (0,2) has 1 well-supported breakpoints 262s Pair 1, 2 has 31 initial LCBs 262s Using scaled bp penalty: 13766.1 262s Pair (1,2) has 1 well-supported breakpoints 262s genome content distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s bp distance matrix: 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 262s Aligning... 262s Aligning node 2 to 3 via 1! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 44 tracking matches 262s There are 88 / 220 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 27 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 3%..7%.. 262s 11%..14%..18%.. 262s 22%..25%..29%.. 262s 33%..37%.. 262s 40%..44%..48%.. 262s 51%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 57862 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 0,0 has an additional 5 matches 262s Restoring backed up alignment tree... 262s 1,0 has 5 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 35 tracking matches 262s There are 70 / 175 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 7 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 262s 14%.. 262s 28%..done 262s Arrived at 3 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 8 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 3 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 57862, new anchor score: 50704 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Aligning node 1 to 4 via 0! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 60 tracking matches 262s There are 239 / 300 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 89 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 1%..2%..3%..4%..5%..6%..7%..8%.. 262s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 262s 20%..21%..22%..23%..24%..25%..26%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 5 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 99201 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 3 new matches outside LCBs 262s 1,0 have 1 new matches outside LCBs 262s 0,0 has an additional 3 matches 262s 1,0 has an additional 1 matches 262s Restoring backed up alignment tree... 262s 0,2 has 3 pairwise matches 262s 1,2 has 1 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 99201, new anchor score: 102789 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 1,0 have 0 new matches outside LCBs 262s Restoring backed up alignment tree... 262s 0,2 has 0 pairwise matches 262s 1,2 has 0 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 102789, new anchor score: 102789 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Performing final pass iterative refinement 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s root alignment has 1 superintervals 262s root alignment length: 2328 262s Organisms have 52.8% GC 262s Storing raw sequence at /tmp/rawseq1388.000 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Storing raw sequence at /tmp/rawseq1388.001 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Storing raw sequence at /tmp/rawseq1388.002 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Using weight 9 mers for initial seeds 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s 33%.. 262s 66%.. 262s 99%.. 262s done. 262s using default bp penalty: 77720 262s using default bp estimate min score: 233160 262s Starting with 152 multi-matches 262s Computing genome content distance matrix... 262s 262s 262s Genome conservation distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s Writing guide tree to /tmp/guide_tree1388.000 262s reading tree... 262s initializing alignment tree... 262s Constructing seed occurrence lists for repeat detection 262s Calculating pairwise breakpoint distances 262s Pair 0, 1 has 30 initial LCBs 262s Using scaled bp penalty: 22995.7 262s Pair (0,1) has 1 well-supported breakpoints 262s Pair 0, 2 has 29 initial LCBs 262s Using scaled bp penalty: 10025.6 262s Pair (0,2) has 1 well-supported breakpoints 262s Pair 1, 2 has 31 initial LCBs 262s Using scaled bp penalty: 13766.1 262s Pair (1,2) has 1 well-supported breakpoints 262s genome content distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s bp distance matrix: 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 262s Aligning... 262s Aligning node 2 to 3 via 1! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 44 tracking matches 262s There are 88 / 220 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 27 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 3%..7%.. 262s 11%..14%..18%.. 262s 22%..25%..29%.. 262s 33%..37%.. 262s 40%..44%..48%.. 262s 51%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 57862 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 0,0 has an additional 5 matches 262s Restoring backed up alignment tree... 262s 1,0 has 5 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 35 tracking matches 262s There are 70 / 175 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 7 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 262s 14%.. 262s 28%..done 262s Arrived at 3 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 8 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 3 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 57862, new anchor score: 50704 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Aligning node 1 to 4 via 0! