0s autopkgtest [19:57:02]: starting date and time: 2024-03-14 19:57:02+0000 0s autopkgtest [19:57:02]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:57:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qeyodvu6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-18.secgroup --name adt-noble-ppc64el-pbsuite-20240314-195702-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/ 180s autopkgtest [20:00:02]: testbed dpkg architecture: ppc64el 180s autopkgtest [20:00:02]: testbed apt version: 2.7.12 180s autopkgtest [20:00:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 181s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 181s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 181s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB] 181s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3020 kB] 182s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [48.4 kB] 182s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB] 182s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 182s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 182s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 182s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3317 kB] 182s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 182s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.8 kB] 182s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 185s Fetched 7625 kB in 2s (3321 kB/s) 185s Reading package lists... 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Calculating upgrade... 188s The following packages will be REMOVED: 188s libssl3 188s The following NEW packages will be installed: 188s libssl3t64 188s The following packages will be upgraded: 188s openssl 189s 1 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 189s Need to get 3195 kB of archives. 189s After this operation, 6144 B of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu1 [1028 kB] 189s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu1 [2168 kB] 190s Fetched 3195 kB in 1s (4597 kB/s) 190s (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 ... 70095 files and directories currently installed.) 190s Preparing to unpack .../openssl_3.0.13-0ubuntu1_ppc64el.deb ... 190s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 190s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 190s wget depends on libssl3 (>= 3.0.0). 190s tnftp depends on libssl3 (>= 3.0.0). 190s tcpdump depends on libssl3 (>= 3.0.0). 190s systemd-resolved depends on libssl3 (>= 3.0.0). 190s systemd depends on libssl3 (>= 3.0.0). 190s sudo depends on libssl3 (>= 3.0.0). 190s rsync depends on libssl3 (>= 3.0.0). 190s python3-cryptography depends on libssl3 (>= 3.0.0). 190s openssh-server depends on libssl3 (>= 3.0.10). 190s openssh-client depends on libssl3 (>= 3.0.10). 190s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 190s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 190s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 190s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 190s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 190s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 190s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 190s libnvme1 depends on libssl3 (>= 3.0.0). 190s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 190s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 190s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 190s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 190s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 190s kmod depends on libssl3 (>= 3.0.0). 190s dhcpcd-base depends on libssl3 (>= 3.0.0). 190s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 190s 190s (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 ... 70095 files and directories currently installed.) 190s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 190s Selecting previously unselected package libssl3t64:ppc64el. 190s (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 ... 70084 files and directories currently installed.) 190s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_ppc64el.deb ... 190s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 190s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu1) ... 190s Setting up openssl (3.0.13-0ubuntu1) ... 190s Processing triggers for man-db (2.12.0-3) ... 191s Processing triggers for libc-bin (2.39-0ubuntu2) ... 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 191s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 192s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 192s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 192s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 194s Reading package lists... 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Calculating upgrade... 