0s autopkgtest [14:06:08]: starting date and time: 2024-03-20 14:06:08+0000
  0s autopkgtest [14:06:08]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [14:06:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q07nf6g6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:crac,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade crac --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=crac/2.5.2+dfsg-6 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@bos03-arm64-14.secgroup --name adt-noble-arm64-crac-20240320-140608-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
106s autopkgtest [14:07:54]: testbed dpkg architecture: arm64
107s autopkgtest [14:07:55]: testbed apt version: 2.7.12
107s autopkgtest [14:07:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup
107s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
107s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB]
107s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3804 kB]
108s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
108s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
108s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [680 kB]
108s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
108s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [41.7 kB]
109s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
109s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4219 kB]
109s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
109s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [56.7 kB]
109s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
111s Fetched 9487 kB in 3s (3558 kB/s)
111s Reading package lists...
114s Reading package lists...
115s Building dependency tree...
115s Reading state information...
115s Calculating upgrade...
115s The following packages will be REMOVED:
115s   libssl3
115s The following NEW packages will be installed:
115s   libssl3t64
115s The following packages have been kept back:
115s   curl
115s The following packages will be upgraded:
115s   openssl
116s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
116s Need to get 2777 kB of archives.
116s After this operation, 139 kB of additional disk space will be used.
116s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
116s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
117s Fetched 2777 kB in 1s (3880 kB/s)
117s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
117s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
117s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
117s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
117s  wget depends on libssl3 (>= 3.0.0).
117s  u-boot-tools depends on libssl3 (>= 3.0.0).
117s  tnftp depends on libssl3 (>= 3.0.0).
117s  tcpdump depends on libssl3 (>= 3.0.0).
117s  systemd-resolved depends on libssl3 (>= 3.0.0).
117s  systemd depends on libssl3 (>= 3.0.0).
117s  sudo depends on libssl3 (>= 3.0.0).
117s  sbsigntool depends on libssl3 (>= 3.0.0).
117s  rsync depends on libssl3 (>= 3.0.0).
117s  python3-cryptography depends on libssl3 (>= 3.0.0).
117s  openssh-server depends on libssl3 (>= 3.0.10).
117s  openssh-client depends on libssl3 (>= 3.0.10).
117s  mtd-utils depends on libssl3 (>= 3.0.0).
117s  mokutil depends on libssl3 (>= 3.0.0).
117s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
117s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
117s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
117s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
117s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
117s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
117s  libnvme1 depends on libssl3 (>= 3.0.0).
117s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
117s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
117s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
117s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
117s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
117s  kmod depends on libssl3 (>= 3.0.0).
117s  dhcpcd-base depends on libssl3 (>= 3.0.0).
117s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
117s 
117s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74758 files and directories currently installed.)
117s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
117s Selecting previously unselected package libssl3t64:arm64.
118s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
118s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
118s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
118s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
118s Setting up openssl (3.0.13-0ubuntu2) ...
118s Processing triggers for man-db (2.12.0-3) ...
118s Processing triggers for libc-bin (2.39-0ubuntu2) ...
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
119s 0 upgraded, 0 newly installed, 0 to remove and 1 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
120s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
122s Reading package lists...
122s Reading package lists...
122s Building dependency tree...
122s Reading state information...
123s Calculating upgrade...
