0s autopkgtest [03:36:50]: starting date and time: 2026-02-05 03:36:50+0000 0s autopkgtest [03:36:50]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [03:36:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wx3971h8/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade fasta3 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-29.secgroup --name adt-resolute-ppc64el-fasta3-20260205-033649-juju-7f2275-prod-proposed-migration-environment-2-e39a6195-353d-4a1f-9ea2-f4a2a2fbd8a7 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-ppc64el-fasta3-20260205-033649-juju-7f2275-prod-proposed-migration-environment-2-e39a6195-353d-4a1f-9ea2-f4a2a2fbd8a7 from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 66s autopkgtest [03:37:56]: testbed dpkg architecture: ppc64el 66s autopkgtest [03:37:56]: testbed apt version: 3.1.14 66s autopkgtest [03:37:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s autopkgtest [03:37:56]: testbed release detected to be: None 67s autopkgtest [03:37:57]: updating testbed package index (apt update) 67s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 68s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 68s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 68s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 68s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [257 kB] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1449 kB] 68s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.6 kB] 68s Fetched 3839 kB in 1s (5014 kB/s) 69s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 71s The following packages will be upgraded: 71s libc-bin libc-gconv-modules-extra libc6 locales pollinate 71s python3-referencing sed 71s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 8612 kB of archives. 71s After this operation, 0 B of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 73s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 73s dpkg-preconfigure: unable to re-open stdin: No such file or directory 73s Fetched 8612 kB in 2s (4673 kB/s) 74s (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 ... 82008 files and directories currently installed.) 74s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 74s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 74s Setting up sed (4.9-2build3) ... 74s (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 ... 82008 files and directories currently installed.) 74s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 74s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 74s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 74s (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 ... 82008 files and directories currently installed.) 74s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 75s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 75s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 75s (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 ... 82008 files and directories currently installed.) 75s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 75s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 75s Setting up libc-bin (2.42-2ubuntu5) ... 75s (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 ... 82008 files and directories currently installed.) 75s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 75s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 76s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 76s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 76s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 76s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 76s Setting up locales (2.42-2ubuntu5) ... 77s Generating locales (this might take a while)... 78s en_US.UTF-8... done 78s Generation complete. 78s Setting up pollinate (4.33-4ubuntu5) ... 89s Setting up python3-referencing (0.36.2-1ubuntu2) ... 89s Processing triggers for man-db (2.13.1-1) ... 90s Processing triggers for install-info (7.2-5) ... 90s Processing triggers for systemd (259-1ubuntu3) ... 91s autopkgtest [03:38:21]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Solving dependencies... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s autopkgtest [03:38:23]: rebooting testbed after setup commands that affected boot 133s autopkgtest [03:39:03]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 136s autopkgtest [03:39:06]: @@@@@@@@@@@@@@@@@@@@ apt-source fasta3 144s Get:1 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (dsc) [2248 B] 144s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (tar) [1403 kB] 144s Get:3 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (diff) [14.8 kB] 144s gpgv: Signature made Wed Sep 24 06:35:50 2025 UTC 144s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 144s gpgv: issuer "tillea@rki.de" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./fasta3_36.3.8i.14-Nov-2020-4.dsc: no acceptable signature found 144s autopkgtest [03:39:14]: testing package fasta3 version 36.3.8i.14-Nov-2020-4 145s autopkgtest [03:39:15]: build not needed 145s autopkgtest [03:39:15]: test run-unit-test: preparing testbed 145s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Solving dependencies... 146s The following NEW packages will be installed: 146s bedtools fasta3 libclone-perl libdbd-mysql-perl libdbi-perl 146s libencode-locale-perl libfile-listing-perl libhtml-parser-perl 146s libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl 146s libhttp-message-perl libhttp-negotiate-perl libio-html-perl 146s libio-socket-ssl-perl libjson-perl liblwp-mediatypes-perl 146s liblwp-protocol-https-perl libmysqlclient24 libnet-http-perl 146s libnet-ssleay-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl 146s libwww-robotrules-perl libxml-parser-perl libxml-twig-perl mysql-common 146s perl-openssl-defaults python3-mysqldb 146s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 5825 kB of archives. 