0s autopkgtest [18:11:20]: starting date and time: 2024-03-24 18:11:20+0000
  0s autopkgtest [18:11:20]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [18:11:20]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lpdoglmu/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade stringtie --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-19.secgroup --name adt-noble-arm64-stringtie-20240324-175540-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://us.ports.ubuntu.com/ubuntu-ports/
 91s autopkgtest [18:12:51]: testbed dpkg architecture: arm64
 91s autopkgtest [18:12:51]: testbed apt version: 2.7.12
 91s autopkgtest [18:12:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB]
 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB]
 92s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 92s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
 92s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB]
 92s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 92s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB]
 92s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 92s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB]
 93s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 93s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB]
 93s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 95s Fetched 9851 kB in 2s (5389 kB/s)
 95s Reading package lists...
 98s Reading package lists...
 98s Building dependency tree...
 98s Reading state information...
 99s Calculating upgrade...
 99s The following packages will be REMOVED:
 99s   libssl3
 99s The following NEW packages will be installed:
 99s   libssl3t64
 99s The following packages have been kept back:
 99s   curl
 99s The following packages will be upgraded:
 99s   openssl
 99s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 99s Need to get 2777 kB of archives.
 99s After this operation, 139 kB of additional disk space will be used.
 99s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
100s Fetched 2777 kB in 1s (4098 kB/s)
100s (Reading database ... 
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(Reading database ... 75911 files and directories currently installed.)
100s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
100s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
100s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
100s  wget depends on libssl3 (>= 3.0.0).
100s  u-boot-tools depends on libssl3 (>= 3.0.0).
100s  tnftp depends on libssl3 (>= 3.0.0).
100s  tcpdump depends on libssl3 (>= 3.0.0).
100s  systemd-resolved depends on libssl3 (>= 3.0.0).
100s  systemd depends on libssl3 (>= 3.0.0).
100s  sudo depends on libssl3 (>= 3.0.0).
100s  sbsigntool depends on libssl3 (>= 3.0.0).
100s  rsync depends on libssl3 (>= 3.0.0).
100s  python3-cryptography depends on libssl3 (>= 3.0.0).
100s  openssh-server depends on libssl3 (>= 3.0.10).
100s  openssh-client depends on libssl3 (>= 3.0.10).
100s  mtd-utils depends on libssl3 (>= 3.0.0).
100s  mokutil depends on libssl3 (>= 3.0.0).
100s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
100s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
100s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
100s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
100s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
100s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
100s  libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0).
100s  libnvme1 depends on libssl3 (>= 3.0.0).
100s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
100s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
100s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
100s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
100s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
100s  kmod depends on libssl3 (>= 3.0.0).
100s  dhcpcd-base depends on libssl3 (>= 3.0.0).
100s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
100s 
100s (Reading database ... 
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(Reading database ... 75911 files and directories currently installed.)
100s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
100s Selecting previously unselected package libssl3t64:arm64.
100s (Reading database ... 
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(Reading database ... 75900 files and directories currently installed.)
100s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
100s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
100s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
100s Setting up openssl (3.0.13-0ubuntu2) ...
100s Processing triggers for man-db (2.12.0-3) ...
101s Processing triggers for libc-bin (2.39-0ubuntu6) ...
101s Reading package lists...
101s Building dependency tree...
101s Reading state information...
102s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
103s sh: Attempting to set up Debian/Ubuntu apt sources automatically
103s sh: Distribution appears to be Ubuntu
103s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s eatmydata is already the newest version (131-1).
104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
104s Reading package lists...
105s Building dependency tree...
105s Reading state information...
105s dbus is already the newest version (1.14.10-4ubuntu1).
105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
105s Reading package lists...
106s Building dependency tree...
106s Reading state information...
106s rng-tools-debian is already the newest version (2.4).
106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
107s The following packages will be REMOVED:
107s   cloud-init* python3-configobj* python3-debconf*
120s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
120s After this operation, 3256 kB disk space will be freed.
120s (Reading database ... 
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(Reading database ... 75913 files and directories currently installed.)
