0s autopkgtest [02:51:39]: starting date and time: 2026-02-05 02:51:39+0000 0s autopkgtest [02:51:39]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [02:51:39]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.biv552hh/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.239 lxd-armhf-10.145.243.239:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [02:52:00]: testbed dpkg architecture: armhf 23s autopkgtest [02:52:02]: testbed apt version: 3.1.14 27s autopkgtest [02:52:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [02:52:08]: testbed release detected to be: None 37s autopkgtest [02:52:16]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 39s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 39s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 39s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 39s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 39s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 39s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 39s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 40s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [250 kB] 40s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1364 kB] 40s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 41s Fetched 3735 kB in 2s (1870 kB/s) 42s Reading package lists... 48s autopkgtest [02:52:27]: upgrading testbed (apt dist-upgrade and autopurge) 49s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 51s The following packages will be upgraded: 51s libc-bin libc-gconv-modules-extra libc6 locales 51s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 7850 kB of archives. 51s After this operation, 0 B of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 52s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 54s Preconfiguring packages ... 54s Fetched 7850 kB in 3s (2889 kB/s) 54s (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 ... 68395 files and directories currently installed.) 54s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 54s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 54s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 54s (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 ... 68395 files and directories currently installed.) 54s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 54s readlink: /usr/lib/libeatmydata: No such file or directory 54s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 55s Setting up libc6:armhf (2.42-2ubuntu5) ... 55s (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 ... 68395 files and directories currently installed.) 55s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 55s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 55s Setting up libc-bin (2.42-2ubuntu5) ... 55s (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 ... 68395 files and directories currently installed.) 55s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 55s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 55s Setting up locales (2.42-2ubuntu5) ... 56s Generating locales (this might take a while)... 58s en_US.UTF-8... done 58s Generation complete. 58s Processing triggers for systemd (259-1ubuntu3) ... 59s Processing triggers for man-db (2.13.1-1) ... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Solving dependencies... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [02:52:44]: rebooting testbed after setup commands that affected boot 108s autopkgtest [02:53:27]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 133s autopkgtest [02:53:52]: @@@@@@@@@@@@@@@@@@@@ apt-source fasta3 148s Get:1 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (dsc) [2248 B] 148s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (tar) [1403 kB] 148s Get:3 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (diff) [14.8 kB] 148s gpgv: Signature made Wed Sep 24 06:35:50 2025 UTC 148s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 148s gpgv: issuer "tillea@rki.de" 148s gpgv: Can't check signature: No public key 148s dpkg-source: warning: cannot verify inline signature for ./fasta3_36.3.8i.14-Nov-2020-4.dsc: no acceptable signature found 148s autopkgtest [02:54:07]: testing package fasta3 version 36.3.8i.14-Nov-2020-4 150s autopkgtest [02:54:09]: build not needed 153s autopkgtest [02:54:12]: test run-unit-test: preparing testbed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Solving dependencies... 