0s autopkgtest [15:24:47]: starting date and time: 2024-03-23 15:24:47+0000 0s autopkgtest [15:24:47]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:24:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bwbhx4q5/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@bos02-ppc64el-8.secgroup --name adt-noble-ppc64el-pbsuite-20240323-152446-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 403s autopkgtest [15:31:30]: testbed dpkg architecture: ppc64el 403s autopkgtest [15:31:30]: testbed apt version: 2.7.12 403s autopkgtest [15:31:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 404s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 404s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 404s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 404s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 405s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 405s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 405s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 405s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 405s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 405s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 405s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 405s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 405s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 409s Fetched 9623 kB in 2s (3855 kB/s) 409s Reading package lists... 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 412s Calculating upgrade... 412s The following packages will be REMOVED: 412s libssl3 412s The following NEW packages will be installed: 412s libssl3t64 412s The following packages have been kept back: 412s curl 412s The following packages will be upgraded: 412s openssl 412s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 412s Need to get 3151 kB of archives. 412s After this operation, 73.7 kB of additional disk space will be used. 412s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 413s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 413s Fetched 3151 kB in 1s (3880 kB/s) 414s (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 ... 70156 files and directories currently installed.) 414s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 414s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 414s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 414s wget depends on libssl3 (>= 3.0.0). 414s tnftp depends on libssl3 (>= 3.0.0). 414s tcpdump depends on libssl3 (>= 3.0.0). 414s systemd-resolved depends on libssl3 (>= 3.0.0). 414s systemd depends on libssl3 (>= 3.0.0). 414s sudo depends on libssl3 (>= 3.0.0). 414s rsync depends on libssl3 (>= 3.0.0). 414s python3-cryptography depends on libssl3 (>= 3.0.0). 414s openssh-server depends on libssl3 (>= 3.0.10). 414s openssh-client depends on libssl3 (>= 3.0.10). 414s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 414s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 414s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 414s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 414s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 414s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 414s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 414s libnvme1 depends on libssl3 (>= 3.0.0). 414s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 414s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 414s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 414s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 414s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 414s kmod depends on libssl3 (>= 3.0.0). 414s dhcpcd-base depends on libssl3 (>= 3.0.0). 414s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 414s 414s (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 ... 70156 files and directories currently installed.) 414s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 414s Selecting previously unselected package libssl3t64:ppc64el. 414s (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 ... 70145 files and directories currently installed.) 414s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 414s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 414s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 414s Setting up openssl (3.0.13-0ubuntu2) ... 414s Processing triggers for man-db (2.12.0-3) ... 415s Processing triggers for libc-bin (2.39-0ubuntu6) ... 415s Reading package lists... 415s Building dependency tree... 415s Reading state information... 415s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 416s sh: Attempting to set up Debian/Ubuntu apt sources automatically 416s sh: Distribution appears to be Ubuntu 417s Reading package lists... 417s Building dependency tree... 417s Reading state information... 417s eatmydata is already the newest version (131-1). 417s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 417s Reading package lists... 417s Building dependency tree... 417s Reading state information... 418s dbus is already the newest version (1.14.10-4ubuntu1). 418s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 418s Reading package lists... 418s Building dependency tree... 418s Reading state information... 418s rng-tools-debian is already the newest version (2.4). 418s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 418s Reading package lists... 418s Building dependency tree... 418s Reading state information... 419s The following packages will be REMOVED: 419s cloud-init* python3-configobj* python3-debconf* 419s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 419s After this operation, 3256 kB disk space will be freed. 