120s Removing cloud-init (24.1.2-0ubuntu1) ...
120s Removing python3-configobj (5.0.8-3) ...
120s Removing python3-debconf (1.5.86) ...
120s Processing triggers for man-db (2.12.0-3) ...
121s (Reading database ... 
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(Reading database ... 75524 files and directories currently installed.)
121s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
121s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
121s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
121s invoke-rc.d: policy-rc.d denied execution of try-restart.
121s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s linux-generic is already the newest version (6.8.0-11.11+1).
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
123s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
123s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
123s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
125s Reading package lists...
125s Reading package lists...
126s Building dependency tree...
126s Reading state information...
126s Calculating upgrade...
126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
127s Reading package lists...
127s Building dependency tree...
127s Reading state information...
127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s autopkgtest [18:13:28]: rebooting testbed after setup commands that affected boot
277s autopkgtest [18:15:57]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
279s autopkgtest [18:15:59]: @@@@@@@@@@@@@@@@@@@@ apt-source stringtie
281s Get:1 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (dsc) [2391 B]
281s Get:2 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [1756 kB]
281s Get:3 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [295 kB]
281s Get:4 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (diff) [11.8 kB]
281s gpgv: Signature made Fri Jan 26 20:37:21 2024 UTC
281s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
281s gpgv:                issuer "tille@debian.org"
281s gpgv: Can't check signature: No public key
281s dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-3.dsc: no acceptable signature found
282s autopkgtest [18:16:02]: testing package stringtie version 2.2.1+ds-3
282s autopkgtest [18:16:02]: build not needed
283s autopkgtest [18:16:03]: test run-unit-test: preparing testbed
288s Reading package lists...
288s Building dependency tree...
288s Reading state information...
289s Starting pkgProblemResolver with broken count: 0
289s Starting 2 pkgProblemResolver with broken count: 0
289s Done
289s The following additional packages will be installed:
289s   libdeflate0 libhts3 libhtscodecs2 samtools stringtie
289s Suggested packages:
289s   cwltool cufflinks
289s Recommended packages:
289s   stringtie-examples
289s The following NEW packages will be installed:
289s   autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools stringtie
290s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
290s Need to get 1418 kB/1419 kB of archives.
290s After this operation, 3739 kB of additional disk space will be used.
290s Get:1 /tmp/autopkgtest.t3f6Ct/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
290s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
290s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
290s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
290s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB]
290s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 stringtie arm64 2.2.1+ds-3 [290 kB]
291s Fetched 1418 kB in 1s (1697 kB/s)
291s Selecting previously unselected package libdeflate0:arm64.
291s (Reading database ... 
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(Reading database ... 75469 files and directories currently installed.)
291s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ...
291s Unpacking libdeflate0:arm64 (1.19-1) ...
291s Selecting previously unselected package libhtscodecs2:arm64.
291s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ...
291s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
291s Selecting previously unselected package libhts3:arm64.
291s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ...
291s Unpacking libhts3:arm64 (1.18+ds-1) ...
291s Selecting previously unselected package samtools.
291s Preparing to unpack .../3-samtools_1.19.2-1_arm64.deb ...
291s Unpacking samtools (1.19.2-1) ...
291s Selecting previously unselected package stringtie.
291s Preparing to unpack .../4-stringtie_2.2.1+ds-3_arm64.deb ...
291s Unpacking stringtie (2.2.1+ds-3) ...
291s Selecting previously unselected package autopkgtest-satdep.
291s Preparing to unpack .../5-1-autopkgtest-satdep.deb ...
291s Unpacking autopkgtest-satdep (0) ...
291s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
291s Setting up libdeflate0:arm64 (1.19-1) ...
291s Setting up libhts3:arm64 (1.18+ds-1) ...
291s Setting up samtools (1.19.2-1) ...
291s Setting up stringtie (2.2.1+ds-3) ...
291s Setting up autopkgtest-satdep (0) ...
291s Processing triggers for man-db (2.12.0-3) ...
291s Processing triggers for libc-bin (2.39-0ubuntu6) ...