156s The following NEW packages will be installed: 156s bedtools fasta3 libclone-perl libdbd-mysql-perl libdbi-perl 156s libencode-locale-perl libfile-listing-perl libhtml-parser-perl 156s libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl 156s libhttp-message-perl libhttp-negotiate-perl libio-html-perl 156s libio-socket-ssl-perl libjson-perl liblwp-mediatypes-perl 156s liblwp-protocol-https-perl libmysqlclient24 libnet-http-perl 156s libnet-ssleay-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl 156s libwww-robotrules-perl libxml-parser-perl libxml-twig-perl mysql-common 156s perl-openssl-defaults python3-mysqldb 156s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 5547 kB of archives. 156s After this operation, 22.2 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu resolute/universe armhf bedtools armhf 2.31.1+dfsg-3 [638 kB] 156s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse armhf fasta3 armhf 36.3.8i.14-Nov-2020-4 [914 kB] 157s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libclone-perl armhf 0.47-1 [10.0 kB] 157s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libdbi-perl armhf 1.647-1build1 [822 kB] 157s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 157s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libmysqlclient24 armhf 8.4.8-0ubuntu1 [1266 kB] 157s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libdbd-mysql-perl armhf 4.053-1ubuntu1 [79.4 kB] 157s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libencode-locale-perl all 1.05-3 [11.6 kB] 157s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libtimedate-perl all 2.3300-2 [34.0 kB] 157s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libhttp-date-perl all 6.06-1 [10.2 kB] 157s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libfile-listing-perl all 6.16-1 [11.3 kB] 157s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libhtml-tagset-perl all 3.24-1 [14.1 kB] 157s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf liburi-perl all 5.34-2build1 [100 kB] 157s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libhtml-parser-perl armhf 3.83-1build1 [83.1 kB] 157s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libhtml-tree-perl all 5.07-3 [200 kB] 157s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libio-html-perl all 1.004-3 [15.9 kB] 157s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 157s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libhttp-message-perl all 7.01-1ubuntu1 [76.1 kB] 157s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libhttp-cookies-perl all 6.11-1 [18.2 kB] 157s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libhttp-negotiate-perl all 6.01-2 [12.4 kB] 157s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf perl-openssl-defaults armhf 7build4 [6710 B] 157s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libnet-ssleay-perl armhf 1.94-3 [298 kB] 157s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libio-socket-ssl-perl all 2.098-1 [205 kB] 157s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-perl all 4.10000-1 [81.9 kB] 157s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libnet-http-perl all 6.24-1build1 [21.7 kB] 157s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libtry-tiny-perl all 0.32-1 [21.2 kB] 157s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libwww-robotrules-perl all 6.02-1build1 [12.4 kB] 157s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libwww-perl all 6.81-1build1 [141 kB] 157s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf liblwp-protocol-https-perl all 6.14-1 [9040 B] 157s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libxml-parser-perl armhf 2.47-1build4 [199 kB] 157s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libxml-twig-perl all 1:3.54-1build1 [157 kB] 157s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf python3-mysqldb armhf 1.4.6-2build7 [49.9 kB] 158s Fetched 5547 kB in 2s (3385 kB/s) 158s Selecting previously unselected package bedtools. 158s (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 ... 68395 files and directories currently installed.) 158s Preparing to unpack .../00-bedtools_2.31.1+dfsg-3_armhf.deb ... 158s Unpacking bedtools (2.31.1+dfsg-3) ... 158s Selecting previously unselected package fasta3. 158s Preparing to unpack .../01-fasta3_36.3.8i.14-Nov-2020-4_armhf.deb ... 158s Unpacking fasta3 (36.3.8i.14-Nov-2020-4) ... 158s Selecting previously unselected package libclone-perl:armhf. 158s Preparing to unpack .../02-libclone-perl_0.47-1_armhf.deb ... 158s Unpacking libclone-perl:armhf (0.47-1) ... 158s Selecting previously unselected package libdbi-perl:armhf. 158s Preparing to unpack .../03-libdbi-perl_1.647-1build1_armhf.deb ... 158s Unpacking libdbi-perl:armhf (1.647-1build1) ... 