146s After this operation, 26.9 MB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bedtools ppc64el 2.31.1+dfsg-3 [675 kB] 146s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse ppc64el fasta3 ppc64el 36.3.8i.14-Nov-2020-4 [1041 kB] 146s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libclone-perl ppc64el 0.47-1 [11.1 kB] 146s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdbi-perl ppc64el 1.647-1build1 [839 kB] 146s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 146s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmysqlclient24 ppc64el 8.4.8-0ubuntu1 [1304 kB] 146s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libdbd-mysql-perl ppc64el 4.053-1ubuntu1 [94.1 kB] 146s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libencode-locale-perl all 1.05-3 [11.6 kB] 146s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtimedate-perl all 2.3300-2 [34.0 kB] 146s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhttp-date-perl all 6.06-1 [10.2 kB] 146s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfile-listing-perl all 6.16-1 [11.3 kB] 146s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhtml-tagset-perl all 3.24-1 [14.1 kB] 146s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el liburi-perl all 5.34-2build1 [100 kB] 146s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhtml-parser-perl ppc64el 3.83-1build1 [91.8 kB] 146s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhtml-tree-perl all 5.07-3 [200 kB] 146s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libio-html-perl all 1.004-3 [15.9 kB] 146s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 146s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhttp-message-perl all 7.01-1ubuntu1 [76.1 kB] 146s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhttp-cookies-perl all 6.11-1 [18.2 kB] 146s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libhttp-negotiate-perl all 6.01-2 [12.4 kB] 146s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el perl-openssl-defaults ppc64el 7build4 [6710 B] 146s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnet-ssleay-perl ppc64el 1.94-3 [323 kB] 146s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libio-socket-ssl-perl all 2.098-1 [205 kB] 146s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] 146s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnet-http-perl all 6.24-1build1 [21.7 kB] 146s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtry-tiny-perl all 0.32-1 [21.2 kB] 146s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwww-robotrules-perl all 6.02-1build1 [12.4 kB] 146s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwww-perl all 6.81-1build1 [141 kB] 146s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblwp-protocol-https-perl all 6.14-1 [9040 B] 146s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxml-parser-perl ppc64el 2.47-1build4 [205 kB] 146s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxml-twig-perl all 1:3.54-1build1 [157 kB] 146s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-mysqldb ppc64el 1.4.6-2build7 [54.5 kB] 147s Fetched 5825 kB in 1s (7461 kB/s) 147s Selecting previously unselected package bedtools. 147s (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 ... 82008 files and directories currently installed.) 147s Preparing to unpack .../00-bedtools_2.31.1+dfsg-3_ppc64el.deb ... 147s Unpacking bedtools (2.31.1+dfsg-3) ... 147s Selecting previously unselected package fasta3. 147s Preparing to unpack .../01-fasta3_36.3.8i.14-Nov-2020-4_ppc64el.deb ... 147s Unpacking fasta3 (36.3.8i.14-Nov-2020-4) ... 147s Selecting previously unselected package libclone-perl:ppc64el. 147s Preparing to unpack .../02-libclone-perl_0.47-1_ppc64el.deb ... 147s Unpacking libclone-perl:ppc64el (0.47-1) ... 147s Selecting previously unselected package libdbi-perl:ppc64el. 147s Preparing to unpack .../03-libdbi-perl_1.647-1build1_ppc64el.deb ... 147s Unpacking libdbi-perl:ppc64el (1.647-1build1) ... 147s Selecting previously unselected package mysql-common. 147s Preparing to unpack .../04-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 147s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 147s Selecting previously unselected package libmysqlclient24:ppc64el. 147s Preparing to unpack .../05-libmysqlclient24_8.4.8-0ubuntu1_ppc64el.deb ... 147s Unpacking libmysqlclient24:ppc64el (8.4.8-0ubuntu1) ... 147s Selecting previously unselected package libdbd-mysql-perl:ppc64el. 147s Preparing to unpack .../06-libdbd-mysql-perl_4.053-1ubuntu1_ppc64el.deb ... 147s Unpacking libdbd-mysql-perl:ppc64el (4.053-1ubuntu1) ... 147s Selecting previously unselected package libencode-locale-perl. 147s Preparing to unpack .../07-libencode-locale-perl_1.05-3_all.deb ... 147s Unpacking libencode-locale-perl (1.05-3) ... 147s Selecting previously unselected package libtimedate-perl. 147s Preparing to unpack .../08-libtimedate-perl_2.3300-2_all.deb ... 147s Unpacking libtimedate-perl (2.3300-2) ... 147s Selecting previously unselected package libhttp-date-perl. 147s Preparing to unpack .../09-libhttp-date-perl_6.06-1_all.deb ... 147s Unpacking libhttp-date-perl (6.06-1) ... 147s Selecting previously unselected package libfile-listing-perl. 147s Preparing to unpack .../10-libfile-listing-perl_6.16-1_all.deb ... 147s Unpacking libfile-listing-perl (6.16-1) ... 147s Selecting previously unselected package libhtml-tagset-perl. 147s Preparing to unpack .../11-libhtml-tagset-perl_3.24-1_all.deb ... 147s Unpacking libhtml-tagset-perl (3.24-1) ... 147s Selecting previously unselected package liburi-perl. 147s Preparing to unpack .../12-liburi-perl_5.34-2build1_all.deb ... 147s Unpacking liburi-perl (5.34-2build1) ... 147s Selecting previously unselected package libhtml-parser-perl:ppc64el. 147s Preparing to unpack .../13-libhtml-parser-perl_3.83-1build1_ppc64el.deb ... 147s Unpacking libhtml-parser-perl:ppc64el (3.83-1build1) ... 147s Selecting previously unselected package libhtml-tree-perl. 147s Preparing to unpack .../14-libhtml-tree-perl_5.07-3_all.deb ... 147s Unpacking libhtml-tree-perl (5.07-3) ... 147s Selecting previously unselected package libio-html-perl. 147s Preparing to unpack .../15-libio-html-perl_1.004-3_all.deb ... 147s Unpacking libio-html-perl (1.004-3) ... 147s Selecting previously unselected package liblwp-mediatypes-perl. 147s Preparing to unpack .../16-liblwp-mediatypes-perl_6.04-2_all.deb ... 147s Unpacking liblwp-mediatypes-perl (6.04-2) ... 