0s autopkgtest [18:41:43]: starting date and time: 2024-03-24 18:41:43+0000 0s autopkgtest [18:41:43]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:41:43]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bnhfb6la/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 --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 samtools/1.19.2-1build1 numpy/1:1.24.2-3ubuntu1 python3-defaults/3.12.2-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-90.secgroup --name adt-noble-i386-pbsuite-20240324-184143-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 925s autopkgtest [18:57:08]: testbed dpkg architecture: amd64 925s autopkgtest [18:57:08]: testbed apt version: 2.7.12 925s autopkgtest [18:57:08]: test architecture: i386 925s autopkgtest [18:57:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 926s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 926s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 926s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 926s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 926s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 926s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [727 kB] 926s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [488 kB] 926s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 926s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 926s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 926s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 926s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1300 kB] 926s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4419 kB] 926s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 926s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.4 kB] 926s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.4 kB] 926s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 929s Fetched 11.8 MB in 1s (8293 kB/s) 929s Reading package lists... 931s Reading package lists... 931s Building dependency tree... 931s Reading state information... 931s Calculating upgrade... 931s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 931s Reading package lists... 932s Building dependency tree... 932s Reading state information... 932s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 932s sh: Attempting to set up Debian/Ubuntu apt sources automatically 932s sh: Distribution appears to be Ubuntu 933s Reading package lists... 933s Building dependency tree... 933s Reading state information... 933s eatmydata is already the newest version (131-1). 933s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 933s Reading package lists... 934s Building dependency tree... 934s Reading state information... 934s dbus is already the newest version (1.14.10-4ubuntu1). 934s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 934s Reading package lists... 934s Building dependency tree... 934s Reading state information... 934s rng-tools-debian is already the newest version (2.4). 934s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 934s Reading package lists... 935s Building dependency tree... 935s Reading state information... 935s The following packages will be REMOVED: 935s cloud-init* python3-configobj* python3-debconf* 935s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 935s After this operation, 3256 kB disk space will be freed. 935s (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 ... 71864 files and directories currently installed.) 935s Removing cloud-init (24.1.2-0ubuntu1) ... 936s Removing python3-configobj (5.0.8-3) ... 936s Removing python3-debconf (1.5.86) ... 936s Processing triggers for man-db (2.12.0-3) ... 936s (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 ... 71475 files and directories currently installed.) 936s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 937s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 937s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 937s invoke-rc.d: policy-rc.d denied execution of try-restart. 937s Reading package lists... 937s Building dependency tree... 937s Reading state information... 938s linux-generic is already the newest version (6.8.0-11.11+1). 938s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 938s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 938s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 938s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 940s Reading package lists... 940s Reading package lists... 940s Building dependency tree... 940s Reading state information... 940s Calculating upgrade... 941s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 941s Reading package lists... 941s Building dependency tree... 941s Reading state information... 941s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 941s autopkgtest [18:57:24]: rebooting testbed after setup commands that affected boot 959s autopkgtest [18:57:42]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 960s autopkgtest [18:57:43]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 961s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 961s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 961s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 961s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 961s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 961s gpgv: issuer "npatra974@gmail.com" 961s gpgv: Can't check signature: No public key 961s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 962s autopkgtest [18:57:45]: testing package pbsuite version 15.8.24+dfsg-7 962s autopkgtest [18:57:45]: build not needed 962s autopkgtest [18:57:45]: test pbhoney: preparing testbed 964s Note, using file '/tmp/autopkgtest.Y1ZvOC/1-autopkgtest-satdep.dsc' to get the build dependencies 964s Reading package lists... 964s Building dependency tree... 964s Reading state information... 