0s autopkgtest [22:35:52]: starting date and time: 2024-03-25 22:35:52+0000
  0s autopkgtest [22:35:52]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [22:35:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.57dajahj/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:stringtie,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=stringtie/2.2.1+ds-3build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-5.secgroup --name adt-noble-ppc64el-stringtie-20240325-223552-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
215s autopkgtest [22:39:27]: testbed dpkg architecture: ppc64el
215s autopkgtest [22:39:27]: testbed apt version: 2.7.12
215s autopkgtest [22:39:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup
216s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
217s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4039 kB]
218s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B]
218s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB]
218s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
218s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB]
219s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
219s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
219s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
219s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4232 kB]
219s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
219s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB]
219s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
223s Fetched 9723 kB in 4s (2282 kB/s)
223s Reading package lists...
226s Reading package lists...
226s Building dependency tree...
226s Reading state information...
226s Calculating upgrade...
226s The following packages will be REMOVED:
226s   libssl3
226s The following NEW packages will be installed:
226s   libssl3t64
226s The following packages have been kept back:
226s   curl
226s The following packages will be upgraded:
226s   openssl
227s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
227s Need to get 3151 kB of archives.
227s After this operation, 73.7 kB of additional disk space will be used.
227s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
227s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
228s Fetched 3151 kB in 1s (3601 kB/s)
228s (Reading database ... 
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(Reading database ... 70156 files and directories currently installed.)
228s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
228s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
228s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
228s  wget depends on libssl3 (>= 3.0.0).
228s  tnftp depends on libssl3 (>= 3.0.0).
228s  tcpdump depends on libssl3 (>= 3.0.0).
228s  systemd-resolved depends on libssl3 (>= 3.0.0).
228s  systemd depends on libssl3 (>= 3.0.0).
228s  sudo depends on libssl3 (>= 3.0.0).
228s  rsync depends on libssl3 (>= 3.0.0).
228s  python3-cryptography depends on libssl3 (>= 3.0.0).
228s  openssh-server depends on libssl3 (>= 3.0.10).
228s  openssh-client depends on libssl3 (>= 3.0.10).
228s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
228s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
228s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
228s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
228s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
228s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
228s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
228s  libnvme1 depends on libssl3 (>= 3.0.0).
228s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
228s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
228s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
228s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
228s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
228s  kmod depends on libssl3 (>= 3.0.0).
228s  dhcpcd-base depends on libssl3 (>= 3.0.0).
228s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
228s 
228s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70156 files and directories currently installed.)
228s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
228s Selecting previously unselected package libssl3t64:ppc64el.
228s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70145 files and directories currently installed.)
228s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
228s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
228s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
228s Setting up openssl (3.0.13-0ubuntu2) ...
228s Processing triggers for man-db (2.12.0-3) ...
229s Processing triggers for libc-bin (2.39-0ubuntu6) ...
229s Reading package lists...
229s Building dependency tree...
229s Reading state information...
229s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
230s sh: Attempting to set up Debian/Ubuntu apt sources automatically
230s sh: Distribution appears to be Ubuntu
231s Reading package lists...
231s Building dependency tree...
231s Reading state information...
231s eatmydata is already the newest version (131-1).
231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
231s Reading package lists...
231s Building dependency tree...
231s Reading state information...
232s dbus is already the newest version (1.14.10-4ubuntu1).
232s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
232s Reading package lists...
232s Building dependency tree...
232s Reading state information...
232s rng-tools-debian is already the newest version (2.4).
232s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
232s Reading package lists...
232s Building dependency tree...
232s Reading state information...
232s The following packages will be REMOVED:
232s   cloud-init* python3-configobj* python3-debconf*
233s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
233s After this operation, 3256 kB disk space will be freed.
233s (Reading database ... 
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(Reading database ... 70158 files and directories currently installed.)
233s Removing cloud-init (24.1.2-0ubuntu1) ...
233s Removing python3-configobj (5.0.8-3) ...
233s Removing python3-debconf (1.5.86) ...
233s Processing triggers for man-db (2.12.0-3) ...
