0s autopkgtest [17:03:21]: starting date and time: 2024-03-24 17:03:21+0000 0s autopkgtest [17:03:21]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:03:21]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zviyhwma/out --timeout-copy=6000 --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:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-1.secgroup --name adt-noble-arm64-pbsuite-20240324-170321-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 88s autopkgtest [17:04:49]: testbed dpkg architecture: arm64 88s autopkgtest [17:04:49]: testbed apt version: 2.7.12 88s autopkgtest [17:04:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 89s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 89s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 89s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 90s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 90s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 90s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 90s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 90s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 90s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 90s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 90s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 90s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 92s Fetched 9850 kB in 2s (5388 kB/s) 92s Reading package lists... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Calculating upgrade... 96s The following packages will be REMOVED: 96s libssl3 96s The following NEW packages will be installed: 96s libssl3t64 96s The following packages have been kept back: 96s curl 96s The following packages will be upgraded: 96s openssl 96s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 96s Need to get 2777 kB of archives. 96s After this operation, 139 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 96s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 97s Fetched 2777 kB in 1s (4012 kB/s) 97s (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 ... 75911 files and directories currently installed.) 97s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 97s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 97s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 97s wget depends on libssl3 (>= 3.0.0). 97s u-boot-tools depends on libssl3 (>= 3.0.0). 97s tnftp depends on libssl3 (>= 3.0.0). 97s tcpdump depends on libssl3 (>= 3.0.0). 97s systemd-resolved depends on libssl3 (>= 3.0.0). 97s systemd depends on libssl3 (>= 3.0.0). 97s sudo depends on libssl3 (>= 3.0.0). 97s sbsigntool depends on libssl3 (>= 3.0.0). 97s rsync depends on libssl3 (>= 3.0.0). 97s python3-cryptography depends on libssl3 (>= 3.0.0). 97s openssh-server depends on libssl3 (>= 3.0.10). 97s openssh-client depends on libssl3 (>= 3.0.10). 97s mtd-utils depends on libssl3 (>= 3.0.0). 97s mokutil depends on libssl3 (>= 3.0.0). 97s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 97s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 97s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 97s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 97s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 97s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 97s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 97s libnvme1 depends on libssl3 (>= 3.0.0). 97s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 97s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 97s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 97s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 97s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 97s kmod depends on libssl3 (>= 3.0.0). 97s dhcpcd-base depends on libssl3 (>= 3.0.0). 97s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 97s 97s (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 ... 75911 files and directories currently installed.) 97s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 97s Selecting previously unselected package libssl3t64:arm64. 97s (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 ... 75900 files and directories currently installed.) 97s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 97s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 97s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 97s Setting up openssl (3.0.13-0ubuntu2) ... 97s Processing triggers for man-db (2.12.0-3) ... 97s Processing triggers for libc-bin (2.39-0ubuntu6) ... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 99s sh: Attempting to set up Debian/Ubuntu apt sources automatically 99s sh: Distribution appears to be Ubuntu 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s eatmydata is already the newest version (131-1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s dbus is already the newest version (1.14.10-4ubuntu1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s rng-tools-debian is already the newest version (2.4). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s The following packages will be REMOVED: 103s cloud-init* python3-configobj* python3-debconf* 103s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 103s After this operation, 3256 kB disk space will be freed. 