0s autopkgtest [18:08:57]: starting date and time: 2024-03-24 18:08:57+0000 0s autopkgtest [18:08:57]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:08:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sxey1eyo/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:samtools,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=samtools/1.19.2-1build1 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-arm64-13.secgroup --name adt-noble-arm64-pbsuite-20240324-173821-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/ 129s autopkgtest [18:11:06]: testbed dpkg architecture: arm64 130s autopkgtest [18:11:07]: testbed apt version: 2.7.12 130s autopkgtest [18:11:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 131s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 131s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 131s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 132s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 132s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 132s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 132s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 132s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 132s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 132s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 132s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 132s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 132s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 138s Fetched 9851 kB in 3s (3335 kB/s) 138s Reading package lists... 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s Calculating upgrade... 145s The following packages will be REMOVED: 145s libssl3 145s The following NEW packages will be installed: 145s libssl3t64 145s The following packages have been kept back: 145s curl 145s The following packages will be upgraded: 145s openssl 145s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 145s Need to get 2777 kB of archives. 145s After this operation, 139 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 146s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 146s Fetched 2777 kB in 1s (3907 kB/s) 147s (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.) 147s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 147s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 147s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 147s wget depends on libssl3 (>= 3.0.0). 147s u-boot-tools depends on libssl3 (>= 3.0.0). 147s tnftp depends on libssl3 (>= 3.0.0). 147s tcpdump depends on libssl3 (>= 3.0.0). 147s systemd-resolved depends on libssl3 (>= 3.0.0). 147s systemd depends on libssl3 (>= 3.0.0). 147s sudo depends on libssl3 (>= 3.0.0). 147s sbsigntool depends on libssl3 (>= 3.0.0). 147s rsync depends on libssl3 (>= 3.0.0). 147s python3-cryptography depends on libssl3 (>= 3.0.0). 147s openssh-server depends on libssl3 (>= 3.0.10). 147s openssh-client depends on libssl3 (>= 3.0.10). 147s mtd-utils depends on libssl3 (>= 3.0.0). 147s mokutil depends on libssl3 (>= 3.0.0). 147s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 147s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 147s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 147s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 147s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 147s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 147s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 147s libnvme1 depends on libssl3 (>= 3.0.0). 147s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 147s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 147s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 147s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 147s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 147s kmod depends on libssl3 (>= 3.0.0). 147s dhcpcd-base depends on libssl3 (>= 3.0.0). 147s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 147s 147s (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.) 147s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 147s Selecting previously unselected package libssl3t64:arm64. 147s (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.) 147s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 147s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 147s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 147s Setting up openssl (3.0.13-0ubuntu2) ... 147s Processing triggers for man-db (2.12.0-3) ... 148s Processing triggers for libc-bin (2.39-0ubuntu6) ... 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 152s sh: Attempting to set up Debian/Ubuntu apt sources automatically 152s sh: Distribution appears to be Ubuntu 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s eatmydata is already the newest version (131-1). 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 157s dbus is already the newest version (1.14.10-4ubuntu1). 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 167s rng-tools-debian is already the newest version (2.4). 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s The following packages will be REMOVED: 167s cloud-init* python3-configobj* python3-debconf* 167s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 167s After this operation, 3256 kB disk space will be freed. 