234s (Reading database ... 
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(Reading database ... 69769 files and directories currently installed.)
234s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
234s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
234s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
234s invoke-rc.d: policy-rc.d denied execution of try-restart.
235s Reading package lists...
235s Building dependency tree...
235s Reading state information...
235s linux-generic is already the newest version (6.8.0-11.11+1).
235s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
236s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
236s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
236s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
238s Reading package lists...
238s Reading package lists...
239s Building dependency tree...
239s Reading state information...
239s Calculating upgrade...
239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
239s Reading package lists...
239s Building dependency tree...
239s Reading state information...
239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
240s autopkgtest [22:39:52]: rebooting testbed after setup commands that affected boot
403s autopkgtest [22:42:35]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
406s autopkgtest [22:42:38]: @@@@@@@@@@@@@@@@@@@@ apt-source stringtie
408s Get:1 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (dsc) [2391 B]
408s Get:2 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [1756 kB]
408s Get:3 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (tar) [295 kB]
408s Get:4 http://ftpmaster.internal/ubuntu noble/universe stringtie 2.2.1+ds-3 (diff) [11.8 kB]
408s gpgv: Signature made Fri Jan 26 20:37:21 2024 UTC
408s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
408s gpgv:                issuer "tille@debian.org"
408s gpgv: Can't check signature: No public key
408s dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-3.dsc: no acceptable signature found
409s autopkgtest [22:42:41]: testing package stringtie version 2.2.1+ds-3
409s autopkgtest [22:42:41]: build not needed
411s autopkgtest [22:42:43]: test run-unit-test: preparing testbed
415s Reading package lists...
415s Building dependency tree...
415s Reading state information...
415s Starting pkgProblemResolver with broken count: 0
415s Starting 2 pkgProblemResolver with broken count: 0
415s Done
415s The following additional packages will be installed:
415s   libdeflate0 libhts3 libhtscodecs2 samtools stringtie
415s Suggested packages:
415s   cwltool cufflinks
415s Recommended packages:
415s   stringtie-examples
415s The following NEW packages will be installed:
415s   autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools stringtie
415s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
415s Need to get 1783 kB/1784 kB of archives.
415s After this operation, 4922 kB of additional disk space will be used.
415s Get:1 /tmp/autopkgtest.4qByTl/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B]
416s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
416s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
416s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB]
416s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB]
416s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el stringtie ppc64el 2.2.1+ds-3 [390 kB]
417s Fetched 1783 kB in 1s (2201 kB/s)
417s Selecting previously unselected package libdeflate0:ppc64el.
417s (Reading database ... 
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(Reading database ... 69714 files and directories currently installed.)
417s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ...
417s Unpacking libdeflate0:ppc64el (1.19-1) ...
417s Selecting previously unselected package libhtscodecs2:ppc64el.
417s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ...
417s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
417s Selecting previously unselected package libhts3:ppc64el.
417s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ...
417s Unpacking libhts3:ppc64el (1.18+ds-1) ...
417s Selecting previously unselected package samtools.
417s Preparing to unpack .../3-samtools_1.19.2-1_ppc64el.deb ...
417s Unpacking samtools (1.19.2-1) ...
417s Selecting previously unselected package stringtie.
417s Preparing to unpack .../4-stringtie_2.2.1+ds-3_ppc64el.deb ...
417s Unpacking stringtie (2.2.1+ds-3) ...
417s Selecting previously unselected package autopkgtest-satdep.
417s Preparing to unpack .../5-1-autopkgtest-satdep.deb ...
417s Unpacking autopkgtest-satdep (0) ...
417s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
417s Setting up libdeflate0:ppc64el (1.19-1) ...
417s Setting up libhts3:ppc64el (1.18+ds-1) ...
417s Setting up samtools (1.19.2-1) ...
417s Setting up stringtie (2.2.1+ds-3) ...
417s Setting up autopkgtest-satdep (0) ...
417s Processing triggers for man-db (2.12.0-3) ...
418s Processing triggers for libc-bin (2.39-0ubuntu6) ...