419s (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 ... 70158 files and directories currently installed.) 419s Removing cloud-init (24.1.2-0ubuntu1) ... 419s Removing python3-configobj (5.0.8-3) ... 419s Removing python3-debconf (1.5.86) ... 420s Processing triggers for man-db (2.12.0-3) ... 420s (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 ... 69769 files and directories currently installed.) 420s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 421s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 421s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 421s invoke-rc.d: policy-rc.d denied execution of try-restart. 421s Reading package lists... 421s Building dependency tree... 421s Reading state information... 421s linux-generic is already the newest version (6.8.0-11.11+1). 421s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 422s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 422s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 422s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 424s Reading package lists... 424s Reading package lists... 425s Building dependency tree... 425s Reading state information... 425s Calculating upgrade... 425s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 425s Reading package lists... 425s Building dependency tree... 425s Reading state information... 425s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 426s autopkgtest [15:31:53]: rebooting testbed after setup commands that affected boot 594s autopkgtest [15:34:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 597s autopkgtest [15:34:44]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 601s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 601s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 601s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 601s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 601s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 601s gpgv: issuer "npatra974@gmail.com" 601s gpgv: Can't check signature: No public key 601s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 602s autopkgtest [15:34:49]: testing package pbsuite version 15.8.24+dfsg-7 602s autopkgtest [15:34:49]: build not needed 604s autopkgtest [15:34:51]: test pbhoney: preparing testbed 605s Reading package lists... 606s Building dependency tree... 606s Reading state information... 606s Starting pkgProblemResolver with broken count: 0 606s Starting 2 pkgProblemResolver with broken count: 0 606s Done 606s The following additional packages will be installed: 606s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 libhdf5-103-1 606s libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 liblapack3 liblzf1 606s libpbbam2.4.0 libpbcopper2.3.0 libpbseq libsz2 pbdagcon pbhoney pbjelly 606s python3-h5py python3-h5py-serial python3-intervaltree 606s python3-intervaltree-bio python3-networkx python3-numpy python3-pbbanana 606s python3-pbsuite-utils python3-pysam python3-sortedcontainers samtools 606s Suggested packages: 606s python-h5py-doc python-networkx-doc python3-gdal python3-matplotlib 606s python3-pydot python3-pygraphviz python3-scipy gcc gfortran python3-dev 606s python3-pytest python-sortedcontainers-doc cwltool 606s The following NEW packages will be installed: 606s autopkgtest-satdep blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 606s libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 606s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 606s libsz2 pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 606s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 606s python3-pbbanana python3-pbsuite-utils python3-pysam 606s python3-sortedcontainers samtools 606s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 606s Need to get 26.1 MB/26.1 MB of archives. 606s After this operation, 146 MB of additional disk space will be used. 606s Get:1 /tmp/autopkgtest.DuvEdI/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 606s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 606s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 606s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 607s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-cpp-103-1 ppc64el 1.10.10+repack-3ubuntu1 [129 kB] 607s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 607s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 607s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 607s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbcopper2.3.0 ppc64el 2.3.0+dfsg-2 [594 kB] 607s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbbam2.4.0 ppc64el 2.4.0+dfsg-1build1 [751 kB] 607s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libblasr5.3.5 ppc64el 5.3.5+dfsg-6build3 [1255 kB] 607s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbseq ppc64el 5.3.5+dfsg-6build3 [3068 B] 607s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el blasr ppc64el 5.3.5+dfsg-6build4 [264 kB] 607s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 607s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 607s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 607s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 607s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 607s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbdagcon ppc64el 0.3+git20180411.c14c422+dfsg-8build3 [279 kB] 607s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 607s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 