167s (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.) 167s Removing cloud-init (24.1.2-0ubuntu1) ... 167s Removing python3-configobj (5.0.8-3) ... 167s Removing python3-debconf (1.5.86) ... 167s Processing triggers for man-db (2.12.0-3) ... 167s (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.) 167s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 167s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 167s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 167s invoke-rc.d: policy-rc.d denied execution of try-restart. 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s linux-generic is already the newest version (6.8.0-11.11+1). 167s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 167s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 167s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 172s Reading package lists... 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade... 175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s autopkgtest [18:11:54]: rebooting testbed after setup commands that affected boot 332s autopkgtest [18:14:29]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 335s autopkgtest [18:14:32]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 341s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 341s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 341s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 341s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 341s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 341s gpgv: issuer "npatra974@gmail.com" 341s gpgv: Can't check signature: No public key 341s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 341s autopkgtest [18:14:38]: testing package pbsuite version 15.8.24+dfsg-7 342s autopkgtest [18:14:39]: build not needed 343s autopkgtest [18:14:40]: test pbhoney: preparing testbed 350s Reading package lists... 350s Building dependency tree... 350s Reading state information... 351s Starting pkgProblemResolver with broken count: 0 351s Starting 2 pkgProblemResolver with broken count: 0 351s Done 352s The following additional packages will be installed: 352s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 libhdf5-103-1 352s libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 liblapack3 liblzf1 352s libpbbam2.4.0 libpbcopper2.3.0 libpbseq libsz2 pbdagcon pbhoney pbjelly 352s python3-h5py python3-h5py-serial python3-intervaltree 352s python3-intervaltree-bio python3-networkx python3-numpy python3-pbbanana 352s python3-pbsuite-utils python3-pysam python3-sortedcontainers samtools 352s Suggested packages: 352s python-h5py-doc python-networkx-doc python3-gdal python3-matplotlib 352s python3-pydot python3-pygraphviz python3-scipy gcc gfortran python3-dev 352s python3-pytest python-sortedcontainers-doc cwltool 352s The following NEW packages will be installed: 352s autopkgtest-satdep blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 352s libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 352s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 352s libsz2 pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 352s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 352s python3-pbbanana python3-pbsuite-utils python3-pysam 352s python3-sortedcontainers samtools 352s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 352s Need to get 22.6 MB/22.6 MB of archives. 352s After this operation, 124 MB of additional disk space will be used. 352s Get:1 /tmp/autopkgtest.AKH7vQ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 353s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 353s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 353s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 353s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-cpp-103-1 arm64 1.10.10+repack-3ubuntu1 [120 kB] 353s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 353s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 353s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 353s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2 [516 kB] 353s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbbam2.4.0 arm64 2.4.0+dfsg-1build1 [634 kB] 353s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-6build3 [1207 kB] 353s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbseq arm64 5.3.5+dfsg-6build3 [3068 B] 353s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 blasr arm64 5.3.5+dfsg-6build4 [212 kB] 353s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 353s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 353s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 353s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 353s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 353s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 pbdagcon arm64 0.3+git20180411.c14c422+dfsg-8build3 [252 kB] 353s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 353s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 353s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 353s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 pbjelly all 15.8.24+dfsg-7 [966 kB] 353s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 353s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 354s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 354s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 354s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 354s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 354s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 354s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 354s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 pbhoney all 15.8.24+dfsg-7 [1051 kB] 354s Fetched 22.6 MB in 1s (18.4 MB/s) 355s Selecting previously unselected package libaec0:arm64. 