0s autopkgtest [21:26:06]: starting date and time: 2024-03-25 21:26:06+0000
  0s autopkgtest [21:26:06]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [21:26:06]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yxa9d556/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-s390x-7.secgroup --name adt-noble-s390x-segemehl-20240325-212606-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-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/
131s autopkgtest [21:28:17]: testbed dpkg architecture: s390x
131s autopkgtest [21:28:17]: testbed apt version: 2.7.12
131s autopkgtest [21:28:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup
132s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
132s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B]
132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4038 kB]
133s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB]
133s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
133s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB]
134s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
134s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B]
134s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
134s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB]
134s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
134s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB]
134s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
136s Fetched 9603 kB in 3s (2839 kB/s)
136s Reading package lists...
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Calculating upgrade...
140s The following packages will be REMOVED:
140s   libssl3
140s The following NEW packages will be installed:
140s   libssl3t64
140s The following packages have been kept back:
140s   curl
140s The following packages will be upgraded:
140s   openssl
140s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
140s Need to get 2685 kB of archives.
140s After this operation, 239 kB of additional disk space will be used.
140s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB]
140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB]
141s Fetched 2685 kB in 1s (2840 kB/s)
141s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 52170 files and directories currently installed.)
141s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ...
141s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
141s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested:
141s  wget depends on libssl3 (>= 3.0.0).
141s  tnftp depends on libssl3 (>= 3.0.0).
141s  tcpdump depends on libssl3 (>= 3.0.0).
141s  systemd-resolved depends on libssl3 (>= 3.0.0).
141s  systemd depends on libssl3 (>= 3.0.0).
141s  sudo depends on libssl3 (>= 3.0.0).
141s  s390-tools depends on libssl3 (>= 3.0.0).
141s  rsync depends on libssl3 (>= 3.0.0).
141s  python3-cryptography depends on libssl3 (>= 3.0.0).
141s  openssh-server depends on libssl3 (>= 3.0.10).
141s  openssh-client depends on libssl3 (>= 3.0.10).
141s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
141s  libsystemd-shared:s390x depends on libssl3 (>= 3.0.0).
141s  libssh-4:s390x depends on libssl3 (>= 3.0.0).
141s  libsasl2-modules:s390x depends on libssl3 (>= 3.0.0).
141s  libsasl2-2:s390x depends on libssl3 (>= 3.0.0).
141s  libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0).
141s  libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0).
141s  libnvme1 depends on libssl3 (>= 3.0.0).
141s  libkrb5-3:s390x depends on libssl3 (>= 3.0.0).
141s  libkmod2:s390x depends on libssl3 (>= 3.0.0).
141s  libfido2-1:s390x depends on libssl3 (>= 3.0.0).
141s  libcurl4:s390x depends on libssl3 (>= 3.0.0).
141s  libcryptsetup12:s390x depends on libssl3 (>= 3.0.0).
141s  kmod depends on libssl3 (>= 3.0.0).
141s  dhcpcd-base depends on libssl3 (>= 3.0.0).
141s  bind9-libs:s390x depends on libssl3 (>= 3.0.0).
141s 
141s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52170 files and directories currently installed.)
141s Removing libssl3:s390x (3.0.10-1ubuntu4) ...
141s Selecting previously unselected package libssl3t64:s390x.
141s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52159 files and directories currently installed.)
141s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ...
141s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ...
141s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ...
141s Setting up openssl (3.0.13-0ubuntu2) ...
141s Processing triggers for man-db (2.12.0-3) ...
142s Processing triggers for libc-bin (2.39-0ubuntu6) ...
142s Reading package lists...
142s Building dependency tree...
142s Reading state information...
142s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
143s Unknown architecture, assuming PC-style ttyS0
143s sh: Attempting to set up Debian/Ubuntu apt sources automatically
143s sh: Distribution appears to be Ubuntu
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
144s eatmydata is already the newest version (131-1).
144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
145s dbus is already the newest version (1.14.10-4ubuntu1).
145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s Reading package lists...
145s Building dependency tree...
145s Reading state information...
145s rng-tools-debian is already the newest version (2.4).
145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s Reading package lists...
145s Building dependency tree...
145s Reading state information...
146s The following packages will be REMOVED:
146s   cloud-init* python3-configobj* python3-debconf*
146s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
146s After this operation, 3256 kB disk space will be freed.
146s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 52172 files and directories currently installed.)
146s Removing cloud-init (24.1.2-0ubuntu1) ...
146s Removing python3-configobj (5.0.8-3) ...
146s Removing python3-debconf (1.5.86) ...
146s Processing triggers for man-db (2.12.0-3) ...
147s (Reading database ... 
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(Reading database ... 51783 files and directories currently installed.)
147s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
147s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
148s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
148s invoke-rc.d: policy-rc.d denied execution of try-restart.
148s Reading package lists...
148s Building dependency tree...
148s Reading state information...
148s linux-generic is already the newest version (6.8.0-11.11+1).