964s Starting pkgProblemResolver with broken count: 0 964s Starting 2 pkgProblemResolver with broken count: 0 964s Done 965s The following NEW packages will be installed: 965s blasr build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu 965s cpp-x86-64-linux-gnu g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu 965s gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libaec0 libasan8 965s libatomic1 libblas3 libblasr5.3.5 libc-dev-bin libc6-dev libcc1-0 965s libcrypt-dev libdeflate0 libgcc-13-dev libgfortran5 libgomp1 libhdf5-103-1 965s libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 libhwasan0 libisl23 965s libitm1 liblapack3 liblsan0 liblzf1 libmpc3 libpbbam2.4.0 libpbcopper2.3.0 965s libpbseq libquadmath0 libstdc++-13-dev libsz2 libtsan2 libubsan1 965s linux-libc-dev pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 965s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 965s python3-pbbanana python3-pbsuite-utils python3-pysam 965s python3-sortedcontainers rpcsvc-proto samtools 965s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 965s Need to get 92.9 MB of archives. 965s After this operation, 388 MB of additional disk space will be used. 965s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 libaec0 amd64 1.1.2-1 [22.6 kB] 965s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 libsz2 amd64 1.1.2-1 [5416 B] 965s Get:3 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-103-1 amd64 1.10.10+repack-3ubuntu1 [1327 kB] 965s Get:4 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-cpp-103-1 amd64 1.10.10+repack-3ubuntu1 [128 kB] 965s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 965s Get:6 http://ftpmaster.internal/ubuntu noble/universe amd64 libhtscodecs2 amd64 1.6.0-1 [98.9 kB] 965s Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 libhts3 amd64 1.18+ds-1 [428 kB] 965s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [575 kB] 965s Get:9 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1build1 [680 kB] 965s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6build3 [1237 kB] 965s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 libpbseq amd64 5.3.5+dfsg-6build3 [3068 B] 965s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 blasr amd64 5.3.5+dfsg-6build4 [230 kB] 965s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 965s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 965s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 965s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 965s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 965s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 965s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 965s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 965s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 965s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 965s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 965s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 965s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 965s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 965s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 965s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 965s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 965s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 965s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 965s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 965s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 965s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 965s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 965s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 965s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 965s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 965s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 965s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 965s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 965s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 965s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 965s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 965s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 965s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 965s Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-hl-100 amd64 1.10.10+repack-3ubuntu1 [56.2 kB] 965s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 965s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 965s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 pbdagcon amd64 0.3+git20180411.c14c422+dfsg-8build3 [269 kB] 965s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pysam amd64 0.22.0+ds-1 [4556 kB] 965s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 965s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 965s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 pbjelly all 15.8.24+dfsg-7 [966 kB] 965s Get:55 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 965s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 python3-numpy amd64 1:1.24.2-2 [7141 kB] 965s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu1 [1510 kB] 965s Get:58 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 965s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 965s Get:60 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 965s Get:61 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 965s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 samtools amd64 1.19.2-1 [593 kB] 965s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 pbhoney all 15.8.24+dfsg-7 [1051 kB] 966s Fetched 92.9 MB in 1s (135 MB/s) 966s Selecting previously unselected package libaec0:amd64. 966s (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 ... 71420 files and directories currently installed.) 966s Preparing to unpack .../00-libaec0_1.1.2-1_amd64.deb ... 