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 197s autopkgtest [20:00:19]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 197s autopkgtest [20:00:19]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 201s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 201s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 202s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 202s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 202s gpgv: issuer "npatra974@gmail.com" 202s gpgv: Can't check signature: No public key 202s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 202s autopkgtest [20:00:24]: testing package pbsuite version 15.8.24+dfsg-7 202s autopkgtest [20:00:24]: build not needed 203s autopkgtest [20:00:25]: test pbhoney: preparing testbed 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 207s The following additional packages will be installed: 207s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 207s libhdf5-103-1t64 libhdf5-cpp-103-1 libhdf5-hl-100t64 libhts3 libhtscodecs2 207s liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libsz2 pbdagcon 207s pbhoney pbjelly python3-h5py python3-h5py-serial python3-intervaltree 207s python3-intervaltree-bio python3-networkx python3-numpy python3-pbbanana 207s python3-pbsuite-utils python3-pysam python3-sortedcontainers samtools 207s Suggested packages: 207s python-h5py-doc python-networkx-doc python3-gdal python3-matplotlib 207s python3-pydot python3-pygraphviz python3-scipy gcc gfortran python3-dev 207s python3-pytest python-sortedcontainers-doc cwltool 207s The following NEW packages will be installed: 207s autopkgtest-satdep blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 207s libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1 libhdf5-hl-100t64 libhts3 207s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 207s libsz2 pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 207s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 207s python3-pbbanana python3-pbsuite-utils python3-pysam 207s python3-sortedcontainers samtools 207s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 25.4 MB/25.4 MB of archives. 207s After this operation, 141 MB of additional disk space will be used. 207s Get:1 /tmp/autopkgtest.dcLzfs/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 207s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 207s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 207s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu2 [1395 kB] 208s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-cpp-103-1 ppc64el 1.10.10+repack-3ubuntu2 [130 kB] 208s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 208s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 208s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 208s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbcopper2.3.0 ppc64el 2.3.0+dfsg-2 [594 kB] 208s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbbam2.4.0 ppc64el 2.4.0+dfsg-1build1 [751 kB] 208s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libblasr5.3.5 ppc64el 5.3.5+dfsg-6build3 [1255 kB] 208s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpbseq ppc64el 5.3.5+dfsg-6build3 [3068 B] 208s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el blasr ppc64el 5.3.5+dfsg-6build4 [264 kB] 208s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 208s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 208s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu2 [70.9 kB] 208s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 208s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 208s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbdagcon ppc64el 0.3+git20180411.c14c422+dfsg-8build3 [279 kB] 208s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 208s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 208s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 208s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbjelly all 15.8.24+dfsg-7 [966 kB] 208s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 208s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 208s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu2 [955 kB] 209s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py all 3.10.0-1ubuntu2 [7980 B] 209s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB] 209s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-intervaltree all 3.0.2-1.1 [22.4 kB] 209s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-intervaltree-bio all 1.0.1-4 [8260 B] 209s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 209s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el pbhoney all 15.8.24+dfsg-7 [1051 kB] 209s Fetched 25.4 MB in 2s (16.4 MB/s) 209s Selecting previously unselected package libaec0:ppc64el. 209s (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 ... 70097 files and directories currently installed.) 209s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 209s Unpacking libaec0:ppc64el (1.1.2-1) ... 209s Selecting previously unselected package libsz2:ppc64el. 209s Preparing to unpack .../01-libsz2_1.1.2-1_ppc64el.deb ... 209s Unpacking libsz2:ppc64el (1.1.2-1) ... 