420s (Reading database ... 69830 files and directories currently installed.)
420s Removing autopkgtest-satdep (0) ...
421s autopkgtest [22:42:53]: test run-unit-test: [-----------------------
421s + pkg=stringtie
421s ++ pwd
421s + CUR_DIR=/tmp/autopkgtest.4qByTl/build.7Fc/src
421s + '[' /tmp/autopkgtest.4qByTl/autopkgtest_tmp = '' ']'
421s + cp /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/README.md /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/human-chr19_P.gff /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/long_reads.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/long_reads.sam /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/long_reads_guided.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/mix_guides.gff /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/mix_long.sam /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/mix_reads.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/mix_reads_guided.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/mix_short.sam /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/short_reads.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/short_reads.sam /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/short_reads_and_superreads.out_expected.gtf /tmp/autopkgtest.4qByTl/build.7Fc/src/debian-tests-data/short_reads_and_superreads.sam -a /tmp/autopkgtest.4qByTl/autopkgtest_tmp
421s + cd /tmp/autopkgtest.4qByTl/autopkgtest_tmp
421s + 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
421s + for f in *.sam
421s + outfile=long_reads.bam
421s + cat long_reads.sam
421s + samtools view -Sb -
421s + for f in *.sam
421s + outfile=mix_long.bam
421s + cat mix_long.sam
421s + samtools view -Sb -
421s + for f in *.sam
421s + outfile=mix_short.bam
421s + samtools view -Sb -
421s + cat mix_short.sam
421s + for f in *.sam
421s + outfile=short_reads.bam
421s + cat short_reads.sam
421s + samtools view -Sb -
421s + for f in *.sam
421s + outfile=short_reads_and_superreads.bam
421s + cat short_reads_and_superreads.sam
421s + samtools view -Sb -
421s + arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" "mix_short mix_long" "mix_short mix_long")
421s + arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff")
421s + arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" "mix_reads" "mix_reads_guided")
421s + arrmsg=("Short reads" "Short reads and super-reads" "Long reads" "Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides")
421s + for i in ${!arrmsg[@]}
421s + fout=short_reads.out.gtf
421s + /bin/rm -f short_reads.out.gtf
421s + fcmp=short_reads.out_expected.gtf
421s + n=0
421s + echo 0
421s + n=1
421s + echo 'Test 1: Short reads'
421s + fin=short_reads.bam
421s + [[ short_reads =~ ^mix ]]
421s + echo short_reads.out.gtf short_reads.bam
421s + stringtie -o short_reads.out.gtf short_reads.bam
421s 0
421s Test 1: Short reads
421s short_reads.out.gtf short_reads.bam
421s + '[' '!' -f short_reads.out.gtf ']'
421s + diff -q -I '^#' short_reads.out.gtf short_reads.out_expected.gtf
421s + echo '  OK.'
421s   OK.
421s + for i in ${!arrmsg[@]}
421s + fout=short_reads_and_superreads.out.gtf
421s + /bin/rm -f short_reads_and_superreads.out.gtf
421s + fcmp=short_reads_and_superreads.out_expected.gtf
421s + n=1
421s 1
421s + echo 1
421s + n=2
421s Test 2: Short reads and super-reads
421s short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
421s + echo 'Test 2: Short reads and super-reads'
421s + fin=short_reads_and_superreads.bam
421s + [[ short_reads_and_superreads =~ ^mix ]]
421s + echo short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
421s + stringtie -o short_reads_and_superreads.out.gtf short_reads_and_superreads.bam
421s + '[' '!' -f short_reads_and_superreads.out.gtf ']'
421s + diff -q -I '^#' short_reads_and_superreads.out.gtf short_reads_and_superreads.out_expected.gtf
421s + echo '  OK.'
421s   OK.