966s Unpacking libaec0:amd64 (1.1.2-1) ... 966s Selecting previously unselected package libsz2:amd64. 966s Preparing to unpack .../01-libsz2_1.1.2-1_amd64.deb ... 966s Unpacking libsz2:amd64 (1.1.2-1) ... 966s Selecting previously unselected package libhdf5-103-1:amd64. 966s Preparing to unpack .../02-libhdf5-103-1_1.10.10+repack-3ubuntu1_amd64.deb ... 966s Unpacking libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 966s Selecting previously unselected package libhdf5-cpp-103-1:amd64. 966s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu1_amd64.deb ... 966s Unpacking libhdf5-cpp-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 966s Selecting previously unselected package libdeflate0:amd64. 966s Preparing to unpack .../04-libdeflate0_1.19-1_amd64.deb ... 966s Unpacking libdeflate0:amd64 (1.19-1) ... 966s Selecting previously unselected package libhtscodecs2:amd64. 966s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_amd64.deb ... 966s Unpacking libhtscodecs2:amd64 (1.6.0-1) ... 966s Selecting previously unselected package libhts3:amd64. 966s Preparing to unpack .../06-libhts3_1.18+ds-1_amd64.deb ... 966s Unpacking libhts3:amd64 (1.18+ds-1) ... 966s Selecting previously unselected package libpbcopper2.3.0:amd64. 966s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ... 966s Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 966s Selecting previously unselected package libpbbam2.4.0:amd64. 966s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_amd64.deb ... 966s Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1build1) ... 966s Selecting previously unselected package libblasr5.3.5:amd64. 966s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_amd64.deb ... 966s Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6build3) ... 966s Selecting previously unselected package libpbseq:amd64. 966s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_amd64.deb ... 966s Unpacking libpbseq:amd64 (5.3.5+dfsg-6build3) ... 966s Selecting previously unselected package blasr. 966s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_amd64.deb ... 966s Unpacking blasr (5.3.5+dfsg-6build4) ... 966s Selecting previously unselected package libc-dev-bin. 966s Preparing to unpack .../12-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 966s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 966s Selecting previously unselected package linux-libc-dev:amd64. 966s Preparing to unpack .../13-linux-libc-dev_6.8.0-11.11_amd64.deb ... 966s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 966s Selecting previously unselected package libcrypt-dev:amd64. 966s Preparing to unpack .../14-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 966s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 966s Selecting previously unselected package rpcsvc-proto. 966s Preparing to unpack .../15-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 966s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 966s Selecting previously unselected package libc6-dev:amd64. 966s Preparing to unpack .../16-libc6-dev_2.39-0ubuntu6_amd64.deb ... 966s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ... 967s Selecting previously unselected package libisl23:amd64. 967s Preparing to unpack .../17-libisl23_0.26-3_amd64.deb ... 967s Unpacking libisl23:amd64 (0.26-3) ... 967s Selecting previously unselected package libmpc3:amd64. 967s Preparing to unpack .../18-libmpc3_1.3.1-1_amd64.deb ... 967s Unpacking libmpc3:amd64 (1.3.1-1) ... 967s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 967s Preparing to unpack .../19-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 967s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 967s Selecting previously unselected package cpp-13. 967s Preparing to unpack .../20-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 967s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 967s Selecting previously unselected package cpp-x86-64-linux-gnu. 967s Preparing to unpack .../21-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 967s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 967s Selecting previously unselected package cpp. 967s Preparing to unpack .../22-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 967s Unpacking cpp (4:13.2.0-7ubuntu1) ... 967s Selecting previously unselected package libcc1-0:amd64. 967s Preparing to unpack .../23-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libgomp1:amd64. 967s Preparing to unpack .../24-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libitm1:amd64. 967s Preparing to unpack .../25-libitm1_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libatomic1:amd64. 967s Preparing to unpack .../26-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libasan8:amd64. 967s Preparing to unpack .../27-libasan8_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package liblsan0:amd64. 967s Preparing to unpack .../28-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libtsan2:amd64. 967s Preparing to unpack .../29-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libubsan1:amd64. 967s Preparing to unpack .../30-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libhwasan0:amd64. 967s Preparing to unpack .../31-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libquadmath0:amd64. 967s Preparing to unpack .../32-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 967s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 967s Selecting previously unselected package libgcc-13-dev:amd64. 967s Preparing to unpack .../33-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 967s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 967s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 967s Preparing to unpack .../34-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 967s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 968s Selecting previously unselected package gcc-13. 