147s Selecting previously unselected package libhttp-message-perl. 147s Preparing to unpack .../17-libhttp-message-perl_7.01-1ubuntu1_all.deb ... 147s Unpacking libhttp-message-perl (7.01-1ubuntu1) ... 148s Selecting previously unselected package libhttp-cookies-perl. 148s Preparing to unpack .../18-libhttp-cookies-perl_6.11-1_all.deb ... 148s Unpacking libhttp-cookies-perl (6.11-1) ... 148s Selecting previously unselected package libhttp-negotiate-perl. 148s Preparing to unpack .../19-libhttp-negotiate-perl_6.01-2_all.deb ... 148s Unpacking libhttp-negotiate-perl (6.01-2) ... 148s Selecting previously unselected package perl-openssl-defaults:ppc64el. 148s Preparing to unpack .../20-perl-openssl-defaults_7build4_ppc64el.deb ... 148s Unpacking perl-openssl-defaults:ppc64el (7build4) ... 148s Selecting previously unselected package libnet-ssleay-perl:ppc64el. 148s Preparing to unpack .../21-libnet-ssleay-perl_1.94-3_ppc64el.deb ... 148s Unpacking libnet-ssleay-perl:ppc64el (1.94-3) ... 148s Selecting previously unselected package libio-socket-ssl-perl. 148s Preparing to unpack .../22-libio-socket-ssl-perl_2.098-1_all.deb ... 148s Unpacking libio-socket-ssl-perl (2.098-1) ... 148s Selecting previously unselected package libjson-perl. 148s Preparing to unpack .../23-libjson-perl_4.10000-1_all.deb ... 148s Unpacking libjson-perl (4.10000-1) ... 148s Selecting previously unselected package libnet-http-perl. 148s Preparing to unpack .../24-libnet-http-perl_6.24-1build1_all.deb ... 148s Unpacking libnet-http-perl (6.24-1build1) ... 148s Selecting previously unselected package libtry-tiny-perl. 148s Preparing to unpack .../25-libtry-tiny-perl_0.32-1_all.deb ... 148s Unpacking libtry-tiny-perl (0.32-1) ... 148s Selecting previously unselected package libwww-robotrules-perl. 148s Preparing to unpack .../26-libwww-robotrules-perl_6.02-1build1_all.deb ... 148s Unpacking libwww-robotrules-perl (6.02-1build1) ... 148s Selecting previously unselected package libwww-perl. 148s Preparing to unpack .../27-libwww-perl_6.81-1build1_all.deb ... 148s Unpacking libwww-perl (6.81-1build1) ... 148s Selecting previously unselected package liblwp-protocol-https-perl. 148s Preparing to unpack .../28-liblwp-protocol-https-perl_6.14-1_all.deb ... 148s Unpacking liblwp-protocol-https-perl (6.14-1) ... 148s Selecting previously unselected package libxml-parser-perl. 148s Preparing to unpack .../29-libxml-parser-perl_2.47-1build4_ppc64el.deb ... 148s Unpacking libxml-parser-perl (2.47-1build4) ... 148s Selecting previously unselected package libxml-twig-perl. 148s Preparing to unpack .../30-libxml-twig-perl_1%3a3.54-1build1_all.deb ... 148s Unpacking libxml-twig-perl (1:3.54-1build1) ... 148s Selecting previously unselected package python3-mysqldb. 148s Preparing to unpack .../31-python3-mysqldb_1.4.6-2build7_ppc64el.deb ... 148s Unpacking python3-mysqldb (1.4.6-2build7) ... 148s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 148s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 148s Setting up libclone-perl:ppc64el (0.47-1) ... 148s Setting up libhtml-tagset-perl (3.24-1) ... 148s Setting up liblwp-mediatypes-perl (6.04-2) ... 148s Setting up fasta3 (36.3.8i.14-Nov-2020-4) ... 148s Setting up libtry-tiny-perl (0.32-1) ... 148s Setting up perl-openssl-defaults:ppc64el (7build4) ... 148s Setting up libencode-locale-perl (1.05-3) ... 148s Setting up libmysqlclient24:ppc64el (8.4.8-0ubuntu1) ... 148s Setting up python3-mysqldb (1.4.6-2build7) ... 148s Setting up libio-html-perl (1.004-3) ... 148s Setting up libtimedate-perl (2.3300-2) ... 148s Setting up libjson-perl (4.10000-1) ... 148s Setting up bedtools (2.31.1+dfsg-3) ... 148s Setting up liburi-perl (5.34-2build1) ... 148s Setting up libdbi-perl:ppc64el (1.647-1build1) ... 148s Setting up libnet-ssleay-perl:ppc64el (1.94-3) ... 148s Setting up libhttp-date-perl (6.06-1) ... 148s Setting up libfile-listing-perl (6.16-1) ... 148s Setting up libnet-http-perl (6.24-1build1) ... 148s Setting up libdbd-mysql-perl:ppc64el (4.053-1ubuntu1) ... 148s Setting up libwww-robotrules-perl (6.02-1build1) ... 148s Setting up libhtml-parser-perl:ppc64el (3.83-1build1) ... 148s Setting up libio-socket-ssl-perl (2.098-1) ... 148s Setting up libhttp-message-perl (7.01-1ubuntu1) ... 148s Setting up libhttp-negotiate-perl (6.01-2) ... 148s Setting up libhttp-cookies-perl (6.11-1) ... 148s Setting up libhtml-tree-perl (5.07-3) ... 148s Setting up liblwp-protocol-https-perl (6.14-1) ... 148s Setting up libwww-perl (6.81-1build1) ... 148s Setting up libxml-parser-perl (2.47-1build4) ... 148s Setting up libxml-twig-perl (1:3.54-1build1) ... 148s Processing triggers for man-db (2.13.1-1) ... 149s Processing triggers for libc-bin (2.42-2ubuntu5) ... 150s autopkgtest [03:39:20]: test run-unit-test: [----------------------- 150s + pkg=fasta3 150s + export LC_ALL=C.UTF-8 150s + LC_ALL=C.UTF-8 150s + '[' /tmp/autopkgtest.pcCrtN/autopkgtest_tmp = '' ']' 150s + cp -a /usr/share/doc/fasta3/examples/seq/bovgh.seq /usr/share/doc/fasta3/examples/seq/bovprl.seq /usr/share/doc/fasta3/examples/seq/dna_test_s.nlib /usr/share/doc/fasta3/examples/seq/dyr_human.aa /usr/share/doc/fasta3/examples/seq/egmsmg.aa /usr/share/doc/fasta3/examples/seq/grou_drome.pseg /usr/share/doc/fasta3/examples/seq/gst.nlib /usr/share/doc/fasta3/examples/seq/gst.seq /usr/share/doc/fasta3/examples/seq/gstm1_human.vaa /usr/share/doc/fasta3/examples/seq/gstm1b_human.nt /usr/share/doc/fasta3/examples/seq/gstm1b_human_fs.nt /usr/share/doc/fasta3/examples/seq/gstt1_drome.aa /usr/share/doc/fasta3/examples/seq/gtm1_human.aa /usr/share/doc/fasta3/examples/seq/gtt1_drome.aa /usr/share/doc/fasta3/examples/seq/h10_human.aa /usr/share/doc/fasta3/examples/seq/hahu.aa /usr/share/doc/fasta3/examples/seq/hsgstm1b.gcg /usr/share/doc/fasta3/examples/seq/hsgstm1b.seq /usr/share/doc/fasta3/examples/seq/humgstd.seq /usr/share/doc/fasta3/examples/seq/lcbo.aa /usr/share/doc/fasta3/examples/seq/m1r.aa /usr/share/doc/fasta3/examples/seq/m2.aa /usr/share/doc/fasta3/examples/seq/mchu.aa /usr/share/doc/fasta3/examples/seq/mgstm1.3nt /usr/share/doc/fasta3/examples/seq/mgstm1.aa /usr/share/doc/fasta3/examples/seq/mgstm1.aaa /usr/share/doc/fasta3/examples/seq/mgstm1.e05 /usr/share/doc/fasta3/examples/seq/mgstm1.eeq /usr/share/doc/fasta3/examples/seq/mgstm1.esq /usr/share/doc/fasta3/examples/seq/mgstm1.gcg /usr/share/doc/fasta3/examples/seq/mgstm1.lc /usr/share/doc/fasta3/examples/seq/mgstm1.nt /usr/share/doc/fasta3/examples/seq/mgstm1.nt1 /usr/share/doc/fasta3/examples/seq/mgstm1.nt12r /usr/share/doc/fasta3/examples/seq/mgstm1.nt13 /usr/share/doc/fasta3/examples/seq/mgstm1.nt13r /usr/share/doc/fasta3/examples/seq/mgstm1.nt1r /usr/share/doc/fasta3/examples/seq/mgstm1.nts /usr/share/doc/fasta3/examples/seq/mgstm1.raa /usr/share/doc/fasta3/examples/seq/mgstm1.rev /usr/share/doc/fasta3/examples/seq/mgstm1.seq /usr/share/doc/fasta3/examples/seq/mgstm1_genclone.seq /usr/share/doc/fasta3/examples/seq/mgtt2_x.seq /usr/share/doc/fasta3/examples/seq/ms1.aa /usr/share/doc/fasta3/examples/seq/mu.lib /usr/share/doc/fasta3/examples/seq/musplfm.aa /usr/share/doc/fasta3/examples/seq/mwkw.aa /usr/share/doc/fasta3/examples/seq/mwrtc1.aa /usr/share/doc/fasta3/examples/seq/myosin_bp.aa /usr/share/doc/fasta3/examples/seq/n0.aa /usr/share/doc/fasta3/examples/seq/n1.aa /usr/share/doc/fasta3/examples/seq/n2.aa /usr/share/doc/fasta3/examples/seq/n2_fs.lib /usr/share/doc/fasta3/examples/seq/n2s.aa /usr/share/doc/fasta3/examples/seq/n2t.aa /usr/share/doc/fasta3/examples/seq/n_fs.lib /usr/share/doc/fasta3/examples/seq/ngt.aa /usr/share/doc/fasta3/examples/seq/ngts.aa /usr/share/doc/fasta3/examples/seq/oohu.aa /usr/share/doc/fasta3/examples/seq/oohu.raa /usr/share/doc/fasta3/examples/seq/prio_atepa.aa /usr/share/doc/fasta3/examples/seq/prot_test.lib /usr/share/doc/fasta3/examples/seq/prot_test.lseg /usr/share/doc/fasta3/examples/seq/prot_test_s.lseg /usr/share/doc/fasta3/examples/seq/qrhuld.aa /usr/share/doc/fasta3/examples/seq/titin_hum.aa /usr/share/doc/fasta3/examples/seq/titin_hum.seq /usr/share/doc/fasta3/examples/seq/vav_human.aa /usr/share/doc/fasta3/examples/seq/xurt8c.aa /usr/share/doc/fasta3/examples/seq/xurt8c.lc /usr/share/doc/fasta3/examples/seq/xurtg.aa /tmp/autopkgtest.pcCrtN/autopkgtest_tmp 150s + cd /tmp/autopkgtest.pcCrtN/autopkgtest_tmp 150s + /usr/share/fasta3/scripts/test_ann_scripts.sh 150s /usr/share/fasta3/scripts/ann_exons_up_www.pl P09488 151s >P09488 151s 1 - 12 exon_1~1 151s 13 - 37 exon_2~2 151s 38 - 59 exon_3~3 151s 60 - 86 exon_4~4 151s 87 - 120 exon_5~5 151s 121 - 152 exon_6~6 151s 153 - 189 exon_7~7 151s 190 - 218 exon_8~8 151s /usr/share/fasta3/scripts/ann_exons_up_www.pl sp|P09488 151s >sp|P09488 151s 1 - 12 exon_1~1 151s 13 - 37 exon_2~2 151s 38 - 59 exon_3~3 151s 60 - 86 exon_4~4 151s 87 - 120 exon_5~5 151s 121 - 152 exon_6~6 151s 153 - 189 exon_7~7 151s 190 - 218 exon_8~8 151s /usr/share/fasta3/scripts/ann_exons_up_www.pl up|P09488|GSTM1_HUMAN 152s >up|P09488|GSTM1_HUMAN 152s 1 - 12 exon_1~1 152s 13 - 37 exon_2~2 152s 38 - 59 exon_3~3 152s 60 - 86 exon_4~4 152s 87 - 120 exon_5~5 152s 121 - 152 exon_6~6 152s 153 - 189 exon_7~7 152s 190 - 218 exon_8~8 152s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN P09488 152s >SP:GSTM1_HUMAN P09488 152s 1 - 12 exon_1~1 152s 13 - 37 exon_2~2 152s 38 - 59 exon_3~3 152s 60 - 86 exon_4~4 152s 87 - 120 exon_5~5 152s 121 - 152 exon_6~6 152s 153 - 189 exon_7~7 152s 190 - 218 exon_8~8 152s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN 152s *** /usr/share/fasta3/scripts/ann_exons_up_www.pl - accession required: SP:GSTM1_HUMAN at /usr/share/fasta3/scripts/ann_exons_up_www.pl line 130. 153s >SP:GSTM1_HUMAN 153s ***DONE*** /usr/share/fasta3/scripts/ann_exons_up_www.pl Thu Feb 5 03:39:22 UTC 2026 153s /usr/share/fasta3/scripts/ann_feats_up_sql.pl P09488 153s /usr/share/fasta3/scripts/ann_feats_up_sql.pl sp|P09488 153s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_feats_up_sql.pl line 98. 153s /usr/share/fasta3/scripts/ann_feats_up_sql.pl up|P09488|GSTM1_HUMAN 153s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_feats_up_sql.pl line 98. 153s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN P09488 153s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_feats_up_sql.pl line 98. 153s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN 153s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_feats_up_sql.pl line 98. 153s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_feats_up_sql.pl line 98. 153s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_sql.pl Thu Feb 5 03:39:22 UTC 2026 153s /usr/share/fasta3/scripts/ann_feats_up_www2.pl P09488 288s ==:Active site 288s =*:Modified 288s =#:Binding 288s =^:Metal binding 288s =@:Site 288s >P09488 288s /usr/share/fasta3/scripts/ann_feats_up_www2.pl sp|P09488 423s ==:Active site 423s =*:Modified 423s =#:Binding 423s =^:Metal binding 423s =@:Site 423s >sp|P09488 423s /usr/share/fasta3/scripts/ann_feats_up_www2.pl up|P09488|GSTM1_HUMAN 558s ==:Active site 558s =*:Modified 558s =#:Binding 558s =^:Metal binding 558s =@:Site 558s >up|P09488|GSTM1_HUMAN 558s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN P09488 693s ==:Active site 693s =*:Modified 693s =#:Binding 693s =^:Metal binding 693s =@:Site 693s >SP:GSTM1_HUMAN P09488 693s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN 694s ==:Active site 694s =*:Modified 694s =#:Binding 694s =^:Metal binding 694s =@:Site 694s >SP:GSTM1_HUMAN 694s *** /usr/share/fasta3/scripts/ann_feats_up_www2.pl accession required: SP:GSTM1_HUMAN 694s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_www2.pl Thu Feb 5 03:48:23 UTC 2026 694s /usr/share/fasta3/scripts/ann_ipr_www.pl P09488 694s >P09488 694s /usr/share/fasta3/scripts/ann_ipr_www.pl sp|P09488 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 694s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 694s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 694s >sp|P09488 694s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 694s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 694s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 694s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 694s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 694s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 694s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 694s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 694s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 