103s (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 ... 75913 files and directories currently installed.) 103s Removing cloud-init (24.1.2-0ubuntu1) ... 104s Removing python3-configobj (5.0.8-3) ... 104s Removing python3-debconf (1.5.86) ... 104s Processing triggers for man-db (2.12.0-3) ... 104s (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 ... 75524 files and directories currently installed.) 104s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 105s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 105s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 105s invoke-rc.d: policy-rc.d denied execution of try-restart. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s linux-generic is already the newest version (6.8.0-11.11+1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [17:05:11]: rebooting testbed after setup commands that affected boot 263s autopkgtest [17:07:44]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 268s autopkgtest [17:07:49]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 271s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 271s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 271s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 271s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 271s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 271s gpgv: issuer "npatra974@gmail.com" 271s gpgv: Can't check signature: No public key 271s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 272s autopkgtest [17:07:53]: testing package pbsuite version 15.8.24+dfsg-7 272s autopkgtest [17:07:53]: build not needed 273s autopkgtest [17:07:54]: test pbhoney: preparing testbed 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 281s Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 281s The following additional packages will be installed: 281s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 libhdf5-103-1 281s libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 liblapack3 liblzf1 281s libpbbam2.4.0 libpbcopper2.3.0 libpbseq libsz2 pbdagcon pbhoney pbjelly 281s python3-h5py python3-h5py-serial python3-intervaltree 281s python3-intervaltree-bio python3-networkx python3-numpy python3-pbbanana 281s python3-pbsuite-utils python3-pysam python3-sortedcontainers samtools 281s Suggested packages: 281s python-h5py-doc python-networkx-doc python3-gdal python3-matplotlib 281s python3-pydot python3-pygraphviz python3-scipy gcc gfortran python3-dev 281s python3-pytest python-sortedcontainers-doc cwltool 281s The following NEW packages will be installed: 281s autopkgtest-satdep blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 281s libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 281s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 281s libsz2 pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 281s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 281s python3-pbbanana python3-pbsuite-utils python3-pysam 281s python3-sortedcontainers samtools 281s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 281s Need to get 22.6 MB/22.6 MB of archives. 281s After this operation, 124 MB of additional disk space will be used. 281s Get:1 /tmp/autopkgtest.8LRfW8/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 281s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 282s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 282s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 282s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-cpp-103-1 arm64 1.10.10+repack-3ubuntu1 [120 kB] 282s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 282s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 282s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 282s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2 [516 kB] 282s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbbam2.4.0 arm64 2.4.0+dfsg-1build1 [634 kB] 282s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-6build3 [1207 kB] 282s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbseq arm64 5.3.5+dfsg-6build3 [3068 B] 282s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 blasr arm64 5.3.5+dfsg-6build4 [212 kB] 282s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 282s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 282s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 282s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 282s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 282s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 pbdagcon arm64 0.3+git20180411.c14c422+dfsg-8build3 [252 kB] 282s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 282s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 282s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 282s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 pbjelly all 15.8.24+dfsg-7 [966 kB] 282s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 282s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 283s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 283s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 283s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 283s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 283s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 283s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 283s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 pbhoney all 15.8.24+dfsg-7 [1051 kB] 283s Fetched 22.6 MB in 1s (17.0 MB/s) 283s Selecting previously unselected package libaec0:arm64. 