0s autopkgtest [15:50:01]: starting date and time: 2024-03-23 15:50:01+0000
  0s autopkgtest [15:50:01]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [15:50:01]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.16k85hcz/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@bos02-ppc64el-8.secgroup --name adt-noble-ppc64el-stringtie-20240323-155001-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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://ftpmaster.internal/ubuntu/
 89s autopkgtest [15:51:30]: testbed dpkg architecture: ppc64el
 89s autopkgtest [15:51:30]: testbed apt version: 2.7.12
 89s autopkgtest [15:51:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 90s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 90s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 90s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB]
 90s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB]
 90s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB]
 91s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB]
 91s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
 91s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
 91s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
 91s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB]
 92s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
 92s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB]
 92s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
 95s Fetched 9623 kB in 3s (3448 kB/s)
 95s Reading package lists...
 97s Reading package lists...
 98s Building dependency tree...
 98s Reading state information...
 98s Calculating upgrade...
 98s The following packages will be REMOVED:
 98s   libssl3
 98s The following NEW packages will be installed:
 98s   libssl3t64
 98s The following packages have been kept back:
 98s   curl
 98s The following packages will be upgraded:
 98s   openssl
 98s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 98s Need to get 3151 kB of archives.
 98s After this operation, 73.7 kB of additional disk space will be used.
 98s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
 99s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
 99s Fetched 3151 kB in 1s (3647 kB/s)
 99s (Reading database ... 
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(Reading database ... 70156 files and directories currently installed.)
 99s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
 99s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
 99s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
 99s  wget depends on libssl3 (>= 3.0.0).
 99s  tnftp depends on libssl3 (>= 3.0.0).
 99s  tcpdump depends on libssl3 (>= 3.0.0).
 99s  systemd-resolved depends on libssl3 (>= 3.0.0).
 99s  systemd depends on libssl3 (>= 3.0.0).
 99s  sudo depends on libssl3 (>= 3.0.0).
 99s  rsync depends on libssl3 (>= 3.0.0).
 99s  python3-cryptography depends on libssl3 (>= 3.0.0).
 99s  openssh-server depends on libssl3 (>= 3.0.10).
 99s  openssh-client depends on libssl3 (>= 3.0.10).
 99s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 99s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libnvme1 depends on libssl3 (>= 3.0.0).
 99s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
 99s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
 99s  kmod depends on libssl3 (>= 3.0.0).
 99s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 99s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
 99s 
 99s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70156 files and directories currently installed.)
 99s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
 99s Selecting previously unselected package libssl3t64:ppc64el.
 99s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70145 files and directories currently installed.)
 99s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
 99s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
 99s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
 99s Setting up openssl (3.0.13-0ubuntu2) ...
 99s Processing triggers for man-db (2.12.0-3) ...
100s Processing triggers for libc-bin (2.39-0ubuntu6) ...
100s Reading package lists...
100s Building dependency tree...
100s Reading state information...
101s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
101s sh: Attempting to set up Debian/Ubuntu apt sources automatically
101s sh: Distribution appears to be Ubuntu
102s Reading package lists...
102s Building dependency tree...
102s Reading state information...
103s eatmydata is already the newest version (131-1).
103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
103s dbus is already the newest version (1.14.10-4ubuntu1).
103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
103s rng-tools-debian is already the newest version (2.4).
103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
104s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s The following packages will be REMOVED:
104s   cloud-init* python3-configobj* python3-debconf*
104s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
104s After this operation, 3256 kB disk space will be freed.
104s (Reading database ... 
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(Reading database ... 70158 files and directories currently installed.)
104s Removing cloud-init (24.1.2-0ubuntu1) ...
105s Removing python3-configobj (5.0.8-3) ...
105s Removing python3-debconf (1.5.86) ...
105s Processing triggers for man-db (2.12.0-3) ...
105s (Reading database ... 
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(Reading database ... 69769 files and directories currently installed.)
105s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
106s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
106s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
106s invoke-rc.d: policy-rc.d denied execution of try-restart.
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
107s linux-generic is already the newest version (6.8.0-11.11+1).
107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
107s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
107s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
107s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
110s Reading package lists...
110s Reading package lists...
110s Building dependency tree...
110s Reading state information...
111s Calculating upgrade...
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
111s Reading package lists...
111s Building dependency tree...
111s Reading state information...
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
111s autopkgtest [15:51:52]: rebooting testbed after setup commands that affected boot
281s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
287s autopkgtest [15:54:48]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
289s autopkgtest [15:54:50]: @@@@@@@@@@@@@@@@@@@@ apt-source stringtie
292s Get:1 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (dsc) [2391 B]
292s Get:2 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [1756 kB]
292s Get:3 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [295 kB]
292s Get:4 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (diff) [11.8 kB]
292s gpgv: Signature made Fri Jan 26 20:37:21 2024 UTC
292s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
292s gpgv:                issuer "tille@debian.org"
292s gpgv: Can't check signature: No public key
292s dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-3.dsc: no acceptable signature found
292s autopkgtest [15:54:53]: testing package stringtie version 2.2.1+ds-3
293s autopkgtest [15:54:54]: build not needed
295s autopkgtest [15:54:56]: test run-unit-test: preparing testbed
304s Reading package lists...