355s (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.) 355s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 355s Unpacking libaec0:arm64 (1.1.2-1) ... 355s Selecting previously unselected package libsz2:arm64. 355s Preparing to unpack .../01-libsz2_1.1.2-1_arm64.deb ... 355s Unpacking libsz2:arm64 (1.1.2-1) ... 355s Selecting previously unselected package libhdf5-103-1:arm64. 355s Preparing to unpack .../02-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 355s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 355s Selecting previously unselected package libhdf5-cpp-103-1:arm64. 355s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 355s Unpacking libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 355s Selecting previously unselected package libdeflate0:arm64. 355s Preparing to unpack .../04-libdeflate0_1.19-1_arm64.deb ... 355s Unpacking libdeflate0:arm64 (1.19-1) ... 355s Selecting previously unselected package libhtscodecs2:arm64. 355s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 355s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 355s Selecting previously unselected package libhts3:arm64. 355s Preparing to unpack .../06-libhts3_1.18+ds-1_arm64.deb ... 355s Unpacking libhts3:arm64 (1.18+ds-1) ... 355s Selecting previously unselected package libpbcopper2.3.0:arm64. 355s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_arm64.deb ... 355s Unpacking libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 355s Selecting previously unselected package libpbbam2.4.0:arm64. 355s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_arm64.deb ... 355s Unpacking libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 355s Selecting previously unselected package libblasr5.3.5:arm64. 355s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_arm64.deb ... 355s Unpacking libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 355s Selecting previously unselected package libpbseq:arm64. 355s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_arm64.deb ... 355s Unpacking libpbseq:arm64 (5.3.5+dfsg-6build3) ... 355s Selecting previously unselected package blasr. 355s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_arm64.deb ... 355s Unpacking blasr (5.3.5+dfsg-6build4) ... 356s Selecting previously unselected package libblas3:arm64. 356s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 356s Unpacking libblas3:arm64 (3.12.0-3) ... 356s Selecting previously unselected package libgfortran5:arm64. 356s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 356s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 356s Selecting previously unselected package libhdf5-hl-100:arm64. 356s Preparing to unpack .../14-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 356s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 356s Selecting previously unselected package liblapack3:arm64. 356s Preparing to unpack .../15-liblapack3_3.12.0-3_arm64.deb ... 356s Unpacking liblapack3:arm64 (3.12.0-3) ... 356s Selecting previously unselected package liblzf1:arm64. 356s Preparing to unpack .../16-liblzf1_3.6-4_arm64.deb ... 356s Unpacking liblzf1:arm64 (3.6-4) ... 356s Selecting previously unselected package pbdagcon. 356s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_arm64.deb ... 356s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 356s Selecting previously unselected package python3-pysam. 356s Preparing to unpack .../18-python3-pysam_0.22.0+ds-1_arm64.deb ... 356s Unpacking python3-pysam (0.22.0+ds-1) ... 357s Selecting previously unselected package python3-pbsuite-utils. 357s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 357s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 357s Selecting previously unselected package python3-networkx. 357s Preparing to unpack .../20-python3-networkx_2.8.8-1ubuntu1_all.deb ... 357s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 357s Selecting previously unselected package pbjelly. 357s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-7_all.deb ... 357s Unpacking pbjelly (15.8.24+dfsg-7) ... 357s Selecting previously unselected package python3-pbbanana. 357s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 357s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 357s Selecting previously unselected package python3-numpy. 357s Preparing to unpack .../23-python3-numpy_1%3a1.24.2-2_arm64.deb ... 357s Unpacking python3-numpy (1:1.24.2-2) ... 358s Selecting previously unselected package python3-h5py-serial. 358s Preparing to unpack .../24-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 358s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 358s Selecting previously unselected package python3-h5py. 358s Preparing to unpack .../25-python3-h5py_3.10.0-1ubuntu1_all.deb ... 358s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 358s Selecting previously unselected package python3-sortedcontainers. 