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 60 tracking matches 262s There are 239 / 300 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 89 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 1%..2%..3%..4%..5%..6%..7%..8%.. 262s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 262s 20%..21%..22%..23%..24%..25%..26%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 5 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 99201 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 3 new matches outside LCBs 262s 1,0 have 1 new matches outside LCBs 262s 0,0 has an additional 3 matches 262s 1,0 has an additional 1 matches 262s Restoring backed up alignment tree... 262s 0,2 has 3 pairwise matches 262s 1,2 has 1 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 99201, new anchor score: 102789 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 1,0 have 0 new matches outside LCBs 262s Restoring backed up alignment tree... 262s 0,2 has 0 pairwise matches 262s 1,2 has 0 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 102789, new anchor score: 102789 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Performing final pass iterative refinement 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s root alignment has 1 superintervals 262s root alignment length: 2328 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Organisms have 52.8% GC 262s Storing raw sequence at /tmp/rawseq1390.000 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Storing raw sequence at /tmp/rawseq1390.001 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Storing raw sequence at /tmp/rawseq1390.002 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Using weight 9 mers for initial seeds 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s 33%.. 262s 66%.. 262s 99%.. 262s done. 262s Storing raw sequence at /tmp/rawseq1391.000 262s Sequence loaded successfully. 262s genome_1.gbk 2175 base pairs. 262s Storing raw sequence at /tmp/rawseq1391.001 262s Sequence loaded successfully. 262s genome_2.gbk 2199 base pairs. 262s Storing raw sequence at /tmp/rawseq1391.002 262s Sequence loaded successfully. 262s genome_3.gbk 2224 base pairs. 262s Using weight 9 mers for initial seeds 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s Sorted mer list loaded successfully 262s using default bp penalty: 77720 262s using default bp estimate min score: 233160 262s Starting with 152 multi-matches 262s Computing genome content distance matrix... 262s 262s 262s Genome conservation distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s Writing guide tree to /tmp/guide_tree1391.000 262s reading tree... 262s initializing alignment tree... 262s Constructing seed occurrence lists for repeat detection 262s Calculating pairwise breakpoint distances 262s Pair 0, 1 has 30 initial LCBs 262s Using scaled bp penalty: 22995.7 262s Pair (0,1) has 1 well-supported breakpoints 262s Pair 0, 2 has 29 initial LCBs 262s Using scaled bp penalty: 10025.6 262s Pair (0,2) has 1 well-supported breakpoints 262s Pair 1, 2 has 31 initial LCBs 262s Using scaled bp penalty: 13766.1 262s Pair (1,2) has 1 well-supported breakpoints 262s genome content distance matrix: 262s 0 0.4396 0.54463 262s 0.4396 0 0.507065 262s 0.54463 0.507065 0 262s 262s bp distance matrix: 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 0.9 0.9 0.9 262s 262s Aligning... 262s Aligning node 2 to 3 via 1! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 44 tracking matches 262s There are 88 / 220 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 27 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 3%..7%.. 262s 11%..14%..18%.. 262s 22%..25%..29%.. 262s 33%..37%.. 262s 40%..44%..48%.. 262s 51%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 57862 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 0,0 has an additional 5 matches 262s Restoring backed up alignment tree... 262s 1,0 has 5 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 35 tracking matches 262s There are 70 / 175 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 7 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.4396 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 262s 14%.. 262s 28%..done 262s Arrived at 3 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 8 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(2) has 1 intervals 262s descendant 1(3) has 1 intervals 262s propagateDescendantBreakpoints yields 3 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 57862, new anchor score: 50704 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 262s 0%.. 262s 100%..Fix left ends 262s 262s done. 262s Aligning node 1 to 4 via 0! 262s get ancestral matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 60 tracking matches 262s There are 239 / 300 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 89 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s 1%..2%..3%..4%..5%..6%..7%..8%.. 