0s autopkgtest [12:00:41]: starting date and time: 2024-03-21 12:00:41+0000 0s autopkgtest [12:00:41]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [12:00:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._fdjzs4g/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:h5py --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-24.secgroup --name adt-noble-i386-pbsuite-20240321-120041-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 403s autopkgtest [12:07:24]: testbed dpkg architecture: amd64 403s autopkgtest [12:07:24]: testbed apt version: 2.7.12 403s autopkgtest [12:07:24]: test architecture: i386 403s autopkgtest [12:07:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 403s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 403s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 403s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 403s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3770 kB] 403s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 403s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [695 kB] 403s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [459 kB] 403s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 403s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 403s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 403s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 403s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1281 kB] 403s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4237 kB] 403s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 403s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB] 403s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB] 403s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 406s Fetched 11.3 MB in 1s (7859 kB/s) 407s Reading package lists... 408s Reading package lists... 408s Building dependency tree... 408s Reading state information... 409s Calculating upgrade... 409s The following packages will be upgraded: 409s debianutils linux-firmware 409s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 409s Need to get 476 MB of archives. 409s After this operation, 5724 kB of additional disk space will be used. 409s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.17 [89.8 kB] 409s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-firmware amd64 20240318.git3b128b60-0ubuntu1 [475 MB] 413s Fetched 476 MB in 3s (136 MB/s) 413s (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 ... 71803 files and directories currently installed.) 413s Preparing to unpack .../debianutils_5.17_amd64.deb ... 413s Unpacking debianutils (5.17) over (5.16) ... 413s Setting up debianutils (5.17) ... 413s (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 ... 71803 files and directories currently installed.) 413s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_amd64.deb ... 413s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ... 416s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ... 416s Processing triggers for man-db (2.12.0-3) ... 417s Processing triggers for initramfs-tools (0.142ubuntu20) ... 417s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 417s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 425s Reading package lists... 425s Building dependency tree... 425s Reading state information... 425s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 426s sh: Attempting to set up Debian/Ubuntu apt sources automatically 426s sh: Distribution appears to be Ubuntu 426s Reading package lists... 427s Building dependency tree... 427s Reading state information... 427s eatmydata is already the newest version (131-1). 427s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 427s Reading package lists... 427s Building dependency tree... 427s Reading state information... 427s dbus is already the newest version (1.14.10-4ubuntu1). 427s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 427s Reading package lists... 428s Building dependency tree... 428s Reading state information... 428s rng-tools-debian is already the newest version (2.4). 428s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 428s Reading package lists... 428s Building dependency tree... 428s Reading state information... 428s The following packages will be REMOVED: 428s cloud-init* python3-configobj* python3-debconf* 429s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 429s After this operation, 3252 kB disk space will be freed. 429s (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 ... 71865 files and directories currently installed.) 429s Removing cloud-init (24.1.1-0ubuntu1) ... 429s Removing python3-configobj (5.0.8-3) ... 429s Removing python3-debconf (1.5.86) ... 429s Processing triggers for man-db (2.12.0-3) ... 430s (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 ... 71476 files and directories currently installed.) 430s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 430s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 430s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 430s invoke-rc.d: policy-rc.d denied execution of try-restart. 430s Reading package lists... 431s Building dependency tree... 431s Reading state information... 431s linux-generic is already the newest version (6.8.0-11.11+1). 