358s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 358s Unpacking python3-sortedcontainers (2.4.0-2) ... 358s Selecting previously unselected package python3-intervaltree. 358s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 358s Unpacking python3-intervaltree (3.0.2-1.1) ... 358s Selecting previously unselected package python3-intervaltree-bio. 358s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 358s Unpacking python3-intervaltree-bio (1.0.1-4) ... 358s Selecting previously unselected package samtools. 358s Preparing to unpack .../29-samtools_1.19.2-1_arm64.deb ... 358s Unpacking samtools (1.19.2-1) ... 358s Selecting previously unselected package pbhoney. 358s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-7_all.deb ... 358s Unpacking pbhoney (15.8.24+dfsg-7) ... 359s Selecting previously unselected package autopkgtest-satdep. 359s Preparing to unpack .../31-1-autopkgtest-satdep.deb ... 359s Unpacking autopkgtest-satdep (0) ... 359s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 359s Setting up libdeflate0:arm64 (1.19-1) ... 359s Setting up python3-sortedcontainers (2.4.0-2) ... 359s Setting up python3-networkx (2.8.8-1ubuntu1) ... 362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 362s "graph [edge [ source u'u\4200' target u'u\4200' ] " 362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 362s + "node [ id u'u\4200' label b ] ]" 362s Setting up libaec0:arm64 (1.1.2-1) ... 362s Setting up libblas3:arm64 (3.12.0-3) ... 362s 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 362s Setting up liblzf1:arm64 (3.6-4) ... 362s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 362s Setting up libsz2:arm64 (1.1.2-1) ... 362s Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 362s Setting up liblapack3:arm64 (3.12.0-3) ... 362s 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 362s Setting up libhts3:arm64 (1.18+ds-1) ... 362s Setting up python3-pysam (0.22.0+ds-1) ... 363s Setting up python3-intervaltree (3.0.2-1.1) ... 363s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 363s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 363s for i in re.findall("\d+|\^?[ATCGN]+", md): 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 363s splRE = re.compile("\s+") 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 363s splRE = re.compile("\s+") 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 363s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 363s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 363s data = re.split("\s+",line) 363s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 363s data = re.split("\s+",line) 363s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 363s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 363s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 363s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 363s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 363s '\s*Type\s*=\s*(?P\w+)\s*,)?' 363s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 363s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 363s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 363s regex = re.compile("ref\d{7}") 363s Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 363s Setting up samtools (1.19.2-1) ... 363s Setting up python3-numpy (1:1.24.2-2) ... 367s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 367s Setting up libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 367s Setting up python3-intervaltree-bio (1.0.1-4) ... 367s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 367s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 368s Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 368s Setting up python3-h5py (3.10.0-1ubuntu1) ... 368s Setting up libpbseq:arm64 (5.3.5+dfsg-6build3) ... 368s Setting up blasr (5.3.5+dfsg-6build4) ... 368s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 368s Setting up pbjelly (15.8.24+dfsg-7) ... 369s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 369s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 369s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 369s splRE = re.compile("\s+") 369s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 369s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 369s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 369s nprocRe = re.compile("--nproc (\d+)") 369s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 369s """ 369s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 369s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 369s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 369s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 369s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 369s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 369s data = re.split("\s+",line) 369s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 369s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 369s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 369s data = re.split("\s+",line) 369s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 369s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 369s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 369s getContigName = re.compile("(\d+)_contig") 369s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 369s "awk -F\ '{{if ($1 < 500) print $2}}' | " 369s Setting up pbhoney (15.8.24+dfsg-7) ... 