262s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 262s 20%..21%..22%..23%..24%..25%..26%..done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 5 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: -1.79769e+308, new anchor score: 99201 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 3 new matches outside LCBs 262s 1,0 have 1 new matches outside LCBs 262s 0,0 has an additional 3 matches 262s 1,0 has an additional 1 matches 262s Restoring backed up alignment tree... 262s 0,2 has 3 pairwise matches 262s 1,2 has 1 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 99201, new anchor score: 102789 262s Backing up alignment tree... 262s propagating ancestral breakpoints 262s recursive anchor search 262s 0,0 have 0 new matches outside LCBs 262s 1,0 have 0 new matches outside LCBs 262s Restoring backed up alignment tree... 262s 0,2 has 0 pairwise matches 262s 1,2 has 0 pairwise matches 262s Performing Sum-of-pairs Greedy Breakpoint Elimination 262s construct LCB tracking matches 262s There are 38 tracking matches 262s There are 152 / 190 components used 262s init tracking match LCB tracking 262s pairwise score tracking matches 262s get pairwise LCBs 262s there are 2 pairwise LCBs 262s scaling bp penalty by conservation weight: 262s 0.54463 262s 0.507065 262s 262s 262s scaling bp penalty by bp weight: 262s 0.9 262s 0.9 262s 262s Greedy BPE 262s Scoring with scaled breakpoint penalty: 4000 262s done 262s Arrived at 1 intervals 262s Adding unaligned intervals 262s addUnalignedIntervals yields 3 intervals 262s Merging unaligned intervals 262s Marbling gaps 262s Propagating descendant breakpoints 262s descendant 0(1) has 1 intervals 262s descendant 1(4) has 1 intervals 262s propagateDescendantBreakpoints yields 1 intervals 262s Creating ancestral ordering 262s Previous anchoring score: 102789, new anchor score: 102789 262s propagating ancestral breakpoints 262s performing a gapped alignment 262s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Performing final pass iterative refinement 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s root alignment has 1 superintervals 263s root alignment length: 2328 263s Organisms have 52.8% GC 263s Storing raw sequence at /tmp/rawseq1392.000 263s Sequence loaded successfully. 263s genome_1.gbk 2175 base pairs. 263s Storing raw sequence at /tmp/rawseq1392.001 263s Sequence loaded successfully. 263s genome_2.gbk 2199 base pairs. 263s Using weight 9 mers for initial seeds 263s Sorted mer list loaded successfully 263s Sorted mer list loaded successfully 263s 49%.. 263s 99%.. 263s done. 263s using default bp penalty: 50000 263s using default bp estimate min score: 232989 263s Starting with 55 multi-matches 263s Computing genome content distance matrix... 263s 263s 263s Genome conservation distance matrix: 263s 0 0.4396 263s 0.4396 0 263s 263s Writing guide tree to /tmp/guide_tree1392.000 263s reading tree... 263s initializing alignment tree... 263s Constructing seed occurrence lists for repeat detection 263s Calculating pairwise breakpoint distances 263s Pair 0, 1 has 30 initial LCBs 263s Using scaled bp penalty: 22978.9 263s Pair (0,1) has 1 well-supported breakpoints 263s genome content distance matrix: 263s 0 0.4396 263s 0.4396 0 263s 263s bp distance matrix: 263s 0.9 0.9 263s 0.9 0.9 263s 263s Aligning... 263s Aligning node 1 to 2 via 0! 263s get ancestral matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s Exception FileNotOpened thrown from 263s Unknown() in gnFileSource.cpp 67 263s Called by Unknown() 263s construct LCB tracking matches 263s There are 44 tracking matches 263s There are 88 / 132 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 27 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.4396 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 4000 263s 3%..7%.. 263s 11%..14%..18%.. 263s 22%..25%..29%.. 263s 33%..37%.. 263s 40%..44%..48%.. 263s 51%..done 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Previous anchoring score: -1.79769e+308, new anchor score: 57862 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 0 new matches outside LCBs 263s 0,0 has an additional 5 matches 263s Restoring backed up alignment tree... 263s 1,0 has 5 pairwise matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 35 tracking matches 263s There are 70 / 105 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 7 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.4396 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 4000 263s 263s 14%.. 263s 28%..done 263s Arrived at 3 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 8 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 3 intervals 263s Creating ancestral ordering 263s Previous anchoring score: 57862, new anchor score: 50704 263s propagating ancestral breakpoints 263s performing a gapped alignment 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Performing final pass iterative refinement 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s root alignment has 1 superintervals 263s root alignment length: 2249 263s Organisms have 53.2% GC 263s Storing raw sequence at /tmp/rawseq1393.000 263s Sequence loaded successfully. 263s genome_1.gbk 2175 base pairs. 263s Storing raw sequence at /tmp/rawseq1393.001 263s Sequence loaded successfully. 263s genome_2.gbk 2199 base pairs. 263s Storing raw sequence at /tmp/rawseq1393.002 263s Sequence loaded successfully. 