607s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 607s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbjelly all 15.8.24+dfsg-7 [966 kB] 607s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 607s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 607s Get:26 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 607s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 607s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB] 607s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-intervaltree all 3.0.2-1.1 [22.4 kB] 607s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-intervaltree-bio all 1.0.1-4 [8260 B] 607s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 608s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbhoney all 15.8.24+dfsg-7 [1051 kB] 608s Fetched 26.1 MB in 1s (19.1 MB/s) 608s Selecting previously unselected package libaec0:ppc64el. 608s (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 ... 69714 files and directories currently installed.) 608s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 608s Unpacking libaec0:ppc64el (1.1.2-1) ... 608s Selecting previously unselected package libsz2:ppc64el. 608s Preparing to unpack .../01-libsz2_1.1.2-1_ppc64el.deb ... 608s Unpacking libsz2:ppc64el (1.1.2-1) ... 608s Selecting previously unselected package libhdf5-103-1:ppc64el. 608s Preparing to unpack .../02-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 608s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 608s Selecting previously unselected package libhdf5-cpp-103-1:ppc64el. 608s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 608s Unpacking libhdf5-cpp-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 608s Selecting previously unselected package libdeflate0:ppc64el. 608s Preparing to unpack .../04-libdeflate0_1.19-1_ppc64el.deb ... 608s Unpacking libdeflate0:ppc64el (1.19-1) ... 608s Selecting previously unselected package libhtscodecs2:ppc64el. 608s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_ppc64el.deb ... 608s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 608s Selecting previously unselected package libhts3:ppc64el. 608s Preparing to unpack .../06-libhts3_1.18+ds-1_ppc64el.deb ... 608s Unpacking libhts3:ppc64el (1.18+ds-1) ... 608s Selecting previously unselected package libpbcopper2.3.0:ppc64el. 608s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_ppc64el.deb ... 608s Unpacking libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 608s Selecting previously unselected package libpbbam2.4.0:ppc64el. 608s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_ppc64el.deb ... 608s Unpacking libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build1) ... 608s Selecting previously unselected package libblasr5.3.5:ppc64el. 608s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_ppc64el.deb ... 608s Unpacking libblasr5.3.5:ppc64el (5.3.5+dfsg-6build3) ... 608s Selecting previously unselected package libpbseq:ppc64el. 608s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_ppc64el.deb ... 608s Unpacking libpbseq:ppc64el (5.3.5+dfsg-6build3) ... 608s Selecting previously unselected package blasr. 608s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_ppc64el.deb ... 608s Unpacking blasr (5.3.5+dfsg-6build4) ... 608s Selecting previously unselected package libblas3:ppc64el. 608s Preparing to unpack .../12-libblas3_3.12.0-3_ppc64el.deb ... 608s Unpacking libblas3:ppc64el (3.12.0-3) ... 608s Selecting previously unselected package libgfortran5:ppc64el. 608s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 608s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 608s Selecting previously unselected package libhdf5-hl-100:ppc64el. 608s Preparing to unpack .../14-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 608s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 608s Selecting previously unselected package liblapack3:ppc64el. 608s Preparing to unpack .../15-liblapack3_3.12.0-3_ppc64el.deb ... 608s Unpacking liblapack3:ppc64el (3.12.0-3) ... 608s Selecting previously unselected package liblzf1:ppc64el. 608s Preparing to unpack .../16-liblzf1_3.6-4_ppc64el.deb ... 608s Unpacking liblzf1:ppc64el (3.6-4) ... 608s Selecting previously unselected package pbdagcon. 608s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_ppc64el.deb ... 608s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 609s Selecting previously unselected package python3-pysam. 609s Preparing to unpack .../18-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 609s Unpacking python3-pysam (0.22.0+ds-1) ... 609s Selecting previously unselected package python3-pbsuite-utils. 609s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 609s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 609s Selecting previously unselected package python3-networkx. 609s Preparing to unpack .../20-python3-networkx_2.8.8-1ubuntu1_all.deb ... 609s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 609s Selecting previously unselected package pbjelly. 609s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-7_all.deb ... 609s Unpacking pbjelly (15.8.24+dfsg-7) ... 609s Selecting previously unselected package python3-pbbanana. 609s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 609s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 609s Selecting previously unselected package python3-numpy. 609s Preparing to unpack .../23-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 609s Unpacking python3-numpy (1:1.24.2-2) ... 