294s (Reading database ... 75585 files and directories currently installed.)
294s Removing autopkgtest-satdep (0) ...
295s autopkgtest [18:16:15]: test run-unit-test: [-----------------------
295s + pkg=stringtie
295s ++ pwd
295s + CUR_DIR=/tmp/autopkgtest.t3f6Ct/build.0gW/src
295s + '[' /tmp/autopkgtest.t3f6Ct/autopkgtest_tmp = '' ']'
295s + cp /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/README.md /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/human-chr19_P.gff /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/long_reads.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/long_reads.sam /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/long_reads_guided.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/mix_guides.gff /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/mix_long.sam /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/mix_reads.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/mix_reads_guided.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/mix_short.sam /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/short_reads.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/short_reads.sam /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/short_reads_and_superreads.out_expected.gtf /tmp/autopkgtest.t3f6Ct/build.0gW/src/debian-tests-data/short_reads_and_superreads.sam -a /tmp/autopkgtest.t3f6Ct/autopkgtest_tmp
295s + cd /tmp/autopkgtest.t3f6Ct/autopkgtest_tmp
295s + gunzip -r README.md human-chr19_P.gff long_reads.out_expected.gtf long_reads.sam long_reads_guided.out_expected.gtf mix_guides.gff mix_long.sam mix_reads.out_expected.gtf mix_reads_guided.out_expected.gtf mix_short.sam short_reads.out_expected.gtf short_reads.sam short_reads_and_superreads.out_expected.gtf short_reads_and_superreads.sam
295s + for f in *.sam
295s + outfile=long_reads.bam
295s + cat long_reads.sam
295s + samtools view -Sb -
295s + for f in *.sam
295s + outfile=mix_long.bam
295s + cat mix_long.sam
295s + samtools view -Sb -
295s + for f in *.sam
295s + outfile=mix_short.bam
295s + cat mix_short.sam
295s + samtools view -Sb -
295s + for f in *.sam
295s + outfile=short_reads.bam
295s + cat short_reads.sam
295s + samtools view -Sb -
295s + for f in *.sam
295s + outfile=short_reads_and_superreads.bam
295s + cat short_reads_and_superreads.sam
295s + samtools view -Sb -
295s + arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" "mix_short mix_long" "mix_short mix_long")
295s + arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff")
295s + arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" "mix_reads" "mix_reads_guided")
295s + arrmsg=("Short reads" "Short reads and super-reads" "Long reads" "Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides")
295s + for i in ${!arrmsg[@]}
295s + fout=short_reads.out.gtf
295s + /bin/rm -f short_reads.out.gtf
295s + fcmp=short_reads.out_expected.gtf
295s + n=0
295s + echo 0
295s + n=1
295s + echo 'Test 1: Short reads'
295s + fin=short_reads.bam
295s + [[ short_reads =~ ^mix ]]
295s + echo short_reads.out.gtf short_reads.bam
295s + stringtie -o short_reads.out.gtf short_reads.bam
295s 0
295s Test 1: Short reads
295s short_reads.out.gtf short_reads.bam
295s + '[' '!' -f short_reads.out.gtf ']'
295s + diff -q -I '^#' short_reads.out.gtf short_reads.out_expected.gtf
295s   OK.
295s + echo '  OK.'
295s + for i in ${!arrmsg[@]}
295s + fout=short_reads_and_superreads.out.gtf
295s + /bin/rm -f short_reads_and_superreads.out.gtf
295s + fcmp=short_reads_and_superreads.out_expected.gtf
295s + n=1
295s + echo 1
295s + n=2
295s + echo 'Test 2: Short reads and super-reads'
295s + fin=short_reads_and_superreads.bam
295s + [[ short_reads_and_superreads =~ ^mix ]]
295s + echo short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
295s + stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
295s 1
295s Test 2: Short reads and super-reads
295s short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
295s + '[' '!' -f short_reads_and_superreads.out.gtf ']'
295s + diff -q -I '^#' short_reads_and_superreads.out.gtf short_reads_and_superreads.out_expected.gtf
295s + echo '  OK.'