263s genome_3.gbk 2224 base pairs. 263s Using weight 9 mers for initial seeds 263s Sorted mer list loaded successfully 263s Sorted mer list loaded successfully 263s Sorted mer list loaded successfully 263s 33%.. 263s 66%.. 263s 99%.. 263s done. 263s using default bp penalty: 77720 263s using default bp estimate min score: 233160 263s Starting with 152 multi-matches 263s Computing genome content distance matrix... 263s 263s 263s Genome conservation distance matrix: 263s 0 0.4396 0.54463 263s 0.4396 0 0.507065 263s 0.54463 0.507065 0 263s 263s Writing guide tree to /tmp/guide_tree1393.000 263s reading tree... 263s initializing alignment tree... 263s Constructing seed occurrence lists for repeat detection 263s Calculating pairwise breakpoint distances 263s Pair 0, 1 has 30 initial LCBs 263s Using scaled bp penalty: 22995.7 263s Pair (0,1) has 1 well-supported breakpoints 263s Pair 0, 2 has 29 initial LCBs 263s Using scaled bp penalty: 10025.6 263s Pair (0,2) has 1 well-supported breakpoints 263s Pair 1, 2 has 31 initial LCBs 263s Using scaled bp penalty: 13766.1 263s Pair (1,2) has 1 well-supported breakpoints 263s genome content distance matrix: 263s 0 0.4396 0.54463 263s 0.4396 0 0.507065 263s 0.54463 0.507065 0 263s 263s bp distance matrix: 263s 0.9 0.9 0.9 263s 0.9 0.9 0.9 263s 0.9 0.9 0.9 263s 263s Aligning... 263s Aligning node 2 to 3 via 1! 263s get ancestral matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 44 tracking matches 263s There are 88 / 220 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 27 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.4396 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 5000 263s 3%..7%.. 263s 11%..14%..18%.. 263s 22%..25%..29%.. 263s 33%..37%.. 263s 40%..44%..48%.. 263s 51%..done 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(2) has 1 intervals 263s descendant 1(3) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Previous anchoring score: -1.79769e+308, new anchor score: 57862 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 0 new matches outside LCBs 263s 0,0 has an additional 5 matches 263s Restoring backed up alignment tree... 263s 1,0 has 5 pairwise matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 35 tracking matches 263s There are 70 / 175 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 7 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.4396 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 5000 263s 263s 14%.. 263s 28%..done 263s Arrived at 3 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 8 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(2) has 1 intervals 263s descendant 1(3) has 1 intervals 263s propagateDescendantBreakpoints yields 3 intervals 263s Creating ancestral ordering 263s Previous anchoring score: 57862, new anchor score: 48704 263s propagating ancestral breakpoints 263s performing a gapped alignment 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Aligning node 1 to 4 via 0! 263s get ancestral matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 60 tracking matches 263s There are 239 / 300 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 89 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.54463 263s 0.507065 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 5000 263s 1%..2%..3%..4%..5%..6%..7%..8%.. 263s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 263s 20%..21%..22%..23%..24%..25%..26%..done 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 5 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(4) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Previous anchoring score: -1.79769e+308, new anchor score: 99201 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 3 new matches outside LCBs 263s 1,0 have 1 new matches outside LCBs 263s 0,0 has an additional 3 matches 263s 1,0 has an additional 1 matches 263s Restoring backed up alignment tree... 263s 0,2 has 3 pairwise matches 263s 1,2 has 1 pairwise matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 38 tracking matches 263s There are 152 / 190 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 2 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.54463 263s 0.507065 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 5000 263s done 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(4) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Previous anchoring score: 99201, new anchor score: 102789 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 0 new matches outside LCBs 263s 1,0 have 0 new matches outside LCBs 263s Restoring backed up alignment tree... 263s 0,2 has 0 pairwise matches 263s 1,2 has 0 pairwise matches 263s Performing Sum-of-pairs Greedy Breakpoint Elimination 263s construct LCB tracking matches 263s There are 38 tracking matches 263s There are 152 / 190 components used 263s init tracking match LCB tracking 263s pairwise score tracking matches 263s get pairwise LCBs 263s there are 2 pairwise LCBs 263s scaling bp penalty by conservation weight: 263s 0.54463 263s 0.507065 263s 263s 263s scaling bp penalty by bp weight: 263s 0.9 263s 0.9 263s 263s Greedy BPE 263s Scoring with scaled breakpoint penalty: 5000 263s done 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(4) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Previous anchoring score: 102789, new anchor score: 102789 263s propagating ancestral breakpoints 263s performing a gapped alignment 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Performing final pass iterative refinement 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s root alignment has 1 superintervals 263s root alignment length: 2328 263s Organisms have 52.8% GC 263s Sequence loaded successfully. 