968s Preparing to unpack .../35-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 968s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 968s Selecting previously unselected package gcc-x86-64-linux-gnu. 968s Preparing to unpack .../36-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 968s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 968s Selecting previously unselected package gcc. 968s Preparing to unpack .../37-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 968s Unpacking gcc (4:13.2.0-7ubuntu1) ... 968s Selecting previously unselected package libstdc++-13-dev:amd64. 968s Preparing to unpack .../38-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 968s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 968s Selecting previously unselected package g++-13-x86-64-linux-gnu. 968s Preparing to unpack .../39-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 968s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 968s Selecting previously unselected package g++-13. 968s Preparing to unpack .../40-g++-13_13.2.0-17ubuntu2_amd64.deb ... 968s Unpacking g++-13 (13.2.0-17ubuntu2) ... 968s Selecting previously unselected package g++-x86-64-linux-gnu. 968s Preparing to unpack .../41-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 968s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 968s Selecting previously unselected package g++. 968s Preparing to unpack .../42-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 968s Unpacking g++ (4:13.2.0-7ubuntu1) ... 968s Selecting previously unselected package build-essential. 968s Preparing to unpack .../43-build-essential_12.10ubuntu1_amd64.deb ... 968s Unpacking build-essential (12.10ubuntu1) ... 968s Selecting previously unselected package libblas3:amd64. 968s Preparing to unpack .../44-libblas3_3.12.0-3_amd64.deb ... 968s Unpacking libblas3:amd64 (3.12.0-3) ... 968s Selecting previously unselected package libgfortran5:amd64. 968s Preparing to unpack .../45-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 968s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 968s Selecting previously unselected package libhdf5-hl-100:amd64. 968s Preparing to unpack .../46-libhdf5-hl-100_1.10.10+repack-3ubuntu1_amd64.deb ... 968s Unpacking libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ... 968s Selecting previously unselected package liblapack3:amd64. 968s Preparing to unpack .../47-liblapack3_3.12.0-3_amd64.deb ... 968s Unpacking liblapack3:amd64 (3.12.0-3) ... 969s Selecting previously unselected package liblzf1:amd64. 969s Preparing to unpack .../48-liblzf1_3.6-4_amd64.deb ... 969s Unpacking liblzf1:amd64 (3.6-4) ... 969s Selecting previously unselected package pbdagcon. 969s Preparing to unpack .../49-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_amd64.deb ... 969s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 969s Selecting previously unselected package python3-pysam. 969s Preparing to unpack .../50-python3-pysam_0.22.0+ds-1_amd64.deb ... 969s Unpacking python3-pysam (0.22.0+ds-1) ... 969s Selecting previously unselected package python3-pbsuite-utils. 969s Preparing to unpack .../51-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 969s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 969s Selecting previously unselected package python3-networkx. 969s Preparing to unpack .../52-python3-networkx_2.8.8-1ubuntu1_all.deb ... 969s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 969s Selecting previously unselected package pbjelly. 969s Preparing to unpack .../53-pbjelly_15.8.24+dfsg-7_all.deb ... 969s Unpacking pbjelly (15.8.24+dfsg-7) ... 969s Selecting previously unselected package python3-pbbanana. 969s Preparing to unpack .../54-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 969s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 969s Selecting previously unselected package python3-numpy. 969s Preparing to unpack .../55-python3-numpy_1%3a1.24.2-2_amd64.deb ... 969s Unpacking python3-numpy (1:1.24.2-2) ... 970s Selecting previously unselected package python3-h5py-serial. 970s Preparing to unpack .../56-python3-h5py-serial_3.10.0-1ubuntu1_amd64.deb ... 970s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 970s Selecting previously unselected package python3-h5py. 970s Preparing to unpack .../57-python3-h5py_3.10.0-1ubuntu1_all.deb ... 970s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 970s Selecting previously unselected package python3-sortedcontainers. 970s Preparing to unpack .../58-python3-sortedcontainers_2.4.0-2_all.deb ... 970s Unpacking python3-sortedcontainers (2.4.0-2) ... 970s Selecting previously unselected package python3-intervaltree. 970s Preparing to unpack .../59-python3-intervaltree_3.0.2-1.1_all.deb ... 970s Unpacking python3-intervaltree (3.0.2-1.1) ... 970s Selecting previously unselected package python3-intervaltree-bio. 970s Preparing to unpack .../60-python3-intervaltree-bio_1.0.1-4_all.deb ... 970s Unpacking python3-intervaltree-bio (1.0.1-4) ... 970s Selecting previously unselected package samtools. 970s Preparing to unpack .../61-samtools_1.19.2-1_amd64.deb ... 970s Unpacking samtools (1.19.2-1) ... 970s Selecting previously unselected package pbhoney. 970s Preparing to unpack .../62-pbhoney_15.8.24+dfsg-7_all.deb ... 970s Unpacking pbhoney (15.8.24+dfsg-7) ... 970s Setting up libhtscodecs2:amd64 (1.6.0-1) ... 970s Setting up libdeflate0:amd64 (1.19-1) ... 970s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 970s Setting up python3-sortedcontainers (2.4.0-2) ... 970s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 970s Setting up python3-networkx (2.8.8-1ubuntu1) ... 971s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 971s "graph [edge [ source u'u\4200' target u'u\4200' ] " 971s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 971s + "node [ id u'u\4200' label b ] ]" 971s Setting up libaec0:amd64 (1.1.2-1) ... 