123s The following packages have been kept back:
123s   curl
123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
124s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
126s autopkgtest [14:08:14]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
127s autopkgtest [14:08:15]: @@@@@@@@@@@@@@@@@@@@ apt-source crac
129s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (dsc) [2080 B]
129s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (tar) [658 kB]
129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (diff) [15.2 kB]
129s gpgv: Signature made Tue Mar 19 17:30:31 2024 UTC
129s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
129s gpgv: Can't check signature: No public key
129s dpkg-source: warning: cannot verify inline signature for ./crac_2.5.2+dfsg-6.dsc: no acceptable signature found
129s autopkgtest [14:08:17]: testing package crac version 2.5.2+dfsg-6
129s autopkgtest [14:08:17]: build not needed
130s autopkgtest [14:08:18]: test run-unit-test: preparing testbed
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Starting pkgProblemResolver with broken count: 0
134s Starting 2 pkgProblemResolver with broken count: 0
134s Done
135s The following additional packages will be installed:
135s   crac curl libcurl3t64-gnutls libcurl4t64 libdeflate0 libgkarrays1t64
135s   libgnutls30t64 libgzstream0 libhogweed6t64 libhts3t64 libhtscodecs2
135s   libjellyfish-2.0-2 libnettle8t64 libpsl5t64
135s Suggested packages:
135s   gnutls-bin
135s The following packages will be REMOVED:
135s   libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5
135s The following NEW packages will be installed:
135s   autopkgtest-satdep crac libcurl3t64-gnutls libcurl4t64 libdeflate0
135s   libgkarrays1t64 libgnutls30t64 libgzstream0 libhogweed6t64 libhts3t64
135s   libhtscodecs2 libjellyfish-2.0-2 libnettle8t64 libpsl5t64
135s The following packages will be upgraded:
135s   curl
135s 1 upgraded, 14 newly installed, 6 to remove and 0 not upgraded.
135s Need to get 3524 kB/3524 kB of archives.
135s After this operation, 4866 kB of additional disk space will be used.
135s Get:1 /tmp/autopkgtest.urrPnK/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B]
135s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2 [192 kB]
136s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2 [199 kB]
136s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu2 [1042 kB]
136s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB]
136s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB]
136s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB]
136s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl3t64-gnutls arm64 8.5.0-2ubuntu7 [327 kB]
136s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libgkarrays1t64 arm64 2.1.0+dfsg-4.2 [51.5 kB]
136s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libgzstream0 arm64 1.5+git20171107.9a20658-1 [7406 B]
136s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
136s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
136s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3t64 arm64 1.19+ds-1.1build2 [429 kB]
136s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libjellyfish-2.0-2 arm64 2.3.1-2build1 [65.8 kB]
136s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 crac arm64 2.5.2+dfsg-6 [477 kB]
137s Fetched 3524 kB in 1s (4158 kB/s)
137s dpkg: libhogweed6:arm64: dependency problems, but removing anyway as you requested:
137s  librtmp1:arm64 depends on libhogweed6.
137s  libjcat1:arm64 depends on libhogweed6.
137s  libgnutls30:arm64 depends on libhogweed6 (>= 3.6).
137s 
137s (Reading database ... 
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(Reading database ... 74760 files and directories currently installed.)
137s Removing libhogweed6:arm64 (3.9.1-2) ...
137s dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested:
137s  librtmp1:arm64 depends on libnettle8.
137s  libgnutls30:arm64 depends on libnettle8 (>= 3.9~).
137s  libcurl3-gnutls:arm64 depends on libnettle8.
137s  libarchive13:arm64 depends on libnettle8.
137s 
137s Removing libnettle8:arm64 (3.9.1-2) ...
137s Selecting previously unselected package libnettle8t64:arm64.
137s (Reading database ... 
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(Reading database ... 74748 files and directories currently installed.)
137s Preparing to unpack .../libnettle8t64_3.9.1-2.2_arm64.deb ...
137s Unpacking libnettle8t64:arm64 (3.9.1-2.2) ...
137s Selecting previously unselected package libhogweed6t64:arm64.
137s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_arm64.deb ...
137s Unpacking libhogweed6t64:arm64 (3.9.1-2.2) ...
137s dpkg: libgnutls30:arm64: dependency problems, but removing anyway as you requested:
137s  u-boot-tools depends on libgnutls30 (>= 3.7.3).
137s  librtmp1:arm64 depends on libgnutls30 (>= 3.7.2).
137s  libldap2:arm64 depends on libgnutls30 (>= 3.8.2).
137s  libjcat1:arm64 depends on libgnutls30 (>= 3.7.3).