694s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 694s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 694s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 694s /usr/share/fasta3/scripts/ann_ipr_www.pl up|P09488|GSTM1_HUMAN 695s >up|P09488|GSTM1_HUMAN 695s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN P09488 695s >SP:GSTM1_HUMAN P09488 695s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 695s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 695s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 695s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 695s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 695s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 695s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 695s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 695s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 695s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 695s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 695s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 695s >SP:GSTM1_HUMAN 695s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 695s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 695s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 695s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 695s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 695s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 695s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 695s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 695s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 695s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 695s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 695s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 695s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 695s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 695s ***DONE*** /usr/share/fasta3/scripts/ann_ipr_www.pl Thu Feb 5 03:48:24 UTC 2026 695s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl P09488 696s ==:Active site 696s =*:Modified 696s =#:Substrate binding 696s =^:Metal binding 696s =@:Site 696s 696s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/powerpc64le-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 696s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 696s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl sp|P09488 696s 696s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/powerpc64le-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 696s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 696s ==:Active site 696s =*:Modified 696s =#:Substrate binding 696s =^:Metal binding 696s =@:Site 696s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl up|P09488|GSTM1_HUMAN 697s 697s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/powerpc64le-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 697s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 697s ==:Active site 697s =*:Modified 697s =#:Substrate binding 697s =^:Metal binding 697s =@:Site 697s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN P09488 698s ==:Active site 698s =*:Modified 698s =#:Substrate binding 698s =^:Metal binding 698s =@:Site 698s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN 698s 698s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/powerpc64le-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 698s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 698s *** /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl - accession required: SP:GSTM1_HUMAN at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 198. 698s ==:Active site 698s =*:Modified 698s =#:Substrate binding 698s =^:Metal binding 698s =@:Site 698s 698s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/powerpc64le-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 698s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 698s + /usr/share/fasta3/scripts/test_py.sh 698s ***DONE*** /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl Thu Feb 5 03:48:27 UTC 2026 698s get_protein.py 698s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 698s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 698s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 698s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 698s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 698s 699s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 699s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 699s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 699s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 699s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 699s 762s get_refseq.py 762s Traceback (most recent call last): 762s File "/usr/lib/python3.13/urllib/request.py", line 1319, in do_open 762s h.request(req.get_method(), req.selector, req.data, headers, 762s ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s encode_chunked=req.has_header('Transfer-encoding')) 762s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/http/client.py", line 1358, in request 762s self._send_request(method, url, body, headers, encode_chunked) 762s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/http/client.py", line 1404, in _send_request 762s self.endheaders(body, encode_chunked=encode_chunked) 762s ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 762s self._send_output(message_body, encode_chunked=encode_chunked) 762s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 762s self.send(msg) 762s ~~~~~~~~~^^^^^ 762s File "/usr/lib/python3.13/http/client.py", line 1057, in send 762s self.connect() 762s ~~~~~~~~~~~~^^ 762s File "/usr/lib/python3.13/http/client.py", line 1499, in connect 762s self.sock = self._context.wrap_socket(self.sock, 762s ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 762s server_hostname=server_hostname) 762s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/ssl.py", line 455, in wrap_socket 762s return self.sslsocket_class._create( 762s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 762s sock=sock, 762s ^^^^^^^^^^ 762s ...<5 lines>... 