0s autopkgtest [11:52:44]: starting date and time: 2024-03-19 11:52:44+0000 1s autopkgtest [11:52:45]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 1s autopkgtest [11:52:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cxwl1wul/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:wise,src:glib2.0 --apt-upgrade wise --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=wise/2.4.1-24 glib2.0/2.79.3-3ubuntu5' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-1.secgroup --name adt-noble-arm64-wise-20240319-115244-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://us.ports.ubuntu.com/ubuntu-ports/ 183s autopkgtest [11:55:47]: testbed dpkg architecture: arm64 183s autopkgtest [11:55:47]: testbed apt version: 2.7.12 183s autopkgtest [11:55:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 184s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 185s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.7 kB] 185s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [486 kB] 186s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 186s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3768 kB] 188s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [659 kB] 188s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 188s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 188s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 188s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4142 kB] 189s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 189s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [56.7 kB] 189s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 194s Fetched 9334 kB in 5s (1731 kB/s) 195s Reading package lists... 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Calculating upgrade... 203s The following packages will be REMOVED: 203s libglib2.0-0 203s The following NEW packages will be installed: 203s libglib2.0-0t64 xdg-user-dirs 203s The following packages will be upgraded: 203s gir1.2-glib-2.0 libglib2.0-data 203s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 203s Need to get 1774 kB of archives. 203s After this operation, 138 kB of additional disk space will be used. 203s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 203s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 203s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 203s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 204s Fetched 1774 kB in 1s (2574 kB/s) 204s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 204s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 204s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 205s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 205s udisks2 depends on libglib2.0-0 (>= 2.77.0). 205s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 205s python3-gi depends on libglib2.0-0 (>= 2.77.0). 205s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 205s netplan.io depends on libglib2.0-0 (>= 2.70.0). 205s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 205s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 205s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 205s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 205s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 205s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 205s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 205s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 205s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 205s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 205s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 205s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 205s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 205s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 205s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 205s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 205s fwupd depends on libglib2.0-0 (>= 2.79.0). 205s bolt depends on libglib2.0-0 (>= 2.56.0). 205s 205s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 205s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 205s Selecting previously unselected package libglib2.0-0t64:arm64. 205s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75825 files and directories currently installed.) 205s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 205s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 205s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 205s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 205s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 205s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 205s Selecting previously unselected package xdg-user-dirs. 205s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 205s Unpacking xdg-user-dirs (0.18-1) ... 205s Setting up xdg-user-dirs (0.18-1) ... 205s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 205s No schema files found: doing nothing. 205s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 205s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 205s Processing triggers for man-db (2.12.0-3) ... 206s Processing triggers for libc-bin (2.39-0ubuntu2) ... 206s Reading package lists... 207s Building dependency tree... 207s Reading state information... 210s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 210s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 210s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 210s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 210s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 212s Reading package lists... 212s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s Calculating upgrade... 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 216s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s autopkgtest [11:56:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 220s autopkgtest [11:56:24]: @@@@@@@@@@@@@@@@@@@@ apt-source wise 224s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe wise 2.4.1-24 (dsc) [2154 B] 224s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe wise 2.4.1-24 (tar) [3410 kB] 224s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe wise 2.4.1-24 (diff) [38.5 kB] 224s gpgv: Signature made Mon Mar 18 16:53:38 2024 UTC 224s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 224s gpgv: Can't check signature: No public key 224s dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-24.dsc: no acceptable signature found 225s autopkgtest [11:56:29]: testing package wise version 2.4.1-24 227s autopkgtest [11:56:31]: build not needed 259s autopkgtest [11:57:03]: test run-unit-test: preparing testbed 263s Reading package lists... 263s Building dependency tree... 263s Reading state information... 264s Starting pkgProblemResolver with broken count: 0 264s Starting 2 pkgProblemResolver with broken count: 0 264s Done 266s The following additional packages will be installed: 266s wise wise-data 266s Suggested packages: 266s wise-doc 266s The following NEW packages will be installed: 266s autopkgtest-satdep wise wise-data 266s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 266s Need to get 877 kB/877 kB of archives. 