209s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 209s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 209s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 209s Selecting previously unselected package libhdf5-cpp-103-1:ppc64el. 209s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu2_ppc64el.deb ... 209s Unpacking libhdf5-cpp-103-1:ppc64el (1.10.10+repack-3ubuntu2) ... 209s Selecting previously unselected package libdeflate0:ppc64el. 209s Preparing to unpack .../04-libdeflate0_1.19-1_ppc64el.deb ... 209s Unpacking libdeflate0:ppc64el (1.19-1) ... 209s Selecting previously unselected package libhtscodecs2:ppc64el. 209s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_ppc64el.deb ... 209s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 209s Selecting previously unselected package libhts3:ppc64el. 209s Preparing to unpack .../06-libhts3_1.18+ds-1_ppc64el.deb ... 209s Unpacking libhts3:ppc64el (1.18+ds-1) ... 209s Selecting previously unselected package libpbcopper2.3.0:ppc64el. 209s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_ppc64el.deb ... 209s Unpacking libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 209s Selecting previously unselected package libpbbam2.4.0:ppc64el. 209s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_ppc64el.deb ... 209s Unpacking libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build1) ... 209s Selecting previously unselected package libblasr5.3.5:ppc64el. 209s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_ppc64el.deb ... 209s Unpacking libblasr5.3.5:ppc64el (5.3.5+dfsg-6build3) ... 209s Selecting previously unselected package libpbseq:ppc64el. 209s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_ppc64el.deb ... 209s Unpacking libpbseq:ppc64el (5.3.5+dfsg-6build3) ... 209s Selecting previously unselected package blasr. 209s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_ppc64el.deb ... 209s Unpacking blasr (5.3.5+dfsg-6build4) ... 209s Selecting previously unselected package libblas3:ppc64el. 209s Preparing to unpack .../12-libblas3_3.12.0-3_ppc64el.deb ... 209s Unpacking libblas3:ppc64el (3.12.0-3) ... 209s Selecting previously unselected package libgfortran5:ppc64el. 209s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 209s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 209s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 209s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_ppc64el.deb ... 209s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 209s Selecting previously unselected package liblapack3:ppc64el. 209s Preparing to unpack .../15-liblapack3_3.12.0-3_ppc64el.deb ... 209s Unpacking liblapack3:ppc64el (3.12.0-3) ... 209s Selecting previously unselected package liblzf1:ppc64el. 209s Preparing to unpack .../16-liblzf1_3.6-4_ppc64el.deb ... 209s Unpacking liblzf1:ppc64el (3.6-4) ... 209s Selecting previously unselected package pbdagcon. 209s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_ppc64el.deb ... 209s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 209s Selecting previously unselected package python3-pysam. 209s Preparing to unpack .../18-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 209s Unpacking python3-pysam (0.22.0+ds-1) ... 210s Selecting previously unselected package python3-pbsuite-utils. 210s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 210s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 210s Selecting previously unselected package python3-networkx. 210s Preparing to unpack .../20-python3-networkx_2.8.8-1ubuntu1_all.deb ... 210s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 210s Selecting previously unselected package pbjelly. 210s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-7_all.deb ... 210s Unpacking pbjelly (15.8.24+dfsg-7) ... 210s Selecting previously unselected package python3-pbbanana. 210s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 210s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 210s Selecting previously unselected package python3-numpy. 210s Preparing to unpack .../23-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 210s Unpacking python3-numpy (1:1.24.2-2) ... 211s Selecting previously unselected package python3-h5py-serial. 211s Preparing to unpack .../24-python3-h5py-serial_3.10.0-1ubuntu2_ppc64el.deb ... 211s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 211s Selecting previously unselected package python3-h5py. 211s Preparing to unpack .../25-python3-h5py_3.10.0-1ubuntu2_all.deb ... 211s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 211s Selecting previously unselected package python3-sortedcontainers. 211s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 211s Unpacking python3-sortedcontainers (2.4.0-2) ... 211s Selecting previously unselected package python3-intervaltree. 211s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 211s Unpacking python3-intervaltree (3.0.2-1.1) ... 211s Selecting previously unselected package python3-intervaltree-bio. 211s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 211s Unpacking python3-intervaltree-bio (1.0.1-4) ... 211s Selecting previously unselected package samtools. 