283s (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 ... 75469 files and directories currently installed.) 283s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 283s Unpacking libaec0:arm64 (1.1.2-1) ... 283s Selecting previously unselected package libsz2:arm64. 283s Preparing to unpack .../01-libsz2_1.1.2-1_arm64.deb ... 283s Unpacking libsz2:arm64 (1.1.2-1) ... 283s Selecting previously unselected package libhdf5-103-1:arm64. 283s Preparing to unpack .../02-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 283s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 283s Selecting previously unselected package libhdf5-cpp-103-1:arm64. 283s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 283s Unpacking libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 283s Selecting previously unselected package libdeflate0:arm64. 283s Preparing to unpack .../04-libdeflate0_1.19-1_arm64.deb ... 283s Unpacking libdeflate0:arm64 (1.19-1) ... 283s Selecting previously unselected package libhtscodecs2:arm64. 283s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 283s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 283s Selecting previously unselected package libhts3:arm64. 283s Preparing to unpack .../06-libhts3_1.18+ds-1_arm64.deb ... 283s Unpacking libhts3:arm64 (1.18+ds-1) ... 283s Selecting previously unselected package libpbcopper2.3.0:arm64. 283s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_arm64.deb ... 283s Unpacking libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 283s Selecting previously unselected package libpbbam2.4.0:arm64. 283s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_arm64.deb ... 283s Unpacking libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 283s Selecting previously unselected package libblasr5.3.5:arm64. 283s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_arm64.deb ... 283s Unpacking libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 283s Selecting previously unselected package libpbseq:arm64. 283s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_arm64.deb ... 283s Unpacking libpbseq:arm64 (5.3.5+dfsg-6build3) ... 283s Selecting previously unselected package blasr. 283s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_arm64.deb ... 283s Unpacking blasr (5.3.5+dfsg-6build4) ... 283s Selecting previously unselected package libblas3:arm64. 283s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 283s Unpacking libblas3:arm64 (3.12.0-3) ... 283s Selecting previously unselected package libgfortran5:arm64. 283s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 283s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 283s Selecting previously unselected package libhdf5-hl-100:arm64. 283s Preparing to unpack .../14-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 283s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 283s Selecting previously unselected package liblapack3:arm64. 283s Preparing to unpack .../15-liblapack3_3.12.0-3_arm64.deb ... 283s Unpacking liblapack3:arm64 (3.12.0-3) ... 283s Selecting previously unselected package liblzf1:arm64. 283s Preparing to unpack .../16-liblzf1_3.6-4_arm64.deb ... 283s Unpacking liblzf1:arm64 (3.6-4) ... 284s Selecting previously unselected package pbdagcon. 284s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_arm64.deb ... 284s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 284s Selecting previously unselected package python3-pysam. 284s Preparing to unpack .../18-python3-pysam_0.22.0+ds-1_arm64.deb ... 284s Unpacking python3-pysam (0.22.0+ds-1) ... 284s Selecting previously unselected package python3-pbsuite-utils. 284s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 284s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 284s Selecting previously unselected package python3-networkx. 284s Preparing to unpack .../20-python3-networkx_2.8.8-1ubuntu1_all.deb ... 284s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 284s Selecting previously unselected package pbjelly. 284s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-7_all.deb ... 284s Unpacking pbjelly (15.8.24+dfsg-7) ... 284s Selecting previously unselected package python3-pbbanana. 284s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 284s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 284s Selecting previously unselected package python3-numpy. 284s Preparing to unpack .../23-python3-numpy_1%3a1.24.2-2_arm64.deb ... 284s Unpacking python3-numpy (1:1.24.2-2) ... 284s Selecting previously unselected package python3-h5py-serial. 284s Preparing to unpack .../24-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 284s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 284s Selecting previously unselected package python3-h5py. 284s Preparing to unpack .../25-python3-h5py_3.10.0-1ubuntu1_all.deb ... 284s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 284s Selecting previously unselected package python3-sortedcontainers. 285s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 285s Unpacking python3-sortedcontainers (2.4.0-2) ... 