266s After this operation, 3934 kB of additional disk space will be used. 266s Get:1 /tmp/autopkgtest.b5McxR/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 266s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 wise-data all 2.4.1-24 [82.7 kB] 266s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 wise arm64 2.4.1-24 [794 kB] 267s Fetched 877 kB in 1s (1520 kB/s) 267s Selecting previously unselected package wise-data. 267s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75864 files and directories currently installed.) 267s Preparing to unpack .../wise-data_2.4.1-24_all.deb ... 267s Unpacking wise-data (2.4.1-24) ... 267s Selecting previously unselected package wise. 267s Preparing to unpack .../wise_2.4.1-24_arm64.deb ... 267s Unpacking wise (2.4.1-24) ... 268s Selecting previously unselected package autopkgtest-satdep. 268s Preparing to unpack .../1-autopkgtest-satdep.deb ... 268s Unpacking autopkgtest-satdep (0) ... 268s Setting up wise-data (2.4.1-24) ... 268s Setting up wise (2.4.1-24) ... 268s Setting up autopkgtest-satdep (0) ... 268s Processing triggers for man-db (2.12.0-3) ... 274s (Reading database ... 75958 files and directories currently installed.) 274s Removing autopkgtest-satdep (0) ... 274s autopkgtest [11:57:18]: test run-unit-test: [----------------------- 275s >>> Doing promoterwise promoterwise standard test 275s >>> Calling [promoterwise -silent pw.human pw.mouse > TEMP-PW] 275s >>> promoterwise ... Failed 275s >>> Doing basic-cdna cdna test case (protein v cdna), all outputs 275s >>> Calling [estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] 275s >>> basic-cdna ... Failed 275s >>> Doing basic-genomic genomic test case (protein v genomic), all outputs 275s >>> Calling [genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s Warning Error 275s Strangely truncated line in fasta file 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:0 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:1 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:2 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:3 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:4 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:5 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:6 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:7 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:8 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:9 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:10 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:11 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:12 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:13 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:14 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:15 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:16 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:17 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:18 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:19 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:20 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:21 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:22 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:23 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:24 (they must 275s be bound between 0:26, returning 0 here 275s Warning Error 275s Attempting to access CompMat with aminoacid numbers 190:25 (they must 275s be bound between 0:26, returning 0 here 275s >>> basic-genomic ... Failed 275s >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs 275s >>> Calling [estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s >>> hmm-binary-cdna ... Failed 275s >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match 275s >>> Calling [genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s Information 275s In making HSHNCPA1 a genomic sequence, converted 3 bases (0.7%) to 275s N's from non ATGCN 275s GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 275s >>> hmm-wrong-dna ... Passed 275s >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match 275s >>> Calling [estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s Information 275s In making HSHNCPA1 a cdna sequence, converted 3 bases (0.7%) to N's 275s from non ATGCN 275s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 275s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 275s >>> hmm-wrong-dna-est ... Failed 275s >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs 275s >>> Calling [genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s FATAL: No support for non-protein, non-nucleic acid alphabets. 275s >>> Bad exit status - 256 (system - ) 275s >>> hmm-ascii-genomic ... Failed 275s >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while 275s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] 275s Warning Error 275s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 275s Strangely truncated line in fasta file 275s Warning Error 275s Strangely truncated line in fasta file 275s >>> genewise-db ... Passed 275s >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while 275s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] 275s Warning Error 275s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 275s Strangely truncated line in fasta file 275s Warning Error 275s Strangely truncated line in fasta file 275s >>> genewise-db-lite ... Passed 275s >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while 275s >>> Calling [estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] 275s Warning Error 275s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 275s Strangely truncated line in fasta file 275s Warning Error 275s Strangely truncated line in fasta file 275s >>> estwise-db ... Passed 275s >>> Doing pswdb Protein smith waterman db search 275s >>> Calling [pswdb road.pep pep.fa -quiet > TEMP ] 275s Warning Error 275s Strangely truncated line in fasta file 275s Warning Error 275s Before any actual search in db searching 275s Out of memory, trying to realloc 1499031348 bytes 275s 275s Fatal Error 275s Before any actual search in db searching 275s Cannot realloc histogram... going to die... sorry! 275s >>> Bad exit status - 512 (system - ) 275s >>> pswdb ... Failed 275s >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching 275s >>> Calling [genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] 275s Warning Error 275s Strangely truncated line in fasta file 275s >>> genewisedb-pfam-mode ... Failed 275s Tests failed 275s PLEASE: email ewan birney (birney@sanger.ac.uk) with the test.results file 275s 276s autopkgtest [11:57:20]: test run-unit-test: -----------------------] 276s autopkgtest [11:57:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 276s run-unit-test PASS 277s autopkgtest [11:57:21]: @@@@@@@@@@@@@@@@@@@@ summary 277s run-unit-test PASS 299s Creating nova instance adt-noble-arm64-wise-20240319-115244-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240319.img (UUID bd25b89b-8264-4402-95d9-d9c88f21f275)...