304s Building dependency tree...
304s Reading state information...
304s Starting pkgProblemResolver with broken count: 0
304s Starting 2 pkgProblemResolver with broken count: 0
304s Done
304s The following additional packages will be installed:
304s   libdeflate0 libhts3 libhtscodecs2 samtools stringtie
304s Suggested packages:
304s   cwltool cufflinks
304s Recommended packages:
304s   stringtie-examples
304s The following NEW packages will be installed:
304s   autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools stringtie
304s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
304s Need to get 1783 kB/1784 kB of archives.
304s After this operation, 4922 kB of additional disk space will be used.
304s Get:1 /tmp/autopkgtest.WpZyrl/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B]
304s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
305s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
305s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB]
305s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB]
305s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el stringtie ppc64el 2.2.1+ds-3 [390 kB]
305s Fetched 1783 kB in 1s (2674 kB/s)
305s Selecting previously unselected package libdeflate0:ppc64el.
305s (Reading database ... 
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(Reading database ... 69714 files and directories currently installed.)
305s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ...
305s Unpacking libdeflate0:ppc64el (1.19-1) ...
305s Selecting previously unselected package libhtscodecs2:ppc64el.
305s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ...
305s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
305s Selecting previously unselected package libhts3:ppc64el.
305s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ...
305s Unpacking libhts3:ppc64el (1.18+ds-1) ...
305s Selecting previously unselected package samtools.
305s Preparing to unpack .../3-samtools_1.19.2-1_ppc64el.deb ...
305s Unpacking samtools (1.19.2-1) ...
305s Selecting previously unselected package stringtie.
305s Preparing to unpack .../4-stringtie_2.2.1+ds-3_ppc64el.deb ...
305s Unpacking stringtie (2.2.1+ds-3) ...
305s Selecting previously unselected package autopkgtest-satdep.
305s Preparing to unpack .../5-1-autopkgtest-satdep.deb ...
305s Unpacking autopkgtest-satdep (0) ...
305s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
305s Setting up libdeflate0:ppc64el (1.19-1) ...
305s Setting up libhts3:ppc64el (1.18+ds-1) ...
305s Setting up samtools (1.19.2-1) ...
305s Setting up stringtie (2.2.1+ds-3) ...
305s Setting up autopkgtest-satdep (0) ...
305s Processing triggers for man-db (2.12.0-3) ...
306s Processing triggers for libc-bin (2.39-0ubuntu6) ...
308s (Reading database ... 69830 files and directories currently installed.)
308s Removing autopkgtest-satdep (0) ...
308s autopkgtest [15:55:09]: test run-unit-test: [-----------------------
309s + pkg=stringtie
309s ++ pwd
309s + CUR_DIR=/tmp/autopkgtest.WpZyrl/build.Evz/src
309s + '[' /tmp/autopkgtest.WpZyrl/autopkgtest_tmp = '' ']'
309s + cp /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/README.md /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/human-chr19_P.gff /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/long_reads.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/long_reads.sam /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/long_reads_guided.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/mix_guides.gff /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/mix_long.sam /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/mix_reads.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/mix_reads_guided.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/mix_short.sam /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/short_reads.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/short_reads.sam /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/short_reads_and_superreads.out_expected.gtf /tmp/autopkgtest.WpZyrl/build.Evz/src/debian-tests-data/short_reads_and_superreads.sam -a /tmp/autopkgtest.WpZyrl/autopkgtest_tmp
309s + cd /tmp/autopkgtest.WpZyrl/autopkgtest_tmp
309s + 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
309s + for f in *.sam
309s + outfile=long_reads.bam
309s + cat long_reads.sam
309s + samtools view -Sb -
309s + for f in *.sam
309s + outfile=mix_long.bam
309s + cat mix_long.sam
309s + samtools view -Sb -
309s + for f in *.sam
309s + outfile=mix_short.bam
309s + cat mix_short.sam
309s + samtools view -Sb -
309s + for f in *.sam
309s + outfile=short_reads.bam
309s + cat short_reads.sam
309s + samtools view -Sb -
309s + for f in *.sam
309s + outfile=short_reads_and_superreads.bam
309s + cat short_reads_and_superreads.sam
309s + samtools view -Sb -
309s + arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" "mix_short mix_long" "mix_short mix_long")
309s + arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff")
309s + arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" "mix_reads" "mix_reads_guided")
309s + arrmsg=("Short reads" "Short reads and super-reads" "Long reads" "Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides")
309s + for i in ${!arrmsg[@]}
309s + fout=short_reads.out.gtf
309s + /bin/rm -f short_reads.out.gtf
309s + fcmp=short_reads.out_expected.gtf
309s + n=0
309s + echo 0
309s 0
309s + n=1
309s Test 1: Short reads
309s + echo 'Test 1: Short reads'
309s + fin=short_reads.bam
309s + [[ short_reads =~ ^mix ]]
309s short_reads.out.gtf short_reads.bam
309s + echo short_reads.out.gtf short_reads.bam
309s + stringtie -o short_reads.out.gtf short_reads.bam
309s + '[' '!' -f short_reads.out.gtf ']'
309s + diff -q -I '^#' short_reads.out.gtf short_reads.out_expected.gtf
309s + echo '  OK.'