211s Preparing to unpack .../29-samtools_1.19.2-1_ppc64el.deb ... 211s Unpacking samtools (1.19.2-1) ... 211s Selecting previously unselected package pbhoney. 211s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-7_all.deb ... 211s Unpacking pbhoney (15.8.24+dfsg-7) ... 211s Selecting previously unselected package autopkgtest-satdep. 211s Preparing to unpack .../31-1-autopkgtest-satdep.deb ... 211s Unpacking autopkgtest-satdep (0) ... 211s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 211s Setting up libdeflate0:ppc64el (1.19-1) ... 211s Setting up python3-sortedcontainers (2.4.0-2) ... 211s Setting up python3-networkx (2.8.8-1ubuntu1) ... 212s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 212s "graph [edge [ source u'u\4200' target u'u\4200' ] " 212s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 212s + "node [ id u'u\4200' label b ] ]" 213s Setting up libaec0:ppc64el (1.1.2-1) ... 213s Setting up libblas3:ppc64el (3.12.0-3) ... 213s 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 213s Setting up liblzf1:ppc64el (3.6-4) ... 213s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 213s Setting up libsz2:ppc64el (1.1.2-1) ... 213s Setting up libpbcopper2.3.0:ppc64el (2.3.0+dfsg-2) ... 213s Setting up liblapack3:ppc64el (3.12.0-3) ... 213s 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 213s Setting up libhts3:ppc64el (1.18+ds-1) ... 213s Setting up python3-pysam (0.22.0+ds-1) ... 213s Setting up python3-intervaltree (3.0.2-1.1) ... 213s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 213s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 213s for i in re.findall("\d+|\^?[ATCGN]+", md): 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 213s splRE = re.compile("\s+") 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 213s splRE = re.compile("\s+") 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 213s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 213s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 213s data = re.split("\s+",line) 213s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 213s data = re.split("\s+",line) 213s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 213s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 213s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 213s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 213s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 213s '\s*Type\s*=\s*(?P\w+)\s*,)?' 213s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 213s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 213s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 213s regex = re.compile("ref\d{7}") 213s Setting up libpbbam2.4.0:ppc64el (2.4.0+dfsg-1build1) ... 213s Setting up samtools (1.19.2-1) ... 213s Setting up python3-numpy (1:1.24.2-2) ... 215s Setting up python3-intervaltree-bio (1.0.1-4) ... 215s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 215s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu2) ... 215s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 216s Setting up python3-h5py (3.10.0-1ubuntu2) ... 216s Setting up libhdf5-cpp-103-1:ppc64el (1.10.10+repack-3ubuntu2) ... 216s Setting up libblasr5.3.5:ppc64el (5.3.5+dfsg-6build3) ... 216s Setting up libpbseq:ppc64el (5.3.5+dfsg-6build3) ... 216s Setting up blasr (5.3.5+dfsg-6build4) ... 216s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 216s Setting up pbjelly (15.8.24+dfsg-7) ... 216s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 216s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 216s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 216s splRE = re.compile("\s+") 216s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 216s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 216s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 216s nprocRe = re.compile("--nproc (\d+)") 216s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 216s """ 216s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 216s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 216s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 216s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 216s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 216s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 216s data = re.split("\s+",line) 216s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 216s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 216s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 216s data = re.split("\s+",line) 216s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 216s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 216s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 216s getContigName = re.compile("(\d+)_contig") 216s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 216s "awk -F\ '{{if ($1 < 500) print $2}}' | " 216s Setting up pbhoney (15.8.24+dfsg-7) ... 