610s Selecting previously unselected package python3-h5py-serial. 610s Preparing to unpack .../24-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 610s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 610s Selecting previously unselected package python3-h5py. 610s Preparing to unpack .../25-python3-h5py_3.10.0-1ubuntu1_all.deb ... 610s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 610s Selecting previously unselected package python3-sortedcontainers. 610s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 610s Unpacking python3-sortedcontainers (2.4.0-2) ... 610s Selecting previously unselected package python3-intervaltree. 610s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 610s Unpacking python3-intervaltree (3.0.2-1.1) ... 610s Selecting previously unselected package python3-intervaltree-bio. 610s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 610s Unpacking python3-intervaltree-bio (1.0.1-4) ... 610s Selecting previously unselected package samtools. 610s Preparing to unpack .../29-samtools_1.19.2-1_ppc64el.deb ... 610s Unpacking samtools (1.19.2-1) ... 610s Selecting previously unselected package pbhoney. 610s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-7_all.deb ... 610s Unpacking pbhoney (15.8.24+dfsg-7) ... 610s Selecting previously unselected package autopkgtest-satdep. 610s Preparing to unpack .../31-1-autopkgtest-satdep.deb ... 610s Unpacking autopkgtest-satdep (0) ... 610s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 610s Setting up libdeflate0:ppc64el (1.19-1) ... 610s Setting up python3-sortedcontainers (2.4.0-2) ... 610s Setting up python3-networkx (2.8.8-1ubuntu1) ... 611s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 611s "graph [edge [ source u'u\4200' target u'u\4200' ] " 611s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 611s + "node [ id u'u\4200' label b ] ]" 612s Setting up libaec0:ppc64el (1.1.2-1) ... 612s Setting up libblas3:ppc64el (3.12.0-3) ... 612s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 612s Setting up liblzf1:ppc64el (3.6-4) ... 612s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 612s Setting up libsz2:ppc64el (1.1.2-1) ... 612s Setting up libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 612s Setting up liblapack3:ppc64el (3.12.0-3) ... 612s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 612s Setting up libhts3:ppc64el (1.18+ds-1) ... 612s Setting up python3-pysam (0.22.0+ds-1) ... 612s Setting up python3-intervaltree (3.0.2-1.1) ... 612s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 612s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 612s for i in re.findall("\d+|\^?[ATCGN]+", md): 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 612s splRE = re.compile("\s+") 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 612s splRE = re.compile("\s+") 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 612s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 612s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 612s data = re.split("\s+",line) 612s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 612s data = re.split("\s+",line) 612s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 612s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 612s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 612s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 612s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 612s '\s*Type\s*=\s*(?P\w+)\s*,)?' 612s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 612s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 612s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 612s regex = re.compile("ref\d{7}") 612s Setting up libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build1) ... 612s Setting up samtools (1.19.2-1) ... 612s Setting up python3-numpy (1:1.24.2-2) ... 614s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 614s Setting up libhdf5-cpp-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 614s Setting up python3-intervaltree-bio (1.0.1-4) ... 614s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 614s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 615s Setting up libblasr5.3.5:ppc64el (5.3.5+dfsg-6build3) ... 615s Setting up python3-h5py (3.10.0-1ubuntu1) ... 615s Setting up libpbseq:ppc64el (5.3.5+dfsg-6build3) ... 615s Setting up blasr (5.3.5+dfsg-6build4) ... 615s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 615s Setting up pbjelly (15.8.24+dfsg-7) ... 615s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 615s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 615s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 615s splRE = re.compile("\s+") 615s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 615s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 615s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 615s nprocRe = re.compile("--nproc (\d+)") 615s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 615s """ 615s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 615s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 615s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 615s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 615s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 615s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 615s data = re.split("\s+",line) 615s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 615s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 615s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 615s data = re.split("\s+",line) 615s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 615s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 615s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 615s getContigName = re.compile("(\d+)_contig") 615s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 615s "awk -F\ '{{if ($1 < 500) print $2}}' | " 615s Setting up pbhoney (15.8.24+dfsg-7) ... 