431s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 431s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 431s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 431s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 433s Reading package lists... 433s Reading package lists... 434s Building dependency tree... 434s Reading state information... 434s Calculating upgrade... 434s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 434s Reading package lists... 434s Building dependency tree... 434s Reading state information... 434s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 434s autopkgtest [12:07:55]: rebooting testbed after setup commands that affected boot 455s autopkgtest [12:08:16]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 456s autopkgtest [12:08:17]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 458s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 458s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 458s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 458s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 458s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 458s gpgv: issuer "npatra974@gmail.com" 458s gpgv: Can't check signature: No public key 458s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 459s autopkgtest [12:08:20]: testing package pbsuite version 15.8.24+dfsg-7 459s autopkgtest [12:08:20]: build not needed 459s autopkgtest [12:08:20]: test pbhoney: preparing testbed 462s Note, using file '/tmp/autopkgtest.h9Egdu/1-autopkgtest-satdep.dsc' to get the build dependencies 462s Reading package lists... 462s Building dependency tree... 462s Reading state information... 462s Starting pkgProblemResolver with broken count: 0 462s Starting 2 pkgProblemResolver with broken count: 0 462s Done 463s The following NEW packages will be installed: 463s blasr build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu 463s cpp-x86-64-linux-gnu g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu 463s gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libaec0 libasan8 463s libatomic1 libblas3 libblasr5.3.5 libc-dev-bin libc6-dev libcc1-0 463s libcrypt-dev libdeflate0 libgcc-13-dev libgfortran5 libgomp1 libhdf5-103-1 463s libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 libhwasan0 libisl23 463s libitm1 liblapack3 liblsan0 liblzf1 libmpc3 libnsl-dev libpbbam2.4.0 463s libpbcopper2.3.0 libpbseq libquadmath0 libstdc++-13-dev libsz2 libtirpc-dev 463s libtsan2 libubsan1 linux-libc-dev pbdagcon pbhoney pbjelly python3-h5py 463s python3-h5py-serial python3-intervaltree python3-intervaltree-bio 463s python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils 463s python3-pysam python3-sortedcontainers rpcsvc-proto samtools 463s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 463s Need to get 93.2 MB of archives. 463s After this operation, 389 MB of additional disk space will be used. 463s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 libaec0 amd64 1.1.2-1 [22.6 kB] 463s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 libsz2 amd64 1.1.2-1 [5416 B] 463s Get:3 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-103-1 amd64 1.10.10+repack-3ubuntu1 [1327 kB] 463s Get:4 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-cpp-103-1 amd64 1.10.10+repack-3ubuntu1 [128 kB] 463s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 463s Get:6 http://ftpmaster.internal/ubuntu noble/universe amd64 libhtscodecs2 amd64 1.6.0-1 [98.9 kB] 463s Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 libhts3 amd64 1.18+ds-1 [428 kB] 463s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB] 463s Get:9 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build1 [680 kB] 463s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6build3 [1237 kB] 463s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbseq amd64 5.3.5+dfsg-6build3 [3068 B] 463s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 blasr amd64 5.3.5+dfsg-6build4 [230 kB] 463s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] 463s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 463s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 463s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] 463s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] 463s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 463s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] 463s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 463s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 463s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 463s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 463s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 463s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 463s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 463s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 463s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 463s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 463s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 463s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 463s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 463s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 463s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 