0s autopkgtest [22:29:46]: starting date and time: 2024-03-25 22:29:46+0000
  0s autopkgtest [22:29:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [22:29:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l6w037yj/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:segemehl,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade segemehl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=segemehl/0.3.4-5build1 curl/8.5.0-2ubuntu8 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-15.secgroup --name adt-noble-ppc64el-segemehl-20240325-222946-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/
 96s autopkgtest [22:31:22]: testbed dpkg architecture: ppc64el
 96s autopkgtest [22:31:22]: testbed apt version: 2.7.12
 96s autopkgtest [22:31:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B]
 98s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB]
 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB]
101s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
101s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB]
102s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
102s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
102s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
102s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4232 kB]
105s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
105s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB]
105s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
108s Fetched 9665 kB in 9s (1103 kB/s)
108s Reading package lists...
111s Reading package lists...
111s Building dependency tree...
111s Reading state information...
112s Calculating upgrade...
112s The following packages will be REMOVED:
112s   libssl3
112s The following NEW packages will be installed:
112s   libssl3t64
112s The following packages have been kept back:
112s   curl
112s The following packages will be upgraded:
112s   openssl
112s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
112s Need to get 3151 kB of archives.
112s After this operation, 73.7 kB of additional disk space will be used.
112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
113s Fetched 3151 kB in 1s (3871 kB/s)
113s (Reading database ... 
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(Reading database ... 55%
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(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.)
113s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
113s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
113s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
113s  wget depends on libssl3 (>= 3.0.0).
113s  tnftp depends on libssl3 (>= 3.0.0).
113s  tcpdump depends on libssl3 (>= 3.0.0).
113s  systemd-resolved depends on libssl3 (>= 3.0.0).
113s  systemd depends on libssl3 (>= 3.0.0).
113s  sudo depends on libssl3 (>= 3.0.0).
113s  rsync depends on libssl3 (>= 3.0.0).
113s  python3-cryptography depends on libssl3 (>= 3.0.0).
113s  openssh-server depends on libssl3 (>= 3.0.10).
113s  openssh-client depends on libssl3 (>= 3.0.10).
113s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
113s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
113s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
113s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
113s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
113s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
113s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
113s  libnvme1 depends on libssl3 (>= 3.0.0).
113s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
113s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
113s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
113s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
113s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
113s  kmod depends on libssl3 (>= 3.0.0).
113s  dhcpcd-base depends on libssl3 (>= 3.0.0).
113s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
113s 
113s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70156 files and directories currently installed.)
113s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
113s Selecting previously unselected package libssl3t64:ppc64el.
113s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70145 files and directories currently installed.)
113s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
113s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
113s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
113s Setting up openssl (3.0.13-0ubuntu2) ...
113s Processing triggers for man-db (2.12.0-3) ...
114s Processing triggers for libc-bin (2.39-0ubuntu6) ...
114s Reading package lists...
114s Building dependency tree...
114s Reading state information...
115s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
115s sh: Attempting to set up Debian/Ubuntu apt sources automatically
115s sh: Distribution appears to be Ubuntu
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s eatmydata is already the newest version (131-1).
116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
117s dbus is already the newest version (1.14.10-4ubuntu1).
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s rng-tools-debian is already the newest version (2.4).
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s The following packages will be REMOVED:
117s   cloud-init* python3-configobj* python3-debconf*
118s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
118s After this operation, 3256 kB disk space will be freed.
118s (Reading database ... 
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(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.)
118s Removing cloud-init (24.1.2-0ubuntu1) ...
118s Removing python3-configobj (5.0.8-3) ...
118s Removing python3-debconf (1.5.86) ...
118s Processing triggers for man-db (2.12.0-3) ...
119s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 69769 files and directories currently installed.)
119s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
119s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
119s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
119s invoke-rc.d: policy-rc.d denied execution of try-restart.
119s Reading package lists...
120s Building dependency tree...
120s Reading state information...
120s linux-generic is already the newest version (6.8.0-11.11+1).
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
120s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
120s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
123s Reading package lists...
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
123s Calculating upgrade...
123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s autopkgtest [22:31:50]: rebooting testbed after setup commands that affected boot
286s autopkgtest [22:34:32]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
289s autopkgtest [22:34:35]: @@@@@@@@@@@@@@@@@@@@ apt-source segemehl
291s Get:1 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (dsc) [2032 B]
291s Get:2 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (tar) [244 kB]
291s Get:3 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (diff) [7788 B]
292s gpgv: Signature made Tue Aug 24 16:51:21 2021 UTC
292s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
292s gpgv:                issuer "npatra974@gmail.com"
292s gpgv: Can't check signature: No public key
292s dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5.dsc: no acceptable signature found
292s autopkgtest [22:34:38]: testing package segemehl version 0.3.4-5
292s autopkgtest [22:34:38]: build not needed
294s autopkgtest [22:34:40]: test run-unit-test: preparing testbed
296s Reading package lists...