762s session=session 762s ^^^^^^^^^^^^^^^ 762s ) 762s ^ 762s File "/usr/lib/python3.13/ssl.py", line 1076, in _create 762s self.do_handshake() 762s ~~~~~~~~~~~~~~~~~^^ 762s File "/usr/lib/python3.13/ssl.py", line 1372, in do_handshake 762s self._sslobj.do_handshake() 762s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 762s ssl.SSLEOFError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033) 762s 762s During handling of the above exception, another exception occurred: 762s 762s Traceback (most recent call last): 762s File "/usr/share/fasta3/scripts/get_protein.py", line 43, in 762s req = urllib.request.urlopen(url_string) 762s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 762s return opener.open(url, data, timeout) 762s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 762s response = self._open(req, data) 762s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 762s result = self._call_chain(self.handle_open, protocol, protocol + 762s '_open', req) 762s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 762s result = func(*args) 762s File "/usr/lib/python3.13/urllib/request.py", line 1367, in https_open 762s return self.do_open(http.client.HTTPSConnection, req, 762s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 762s context=self._context) 762s ^^^^^^^^^^^^^^^^^^^^^^ 762s File "/usr/lib/python3.13/urllib/request.py", line 1322, in do_open 762s raise URLError(err) 762s urllib.error.URLError: 762s 762s During handling of the above exception, another exception occurred: 762s 762s Traceback (most recent call last): 762s File "/usr/share/fasta3/scripts/get_protein.py", line 46, in 762s sys.stderr.write(e.read().decode('utf-8')+'\n') 762s ^^^^^^ 762s AttributeError: 'URLError' object has no attribute 'read' 763s >NP_000552.2 glutathione S-transferase Mu 1 isoform 1 [Homo sapiens] 763s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI 763s TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE 763s FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFS 763s KMAVWGNK 763s 794s get_uniprot.py 794s urllib3.exceptions.SSLError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033) 794s 794s The above exception was the direct cause of the following exception: 794s 794s Traceback (most recent call last): 794s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 794s resp = conn.urlopen( 794s method=request.method, 794s ...<9 lines>... 794s chunked=chunked, 794s ) 794s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 794s retries = retries.increment( 794s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 794s ) 794s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 519, in increment 794s raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] 794s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 794s urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/efetch.fcgi?db=protein&id=NP_0000552&rettype=fasta (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033)'))) 794s 794s During handling of the above exception, another exception occurred: 794s 794s Traceback (most recent call last): 794s File "/usr/share/fasta3/scripts/get_refseq.py", line 19, in 794s req = requests.get(url_string) 794s File "/usr/lib/python3/dist-packages/requests/api.py", line 73, in get 794s return request("get", url, params=params, **kwargs) 794s File "/usr/lib/python3/dist-packages/requests/api.py", line 59, in request 794s return session.request(method=method, url=url, **kwargs) 794s ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 794s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 794s resp = self.send(prep, **send_kwargs) 794s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 794s r = adapter.send(request, **kwargs) 794s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 675, in send 794s raise SSLError(e, request=request) 794s requests.exceptions.SSLError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/efetch.fcgi?db=protein&id=NP_0000552&rettype=fasta (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033)'))) 794s 794s During handling of the above exception, another exception occurred: 794s 794s Traceback (most recent call last): 794s File "/usr/share/fasta3/scripts/get_refseq.py", line 22, in 794s sys.stderr.print(e.response.text+'\n') 794s ^^^^^^^^^^^^^^^^ 794s AttributeError: '_io.TextIOWrapper' object has no attribute 'print' 795s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 795s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 795s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 795s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 795s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 795s 795s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 795s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 795s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 795s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 795s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 795s 795s ################################################################ 795s map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output 797s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_exons_up_sql.pl line 81. 797s *** ERROR [compacc2e.c:2269] -- get_annot() - premature annotation file end () 797s DBI connect('database=uniprot;host=wrpxdb.its.virginia.edu','web_user',...) failed: Unknown MySQL server host 'wrpxdb.its.virginia.edu' (-2) at /usr/share/fasta3/scripts/ann_exons_up_sql.pl line 81. 797s *** ERROR [compacc2e.c:1873] - premature annotation file end (annot_bline_B2sxf0.annot) 797s *** ERROR [compacc2e.c:1107] - !/usr/share/fasta3/scripts/ann_exons_up_sql.pl --gen_coord --exon_label did not produce annotations for sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 797s #/usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL 797s # fasta36 -q -m 8CBL -V !/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label !/usr/share/fasta3/scripts/get_protein.py+P30711 !