463s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 463s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 463s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 463s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 463s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 463s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 463s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 463s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 464s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 464s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 464s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 464s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 464s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 464s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 464s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-hl-100 amd64 1.10.10+repack-3ubuntu1 [56.2 kB] 464s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 464s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 464s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-8build3 [269 kB] 464s Get:53 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pysam amd64 0.22.0+ds-1 [4556 kB] 464s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 464s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 464s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 pbjelly all 15.8.24+dfsg-7 [966 kB] 464s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 464s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 python3-numpy amd64 1:1.24.2-2 [7141 kB] 464s Get:59 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu1 [1510 kB] 464s Get:60 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 464s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 464s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 464s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 464s Get:64 http://ftpmaster.internal/ubuntu noble/universe amd64 samtools amd64 1.19.2-1 [593 kB] 464s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 pbhoney all 15.8.24+dfsg-7 [1051 kB] 464s Fetched 93.2 MB in 1s (98.3 MB/s) 464s Selecting previously unselected package libaec0:amd64. 464s (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 ... 71421 files and directories currently installed.) 464s Preparing to unpack .../00-libaec0_1.1.2-1_amd64.deb ... 464s Unpacking libaec0:amd64 (1.1.2-1) ... 464s Selecting previously unselected package libsz2:amd64. 464s Preparing to unpack .../01-libsz2_1.1.2-1_amd64.deb ... 464s Unpacking libsz2:amd64 (1.1.2-1) ... 464s Selecting previously unselected package libhdf5-103-1:amd64. 464s Preparing to unpack .../02-libhdf5-103-1_1.10.10+repack-3ubuntu1_amd64.deb ... 464s Unpacking libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 464s Selecting previously unselected package libhdf5-cpp-103-1:amd64. 464s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu1_amd64.deb ... 464s Unpacking libhdf5-cpp-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 465s Selecting previously unselected package libdeflate0:amd64. 465s Preparing to unpack .../04-libdeflate0_1.19-1_amd64.deb ... 465s Unpacking libdeflate0:amd64 (1.19-1) ... 465s Selecting previously unselected package libhtscodecs2:amd64. 465s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_amd64.deb ... 465s Unpacking libhtscodecs2:amd64 (1.6.0-1) ... 465s Selecting previously unselected package libhts3:amd64. 465s Preparing to unpack .../06-libhts3_1.18+ds-1_amd64.deb ... 465s Unpacking libhts3:amd64 (1.18+ds-1) ... 465s Selecting previously unselected package libpbcopper2.3.0:amd64. 465s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ... 465s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 465s Selecting previously unselected package libpbbam2.4.0:amd64. 465s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_amd64.deb ... 465s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build1) ... 465s Selecting previously unselected package libblasr5.3.5:amd64. 465s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_amd64.deb ... 465s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6build3) ... 465s Selecting previously unselected package libpbseq:amd64. 465s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_amd64.deb ... 465s Unpacking libpbseq:amd64 (5.3.5+dfsg-6build3) ... 465s Selecting previously unselected package blasr. 465s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_amd64.deb ... 465s Unpacking blasr (5.3.5+dfsg-6build4) ... 465s Selecting previously unselected package libc-dev-bin. 465s Preparing to unpack .../12-libc-dev-bin_2.39-0ubuntu2_amd64.deb ... 465s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 465s Selecting previously unselected package linux-libc-dev:amd64. 465s Preparing to unpack .../13-linux-libc-dev_6.8.0-11.11_amd64.deb ... 465s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 465s Selecting previously unselected package libcrypt-dev:amd64. 465s Preparing to unpack .../14-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 465s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 465s Selecting previously unselected package libtirpc-dev:amd64. 