158s Selecting previously unselected package mysql-common. 158s Preparing to unpack .../04-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 158s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 158s Selecting previously unselected package libmysqlclient24:armhf. 158s Preparing to unpack .../05-libmysqlclient24_8.4.8-0ubuntu1_armhf.deb ... 158s Unpacking libmysqlclient24:armhf (8.4.8-0ubuntu1) ... 158s Selecting previously unselected package libdbd-mysql-perl:armhf. 158s Preparing to unpack .../06-libdbd-mysql-perl_4.053-1ubuntu1_armhf.deb ... 158s Unpacking libdbd-mysql-perl:armhf (4.053-1ubuntu1) ... 158s Selecting previously unselected package libencode-locale-perl. 158s Preparing to unpack .../07-libencode-locale-perl_1.05-3_all.deb ... 158s Unpacking libencode-locale-perl (1.05-3) ... 159s Selecting previously unselected package libtimedate-perl. 159s Preparing to unpack .../08-libtimedate-perl_2.3300-2_all.deb ... 159s Unpacking libtimedate-perl (2.3300-2) ... 159s Selecting previously unselected package libhttp-date-perl. 159s Preparing to unpack .../09-libhttp-date-perl_6.06-1_all.deb ... 159s Unpacking libhttp-date-perl (6.06-1) ... 159s Selecting previously unselected package libfile-listing-perl. 159s Preparing to unpack .../10-libfile-listing-perl_6.16-1_all.deb ... 159s Unpacking libfile-listing-perl (6.16-1) ... 159s Selecting previously unselected package libhtml-tagset-perl. 159s Preparing to unpack .../11-libhtml-tagset-perl_3.24-1_all.deb ... 159s Unpacking libhtml-tagset-perl (3.24-1) ... 159s Selecting previously unselected package liburi-perl. 159s Preparing to unpack .../12-liburi-perl_5.34-2build1_all.deb ... 159s Unpacking liburi-perl (5.34-2build1) ... 159s Selecting previously unselected package libhtml-parser-perl:armhf. 159s Preparing to unpack .../13-libhtml-parser-perl_3.83-1build1_armhf.deb ... 159s Unpacking libhtml-parser-perl:armhf (3.83-1build1) ... 159s Selecting previously unselected package libhtml-tree-perl. 159s Preparing to unpack .../14-libhtml-tree-perl_5.07-3_all.deb ... 159s Unpacking libhtml-tree-perl (5.07-3) ... 159s Selecting previously unselected package libio-html-perl. 159s Preparing to unpack .../15-libio-html-perl_1.004-3_all.deb ... 159s Unpacking libio-html-perl (1.004-3) ... 159s Selecting previously unselected package liblwp-mediatypes-perl. 159s Preparing to unpack .../16-liblwp-mediatypes-perl_6.04-2_all.deb ... 159s Unpacking liblwp-mediatypes-perl (6.04-2) ... 159s Selecting previously unselected package libhttp-message-perl. 159s Preparing to unpack .../17-libhttp-message-perl_7.01-1ubuntu1_all.deb ... 159s Unpacking libhttp-message-perl (7.01-1ubuntu1) ... 159s Selecting previously unselected package libhttp-cookies-perl. 159s Preparing to unpack .../18-libhttp-cookies-perl_6.11-1_all.deb ... 159s Unpacking libhttp-cookies-perl (6.11-1) ... 159s Selecting previously unselected package libhttp-negotiate-perl. 159s Preparing to unpack .../19-libhttp-negotiate-perl_6.01-2_all.deb ... 159s Unpacking libhttp-negotiate-perl (6.01-2) ... 159s Selecting previously unselected package perl-openssl-defaults:armhf. 159s Preparing to unpack .../20-perl-openssl-defaults_7build4_armhf.deb ... 159s Unpacking perl-openssl-defaults:armhf (7build4) ... 159s Selecting previously unselected package libnet-ssleay-perl:armhf. 159s Preparing to unpack .../21-libnet-ssleay-perl_1.94-3_armhf.deb ... 159s Unpacking libnet-ssleay-perl:armhf (1.94-3) ... 159s Selecting previously unselected package libio-socket-ssl-perl. 159s Preparing to unpack .../22-libio-socket-ssl-perl_2.098-1_all.deb ... 159s Unpacking libio-socket-ssl-perl (2.098-1) ... 159s Selecting previously unselected package libjson-perl. 159s Preparing to unpack .../23-libjson-perl_4.10000-1_all.deb ... 159s Unpacking libjson-perl (4.10000-1) ... 159s Selecting previously unselected package libnet-http-perl. 159s Preparing to unpack .../24-libnet-http-perl_6.24-1build1_all.deb ... 159s Unpacking libnet-http-perl (6.24-1build1) ... 159s Selecting previously unselected package libtry-tiny-perl. 159s Preparing to unpack .../25-libtry-tiny-perl_0.32-1_all.deb ... 159s Unpacking libtry-tiny-perl (0.32-1) ... 159s Selecting previously unselected package libwww-robotrules-perl. 159s Preparing to unpack .../26-libwww-robotrules-perl_6.02-1build1_all.deb ... 159s Unpacking libwww-robotrules-perl (6.02-1build1) ... 159s Selecting previously unselected package libwww-perl. 159s Preparing to unpack .../27-libwww-perl_6.81-1build1_all.deb ... 159s Unpacking libwww-perl (6.81-1build1) ... 