263s all_virii.fasta 2175 base pairs. 263s Sequence loaded successfully. 263s all_virii.fasta 2199 base pairs. 263s Sequence loaded successfully. 263s all_virii.fasta 2224 base pairs. 263s Using 9-mers for initial seeds 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s 263s Searching with seed pattern 11100100100100111 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s 32%.. 263s 65%.. 263s 99%.. 263s 263s Searching with seed pattern 111001010100111 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s 33%.. 263s 66%.. 263s 99%.. 263s 263s Searching with seed pattern 111010010010111 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s Creating sorted mer list 263s Create time was: 0 seconds. 263s 32%.. 263s 65%.. 263s 99%.. 263s done 263s using default bp penalty: 77720 263s using default bp estimate min score: 233160 263s 263s Assuming collinear genomes... 263s Starting with 291 multi-matches 263s Computing genome content distance matrix... 263s 263s 263s Genome conservation distance matrix: 263s 0 0.220697 0.310296 263s 0.220697 0 0.291861 263s 0.310296 0.291861 0 263s 263s Writing guide tree to /tmp/guide_tree1394.000 263s reading tree... 263s initializing alignment tree... 263s Aligning... 263s Aligning node 3 to 4 via 1! 263s get ancestral matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(3) has 1 intervals 263s descendant 1(4) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 18446744073709551615, new alignment length: 3832 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 0 new matches outside LCBs 263s Restoring backed up alignment tree... 263s 1,0 has 0 pairwise matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(3) has 1 intervals 263s descendant 1(4) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 3832, new alignment length: 3832 263s propagating ancestral breakpoints 263s performing a gapped alignment 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Aligning node 1 to 2 via 0! 263s get ancestral matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 5 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 18446744073709551615, new alignment length: 4373 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 14 new matches outside LCBs 263s 1,0 have 17 new matches outside LCBs 263s 0,0 has an additional 38 matches 263s 1,0 has an additional 41 matches 263s Restoring backed up alignment tree... 263s 0,2 has 38 pairwise matches 263s 1,2 has 41 pairwise matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 3 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 4373, new alignment length: 3825 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 2 new matches outside LCBs 263s 1,0 have 1 new matches outside LCBs 263s 0,0 has an additional 2 matches 263s 1,0 has an additional 1 matches 263s Restoring backed up alignment tree... 263s 0,2 has 2 pairwise matches 263s 1,2 has 1 pairwise matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 1 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 3825, new alignment length: 3802 263s Backing up alignment tree... 263s propagating ancestral breakpoints 263s recursive anchor search 263s 0,0 have 0 new matches outside LCBs 263s 1,0 have 0 new matches outside LCBs 263s Restoring backed up alignment tree... 263s 0,2 has 0 pairwise matches 263s 1,2 has 0 pairwise matches 263s Arrived at 1 intervals 263s Adding unaligned intervals 263s addUnalignedIntervals yields 1 intervals 263s Merging unaligned intervals 263s Marbling gaps 263s Propagating descendant breakpoints 263s descendant 0(1) has 1 intervals 263s descendant 1(2) has 1 intervals 263s propagateDescendantBreakpoints yields 1 intervals 263s Creating ancestral ordering 263s Prev alignment len: 3802, new alignment length: 3802 263s propagating ancestral breakpoints 263s performing a gapped alignment 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s Performing final pass iterative refinement 263s 263s 0%.. 263s 100%..Fix left ends 263s 263s done. 263s root alignment has 1 superintervals 263s root alignment length: 2328 263s autopkgtest [13:38:45]: test run-unit-test: -----------------------] 264s autopkgtest [13:38:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 264s run-unit-test PASS 264s autopkgtest [13:38:46]: @@@@@@@@@@@@@@@@@@@@ summary 264s run-unit-test PASS 283s nova [W] Using flock in prodstack6-arm64 283s Creating nova instance adt-plucky-arm64-progressivemauve-20250315-133421-juju-7f2275-prod-proposed-migration-environment-2-ed8170b6-7882-42b1-950b-1cf197d0299f from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 283s nova [W] Timed out waiting for 57db63de-6a44-4e08-a7cd-bebafdb73f19 to get deleted.