285s Selecting previously unselected package python3-intervaltree. 285s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 285s Unpacking python3-intervaltree (3.0.2-1.1) ... 285s Selecting previously unselected package python3-intervaltree-bio. 285s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 285s Unpacking python3-intervaltree-bio (1.0.1-4) ... 285s Selecting previously unselected package samtools. 285s Preparing to unpack .../29-samtools_1.19.2-1_arm64.deb ... 285s Unpacking samtools (1.19.2-1) ... 285s Selecting previously unselected package pbhoney. 285s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-7_all.deb ... 285s Unpacking pbhoney (15.8.24+dfsg-7) ... 285s Selecting previously unselected package autopkgtest-satdep. 285s Preparing to unpack .../31-1-autopkgtest-satdep.deb ... 285s Unpacking autopkgtest-satdep (0) ... 285s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 285s Setting up libdeflate0:arm64 (1.19-1) ... 285s Setting up python3-sortedcontainers (2.4.0-2) ... 285s Setting up python3-networkx (2.8.8-1ubuntu1) ... 286s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 286s "graph [edge [ source u'u\4200' target u'u\4200' ] " 286s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 286s + "node [ id u'u\4200' label b ] ]" 286s Setting up libaec0:arm64 (1.1.2-1) ... 286s Setting up libblas3:arm64 (3.12.0-3) ... 286s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 286s Setting up liblzf1:arm64 (3.6-4) ... 286s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 286s Setting up libsz2:arm64 (1.1.2-1) ... 286s Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 286s Setting up liblapack3:arm64 (3.12.0-3) ... 286s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 286s Setting up libhts3:arm64 (1.18+ds-1) ... 286s Setting up python3-pysam (0.22.0+ds-1) ... 286s Setting up python3-intervaltree (3.0.2-1.1) ... 286s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 286s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 286s for i in re.findall("\d+|\^?[ATCGN]+", md): 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 286s splRE = re.compile("\s+") 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 286s splRE = re.compile("\s+") 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 286s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 286s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 286s data = re.split("\s+",line) 286s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 286s data = re.split("\s+",line) 286s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 286s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 286s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 286s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 286s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 286s '\s*Type\s*=\s*(?P\w+)\s*,)?' 286s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 286s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 286s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 286s regex = re.compile("ref\d{7}") 286s Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 286s Setting up samtools (1.19.2-1) ... 286s Setting up python3-numpy (1:1.24.2-2) ... 288s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 288s Setting up libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 288s Setting up python3-intervaltree-bio (1.0.1-4) ... 288s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 288s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 288s Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 288s Setting up python3-h5py (3.10.0-1ubuntu1) ... 288s Setting up libpbseq:arm64 (5.3.5+dfsg-6build3) ... 288s Setting up blasr (5.3.5+dfsg-6build4) ... 288s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 288s Setting up pbjelly (15.8.24+dfsg-7) ... 288s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 288s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 288s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 288s splRE = re.compile("\s+") 288s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 288s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 288s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 288s nprocRe = re.compile("--nproc (\d+)") 288s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 288s """ 288s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 288s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 288s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 289s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 289s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 289s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 289s data = re.split("\s+",line) 289s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 289s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 289s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 289s data = re.split("\s+",line) 289s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 289s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 289s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 289s getContigName = re.compile("(\d+)_contig") 289s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 289s "awk -F\ '{{if ($1 < 500) print $2}}' | " 289s Setting up pbhoney (15.8.24+dfsg-7) ... 