137s  libcurl3-gnutls:arm64 depends on libgnutls30 (>= 3.8.2).
137s  fwupd depends on libgnutls30 (>= 3.7.3).
137s  dirmngr depends on libgnutls30 (>= 3.8.1).
137s  apt depends on libgnutls30 (>= 3.8.1).
137s 
137s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74762 files and directories currently installed.)
137s Removing libgnutls30:arm64 (3.8.3-1ubuntu1) ...
137s Selecting previously unselected package libgnutls30t64:arm64.
137s (Reading database ... 
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(Reading database ... 74753 files and directories currently installed.)
137s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_arm64.deb ...
137s Unpacking libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ...
137s dpkg: libcurl4:arm64: dependency problems, but removing anyway as you requested:
137s  curl depends on libcurl4 (= 8.5.0-2ubuntu2).
137s 
137s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74781 files and directories currently installed.)
137s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ...
137s Selecting previously unselected package libcurl4t64:arm64.
137s (Reading database ... 
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(Reading database ... 74776 files and directories currently installed.)
137s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ...
137s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ...
137s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ...
137s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ...
138s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested:
138s  wget depends on libpsl5 (>= 0.16.0).
138s  libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0).
138s 
138s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74782 files and directories currently installed.)
138s Removing libpsl5:arm64 (0.21.2-1build1) ...
138s Selecting previously unselected package libpsl5t64:arm64.
138s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74777 files and directories currently installed.)
138s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ...
138s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ...
138s dpkg: libcurl3-gnutls:arm64: dependency problems, but removing anyway as you requested:
138s  libfwupd2:arm64 depends on libcurl3-gnutls (>= 7.63.0).
138s  fwupd depends on libcurl3-gnutls (>= 7.63.0).
138s 
138s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74783 files and directories currently installed.)
138s Removing libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ...
138s Selecting previously unselected package libcurl3t64-gnutls:arm64.
138s (Reading database ... 
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(Reading database ... 74776 files and directories currently installed.)
138s Preparing to unpack .../0-libcurl3t64-gnutls_8.5.0-2ubuntu7_arm64.deb ...
138s Unpacking libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ...
138s Selecting previously unselected package libgkarrays1t64.
138s Preparing to unpack .../1-libgkarrays1t64_2.1.0+dfsg-4.2_arm64.deb ...
138s Unpacking libgkarrays1t64 (2.1.0+dfsg-4.2) ...
138s Selecting previously unselected package libgzstream0:arm64.
138s Preparing to unpack .../2-libgzstream0_1.5+git20171107.9a20658-1_arm64.deb ...
138s Unpacking libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
138s Selecting previously unselected package libdeflate0:arm64.
138s Preparing to unpack .../3-libdeflate0_1.19-1_arm64.deb ...
138s Unpacking libdeflate0:arm64 (1.19-1) ...
138s Selecting previously unselected package libhtscodecs2:arm64.
138s Preparing to unpack .../4-libhtscodecs2_1.6.0-1_arm64.deb ...
138s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
138s Selecting previously unselected package libhts3t64:arm64.
138s Preparing to unpack .../5-libhts3t64_1.19+ds-1.1build2_arm64.deb ...
138s Unpacking libhts3t64:arm64 (1.19+ds-1.1build2) ...
138s Selecting previously unselected package libjellyfish-2.0-2:arm64.
138s Preparing to unpack .../6-libjellyfish-2.0-2_2.3.1-2build1_arm64.deb ...
138s Unpacking libjellyfish-2.0-2:arm64 (2.3.1-2build1) ...
138s Selecting previously unselected package crac.
138s Preparing to unpack .../7-crac_2.5.2+dfsg-6_arm64.deb ...
138s Unpacking crac (2.5.2+dfsg-6) ...
138s Selecting previously unselected package autopkgtest-satdep.
138s Preparing to unpack .../8-1-autopkgtest-satdep.deb ...
138s Unpacking autopkgtest-satdep (0) ...
138s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
138s Setting up libpsl5t64:arm64 (0.21.2-1.1) ...