465s Preparing to unpack .../15-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... 465s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 465s Selecting previously unselected package libnsl-dev:amd64. 465s Preparing to unpack .../16-libnsl-dev_1.3.0-3_amd64.deb ... 465s Unpacking libnsl-dev:amd64 (1.3.0-3) ... 465s Selecting previously unselected package rpcsvc-proto. 465s Preparing to unpack .../17-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 465s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 465s Selecting previously unselected package libc6-dev:amd64. 465s Preparing to unpack .../18-libc6-dev_2.39-0ubuntu2_amd64.deb ... 465s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ... 465s Selecting previously unselected package libisl23:amd64. 465s Preparing to unpack .../19-libisl23_0.26-3_amd64.deb ... 465s Unpacking libisl23:amd64 (0.26-3) ... 465s Selecting previously unselected package libmpc3:amd64. 465s Preparing to unpack .../20-libmpc3_1.3.1-1_amd64.deb ... 465s Unpacking libmpc3:amd64 (1.3.1-1) ... 465s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 465s Preparing to unpack .../21-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 465s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 465s Selecting previously unselected package cpp-13. 466s Preparing to unpack .../22-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 466s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 466s Selecting previously unselected package cpp-x86-64-linux-gnu. 466s Preparing to unpack .../23-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 466s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 466s Selecting previously unselected package cpp. 466s Preparing to unpack .../24-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 466s Unpacking cpp (4:13.2.0-7ubuntu1) ... 466s Selecting previously unselected package libcc1-0:amd64. 466s Preparing to unpack .../25-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libgomp1:amd64. 466s Preparing to unpack .../26-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libitm1:amd64. 466s Preparing to unpack .../27-libitm1_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libatomic1:amd64. 466s Preparing to unpack .../28-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libasan8:amd64. 466s Preparing to unpack .../29-libasan8_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package liblsan0:amd64. 466s Preparing to unpack .../30-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libtsan2:amd64. 466s Preparing to unpack .../31-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libubsan1:amd64. 466s Preparing to unpack .../32-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libhwasan0:amd64. 466s Preparing to unpack .../33-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libquadmath0:amd64. 466s Preparing to unpack .../34-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 466s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 466s Selecting previously unselected package libgcc-13-dev:amd64. 466s Preparing to unpack .../35-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 466s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 466s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 466s Preparing to unpack .../36-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 466s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 466s Selecting previously unselected package gcc-13. 466s Preparing to unpack .../37-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 466s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 466s Selecting previously unselected package gcc-x86-64-linux-gnu. 466s Preparing to unpack .../38-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 466s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 467s Selecting previously unselected package gcc. 467s Preparing to unpack .../39-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 467s Unpacking gcc (4:13.2.0-7ubuntu1) ... 467s Selecting previously unselected package libstdc++-13-dev:amd64. 467s Preparing to unpack .../40-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 467s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 467s Selecting previously unselected package g++-13-x86-64-linux-gnu. 467s Preparing to unpack .../41-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 467s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 467s Selecting previously unselected package g++-13. 467s Preparing to unpack .../42-g++-13_13.2.0-17ubuntu2_amd64.deb ... 467s Unpacking g++-13 (13.2.0-17ubuntu2) ... 467s Selecting previously unselected package g++-x86-64-linux-gnu. 467s Preparing to unpack .../43-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 467s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 467s Selecting previously unselected package g++. 467s Preparing to unpack .../44-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 467s Unpacking g++ (4:13.2.0-7ubuntu1) ... 467s Selecting previously unselected package build-essential. 467s Preparing to unpack .../45-build-essential_12.10ubuntu1_amd64.deb ... 467s Unpacking build-essential (12.10ubuntu1) ... 467s Selecting previously unselected package libblas3:amd64. 467s Preparing to unpack .../46-libblas3_3.12.0-3_amd64.deb ... 