289s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 289s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 289s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 289s """ 289s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 289s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 289s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 289s for i in re.findall("\d+|\^?[ATCGN]+", md): 289s Setting up autopkgtest-satdep (0) ... 289s Processing triggers for man-db (2.12.0-3) ... 289s Processing triggers for libc-bin (2.39-0ubuntu6) ... 293s (Reading database ... 78198 files and directories currently installed.) 293s Removing autopkgtest-satdep (0) ... 293s autopkgtest [17:08:14]: test pbhoney: [----------------------- 293s PIEMapping 294s 294s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 294s Reid. "PBHoney: identyfying genomic variants via 294s long-read discordance and interrupted mapping." 294s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 294s doi:10.1186/1471-2105-15-180 294s 294s 2024-03-24 17:08:15,081 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 294s 2024-03-24 17:08:15,081 [INFO] Running Blasr 325s 2024-03-24 17:08:46,333 [INFO] [0, b'[INFO] 2024-03-24T17:08:15 [blasr] started.\n[INFO] 2024-03-24T17:08:46 [blasr] ended.\n', None] 325s 2024-03-24 17:08:46,333 [INFO] Mapping Tails 325s 2024-03-24 17:08:46,334 [INFO] Extracting tails 325s 2024-03-24 17:08:46,523 [INFO] Parsed 433 reads 325s 2024-03-24 17:08:46,523 [INFO] Found 278 tails 325s 2024-03-24 17:08:46,524 [INFO] 21 reads had double tails 325s 2024-03-24 17:08:46,524 [INFO] Running Blasr 331s 2024-03-24 17:08:52,934 [INFO] [0, b'[INFO] 2024-03-24T17:08:46 [blasr] started.\n[INFO] 2024-03-24T17:08:52 [blasr] ended.\n', None] 331s 2024-03-24 17:08:52,935 [INFO] Consolidating alignments 331s 2024-03-24 17:08:52,955 [INFO] 172 tails mapped 332s Sam To Bam 332s Calling Tails 332s 332s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 332s Reid. "PBHoney: identyfying genomic variants via 332s long-read discordance and interrupted mapping." 332s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 332s doi:10.1186/1471-2105-15-180 332s 332s 2024-03-24 17:08:53,388 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 332s 2024-03-24 17:08:53,388 [INFO] Parsing lambda_NEB3011 332s 2024-03-24 17:08:53,408 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 332s 2024-03-24 17:08:53,418 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 332s 2024-03-24 17:08:53,419 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 332s 2024-03-24 17:08:53,419 [INFO] Finished 332s Calling Spots 332s 332s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 332s Reid. "PBHoney: identyfying genomic variants via 332s long-read discordance and interrupted mapping." 332s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 332s doi:10.1186/1471-2105-15-180 332s 332s 2024-03-24 17:08:53,685 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 332s 2024-03-24 17:08:53,696 [INFO] Starting lambda_NEB3011:ErrorCounter 332s 2024-03-24 17:08:53,704 [INFO] 605 reads to parse in lambda_NEB3011 332s 2024-03-24 17:08:53,707 [INFO] 5% complete 332s 2024-03-24 17:08:53,708 [INFO] 10% complete 332s 2024-03-24 17:08:53,711 [INFO] 15% complete 332s 2024-03-24 17:08:53,712 [INFO] 20% complete 332s 2024-03-24 17:08:53,713 [INFO] 25% complete 332s 2024-03-24 17:08:53,715 [INFO] 30% complete 332s 2024-03-24 17:08:53,717 [INFO] 35% complete 332s 2024-03-24 17:08:53,719 [INFO] 40% complete 332s 2024-03-24 17:08:53,719 [INFO] 45% complete 332s 2024-03-24 17:08:53,721 [INFO] 50% complete 332s 2024-03-24 17:08:53,722 [INFO] 55% complete 332s 2024-03-24 17:08:53,724 [INFO] 60% complete 332s 2024-03-24 17:08:53,726 [INFO] 65% complete 332s 2024-03-24 17:08:53,727 [INFO] 70% complete 332s 2024-03-24 17:08:53,728 [INFO] 75% complete 332s 2024-03-24 17:08:53,730 [INFO] 80% complete 332s 2024-03-24 17:08:53,732 [INFO] 85% complete 332s 2024-03-24 17:08:53,733 [INFO] 90% complete 332s 2024-03-24 17:08:53,734 [INFO] 95% complete 332s 2024-03-24 17:08:53,748 [INFO] lambda_NEB3011:ErrorCounter -> spot 332s 2024-03-24 17:08:53,749 [INFO] Starting lambda_NEB3011:SpotCaller 332s 2024-03-24 17:08:53,758 [INFO] |lambda_NEB3011:SpotCaller|COV processing 332s 2024-03-24 17:08:53,758 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 332s 2024-03-24 17:08:53,758 [INFO] |lambda_NEB3011:SpotCaller|INS processing 332s 2024-03-24 17:08:53,762 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 332s 2024-03-24 17:08:53,762 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 332s 2024-03-24 17:08:53,765 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 332s 2024-03-24 17:08:53,767 [INFO] Finished 332s 2024-03-24 17:08:53,768 [INFO] Thread Consumer-1: Exiting 333s autopkgtest [17:08:54]: test pbhoney: -----------------------] 333s autopkgtest [17:08:54]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 333s pbhoney PASS 333s autopkgtest [17:08:54]: @@@@@@@@@@@@@@@@@@@@ summary 333s pbhoney PASS 346s Creating nova instance adt-noble-arm64-pbsuite-20240324-170321-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...