296s Building dependency tree...
296s Reading state information...
296s Starting pkgProblemResolver with broken count: 0
296s Starting 2 pkgProblemResolver with broken count: 0
296s Done
296s The following additional packages will be installed:
296s   libdeflate0 libhts3 libhtscodecs2 segemehl
296s The following NEW packages will be installed:
296s   autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 segemehl
296s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.
296s Need to get 953 kB/954 kB of archives.
296s After this operation, 2674 kB of additional disk space will be used.
296s Get:1 /tmp/autopkgtest.POGZim/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B]
297s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
297s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
297s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB]
297s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el segemehl ppc64el 0.3.4-5 [229 kB]
298s Fetched 953 kB in 1s (917 kB/s)
298s Selecting previously unselected package libdeflate0:ppc64el.
298s (Reading database ... 
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(Reading database ... 50%
(Reading database ... 55%
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(Reading database ... 75%
(Reading database ... 80%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 69714 files and directories currently installed.)
298s Preparing to unpack .../libdeflate0_1.19-1_ppc64el.deb ...
298s Unpacking libdeflate0:ppc64el (1.19-1) ...
298s Selecting previously unselected package libhtscodecs2:ppc64el.
298s Preparing to unpack .../libhtscodecs2_1.6.0-1_ppc64el.deb ...
298s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
298s Selecting previously unselected package libhts3:ppc64el.
298s Preparing to unpack .../libhts3_1.18+ds-1_ppc64el.deb ...
298s Unpacking libhts3:ppc64el (1.18+ds-1) ...
298s Selecting previously unselected package segemehl.
298s Preparing to unpack .../segemehl_0.3.4-5_ppc64el.deb ...
298s Unpacking segemehl (0.3.4-5) ...
298s Selecting previously unselected package autopkgtest-satdep.
298s Preparing to unpack .../1-autopkgtest-satdep.deb ...
298s Unpacking autopkgtest-satdep (0) ...
298s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
298s Setting up libdeflate0:ppc64el (1.19-1) ...
298s Setting up libhts3:ppc64el (1.18+ds-1) ...
298s Setting up segemehl (0.3.4-5) ...
298s Setting up autopkgtest-satdep (0) ...
298s Processing triggers for man-db (2.12.0-3) ...
298s Processing triggers for libc-bin (2.39-0ubuntu6) ...
301s (Reading database ... 69750 files and directories currently installed.)
301s Removing autopkgtest-satdep (0) ...
301s autopkgtest [22:34:47]: test run-unit-test: [-----------------------
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading database sequences.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 1 database sequences found.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: total length of db sequences: 250
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: assigning all reads to default read group 'A1'.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reads assigned to read group 'A1'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: compiled sam header.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alphabet of size (5): ACGT
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: size of db sequence: 251
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing suftab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusort: classify.
301s init bit array of 32
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusort: getting bit.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: bit alurusort: alloc B of size 124.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusort: initbitarray of size 124.
301s init bit array of 16
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusort: Qmaxdist in cl of size 251.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: enter alurusort: substringsort.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: setting bit array to zero
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: allocating space for buckets and buffers
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: memsetting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: substring sort ... ok
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: checking valbitarray.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: enter Tprime calculation.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: init arrays.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: scan B
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: iterating i=251 elements with lenB=124.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: exit
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: enter alursortint.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: classify int.
301s init bit array of 16
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: getting bit.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: init bcktsA.
301s init bit array of 16
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: countingsort.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countingsortint: init buffers and A
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: setting buffer to zero
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (1 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (2 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (3 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (to set borders)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: Sorting type S suffixes. Init bcktsB.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 55	69	124.
301s 
301s init bit array of 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: allocating B with 55 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: iterating to lenA=124.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter Qmaxdist.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter Qdist.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter distCount.
301s init bit array of 16
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter get listsS.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: memsetting list of 121 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: iter up to 124.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: scan A
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: set accidst
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: freeing stuff.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter sortlistsS.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: allocating stuff.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: iterating 55 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: looping 121 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: iterating 124 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistsS: exiting happily!
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter tprime.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: init arrays.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: scan B
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: iterating i=124 elements with lenB=55.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: tprime: exit
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter alurusortint.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: classify int.