615s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 615s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 615s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 615s """ 615s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 615s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 615s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 615s for i in re.findall("\d+|\^?[ATCGN]+", md): 615s Setting up autopkgtest-satdep (0) ... 615s Processing triggers for man-db (2.12.0-3) ... 616s Processing triggers for libc-bin (2.39-0ubuntu6) ... 619s (Reading database ... 72443 files and directories currently installed.) 619s Removing autopkgtest-satdep (0) ... 620s autopkgtest [15:35:07]: test pbhoney: [----------------------- 620s PIEMapping 620s 620s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 620s Reid. "PBHoney: identyfying genomic variants via 620s long-read discordance and interrupted mapping." 620s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 620s doi:10.1186/1471-2105-15-180 620s 620s 2024-03-23 15:35:08,958 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 620s 2024-03-23 15:35:08,958 [INFO] Running Blasr 665s 2024-03-23 15:35:52,499 [INFO] [0, b'[INFO] 2024-03-23T15:35:08 [blasr] started.\n[INFO] 2024-03-23T15:35:52 [blasr] ended.\n', None] 665s 2024-03-23 15:35:52,500 [INFO] Mapping Tails 665s 2024-03-23 15:35:52,500 [INFO] Extracting tails 665s 2024-03-23 15:35:52,771 [INFO] Parsed 433 reads 665s 2024-03-23 15:35:52,771 [INFO] Found 278 tails 665s 2024-03-23 15:35:52,772 [INFO] 21 reads had double tails 665s 2024-03-23 15:35:52,772 [INFO] Running Blasr 675s 2024-03-23 15:36:02,027 [INFO] [0, b'[INFO] 2024-03-23T15:35:52 [blasr] started.\n[INFO] 2024-03-23T15:36:02 [blasr] ended.\n', None] 675s 2024-03-23 15:36:02,027 [INFO] Consolidating alignments 675s 2024-03-23 15:36:02,060 [INFO] 172 tails mapped 675s Sam To Bam 675s Calling Tails 675s 675s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 675s Reid. "PBHoney: identyfying genomic variants via 675s long-read discordance and interrupted mapping." 675s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 675s doi:10.1186/1471-2105-15-180 675s 675s 2024-03-23 15:36:02,561 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 675s 2024-03-23 15:36:02,561 [INFO] Parsing lambda_NEB3011 675s 2024-03-23 15:36:02,592 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 675s 2024-03-23 15:36:02,607 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 675s 2024-03-23 15:36:02,609 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 675s 2024-03-23 15:36:02,609 [INFO] Finished 675s Calling Spots 675s 675s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 675s Reid. "PBHoney: identyfying genomic variants via 675s long-read discordance and interrupted mapping." 675s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 675s doi:10.1186/1471-2105-15-180 675s 675s 2024-03-23 15:36:02,895 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 675s 2024-03-23 15:36:02,927 [INFO] Starting lambda_NEB3011:ErrorCounter 675s 2024-03-23 15:36:02,941 [INFO] 605 reads to parse in lambda_NEB3011 675s 2024-03-23 15:36:02,945 [INFO] 5% complete 675s 2024-03-23 15:36:02,946 [INFO] 10% complete 675s 2024-03-23 15:36:02,950 [INFO] 15% complete 675s 2024-03-23 15:36:02,953 [INFO] 20% complete 675s 2024-03-23 15:36:02,954 [INFO] 25% complete 675s 2024-03-23 15:36:02,957 [INFO] 30% complete 676s 2024-03-23 15:36:02,960 [INFO] 35% complete 676s 2024-03-23 15:36:02,963 [INFO] 40% complete 676s 2024-03-23 15:36:02,964 [INFO] 45% complete 676s 2024-03-23 15:36:02,967 [INFO] 50% complete 676s 2024-03-23 15:36:02,968 [INFO] 55% complete 676s 2024-03-23 15:36:02,971 [INFO] 60% complete 676s 2024-03-23 15:36:02,974 [INFO] 65% complete 676s 2024-03-23 15:36:02,976 [INFO] 70% complete 676s 2024-03-23 15:36:02,978 [INFO] 75% complete 676s 2024-03-23 15:36:02,980 [INFO] 80% complete 676s 2024-03-23 15:36:02,983 [INFO] 85% complete 676s 2024-03-23 15:36:02,985 [INFO] 90% complete 676s 2024-03-23 15:36:02,987 [INFO] 95% complete 676s 2024-03-23 15:36:03,005 [INFO] lambda_NEB3011:ErrorCounter -> spot 676s 2024-03-23 15:36:03,006 [INFO] Starting lambda_NEB3011:SpotCaller 676s 2024-03-23 15:36:03,022 [INFO] |lambda_NEB3011:SpotCaller|COV processing 676s 2024-03-23 15:36:03,022 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 676s 2024-03-23 15:36:03,022 [INFO] |lambda_NEB3011:SpotCaller|INS processing 676s 2024-03-23 15:36:03,029 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 676s 2024-03-23 15:36:03,030 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 676s 2024-03-23 15:36:03,037 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 676s 2024-03-23 15:36:03,039 [INFO] Thread Consumer-1: Exiting 676s 2024-03-23 15:36:03,039 [INFO] Finished 676s autopkgtest [15:36:03]: test pbhoney: -----------------------] 676s pbhoney PASS 676s autopkgtest [15:36:03]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 677s autopkgtest [15:36:04]: @@@@@@@@@@@@@@@@@@@@ summary 677s pbhoney PASS 696s Creating nova instance adt-noble-ppc64el-pbsuite-20240323-152446-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...