309s   OK.
309s + for i in ${!arrmsg[@]}
309s + fout=short_reads_and_superreads.out.gtf
309s + /bin/rm -f short_reads_and_superreads.out.gtf
309s + fcmp=short_reads_and_superreads.out_expected.gtf
309s + n=1
309s 1
309s Test 2: Short reads and super-reads
309s short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
309s + echo 1
309s + n=2
309s + echo 'Test 2: Short reads and super-reads'
309s + fin=short_reads_and_superreads.bam
309s + [[ short_reads_and_superreads =~ ^mix ]]
309s + echo short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
309s + stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
309s + '[' '!' -f short_reads_and_superreads.out.gtf ']'
309s + diff -q -I '^#' short_reads_and_superreads.out.gtf short_reads_and_superreads.out_expected.gtf
309s + echo '  OK.'
309s   OK.
309s + for i in ${!arrmsg[@]}
309s + fout=long_reads.out.gtf
309s + /bin/rm -f long_reads.out.gtf
309s 2
309s Test 3: Long reads
309s -L long_reads.out.gtf long_reads.bam
309s + fcmp=long_reads.out_expected.gtf
309s + n=2
309s + echo 2
309s + n=3
309s + echo 'Test 3: Long reads'
309s + fin=long_reads.bam
309s + [[ long_reads =~ ^mix ]]
309s + echo -L long_reads.out.gtf long_reads.bam
309s + stringtie -L -o long_reads.out.gtf long_reads.bam
309s + '[' '!' -f long_reads.out.gtf ']'
309s + diff -q -I '^#' long_reads.out.gtf long_reads.out_expected.gtf
309s + echo '  OK.'
309s   OK.
309s + for i in ${!arrmsg[@]}
309s + fout=long_reads_guided.out.gtf
309s + /bin/rm -f long_reads_guided.out.gtf
309s + fcmp=long_reads_guided.out_expected.gtf
309s + n=3
309s 3
309s Test 4: Long reads with annotation guides
309s -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
309s + echo 3
309s + n=4
309s + echo 'Test 4: Long reads with annotation guides'
309s + fin=long_reads.bam
309s + [[ long_reads =~ ^mix ]]
309s + echo -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
309s + stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
309s + '[' '!' -f long_reads_guided.out.gtf ']'
309s + diff -q -I '^#' long_reads_guided.out.gtf long_reads_guided.out_expected.gtf
309s   OK.
309s + echo '  OK.'
309s + for i in ${!arrmsg[@]}
309s + fout=mix_reads.out.gtf
309s + /bin/rm -f mix_reads.out.gtf
309s + fcmp=mix_reads.out_expected.gtf
309s + n=4
309s 4
309s + echo 4
309s Test 5: Mixed reads
309s --mix mix_reads.out.gtf mix_short.bam mix_long.bam
309s + n=5
309s + echo 'Test 5: Mixed reads'
309s + fin='mix_short mix_long.bam'
309s + [[ mix_short mix_long =~ ^mix ]]
309s + ins=(${arrins[$i]})
309s + fin='mix_short.bam mix_long.bam'
309s + echo --mix mix_reads.out.gtf mix_short.bam mix_long.bam
309s + stringtie --mix -o mix_reads.out.gtf mix_short.bam mix_long.bam
309s + '[' '!' -f mix_reads.out.gtf ']'
309s + diff -q -I '^#' mix_reads.out.gtf mix_reads.out_expected.gtf
309s + echo '  OK.'
309s   OK.
309s + for i in ${!arrmsg[@]}
309s + fout=mix_reads_guided.out.gtf
309s + /bin/rm -f mix_reads_guided.out.gtf
309s + fcmp=mix_reads_guided.out_expected.gtf
309s + n=5
309s 5
309s Test 6: Mixed reads with annotation guides
309s --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
309s + echo 5
309s + n=6
309s + echo 'Test 6: Mixed reads with annotation guides'
309s + fin='mix_short mix_long.bam'
309s + [[ mix_short mix_long =~ ^mix ]]
309s + ins=(${arrins[$i]})
309s + fin='mix_short.bam mix_long.bam'
309s + echo --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
309s + stringtie --mix -G mix_guides.gff -o mix_reads_guided.out.gtf mix_short.bam mix_long.bam
309s + '[' '!' -f mix_reads_guided.out.gtf ']'
309s + diff -q -I '^#' mix_reads_guided.out.gtf mix_reads_guided.out_expected.gtf
309s   OK.
309s + echo '  OK.'
310s autopkgtest [15:55:11]: test run-unit-test: -----------------------]
310s autopkgtest [15:55:11]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
310s run-unit-test        PASS
310s autopkgtest [15:55:11]: @@@@@@@@@@@@@@@@@@@@ summary
310s run-unit-test        PASS
321s Creating nova instance adt-noble-ppc64el-stringtie-20240323-155001-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...