301s init bit array of 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: getting bit.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: init bcktsA.
301s init bit array of 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: countingsort.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countingsortint: init buffers and A
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: setting buffer to zero
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (1 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (2 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (3 of 3)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: scanning buffer (to set borders)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: countsortint: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: Sorting type S suffixes. Init bcktsB.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 27	28	55.
301s 
301s init bit array of 4
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: allocating B with 27 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: iterating to lenA=55.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: arrayB: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter Qmaxdist.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter Qdist.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter distCount.
301s init bit array of 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter get listsS.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: memsetting list of 54 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: iter up to 55.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: scan A
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: set accidst
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: getlistsS: exiting
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: freeing stuff.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: enter sortlistsS.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: allocating stuff.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: iterating 27 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: looping 54 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistS: iterating 55 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: sortlistsS: exiting happily!
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: alurusortint: valbitarraysortedS.
301s init bit array of 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstructintS.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: init.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: iteration over 124 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: scan B (size: 55).
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: exit.
301s init bit array of 16
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: enter reconstruction.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: init.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: iteration over 251 elems.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: scan B (size: 124).
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reconstruct: exit.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: enter aluruSuffixArrayL start.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: aluruSuffixArrayL: initalizning arrays.
301s init bit array of 32
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: aluruSuffixArrayL: memsetting count.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: aluruSuffixArrayL: setting b.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: aluruSuffixArrayL: iteration.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: aluruSuffixArrayL: exit ok.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing inv_suftab (251).
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: inv_suftab constructed.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing lcp.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: deleting inv_suftab
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing child tab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing suffix links.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing id.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing suflinks - bottom up.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: constructing suflinks - top down.
301s suflink construction. pushes: 177, maxstack: 7
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: building  the suffix array has taken 0.000000 seconds.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: total length of suffix array was 250.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: writing suffix array 'index.idx' to disk.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: Mapping stats:
301s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
301s all	0	0	nan%	0	nan%	0	nan%	0	nan%
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 
301s Goodbye.
301s  "Wir sind hier nicht in Seattle Dirk!" (Tocotronic)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading queries in 'myseq.fa'.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 1 query sequences found.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading database sequences.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 1 database sequences found.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: total length of db sequences: 250
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: assigning all reads to default read group 'A1'.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reads assigned to read group 'A1'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: compiled sam header.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading suffix array 'index.idx' from disk.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading lcpc/vtab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading childtab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading suflinks.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading lsint id.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: read suffix array 'index.idx' with 251 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: md5 keys of index and db match.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading the suffix array has taken 0.000000 seconds.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: matching w/ suffixarray has taken 0.000000 seconds.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: Mapping stats:
301s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
301s all	1	0	0.00%	0	0.00%	0	0.00%	0	0.00%
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 
301s Goodbye.
301s  "Wir sind hier nicht in Seattle Dirk!" (Tocotronic)
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading queries in 'seq2.fa'.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 1 query sequences found.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading database sequences.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 1 database sequences found.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: total length of db sequences: 250
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: assigning all reads to default read group 'A1'.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reads assigned to read group 'A1'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: compiled sam header.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading suffix array 'index.idx' from disk.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading lcpc/vtab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading childtab.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading suflinks.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading lsint id.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: read suffix array 'index.idx' with 251 elements.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: md5 keys of index and db match.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: reading the suffix array has taken 0.000000 seconds.
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: writing multi splits to 'seq2.mult.bed'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: writing sngle splits to 'seq2.sngl.bed'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: writing trans splits to 'seq2.trns.txt'
301s [SEGEMEHL] Mon Mar 25 22:34:47 2024: matching w/ suffixarray has taken 0.000000 seconds.
302s [SEGEMEHL] Mon Mar 25 22:34:47 2024: Mapping stats:
302s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
302s all	1	0	0.00%	0	0.00%	0	0.00%	0	0.00%
302s [SEGEMEHL] Mon Mar 25 22:34:47 2024: 
302s Goodbye.
302s  "Wir sind hier nicht in Seattle Dirk!" (Tocotronic)
302s PASS Test
302s autopkgtest [22:34:48]: test run-unit-test: -----------------------]
302s run-unit-test        PASS
302s autopkgtest [22:34:48]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
303s autopkgtest [22:34:49]: @@@@@@@@@@@@@@@@@@@@ summary
303s run-unit-test        PASS
315s Creating nova instance adt-noble-ppc64el-segemehl-20240325-222946-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...