971s Setting up libblas3:amd64 (3.12.0-3) ... 971s 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 971s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 971s Setting up liblzf1:amd64 (3.6-4) ... 971s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libmpc3:amd64 (1.3.1-1) ... 971s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 971s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libisl23:amd64 (0.26-3) ... 971s Setting up libc-dev-bin (2.39-0ubuntu6) ... 971s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 971s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libsz2:amd64 (1.1.2-1) ... 971s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 971s Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... 971s Setting up liblapack3:amd64 (3.12.0-3) ... 971s 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 971s Setting up libhts3:amd64 (1.18+ds-1) ... 971s Setting up python3-pysam (0.22.0+ds-1) ... 971s Setting up python3-intervaltree (3.0.2-1.1) ... 971s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 971s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 971s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 971s for i in re.findall("\d+|\^?[ATCGN]+", md): 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 971s splRE = re.compile("\s+") 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 971s splRE = re.compile("\s+") 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 971s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 971s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 971s data = re.split("\s+",line) 971s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 971s data = re.split("\s+",line) 971s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 971s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 971s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 971s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 971s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 971s '\s*Type\s*=\s*(?P\w+)\s*,)?' 971s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 971s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 971s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 971s regex = re.compile("ref\d{7}") 971s Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1build1) ... 971s Setting up samtools (1.19.2-1) ... 971s Setting up python3-numpy (1:1.24.2-2) ... 973s Setting up libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 973s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 973s Setting up libhdf5-cpp-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 973s Setting up python3-intervaltree-bio (1.0.1-4) ... 973s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 973s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 973s Setting up libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ... 973s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 973s Setting up cpp-13 (13.2.0-17ubuntu2) ... 973s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 973s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 973s Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6build3) ... 973s Setting up python3-h5py (3.10.0-1ubuntu1) ... 973s Setting up gcc-13 (13.2.0-17ubuntu2) ... 973s Setting up libpbseq:amd64 (5.3.5+dfsg-6build3) ... 973s Setting up cpp (4:13.2.0-7ubuntu1) ... 973s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 973s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 973s Setting up blasr (5.3.5+dfsg-6build4) ... 973s Setting up gcc (4:13.2.0-7ubuntu1) ... 973s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 973s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 973s Setting up pbjelly (15.8.24+dfsg-7) ... 973s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 973s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 973s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 973s splRE = re.compile("\s+") 973s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 973s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 973s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 973s nprocRe = re.compile("--nproc (\d+)") 973s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 973s """ 973s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 973s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 973s Setting up g++-13 (13.2.0-17ubuntu2) ... 973s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 973s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 973s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 973s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 973s data = re.split("\s+",line) 973s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 973s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 973s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 973s data = re.split("\s+",line) 973s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 973s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 973s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 973s getContigName = re.compile("(\d+)_contig") 973s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 973s "awk -F\ '{{if ($1 < 500) print $2}}' | " 973s Setting up g++ (4:13.2.0-7ubuntu1) ... 973s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 973s Setting up build-essential (12.10ubuntu1) ... 973s Setting up pbhoney (15.8.24+dfsg-7) ... 973s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 973s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 974s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 974s """ 974s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 974s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 974s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 974s for i in re.findall("\d+|\^?