295s + for i in ${!arrmsg[@]}
295s + fout=long_reads.out.gtf
295s + /bin/rm -f long_reads.out.gtf
295s   OK.
295s 2
295s + fcmp=long_reads.out_expected.gtf
295s + n=2
295s + echo 2
295s + n=3
295s Test 3: Long reads
295s -L long_reads.out.gtf long_reads.bam
295s + echo 'Test 3: Long reads'
295s + fin=long_reads.bam
295s + [[ long_reads =~ ^mix ]]
295s + echo -L long_reads.out.gtf long_reads.bam
295s + stringtie -L -o long_reads.out.gtf long_reads.bam
295s + '[' '!' -f long_reads.out.gtf ']'
295s + diff -q -I '^#' long_reads.out.gtf long_reads.out_expected.gtf
295s + echo '  OK.'
295s + for i in ${!arrmsg[@]}
295s   OK.
295s + fout=long_reads_guided.out.gtf
295s + /bin/rm -f long_reads_guided.out.gtf
295s 3
295s + fcmp=long_reads_guided.out_expected.gtf
295s + n=3
295s + echo 3
295s + n=4
295s + echo 'Test 4: Long reads with annotation guides'
295s + fin=long_reads.bam
295s + [[ long_reads =~ ^mix ]]
295s + echo -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
295s + stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
295s Test 4: Long reads with annotation guides
295s -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
295s + '[' '!' -f long_reads_guided.out.gtf ']'
295s + diff -q -I '^#' long_reads_guided.out.gtf long_reads_guided.out_expected.gtf
295s + echo '  OK.'
295s + for i in ${!arrmsg[@]}
295s + fout=mix_reads.out.gtf
295s   OK.
295s + /bin/rm -f mix_reads.out.gtf
295s + fcmp=mix_reads.out_expected.gtf
295s + n=4
295s + echo 4
295s 4
295s + n=5
295s + echo 'Test 5: Mixed reads'
295s + fin='mix_short mix_long.bam'
295s + [[ mix_short mix_long =~ ^mix ]]
295s + ins=(${arrins[$i]})
295s + fin='mix_short.bam mix_long.bam'
295s + echo --mix mix_reads.out.gtf mix_short.bam mix_long.bam
295s + stringtie --mix -o mix_reads.out.gtf mix_short.bam mix_long.bam
295s Test 5: Mixed reads
295s --mix mix_reads.out.gtf mix_short.bam mix_long.bam
295s + '[' '!' -f mix_reads.out.gtf ']'
295s + diff -q -I '^#' mix_reads.out.gtf mix_reads.out_expected.gtf
295s + echo '  OK.'
295s   OK.
295s + for i in ${!arrmsg[@]}
295s + fout=mix_reads_guided.out.gtf
295s + /bin/rm -f mix_reads_guided.out.gtf
295s + fcmp=mix_reads_guided.out_expected.gtf
295s + n=5
295s + echo 5
295s + n=6
295s + echo 'Test 6: Mixed reads with annotation guides'
295s + fin='mix_short mix_long.bam'
295s + [[ mix_short mix_long =~ ^mix ]]
295s 5
295s Test 6: Mixed reads with annotation guides
295s + ins=(${arrins[$i]})
295s --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
295s + fin='mix_short.bam mix_long.bam'
295s + echo --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
295s + stringtie --mix -G mix_guides.gff -o mix_reads_guided.out.gtf mix_short.bam mix_long.bam
295s + '[' '!' -f mix_reads_guided.out.gtf ']'
295s + diff -q -I '^#' mix_reads_guided.out.gtf mix_reads_guided.out_expected.gtf
295s + echo '  OK.'
295s   OK.
296s autopkgtest [18:16:16]: test run-unit-test: -----------------------]
296s autopkgtest [18:16:16]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
296s run-unit-test        PASS
296s autopkgtest [18:16:16]: @@@@@@@@@@@@@@@@@@@@ summary
296s run-unit-test        PASS
312s Creating nova instance adt-noble-arm64-stringtie-20240324-175540-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...