421s + for i in ${!arrmsg[@]}
421s + fout=long_reads.out.gtf
421s + /bin/rm -f long_reads.out.gtf
422s + fcmp=long_reads.out_expected.gtf
422s + n=2
422s 2
422s Test 3: Long reads
422s + echo 2
422s + n=3
422s + echo 'Test 3: Long reads'
422s -L long_reads.out.gtf long_reads.bam
422s + fin=long_reads.bam
422s + [[ long_reads =~ ^mix ]]
422s + echo -L long_reads.out.gtf long_reads.bam
422s + stringtie -L -o long_reads.out.gtf long_reads.bam
422s + '[' '!' -f long_reads.out.gtf ']'
422s + diff -q -I '^#' long_reads.out.gtf long_reads.out_expected.gtf
422s + echo '  OK.'
422s   OK.
422s + for i in ${!arrmsg[@]}
422s + fout=long_reads_guided.out.gtf
422s + /bin/rm -f long_reads_guided.out.gtf
422s + fcmp=long_reads_guided.out_expected.gtf
422s + n=3
422s + echo 3
422s 3
422s + n=4
422s + echo 'Test 4: Long reads with annotation guides'
422s Test 4: Long reads with annotation guides
422s -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
422s + fin=long_reads.bam
422s + [[ long_reads =~ ^mix ]]
422s + echo -L -G human-chr19_P.gff long_reads_guided.out.gtf long_reads.bam
422s + stringtie -L -G human-chr19_P.gff -o long_reads_guided.out.gtf long_reads.bam
422s + '[' '!' -f long_reads_guided.out.gtf ']'
422s + diff -q -I '^#' long_reads_guided.out.gtf long_reads_guided.out_expected.gtf
422s + echo '  OK.'
422s   OK.
422s + for i in ${!arrmsg[@]}
422s + fout=mix_reads.out.gtf
422s + /bin/rm -f mix_reads.out.gtf
422s + fcmp=mix_reads.out_expected.gtf
422s + n=4
422s + echo 4
422s 4
422s + n=5
422s + echo 'Test 5: Mixed reads'
422s Test 5: Mixed reads
422s + fin='mix_short mix_long.bam'
422s + [[ mix_short mix_long =~ ^mix ]]
422s + ins=(${arrins[$i]})
422s + fin='mix_short.bam mix_long.bam'
422s --mix mix_reads.out.gtf mix_short.bam mix_long.bam
422s + echo --mix mix_reads.out.gtf mix_short.bam mix_long.bam
422s + stringtie --mix -o mix_reads.out.gtf mix_short.bam mix_long.bam
422s + '[' '!' -f mix_reads.out.gtf ']'
422s + diff -q -I '^#' mix_reads.out.gtf mix_reads.out_expected.gtf
422s   OK.
422s + echo '  OK.'
422s + for i in ${!arrmsg[@]}
422s + fout=mix_reads_guided.out.gtf
422s + /bin/rm -f mix_reads_guided.out.gtf
422s + fcmp=mix_reads_guided.out_expected.gtf
422s + n=5
422s + echo 5
422s 5
422s Test 6: Mixed reads with annotation guides
422s --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
422s + n=6
422s + echo 'Test 6: Mixed reads with annotation guides'
422s + fin='mix_short mix_long.bam'
422s + [[ mix_short mix_long =~ ^mix ]]
422s + ins=(${arrins[$i]})
422s + fin='mix_short.bam mix_long.bam'
422s + echo --mix -G mix_guides.gff mix_reads_guided.out.gtf mix_short.bam mix_long.bam
422s + stringtie --mix -G mix_guides.gff -o mix_reads_guided.out.gtf mix_short.bam mix_long.bam
422s + '[' '!' -f mix_reads_guided.out.gtf ']'
422s + diff -q -I '^#' mix_reads_guided.out.gtf mix_reads_guided.out_expected.gtf
422s + echo '  OK.'
422s   OK.
422s autopkgtest [22:42:54]: test run-unit-test: -----------------------]
423s autopkgtest [22:42:55]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
423s run-unit-test        PASS
423s autopkgtest [22:42:55]: @@@@@@@@@@@@@@@@@@@@ summary
423s run-unit-test        PASS
442s Creating nova instance adt-noble-ppc64el-stringtie-20240325-223552-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...