148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
149s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
149s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
149s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
151s Reading package lists...
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s Calculating upgrade...
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s Reading package lists...
152s Building dependency tree...
152s Reading state information...
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s autopkgtest [21:28:38]: rebooting testbed after setup commands that affected boot
168s autopkgtest [21:28:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024
171s autopkgtest [21:28:57]: @@@@@@@@@@@@@@@@@@@@ apt-source segemehl
173s Get:1 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (dsc) [2032 B]
173s Get:2 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (tar) [244 kB]
173s Get:3 http://ftpmaster.internal/ubuntu noble/universe segemehl 0.3.4-5 (diff) [7788 B]
173s gpgv: Signature made Tue Aug 24 16:51:21 2021 UTC
173s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
173s gpgv:                issuer "npatra974@gmail.com"
173s gpgv: Can't check signature: No public key
173s dpkg-source: warning: cannot verify inline signature for ./segemehl_0.3.4-5.dsc: no acceptable signature found
174s autopkgtest [21:29:00]: testing package segemehl version 0.3.4-5
174s autopkgtest [21:29:00]: build not needed
176s autopkgtest [21:29:02]: test run-unit-test: preparing testbed
181s Reading package lists...
181s Building dependency tree...
181s Reading state information...
181s Starting pkgProblemResolver with broken count: 0
181s Starting 2 pkgProblemResolver with broken count: 0
181s Done
182s The following additional packages will be installed:
182s   libdeflate0 libhts3 libhtscodecs2 segemehl
182s The following NEW packages will be installed:
182s   autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 segemehl
182s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.
182s Need to get 807 kB/808 kB of archives.
182s After this operation, 1940 kB of additional disk space will be used.
182s Get:1 /tmp/autopkgtest.AHT7Io/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B]
182s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB]
182s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB]
182s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB]
182s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x segemehl s390x 0.3.4-5 [211 kB]
183s Fetched 807 kB in 1s (1253 kB/s)
183s Selecting previously unselected package libdeflate0:s390x.
183s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 51728 files and directories currently installed.)
183s Preparing to unpack .../libdeflate0_1.19-1_s390x.deb ...
183s Unpacking libdeflate0:s390x (1.19-1) ...
183s Selecting previously unselected package libhtscodecs2:s390x.
183s Preparing to unpack .../libhtscodecs2_1.6.0-1_s390x.deb ...
183s Unpacking libhtscodecs2:s390x (1.6.0-1) ...
183s Selecting previously unselected package libhts3:s390x.
183s Preparing to unpack .../libhts3_1.18+ds-1_s390x.deb ...
183s Unpacking libhts3:s390x (1.18+ds-1) ...
183s Selecting previously unselected package segemehl.
183s Preparing to unpack .../segemehl_0.3.4-5_s390x.deb ...
183s Unpacking segemehl (0.3.4-5) ...
183s Selecting previously unselected package autopkgtest-satdep.
183s Preparing to unpack .../1-autopkgtest-satdep.deb ...
183s Unpacking autopkgtest-satdep (0) ...
183s Setting up libhtscodecs2:s390x (1.6.0-1) ...
183s Setting up libdeflate0:s390x (1.19-1) ...
183s Setting up libhts3:s390x (1.18+ds-1) ...
183s Setting up segemehl (0.3.4-5) ...
183s Setting up autopkgtest-satdep (0) ...
183s Processing triggers for man-db (2.12.0-3) ...
184s Processing triggers for libc-bin (2.39-0ubuntu6) ...
186s (Reading database ... 51764 files and directories currently installed.)
186s Removing autopkgtest-satdep (0) ...
187s autopkgtest [21:29:13]: test run-unit-test: [-----------------------
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading database sequences.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 1 database sequences found.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: total length of db sequences: 250
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: assigning all reads to default read group 'A1'.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reads assigned to read group 'A1'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: compiled sam header.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alphabet of size (5): ACGT
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: size of db sequence: 251
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing suftab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusort: classify.
187s init bit array of 32
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusort: getting bit.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: bit alurusort: alloc B of size 124.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusort: initbitarray of size 124.
187s init bit array of 16
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusort: Qmaxdist in cl of size 251.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: enter alurusort: substringsort.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: setting bit array to zero
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: allocating space for buckets and buffers
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: memsetting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: substring sort ... ok
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: checking valbitarray.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: enter Tprime calculation.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: init arrays.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: scan B
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: iterating i=251 elements with lenB=124.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: exit
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: enter alursortint.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: classify int.
187s init bit array of 16
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: getting bit.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: init bcktsA.
187s init bit array of 16
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: countingsort.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countingsortint: init buffers and A
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: setting buffer to zero
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (1 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (2 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (3 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (to set borders)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: Sorting type S suffixes. Init bcktsB.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 55	69	124.
187s 
187s init bit array of 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: allocating B with 55 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: iterating to lenA=124.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter Qmaxdist.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter Qdist.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter distCount.