[ATCGN]+", md): 974s Processing triggers for man-db (2.12.0-3) ... 974s Processing triggers for libc-bin (2.39-0ubuntu6) ... 980s Reading package lists... 981s Building dependency tree... 981s Reading state information... 981s Starting pkgProblemResolver with broken count: 0 981s Starting 2 pkgProblemResolver with broken count: 0 981s Done 981s The following NEW packages will be installed: 981s autopkgtest-satdep 981s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 981s Need to get 0 B/696 B of archives. 981s After this operation, 0 B of additional disk space will be used. 981s Get:1 /tmp/autopkgtest.Y1ZvOC/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 982s Selecting previously unselected package autopkgtest-satdep. 982s (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 ... 77034 files and directories currently installed.) 982s Preparing to unpack .../2-autopkgtest-satdep.deb ... 982s Unpacking autopkgtest-satdep (0) ... 982s Setting up autopkgtest-satdep (0) ... 982s autopkgtest: WARNING: package pbhoney:i386 is not installed though it should be 983s (Reading database ... 77034 files and directories currently installed.) 983s Removing autopkgtest-satdep (0) ... 983s autopkgtest [18:58:06]: test pbhoney: [----------------------- 983s PIEMapping 984s 984s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 984s Reid. "PBHoney: identyfying genomic variants via 984s long-read discordance and interrupted mapping." 984s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 984s doi:10.1186/1471-2105-15-180 984s 984s 2024-03-24 18:58:07,118 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 984s 2024-03-24 18:58:07,119 [INFO] Running Blasr 1017s 2024-03-24 18:58:40,857 [INFO] [0, b'[INFO] 2024-03-24T18:58:07 [blasr] started.\n[INFO] 2024-03-24T18:58:40 [blasr] ended.\n', None] 1017s 2024-03-24 18:58:40,857 [INFO] Mapping Tails 1017s 2024-03-24 18:58:40,857 [INFO] Extracting tails 1018s 2024-03-24 18:58:41,036 [INFO] Parsed 433 reads 1018s 2024-03-24 18:58:41,036 [INFO] Found 278 tails 1018s 2024-03-24 18:58:41,036 [INFO] 21 reads had double tails 1018s 2024-03-24 18:58:41,036 [INFO] Running Blasr 1024s 2024-03-24 18:58:47,921 [INFO] [0, b'[INFO] 2024-03-24T18:58:41 [blasr] started.\n[INFO] 2024-03-24T18:58:47 [blasr] ended.\n', None] 1024s 2024-03-24 18:58:47,921 [INFO] Consolidating alignments 1024s 2024-03-24 18:58:47,943 [INFO] 172 tails mapped 1024s Sam To Bam 1025s Calling Tails 1025s 1025s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 1025s Reid. "PBHoney: identyfying genomic variants via 1025s long-read discordance and interrupted mapping." 1025s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 1025s doi:10.1186/1471-2105-15-180 1025s 1025s 2024-03-24 18:58:48,365 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 1025s 2024-03-24 18:58:48,366 [INFO] Parsing lambda_NEB3011 1025s 2024-03-24 18:58:48,387 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 1025s 2024-03-24 18:58:48,399 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 1025s 2024-03-24 18:58:48,400 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 1025s 2024-03-24 18:58:48,400 [INFO] Finished 1025s Calling Spots 1025s 1025s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 1025s Reid. "PBHoney: identyfying genomic variants via 1025s long-read discordance and interrupted mapping." 1025s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 1025s doi:10.1186/1471-2105-15-180 1025s 1025s 2024-03-24 18:58:48,645 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 1025s 2024-03-24 18:58:48,659 [INFO] Starting lambda_NEB3011:ErrorCounter 1025s 2024-03-24 18:58:48,668 [INFO] 605 reads to parse in lambda_NEB3011 1025s 2024-03-24 18:58:48,671 [INFO] 5% complete 1025s 2024-03-24 18:58:48,672 [INFO] 10% complete 1025s 2024-03-24 18:58:48,675 [INFO] 15% complete 1025s 2024-03-24 18:58:48,677 [INFO] 20% complete 1025s 2024-03-24 18:58:48,678 [INFO] 25% complete 1025s 2024-03-24 18:58:48,680 [INFO] 30% complete 1025s 2024-03-24 18:58:48,683 [INFO] 35% complete 1025s 2024-03-24 18:58:48,684 [INFO] 40% complete 1025s 2024-03-24 18:58:48,685 [INFO] 45% complete 1025s 2024-03-24 18:58:48,687 [INFO] 50% complete 1025s 2024-03-24 18:58:48,689 [INFO] 55% complete 1025s 2024-03-24 18:58:48,691 [INFO] 60% complete 1025s 2024-03-24 18:58:48,693 [INFO] 65% complete 1025s 2024-03-24 18:58:48,695 [INFO] 70% complete 1025s 2024-03-24 18:58:48,696 [INFO] 75% complete 1025s 2024-03-24 18:58:48,698 [INFO] 80% complete 1025s 2024-03-24 18:58:48,700 [INFO] 85% complete 1025s 2024-03-24 18:58:48,702 [INFO] 90% complete 1025s 2024-03-24 18:58:48,703 [INFO] 95% complete 1025s 2024-03-24 18:58:48,722 [INFO] lambda_NEB3011:ErrorCounter -> spot 1025s 2024-03-24 18:58:48,722 [INFO] Starting lambda_NEB3011:SpotCaller 1025s 2024-03-24 18:58:48,733 [INFO] |lambda_NEB3011:SpotCaller|COV processing 1025s 2024-03-24 18:58:48,733 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 1025s 2024-03-24 18:58:48,733 [INFO] |lambda_NEB3011:SpotCaller|INS processing 1025s 2024-03-24 18:58:48,736 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 1025s 2024-03-24 18:58:48,736 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 1025s 2024-03-24 18:58:48,739 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 1025s 2024-03-24 18:58:48,742 [INFO] Finished 1025s 2024-03-24 18:58:48,743 [INFO] Thread Consumer-1: Exiting 1026s autopkgtest [18:58:49]: test pbhoney: -----------------------] 1027s autopkgtest [18:58:49]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 1027s pbhoney PASS 1027s autopkgtest [18:58:49]: @@@@@@@@@@@@@@@@@@@@ summary 1027s pbhoney PASS 1042s Creating nova instance adt-noble-i386-pbsuite-20240324-184143-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240324.img (UUID 4e56ccec-954f-4884-8b9c-3e1a29e50308)...