467s Unpacking libblas3:amd64 (3.12.0-3) ... 467s Selecting previously unselected package libgfortran5:amd64. 467s Preparing to unpack .../47-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 467s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 467s Selecting previously unselected package libhdf5-hl-100:amd64. 467s Preparing to unpack .../48-libhdf5-hl-100_1.10.10+repack-3ubuntu1_amd64.deb ... 467s Unpacking libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ... 467s Selecting previously unselected package liblapack3:amd64. 467s Preparing to unpack .../49-liblapack3_3.12.0-3_amd64.deb ... 467s Unpacking liblapack3:amd64 (3.12.0-3) ... 467s Selecting previously unselected package liblzf1:amd64. 467s Preparing to unpack .../50-liblzf1_3.6-4_amd64.deb ... 467s Unpacking liblzf1:amd64 (3.6-4) ... 467s Selecting previously unselected package pbdagcon. 467s Preparing to unpack .../51-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_amd64.deb ... 467s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 467s Selecting previously unselected package python3-pysam. 467s Preparing to unpack .../52-python3-pysam_0.22.0+ds-1_amd64.deb ... 467s Unpacking python3-pysam (0.22.0+ds-1) ... 467s Selecting previously unselected package python3-pbsuite-utils. 467s Preparing to unpack .../53-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 467s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 468s Selecting previously unselected package python3-networkx. 468s Preparing to unpack .../54-python3-networkx_2.8.8-1ubuntu1_all.deb ... 468s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 468s Selecting previously unselected package pbjelly. 468s Preparing to unpack .../55-pbjelly_15.8.24+dfsg-7_all.deb ... 468s Unpacking pbjelly (15.8.24+dfsg-7) ... 468s Selecting previously unselected package python3-pbbanana. 468s Preparing to unpack .../56-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 468s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 468s Selecting previously unselected package python3-numpy. 468s Preparing to unpack .../57-python3-numpy_1%3a1.24.2-2_amd64.deb ... 468s Unpacking python3-numpy (1:1.24.2-2) ... 468s Selecting previously unselected package python3-h5py-serial. 468s Preparing to unpack .../58-python3-h5py-serial_3.10.0-1ubuntu1_amd64.deb ... 468s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 468s Selecting previously unselected package python3-h5py. 468s Preparing to unpack .../59-python3-h5py_3.10.0-1ubuntu1_all.deb ... 468s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 468s Selecting previously unselected package python3-sortedcontainers. 468s Preparing to unpack .../60-python3-sortedcontainers_2.4.0-2_all.deb ... 468s Unpacking python3-sortedcontainers (2.4.0-2) ... 468s Selecting previously unselected package python3-intervaltree. 468s Preparing to unpack .../61-python3-intervaltree_3.0.2-1.1_all.deb ... 468s Unpacking python3-intervaltree (3.0.2-1.1) ... 468s Selecting previously unselected package python3-intervaltree-bio. 468s Preparing to unpack .../62-python3-intervaltree-bio_1.0.1-4_all.deb ... 468s Unpacking python3-intervaltree-bio (1.0.1-4) ... 468s Selecting previously unselected package samtools. 468s Preparing to unpack .../63-samtools_1.19.2-1_amd64.deb ... 468s Unpacking samtools (1.19.2-1) ... 468s Selecting previously unselected package pbhoney. 468s Preparing to unpack .../64-pbhoney_15.8.24+dfsg-7_all.deb ... 468s Unpacking pbhoney (15.8.24+dfsg-7) ... 469s Setting up libhtscodecs2:amd64 (1.6.0-1) ... 469s Setting up libdeflate0:amd64 (1.19-1) ... 469s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 469s Setting up python3-sortedcontainers (2.4.0-2) ... 469s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 469s Setting up python3-networkx (2.8.8-1ubuntu1) ... 470s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 470s "graph [edge [ source u'u\4200' target u'u\4200' ] " 470s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 470s + "node [ id u'u\4200' label b ] ]" 470s Setting up libaec0:amd64 (1.1.2-1) ... 470s Setting up libblas3:amd64 (3.12.0-3) ... 470s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 470s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 470s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 470s Setting up liblzf1:amd64 (3.6-4) ... 470s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libmpc3:amd64 (1.3.1-1) ... 470s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libnsl-dev:amd64 (1.3.0-3) ... 470s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 470s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libisl23:amd64 (0.26-3) ... 470s Setting up libc-dev-bin (2.39-0ubuntu2) ... 470s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 470s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libsz2:amd64 (1.1.2-1) ... 470s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 470s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 470s Setting up liblapack3:amd64 (3.12.0-3) ... 470s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 470s Setting up libhts3:amd64 (1.18+ds-1) ... 470s Setting up python3-pysam (0.22.0+ds-1) ... 470s Setting up python3-intervaltree (3.0.2-1.1) ... 