/usr/share/fasta3/scripts/get_protein.py+P20135 797s # FASTA 36.3.8i Nov, 2022 797s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 797s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 797s # Fields: query id, query length, subject id, subject length, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, BTOP 797s # 1 hits found 797s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 4.3e-58 206.5 15ASVI4KRKT1DN4LFRKIH1DE1IF1-D-S-V-L-G-K-K-P-A-A-A-S-G-A-E-R-P-R-T1QPHSLN1DEAGFDAGQKVINSPL5AV8TA1SCVT6TS3KNVT2YH3QS1LIQKAK2RQ5AS1QH1TATNLI1RASNCALPRKATLM1HI2MLFI1VL1LT1EQ1VQSPPSQETK1AQAETVLMAEEG1DSVTTS1QKLQLF1DEKR3ND3LITI1PSHE9TV3HQ3AV2QDVI2GD2KR1AMTE2QR3AE3EKDE2QFEQ3VM2KNAI1DEFLPS-N-IPQAI2TQIL1QEKH1MA1WVVLLMAK1ILRK | 15ASVI4KRKT1DN4LFRKIH1DE1IF1-D-S-V-L-G-K-K-P-A-A-A-S-G-A-E-R-P-R-T1QPHSLN1DEAGFDAGQKVINSPL5AV8TA1SCVT6TS3KNVT2YH3QS1LIQKAK2RQ5AS1QH1TATNLI1RASNCALPRKATLM1HI2MLFI1VL1LT1EQ1VQSPPSQETK1AQAETVLMAEEG1DSVTTS1QKLQLF1DEKR3ND3LITI1PSHE9TV3HQ3AV2QDVI2GD2KR1AMTE2QR3AE3EKDE2QFEQ3VM2KNAI1DEFLPS-N-IPQAI2TQIL1QEKH1MA1WVVLLMAK1ILRK 797s # FASTA processed 1 queries 797s rename_exons.py -- look for exon_X in output 797s # fasta36 -q -m 8CBL -V !/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q!/usr/share/fasta3/scripts/ann_exons_up_sql.pl+--gen_coord+--exon_label !/usr/share/fasta3/scripts/get_protein.py+P30711 !/usr/share/fasta3/scripts/get_protein.py+P20135 797s # FASTA 36.3.8i Nov, 2022 797s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 797s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 797s # Fields: query id, query length, subject id, subject length, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, BTOP 797s # 1 hits found 797s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 4.3e-58 206.5 15ASVI4KRKT1DN4LFRKIH1DE1IF1-D-S-V-L-G-K-K-P-A-A-A-S-G-A-E-R-P-R-T1QPHSLN1DEAGFDAGQKVINSPL5AV8TA1SCVT6TS3KNVT2YH3QS1LIQKAK2RQ5AS1QH1TATNLI1RASNCALPRKATLM1HI2MLFI1VL1LT1EQ1VQSPPSQETK1AQAETVLMAEEG1DSVTTS1QKLQLF1DEKR3ND3LITI1PSHE9TV3HQ3AV2QDVI2GD2KR1AMTE2QR3AE3EKDE2QFEQ3VM2KNAI1DEFLPS-N-IPQAI2TQIL1QEKH1MA1WVVLLMAK1ILRK 797s # FASTA processed 1 queries 797s # fasta36 -q mgstm1.aa prot_test.lseg 797s FASTA searches a protein or DNA sequence data bank 797s version 36.3.8i Nov, 2022 797s Please cite: 797s W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 797s 797s + fasta36 -q mgstm1.aa prot_test.lseg 797s Query: mgstm1.aa 797s 1>>>sp|P10649|GSTM1_MOUSE Glutathione S-transferase Mu 1; GST 1-1; GST class-mu 1; Glutathione S-transferase GT8.7; pmGT10 - 218 aa 797s Library: prot_test.lseg 797s 2267 residues in 12 sequences 797s 797s Statistics: (shuffled [493]) MLE statistics: Lambda= 0.1558; K=0.003821 797s statistics sampled from 4 (4) to 492 sequences 797s Algorithm: FASTA (3.8 Nov 2011) [optimized] 797s Parameters: BL50 matrix (15:-5), open/ext: -10/-2 797s ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 797s Scan time: 0.000 797s 797s The best scores are: opt bits E(12) 797s sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 289.0 5.8e-82 797s sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 63.0 6.2e-14 797s sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.2 0.15 797s sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.4 1.3 797s sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.8 1.5 797s sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.7 2.4 797s sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.5 2.7 797s sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.5 3.8 797s sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.6 4.1 797s sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.3 797s sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.1 4.4 797s sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.3 797s 797s >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) 797s initn: 1242 init1: 1242 opt: 1242 Z-score: 1523.3 bits: 289.0 E(12): 5.8e-82 797s Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 797s 797s 10 20 30 40 50 60 797s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNL 797s ::::::::..:::.: ::.:::::::::.::.::::::::.::::::::::::::::::: 797s sp|P09 MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 797s 10 20 30 40 50 60 797s 797s 70 80 90 100 110 120 797s sp|P10 PYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDF 797s ::::::.:::::::::: :.::::.: ::::::.::.::.:::.::..::: :.::::.: 797s sp|P09 PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 797s 70 80 90 100 110 120 797s 797s 130 140 150 160 170 180 797s sp|P10 EKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPN 797s :: ::..:. .:::.:::::::::::::::.:.:.::::.::.:: .:.::::::::::: 797s sp|P09 EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 797s 130 140 150 160 170 180 797s 797s 190 200 210 797s sp|P10 LRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 797s :.::..:::::.::::::::::.. :.::::: :.:: 797s sp|P09 LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 797s 190 200 210 797s 797s >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) 797s initn: 204 init1: 73 opt: 237 Z-score: 302.0 bits: 63.0 E(12): 6.2e-14 797s Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 797s 797s 10 20 30 40 50 797s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLD 797s .: :.:.:: . :: :: . .::: : .: ::.: .: 797s sp|P00 MSGKPVLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLM 797s 10 20 30 40 50 797s 797s 60 70 80 90 100 110 797s sp|P10 FPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIML 797s : ..:.. ::: :..:. ::: :.: :. : :. .:: :. . ..: :.: . .. 797s sp|P00 FDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLV 797s 60 70 80 90 100 110 797s 797s 120 130 140 150 160 170 797s sp|P10 CYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMF 797s :: .. : . : : . . . . : . . ...:...: ::. ..: . : 797s sp|P00 ICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEF 797s 120 130 140 150 160 170 797s 797s 180 190 200 210 797s sp|P10 EPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 797s . . : .:: :. : .:. .: ... ... . :. .:. . . : 797s sp|P00 DASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARKIFKF 797s 180 190 200 210 220 797s 797s >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) 797s initn: 40 init1: 40 opt: 51 Z-score: 79.5 bits: 21.2 E(12): 0.15 797s Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 797s 797s 150 160 170 180 190 200 797s sp|P10 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA 797s .::. . .. .:. :.. :: .:. .. .: 797s sp|P69 ADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFD-LSHGSAQVKGHGKKVA 797s 10 20 30 40 50 60 797s 797s 210 797s sp|P10 TPIFSKMAHWSNK 797s . . .:: 797s sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 797s 70 80 90 100 110 120 797s 797s >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) 797s initn: 43 init1: 43 opt: 43 Z-score: 62.7 bits: 19.4 E(12): 1.3 797s Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 797s 797s 110 120 130 140 150 160 797s sp|P10 TRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQ 797s .: : :.:: . . . .. . 