138s Setting up libdeflate0:arm64 (1.19-1) ...
138s Setting up libgkarrays1t64 (2.1.0+dfsg-4.2) ...
138s Setting up libjellyfish-2.0-2:arm64 (2.3.1-2build1) ...
138s Setting up libnettle8t64:arm64 (3.9.1-2.2) ...
138s Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
138s Setting up libhogweed6t64:arm64 (3.9.1-2.2) ...
138s Setting up libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ...
138s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ...
138s Setting up libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu7) ...
138s Setting up libhts3t64:arm64 (1.19+ds-1.1build2) ...
138s Setting up crac (2.5.2+dfsg-6) ...
138s Setting up curl (8.5.0-2ubuntu7) ...
138s Setting up autopkgtest-satdep (0) ...
138s Processing triggers for man-db (2.12.0-3) ...
139s Processing triggers for libc-bin (2.39-0ubuntu2) ...
143s (Reading database ... 74955 files and directories currently installed.)
143s Removing autopkgtest-satdep (0) ...
144s autopkgtest [14:08:32]: test run-unit-test: [-----------------------
145s Launching ' crac -i ../../test_f/cigar/genome -r reads_k18.fasta -k 18 -o ../../test_f/cigar/consistency2.sam'
145s ==> ../../test_f/cigar/consistency2.tap
145s 
145s Launching ' crac -i ../../test_f/cigar/genome -r reads_sam1.fasta reads_sam2.fasta -k 10 -o ../../test_f/cigar/consistency3.sam --treat-multiple 100 --use-x-in-cigar'
145s ==> ../../test_f/cigar/consistency3.tap
145s 
145s Launching ' crac -i ../../test_f/cigar/genome -r reads.fasta -k 22 -o ../../test_f/cigar/consistency.sam --detailed-sam --reads-index GKARRAYS --use-x-in-cigar --min-chimera-score 0'
145s ==> ../../test_f/cigar/consistency.tap
145s 
145s Launching ' crac -i ../../test_f/bug/bug-16502-genome -r bug-16502-read.fa -k 22 -o ../../test_f/bug/bug-16502.sam --reads-index GKARRAYS'
145s ==> ../../test_f/bug/bug-16502.tap
145s 
145s Launching ' crac -i ../../test_f/bug/bug-18524-genome -r bug-18524-read.fa -k 22 -o ../../test_f/bug/bug-18524.sam --detailed-sam'
146s ==> ../../test_f/bug/bug-18524.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18409-genome -r bug-18409-read.fa --detailed-sam -k 22 -o /dev/stdout | tr ';' '\n''
146s ==> ./bug-18409.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15672-genome -r bug-15672-read.fa -k 22 -o ../../test_f/bug/bug-15672.sam --detailed-sam'
146s ==> ../../test_f/bug/bug-15672.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15639-genome -r bug-15639-read.fa -k 22 -o ../../test_f/bug/bug-15639.sam'
146s ==> ../../test_f/bug/bug-15639.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15649-genome-2 -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649-2.sam'
146s ==> ../../test_f/bug/bug-15649-2.tap
146s 
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15605_2-genome -r bug-15605_2-read.fa -k 22 -o ../../test_f/bug/bug-15605_2.sam --detailed-sam'
146s ==> ../../test_f/bug/bug-15605_2.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18793-genome -r bug-18793-read.fa -k 22 -o ../../test_f/bug/bug-18793.sam --detailed-sam --reads-index GKARRAYS'
146s ==> ../../test_f/bug/bug-18793.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15677-genome -r bug-15677-read.fa -k 22 -o ../../test_f/bug/bug-15677.sam'
146s ==> ../../test_f/bug/bug-15677.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-16403-genome -r bug-16403-read.fa -k 20 -o ../../test_f/bug/bug-16931.sam'
146s ==> ../../test_f/bug/bug-16931.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-16581-genome -r bug-16581-read.fq -m 25 -k 22 -o ../../test_f/bug/bug-16581.sam'