470s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 470s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 470s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 470s for i in re.findall("\d+|\^?[ATCGN]+", md): 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 470s splRE = re.compile("\s+") 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 470s splRE = re.compile("\s+") 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 470s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 470s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 470s data = re.split("\s+",line) 470s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 470s data = re.split("\s+",line) 470s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 470s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 470s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 470s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 470s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 470s '\s*Type\s*=\s*(?P\w+)\s*,)?' 470s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 470s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 470s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 470s regex = re.compile("ref\d{7}") 470s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build1) ... 470s Setting up samtools (1.19.2-1) ... 470s Setting up python3-numpy (1:1.24.2-2) ... 472s Setting up libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 472s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 472s Setting up libhdf5-cpp-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 472s Setting up python3-intervaltree-bio (1.0.1-4) ... 472s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ... 472s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 472s Setting up libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ... 472s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 472s Setting up cpp-13 (13.2.0-17ubuntu2) ... 472s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 472s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 472s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6build3) ... 472s Setting up python3-h5py (3.10.0-1ubuntu1) ... 472s Setting up gcc-13 (13.2.0-17ubuntu2) ... 472s Setting up libpbseq:amd64 (5.3.5+dfsg-6build3) ... 472s Setting up cpp (4:13.2.0-7ubuntu1) ... 472s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 472s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 472s Setting up blasr (5.3.5+dfsg-6build4) ... 472s Setting up gcc (4:13.2.0-7ubuntu1) ... 472s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 472s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 472s Setting up pbjelly (15.8.24+dfsg-7) ... 472s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 472s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 472s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 472s splRE = re.compile("\s+") 472s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 472s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 472s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 472s nprocRe = re.compile("--nproc (\d+)") 472s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 472s """ 472s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 472s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 472s Setting up g++-13 (13.2.0-17ubuntu2) ... 472s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 472s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 472s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 472s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 472s data = re.split("\s+",line) 472s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 472s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 472s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 472s data = re.split("\s+",line) 472s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 472s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 472s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 472s getContigName = re.compile("(\d+)_contig") 472s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 472s "awk -F\ '{{if ($1 < 500) print $2}}' | " 472s Setting up g++ (4:13.2.0-7ubuntu1) ... 472s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 472s Setting up build-essential (12.10ubuntu1) ... 472s Setting up pbhoney (15.8.24+dfsg-7) ... 473s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 473s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 473s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 473s """ 473s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 473s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 473s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 473s for i in re.findall("\d+|\^?[ATCGN]+", md): 473s Processing triggers for man-db (2.12.0-3) ... 474s Processing triggers for libc-bin (2.39-0ubuntu2) ... 475s Reading package lists... 475s Building dependency tree... 475s Reading state information... 475s Starting pkgProblemResolver with broken count: 0 475s Starting 2 pkgProblemResolver with broken count: 0 475s Done 476s The following NEW packages will be installed: 476s autopkgtest-satdep 476s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 476s Need to get 0 B/700 B of archives. 