216s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 216s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 216s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 216s """ 216s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 216s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 216s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 216s for i in re.findall("\d+|\^?[ATCGN]+", md): 216s Setting up autopkgtest-satdep (0) ... 216s Processing triggers for man-db (2.12.0-3) ... 217s Processing triggers for libc-bin (2.39-0ubuntu2) ... 220s (Reading database ... 72804 files and directories currently installed.) 220s Removing autopkgtest-satdep (0) ... 220s autopkgtest [20:00:42]: test pbhoney: [----------------------- 221s PIEMapping 221s 221s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 221s Reid. "PBHoney: identyfying genomic variants via 221s long-read discordance and interrupted mapping." 221s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 221s doi:10.1186/1471-2105-15-180 221s 221s 2024-03-14 20:00:43,273 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 221s 2024-03-14 20:00:43,273 [INFO] Running Blasr 266s 2024-03-14 20:01:28,230 [INFO] [0, b'[INFO] 2024-03-14T20:00:43 [blasr] started.\n[INFO] 2024-03-14T20:01:28 [blasr] ended.\n', None] 266s 2024-03-14 20:01:28,230 [INFO] Mapping Tails 266s 2024-03-14 20:01:28,231 [INFO] Extracting tails 266s 2024-03-14 20:01:28,505 [INFO] Parsed 433 reads 266s 2024-03-14 20:01:28,505 [INFO] Found 278 tails 266s 2024-03-14 20:01:28,505 [INFO] 21 reads had double tails 266s 2024-03-14 20:01:28,506 [INFO] Running Blasr 275s 2024-03-14 20:01:37,680 [INFO] [0, b'[INFO] 2024-03-14T20:01:28 [blasr] started.\n[INFO] 2024-03-14T20:01:37 [blasr] ended.\n', None] 275s 2024-03-14 20:01:37,680 [INFO] Consolidating alignments 275s 2024-03-14 20:01:37,710 [INFO] 172 tails mapped 275s Sam To Bam 275s Calling Tails 276s 276s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 276s Reid. "PBHoney: identyfying genomic variants via 276s long-read discordance and interrupted mapping." 276s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 276s doi:10.1186/1471-2105-15-180 276s 276s 2024-03-14 20:01:38,190 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 276s 2024-03-14 20:01:38,191 [INFO] Parsing lambda_NEB3011 276s 2024-03-14 20:01:38,221 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 276s 2024-03-14 20:01:38,237 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 276s 2024-03-14 20:01:38,239 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 276s 2024-03-14 20:01:38,239 [INFO] Finished 276s Calling Spots 276s 276s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 276s Reid. "PBHoney: identyfying genomic variants via 276s long-read discordance and interrupted mapping." 276s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 276s doi:10.1186/1471-2105-15-180 276s 276s 2024-03-14 20:01:38,517 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 276s 2024-03-14 20:01:38,528 [INFO] Starting lambda_NEB3011:ErrorCounter 276s 2024-03-14 20:01:38,541 [INFO] 605 reads to parse in lambda_NEB3011 276s 2024-03-14 20:01:38,546 [INFO] 5% complete 276s 2024-03-14 20:01:38,547 [INFO] 10% complete 276s 2024-03-14 20:01:38,551 [INFO] 15% complete 276s 2024-03-14 20:01:38,553 [INFO] 20% complete 276s 2024-03-14 20:01:38,555 [INFO] 25% complete 276s 2024-03-14 20:01:38,557 [INFO] 30% complete 276s 2024-03-14 20:01:38,561 [INFO] 35% complete 276s 2024-03-14 20:01:38,563 [INFO] 40% complete 276s 2024-03-14 20:01:38,564 [INFO] 45% complete 276s 2024-03-14 20:01:38,567 [INFO] 50% complete 276s 2024-03-14 20:01:38,569 [INFO] 55% complete 276s 2024-03-14 20:01:38,571 [INFO] 60% complete 276s 2024-03-14 20:01:38,574 [INFO] 65% complete 276s 2024-03-14 20:01:38,576 [INFO] 70% complete 276s 2024-03-14 20:01:38,578 [INFO] 75% complete 276s 2024-03-14 20:01:38,580 [INFO] 80% complete 276s 2024-03-14 20:01:38,583 [INFO] 85% complete 276s 2024-03-14 20:01:38,585 [INFO] 90% complete 276s 2024-03-14 20:01:38,587 [INFO] 95% complete 276s 2024-03-14 20:01:38,606 [INFO] lambda_NEB3011:ErrorCounter -> spot 276s 2024-03-14 20:01:38,606 [INFO] Starting lambda_NEB3011:SpotCaller 276s 2024-03-14 20:01:38,622 [INFO] |lambda_NEB3011:SpotCaller|COV processing 276s 2024-03-14 20:01:38,622 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 276s 2024-03-14 20:01:38,622 [INFO] |lambda_NEB3011:SpotCaller|INS processing 276s 2024-03-14 20:01:38,629 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 276s 2024-03-14 20:01:38,630 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 276s 2024-03-14 20:01:38,637 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 276s 2024-03-14 20:01:38,639 [INFO] Finished 276s 2024-03-14 20:01:38,640 [INFO] Thread Consumer-1: Exiting 277s autopkgtest [20:01:39]: test pbhoney: -----------------------] 278s autopkgtest [20:01:40]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 278s pbhoney PASS 278s autopkgtest [20:01:40]: @@@@@@@@@@@@@@@@@@@@ summary 278s pbhoney PASS 297s Creating nova instance adt-noble-ppc64el-pbsuite-20240314-195702-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID a031584c-aec8-4412-bff6-4238354f4d17)...