146s ==> ../../test_f/bug/bug-16581.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-case-sensitive-genome -r bug-case-sensitive-read.fa -k 12 -o ../../test_f/bug/bug-case-sensitive.sam --detailed-sam'
146s ==> ../../test_f/bug/bug-case-sensitive.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15847-genome -r bug-15847-read.fa -k 22 --treat-multiple 36 --detailed-sam -o ../../test_f/bug/bug-15847.sam'
146s ==> ../../test_f/bug/bug-15847.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15646-genome -r bug-15646-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15646.sam'
146s ==> ../../test_f/bug/bug-15646.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18522-genome -r bug-18522-read.fa -k 10 -o ../../test_f/bug/bug-18522.sam --treat-multiple 2'
146s ==> ../../test_f/bug/bug-18522.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15630-genome -r bug-15630-read.fa --detailed-sam -k 18 -o ../../test_f/bug/bug-15630.sam'
146s ==> ../../test_f/bug/bug-15630.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18180-genome -r bug-18180-read.fa --detailed-sam --emt -k 18 -o ../../test_f/bug/bug-18180.sam'
146s Warning: Running CRAC--emt with k=18 which means that it only maps the first located kmer of length 18 for each read
146s ==> ../../test_f/bug/bug-18180.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-17749-genome -r bug-17749-read.fa -k 22 -o ../../test_f/bug/bug-17749.sam --max-splice-length 100 --max-extension-length 2 --min-chimera-score 0'
146s ==> ../../test_f/bug/bug-17749.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-17175-genome -r bug-17175-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-17175.sam --use-x-in-cigar'
146s ==> ../../test_f/bug/bug-17175.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-2015-12-08-genome -r bug-2015-12-08-read1.fa bug-2015-12-08-read2.fa -k 22 -o ../../test_f/bug/bug-2015-12-08.sam --detailed-sam --reads-index GKARRAYS'
146s ==> ../../test_f/bug/bug-2015-12-08.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18435-genome -r bug-18435-read.fa -k 22 -o ../../test_f/bug/bug-18435.sam'
146s ==> ../../test_f/bug/bug-18435.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15649-genome -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649.sam'
146s ==> ../../test_f/bug/bug-15649.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-15605-genome -r bug-15605-read.fa -k 22 -o ../../test_f/bug/bug-15605.sam --detailed-sam'
146s ==> ../../test_f/bug/bug-15605.tap
146s 
146s Launching ' crac -i ../../test_f/bug/bug-18568-genome -r bug-18568-read.fa -k 22 -o ../../test_f/bug/bug-18568.sam --detailed-sam --reads-index GKARRAYS'
146s ==> ../../test_f/bug/bug-18568.tap
146s 
146s Launching ' crac -i ../../test_f/causes/genome -r snp.fa -k 22 --deep-snv --nb-nucleotides-snv-comparison 3 -o ../../test_f/causes/snp.sam --detailed-sam --use-x-in-cigar'
146s ==> ../../test_f/causes/snp.fa.tap
146s 
147s Launching ' crac -i ../../test_f/causes/genome -r biotag.fa -k 22 -o ../../test_f/causes/biotag.sam --detailed-sam --use-x-in-cigar'
147s ==> ../../test_f/causes/biotag.fa.tap
147s 
147s Launching ' crac -i ../../test_f/splices_adjust/genome -r splice.fa -k 22 -o ../../test_f/splices_adjust/splice.sam --detailed-sam'
147s ==> ../../test_f/splices_adjust/splice.tap
147s 
148s autopkgtest [14:08:36]: test run-unit-test: -----------------------]
148s run-unit-test        PASS
148s autopkgtest [14:08:36]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
148s autopkgtest [14:08:36]: @@@@@@@@@@@@@@@@@@@@ summary
148s run-unit-test        PASS
160s Creating nova instance adt-noble-arm64-crac-20240320-140608-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240320.img (UUID e0f61a12-2f1c-4e49-a68b-f68d2ad5dd10)...