369s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 369s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 369s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 369s """ 369s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 369s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 369s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 369s for i in re.findall("\d+|\^?[ATCGN]+", md): 370s Setting up autopkgtest-satdep (0) ... 370s Processing triggers for man-db (2.12.0-3) ... 370s Processing triggers for libc-bin (2.39-0ubuntu6) ... 377s (Reading database ... 78198 files and directories currently installed.) 377s Removing autopkgtest-satdep (0) ... 378s autopkgtest [18:15:15]: test pbhoney: [----------------------- 378s PIEMapping 378s 378s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 378s Reid. "PBHoney: identyfying genomic variants via 378s long-read discordance and interrupted mapping." 378s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 378s doi:10.1186/1471-2105-15-180 378s 378s 2024-03-24 18:15:15,978 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 378s 2024-03-24 18:15:15,979 [INFO] Running Blasr 428s 2024-03-24 18:16:05,095 [INFO] [0, b'[INFO] 2024-03-24T18:15:16 [blasr] started.\n[INFO] 2024-03-24T18:16:05 [blasr] ended.\n', None] 428s 2024-03-24 18:16:05,095 [INFO] Mapping Tails 428s 2024-03-24 18:16:05,096 [INFO] Extracting tails 428s 2024-03-24 18:16:05,504 [INFO] Parsed 433 reads 428s 2024-03-24 18:16:05,504 [INFO] Found 278 tails 428s 2024-03-24 18:16:05,505 [INFO] 21 reads had double tails 428s 2024-03-24 18:16:05,505 [INFO] Running Blasr 438s 2024-03-24 18:16:15,744 [INFO] [0, b'[INFO] 2024-03-24T18:16:05 [blasr] started.\n[INFO] 2024-03-24T18:16:15 [blasr] ended.\n', None] 438s 2024-03-24 18:16:15,744 [INFO] Consolidating alignments 438s 2024-03-24 18:16:15,810 [INFO] 172 tails mapped 439s Sam To Bam 439s Calling Tails 440s 440s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 440s Reid. "PBHoney: identyfying genomic variants via 440s long-read discordance and interrupted mapping." 440s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 440s doi:10.1186/1471-2105-15-180 440s 440s Calling Spots 440s 2024-03-24 18:16:16,841 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 440s 2024-03-24 18:16:16,842 [INFO] Parsing lambda_NEB3011 440s 2024-03-24 18:16:16,880 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 440s 2024-03-24 18:16:16,903 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 440s 2024-03-24 18:16:16,906 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 440s 2024-03-24 18:16:16,907 [INFO] Finished 440s 440s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 440s Reid. "PBHoney: identyfying genomic variants via 440s long-read discordance and interrupted mapping." 440s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 440s doi:10.1186/1471-2105-15-180 440s 440s 2024-03-24 18:16:17,615 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 440s 2024-03-24 18:16:17,642 [INFO] Starting lambda_NEB3011:ErrorCounter 440s 2024-03-24 18:16:17,656 [INFO] 605 reads to parse in lambda_NEB3011 440s 2024-03-24 18:16:17,663 [INFO] 5% complete 440s 2024-03-24 18:16:17,665 [INFO] 10% complete 440s 2024-03-24 18:16:17,672 [INFO] 15% complete 440s 2024-03-24 18:16:17,676 [INFO] 20% complete 440s 2024-03-24 18:16:17,679 [INFO] 25% complete 440s 2024-03-24 18:16:17,683 [INFO] 30% complete 440s 2024-03-24 18:16:17,689 [INFO] 35% complete 440s 2024-03-24 18:16:17,694 [INFO] 40% complete 440s 2024-03-24 18:16:17,696 [INFO] 45% complete 440s 2024-03-24 18:16:17,701 [INFO] 50% complete 440s 2024-03-24 18:16:17,704 [INFO] 55% complete 440s 2024-03-24 18:16:17,709 [INFO] 60% complete 440s 2024-03-24 18:16:17,713 [INFO] 65% complete 440s 2024-03-24 18:16:17,716 [INFO] 70% complete 440s 2024-03-24 18:16:17,719 [INFO] 75% complete 440s 2024-03-24 18:16:17,724 [INFO] 80% complete 440s 2024-03-24 18:16:17,728 [INFO] 85% complete 440s 2024-03-24 18:16:17,732 [INFO] 90% complete 440s 2024-03-24 18:16:17,735 [INFO] 95% complete 440s 2024-03-24 18:16:17,766 [INFO] lambda_NEB3011:ErrorCounter -> spot 440s 2024-03-24 18:16:17,767 [INFO] Starting lambda_NEB3011:SpotCaller 440s 2024-03-24 18:16:17,784 [INFO] |lambda_NEB3011:SpotCaller|COV processing 440s 2024-03-24 18:16:17,784 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 440s 2024-03-24 18:16:17,785 [INFO] |lambda_NEB3011:SpotCaller|INS processing 440s 2024-03-24 18:16:17,793 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 440s 2024-03-24 18:16:17,794 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 440s 2024-03-24 18:16:17,803 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 440s 2024-03-24 18:16:17,808 [INFO] Thread Consumer-1: Exiting 440s 2024-03-24 18:16:17,807 [INFO] Finished 441s autopkgtest [18:16:18]: test pbhoney: -----------------------] 441s pbhoney PASS 441s autopkgtest [18:16:18]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 442s autopkgtest [18:16:19]: @@@@@@@@@@@@@@@@@@@@ summary 442s pbhoney PASS 462s Creating nova instance adt-noble-arm64-pbsuite-20240324-173821-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...