797s sp|P00 LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF 797s 200 210 220 230 240 250 797s 797s 170 180 190 200 210 797s sp|P10 YRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 797s : : . :: :. :: .::. .:. ...:: 797s sp|P00 PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK 797s 260 270 280 290 300 310 797s 797s sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 797s 320 330 340 350 797s 797s >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) 797s initn: 56 init1: 36 opt: 36 Z-score: 61.4 bits: 17.8 E(12): 1.5 797s Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 797s 797s 10 20 30 797s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG 797s ::.. :: 797s sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP 797s 20 30 40 50 60 70 797s 797s 40 50 60 70 80 90 797s sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR 797s 797s sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG 797s 80 90 100 110 120 130 797s 797s >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) 797s initn: 31 init1: 31 opt: 31 Z-score: 57.3 bits: 16.7 E(12): 2.4 797s Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 797s 797s 120 130 140 150 160 170 797s sp|P10 FEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDI---LDQYRMFE---PK 797s ::.:: . . :: :. :.. :: 797s sp|P01 DIQMTQSPSSLSASVGDRVTITCQASQDINHYLNWYQQGPKKAPK 797s 10 20 30 40 797s 797s 180 190 200 210 797s sp|P10 CL--DAFPNLRDFL-ARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 797s : :: ::. . .:: : 797s sp|P01 ILIYDA-SNLETGVPSRFSGSGFGTDFTFTISGLQPEDIATYYCQQYDTLPRTFGQGTKL 797s 50 60 70 80 90 100 797s 797s >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) 797s initn: 30 init1: 30 opt: 30 Z-score: 56.3 bits: 16.5 E(12): 2.7 797s Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 797s 797s 100 110 120 130 140 150 797s sp|P10 IVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWF---AGDKVTY 797s :: :. :... :. : . :..: 797s sp|P99 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKG 797s 10 20 30 40 50 797s 797s 160 170 180 190 200 210 797s sp|P10 VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW 797s . . . : : .: . .:: .:. . . : :.:: 797s sp|P99 I-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKKKEERADLIAYLKKATNE 797s 60 70 80 90 100 797s 797s 797s sp|P10 SNK 797s 797s >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) 797s initn: 30 init1: 30 opt: 30 Z-score: 53.0 bits: 16.5 E(12): 3.8 797s Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 797s 797s 20 30 40 50 60 70 797s sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- 797s :. . .:: ..:. . ::. :. 797s sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK 797s 10 20 30 797s 797s 80 90 100 110 120 797s sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL 797s . ....:.:.. :..::. :: 797s sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 797s 40 50 60 70 80 90 797s 797s >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) 797s initn: 26 init1: 26 opt: 26 Z-score: 52.2 bits: 15.6 E(12): 4.1 797s Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 797s 797s 90 100 110 120 130 140 797s sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK 797s : :: ::.: 797s sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG 797s 60 70 80 90 797s 797s 150 160 170 180 190 200 797s sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI 797s 797s >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) 797s initn: 22 init1: 22 opt: 22 Z-score: 51.8 bits: 14.7 E(12): 4.3 797s Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 797s 797s 150 160 170 180 190 200 797s sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS 797s .:.: 797s sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV 797s 10 20 30 40 797s 797s 210 797s sp|P10 SRYIATPIFSKMAHWSNK 797s 797s sp|P00 CPVGAPNPED 797s 50 797s 797s >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) 797s initn: 37 init1: 37 opt: 37 Z-score: 51.6 bits: 18.1 E(12): 4.4 797s Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 797s 797s 50 60 70 80 90 100 797s sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN 797s : ... .: :... : : . : . .:. 797s sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK 797s 370 380 390 400 410 420 797s 797s 110 120 130 140 150 160 797s sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD 797s : ::...: 797s sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 797s 430 440 450 460 470 480 797s 797s >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) 797s initn: 23 init1: 23 opt: 23 Z-score: 47.7 bits: 14.9 E(12): 6.3 797s Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 797s 797s 30 40 50 60 70 80 797s sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH 797s :. : .:. ... .: : . . 797s sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK 797s 10 20 30 40 797s 797s 90 100 110 120 130 140 797s sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG 797s .:. . . ...:.. :. ..: . . :.::.: 797s sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 797s 50 60 70 80 90 100 797s 797s 150 160 170 180 190 200 797s sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY 797s 797s sp|P01 NRGEC 797s 797s 797s 797s 797s 218 residues in 1 query sequences 797s 2267 residues in 12 library sequences 797s Tcomplib [36.3.8i Nov, 2022] (2 proc in memory [0G]) 797s start: Thu Feb 5 03:50:06 2026 done: Thu Feb 5 03:50:06 2026 797s Total Scan time: 0.000 Total Display time: 0.010 797s 797s Function used was FASTA [36.3.8i Nov, 2022] 797s autopkgtest [03:50:07]: test run-unit-test: -----------------------] 801s autopkgtest [03:50:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 801s run-unit-test PASS 802s autopkgtest [03:50:12]: @@@@@@@@@@@@@@@@@@@@ summary 802s run-unit-test PASS