187s init bit array of 16
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter get listsS.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: memsetting list of 121 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: iter up to 124.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: scan A
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: set accidst
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: freeing stuff.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter sortlistsS.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: allocating stuff.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: iterating 55 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: looping 121 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: iterating 124 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistsS: exiting happily!
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter tprime.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: init arrays.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: scan B
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: iterating i=124 elements with lenB=55.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: tprime: exit
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter alurusortint.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: classify int.
187s init bit array of 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: getting bit.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: init bcktsA.
187s init bit array of 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: countingsort.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countingsortint: init buffers and A
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: setting buffer to zero
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (1 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (2 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (3 of 3)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: scanning buffer (to set borders)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: countsortint: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: Sorting type S suffixes. Init bcktsB.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 27	28	55.
187s 
187s init bit array of 4
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: allocating B with 27 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: iterating to lenA=55.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: arrayB: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter Qmaxdist.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter Qdist.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter distCount.
187s init bit array of 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter get listsS.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: memsetting list of 54 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: iter up to 55.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: scan A
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: set accidst
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: getlistsS: exiting
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: freeing stuff.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: enter sortlistsS.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: allocating stuff.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: iterating 27 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: looping 54 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistS: iterating 55 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: sortlistsS: exiting happily!
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: alurusortint: valbitarraysortedS.
187s init bit array of 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstructintS.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: init.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: iteration over 124 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: scan B (size: 55).
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: exit.
187s init bit array of 16
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: enter reconstruction.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: init.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: iteration over 251 elems.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: scan B (size: 124).
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reconstruct: exit.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: enter aluruSuffixArrayL start.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: aluruSuffixArrayL: initalizning arrays.
187s init bit array of 32
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: aluruSuffixArrayL: memsetting count.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: aluruSuffixArrayL: setting b.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: aluruSuffixArrayL: iteration.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: aluruSuffixArrayL: exit ok.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing inv_suftab (251).
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: inv_suftab constructed.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing lcp.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: deleting inv_suftab
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing child tab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing suffix links.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing id.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing suflinks - bottom up.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: constructing suflinks - top down.
187s suflink construction. pushes: 177, maxstack: 7
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: building  the suffix array has taken 0.000000 seconds.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: total length of suffix array was 250.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: writing suffix array 'index.idx' to disk.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: Mapping stats:
187s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
187s all	0	0	nan%	0	nan%	0	nan%	0	nan%
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 
187s Goodbye.
187s  "Mahlzeit!" (Ditsche, Ingo, Schildkroede)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading queries in 'myseq.fa'.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 1 query sequences found.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading database sequences.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 1 database sequences found.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: total length of db sequences: 250
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: assigning all reads to default read group 'A1'.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reads assigned to read group 'A1'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: compiled sam header.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading suffix array 'index.idx' from disk.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading lcpc/vtab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading childtab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading suflinks.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading lsint id.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: read suffix array 'index.idx' with 251 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: md5 keys of index and db match.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading the suffix array has taken 0.000000 seconds.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: matching w/ suffixarray has taken 0.000000 seconds.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: Mapping stats:
187s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
187s all	1	0	0.00%	0	0.00%	0	0.00%	0	0.00%
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 
187s Goodbye.
187s  "Mahlzeit!" (Ditsche, Ingo, Schildkroede)
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading queries in 'seq2.fa'.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 1 query sequences found.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading database sequences.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 1 database sequences found.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: total length of db sequences: 250
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: assigning all reads to default read group 'A1'.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: additional read group default values '	SM:sample1	LB:library1	PU:unit1	PL:illumina'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reads assigned to read group 'A1'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: compiled sam header.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading suffix array 'index.idx' from disk.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading lcpc/vtab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading childtab.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading suflinks.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading lsint id.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: PASS Test
187s read suffix array 'index.idx' with 251 elements.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: md5 keys of index and db match.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: reading the suffix array has taken 0.000000 seconds.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: writing multi splits to 'seq2.mult.bed'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: writing sngle splits to 'seq2.sngl.bed'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: writing trans splits to 'seq2.trns.txt'
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: matching w/ suffixarray has taken 0.000000 seconds.
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: Mapping stats:
187s 	total	mapped	(%)	unique	(%)	multi	(%)	split	(%)
187s all	1	0	0.00%	0	0.00%	0	0.00%	0	0.00%
187s [SEGEMEHL] Mon Mar 25 21:29:11 2024: 
187s Goodbye.
187s  "Mahlzeit!" (Ditsche, Ingo, Schildkroede)
187s autopkgtest [21:29:13]: test run-unit-test: -----------------------]
188s run-unit-test        PASS
188s autopkgtest [21:29:14]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
188s autopkgtest [21:29:14]: @@@@@@@@@@@@@@@@@@@@ summary
188s run-unit-test        PASS
200s Creating nova instance adt-noble-s390x-segemehl-20240325-212606-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...