476s After this operation, 0 B of additional disk space will be used. 476s Get:1 /tmp/autopkgtest.h9Egdu/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 476s Selecting previously unselected package autopkgtest-satdep. 476s (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 ... 77136 files and directories currently installed.) 476s Preparing to unpack .../2-autopkgtest-satdep.deb ... 476s Unpacking autopkgtest-satdep (0) ... 476s Setting up autopkgtest-satdep (0) ... 476s autopkgtest: WARNING: package pbhoney:i386 is not installed though it should be 478s (Reading database ... 77136 files and directories currently installed.) 478s Removing autopkgtest-satdep (0) ... 478s autopkgtest [12:08:39]: test pbhoney: [----------------------- 478s PIEMapping 478s 478s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 478s Reid. "PBHoney: identyfying genomic variants via 478s long-read discordance and interrupted mapping." 478s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 478s doi:10.1186/1471-2105-15-180 478s 478s 2024-03-21 12:08:40,115 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 478s 2024-03-21 12:08:40,115 [INFO] Running Blasr 512s 2024-03-21 12:09:13,954 [INFO] [0, b'[INFO] 2024-03-21T12:08:40 [blasr] started.\n[INFO] 2024-03-21T12:09:13 [blasr] ended.\n', None] 512s 2024-03-21 12:09:13,955 [INFO] Mapping Tails 512s 2024-03-21 12:09:13,955 [INFO] Extracting tails 513s 2024-03-21 12:09:14,152 [INFO] Parsed 433 reads 513s 2024-03-21 12:09:14,152 [INFO] Found 278 tails 513s 2024-03-21 12:09:14,152 [INFO] 21 reads had double tails 513s 2024-03-21 12:09:14,152 [INFO] Running Blasr 520s 2024-03-21 12:09:21,151 [INFO] [0, b'[INFO] 2024-03-21T12:09:14 [blasr] started.\n[INFO] 2024-03-21T12:09:21 [blasr] ended.\n', None] 520s 2024-03-21 12:09:21,151 [INFO] Consolidating alignments 520s 2024-03-21 12:09:21,176 [INFO] 172 tails mapped 520s Sam To Bam 520s Calling Tails 520s 520s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 520s Reid. "PBHoney: identyfying genomic variants via 520s long-read discordance and interrupted mapping." 520s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 520s doi:10.1186/1471-2105-15-180 520s 520s 2024-03-21 12:09:21,623 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 520s 2024-03-21 12:09:21,623 [INFO] Parsing lambda_NEB3011 520s 2024-03-21 12:09:21,644 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 520s 2024-03-21 12:09:21,657 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 520s 2024-03-21 12:09:21,658 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 520s 2024-03-21 12:09:21,658 [INFO] Finished 520s Calling Spots 520s 520s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 520s Reid. "PBHoney: identyfying genomic variants via 520s long-read discordance and interrupted mapping." 520s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 520s doi:10.1186/1471-2105-15-180 520s 520s 2024-03-21 12:09:21,920 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 520s 2024-03-21 12:09:21,935 [INFO] Starting lambda_NEB3011:ErrorCounter 520s 2024-03-21 12:09:21,944 [INFO] 605 reads to parse in lambda_NEB3011 520s 2024-03-21 12:09:21,947 [INFO] 5% complete 520s 2024-03-21 12:09:21,948 [INFO] 10% complete 520s 2024-03-21 12:09:21,951 [INFO] 15% complete 520s 2024-03-21 12:09:21,953 [INFO] 20% complete 520s 2024-03-21 12:09:21,954 [INFO] 25% complete 520s 2024-03-21 12:09:21,956 [INFO] 30% complete 520s 2024-03-21 12:09:21,959 [INFO] 35% complete 520s 2024-03-21 12:09:21,961 [INFO] 40% complete 520s 2024-03-21 12:09:21,962 [INFO] 45% complete 520s 2024-03-21 12:09:21,964 [INFO] 50% complete 520s 2024-03-21 12:09:21,965 [INFO] 55% complete 520s 2024-03-21 12:09:21,968 [INFO] 60% complete 520s 2024-03-21 12:09:21,970 [INFO] 65% complete 520s 2024-03-21 12:09:21,972 [INFO] 70% complete 520s 2024-03-21 12:09:21,973 [INFO] 75% complete 520s 2024-03-21 12:09:21,975 [INFO] 80% complete 520s 2024-03-21 12:09:21,977 [INFO] 85% complete 520s 2024-03-21 12:09:21,979 [INFO] 90% complete 520s 2024-03-21 12:09:21,980 [INFO] 95% complete 520s 2024-03-21 12:09:21,999 [INFO] lambda_NEB3011:ErrorCounter -> spot 520s 2024-03-21 12:09:22,000 [INFO] Starting lambda_NEB3011:SpotCaller 521s 2024-03-21 12:09:22,009 [INFO] |lambda_NEB3011:SpotCaller|COV processing 521s 2024-03-21 12:09:22,009 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 521s 2024-03-21 12:09:22,009 [INFO] |lambda_NEB3011:SpotCaller|INS processing 521s 2024-03-21 12:09:22,012 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 521s 2024-03-21 12:09:22,012 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 521s 2024-03-21 12:09:22,015 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 521s 2024-03-21 12:09:22,017 [INFO] Finished 521s 2024-03-21 12:09:22,018 [INFO] Thread Consumer-1: Exiting 521s autopkgtest [12:09:22]: test pbhoney: -----------------------] 521s pbhoney PASS 521s autopkgtest [12:09:22]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 521s autopkgtest [12:09:22]: @@@@@@@@@@@@@@@@@@@@ summary 521s pbhoney PASS 532s Creating nova instance adt-noble-i386-pbsuite-20240321-120041-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240320.img (UUID 3219a3f4-90ea-47d9-8dfb-3912f2ae9f95)...