159s Selecting previously unselected package liblwp-protocol-https-perl. 159s Preparing to unpack .../28-liblwp-protocol-https-perl_6.14-1_all.deb ... 159s Unpacking liblwp-protocol-https-perl (6.14-1) ... 159s Selecting previously unselected package libxml-parser-perl. 159s Preparing to unpack .../29-libxml-parser-perl_2.47-1build4_armhf.deb ... 159s Unpacking libxml-parser-perl (2.47-1build4) ... 159s Selecting previously unselected package libxml-twig-perl. 160s Preparing to unpack .../30-libxml-twig-perl_1%3a3.54-1build1_all.deb ... 160s Unpacking libxml-twig-perl (1:3.54-1build1) ... 160s Selecting previously unselected package python3-mysqldb. 160s Preparing to unpack .../31-python3-mysqldb_1.4.6-2build7_armhf.deb ... 160s Unpacking python3-mysqldb (1.4.6-2build7) ... 160s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 160s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 160s Setting up libclone-perl:armhf (0.47-1) ... 160s Setting up libhtml-tagset-perl (3.24-1) ... 160s Setting up liblwp-mediatypes-perl (6.04-2) ... 160s Setting up fasta3 (36.3.8i.14-Nov-2020-4) ... 160s Setting up libtry-tiny-perl (0.32-1) ... 160s Setting up perl-openssl-defaults:armhf (7build4) ... 160s Setting up libencode-locale-perl (1.05-3) ... 160s Setting up libmysqlclient24:armhf (8.4.8-0ubuntu1) ... 160s Setting up python3-mysqldb (1.4.6-2build7) ... 160s Setting up libio-html-perl (1.004-3) ... 160s Setting up libtimedate-perl (2.3300-2) ... 160s Setting up libjson-perl (4.10000-1) ... 160s Setting up bedtools (2.31.1+dfsg-3) ... 160s Setting up liburi-perl (5.34-2build1) ... 160s Setting up libdbi-perl:armhf (1.647-1build1) ... 160s Setting up libnet-ssleay-perl:armhf (1.94-3) ... 160s Setting up libhttp-date-perl (6.06-1) ... 160s Setting up libfile-listing-perl (6.16-1) ... 160s Setting up libnet-http-perl (6.24-1build1) ... 160s Setting up libdbd-mysql-perl:armhf (4.053-1ubuntu1) ... 160s Setting up libwww-robotrules-perl (6.02-1build1) ... 160s Setting up libhtml-parser-perl:armhf (3.83-1build1) ... 160s Setting up libio-socket-ssl-perl (2.098-1) ... 160s Setting up libhttp-message-perl (7.01-1ubuntu1) ... 160s Setting up libhttp-negotiate-perl (6.01-2) ... 160s Setting up libhttp-cookies-perl (6.11-1) ... 160s Setting up libhtml-tree-perl (5.07-3) ... 160s Setting up liblwp-protocol-https-perl (6.14-1) ... 160s Setting up libwww-perl (6.81-1build1) ... 160s Setting up libxml-parser-perl (2.47-1build4) ... 160s Setting up libxml-twig-perl (1:3.54-1build1) ... 160s Processing triggers for man-db (2.13.1-1) ... 160s Processing triggers for libc-bin (2.42-2ubuntu5) ... 169s autopkgtest [02:54:28]: test run-unit-test: [----------------------- 171s + pkg=fasta3 171s + export LC_ALL=C.UTF-8 171s + LC_ALL=C.UTF-8 171s + '[' /tmp/autopkgtest.RAhFHb/autopkgtest_tmp = '' ']' 171s + 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.RAhFHb/autopkgtest_tmp 171s /usr/share/fasta3/scripts/ann_exons_up_www.pl P09488 171s + cd /tmp/autopkgtest.RAhFHb/autopkgtest_tmp 171s + /usr/share/fasta3/scripts/test_ann_scripts.sh 172s >P09488 172s 1 - 12 exon_1~1 172s 13 - 37 exon_2~2 172s 38 - 59 exon_3~3 172s 60 - 86 exon_4~4 172s 87 - 120 exon_5~5 172s 121 - 152 exon_6~6 172s 153 - 189 exon_7~7 172s 190 - 218 exon_8~8 172s /usr/share/fasta3/scripts/ann_exons_up_www.pl sp|P09488 173s >sp|P09488 173s 1 - 12 exon_1~1 173s 13 - 37 exon_2~2 173s 38 - 59 exon_3~3 173s 60 - 86 exon_4~4 173s 87 - 120 exon_5~5 173s 121 - 152 exon_6~6 173s 153 - 189 exon_7~7 173s 190 - 218 exon_8~8 173s /usr/share/fasta3/scripts/ann_exons_up_www.pl up|P09488|GSTM1_HUMAN 174s >up|P09488|GSTM1_HUMAN 174s 1 - 12 exon_1~1 174s 13 - 37 exon_2~2 174s 38 - 59 exon_3~3 174s 60 - 86 exon_4~4 174s 87 - 120 exon_5~5 174s 121 - 152 exon_6~6 174s 153 - 189 exon_7~7 174s 190 - 218 exon_8~8 174s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN P09488 175s >SP:GSTM1_HUMAN P09488 175s 1 - 12 exon_1~1 175s 13 - 37 exon_2~2 175s 38 - 59 exon_3~3 175s 60 - 86 exon_4~4 175s 87 - 120 exon_5~5 175s 121 - 152 exon_6~6 175s 153 - 189 exon_7~7 175s 190 - 218 exon_8~8 175s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN 175s *** /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. 175s >SP:GSTM1_HUMAN 175s ***DONE*** /usr/share/fasta3/scripts/ann_exons_up_www.pl Thu Feb 5 02:54:34 UTC 2026 175s /usr/share/fasta3/scripts/ann_feats_up_sql.pl P09488 176s 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. 176s /usr/share/fasta3/scripts/ann_feats_up_sql.pl sp|P09488 176s 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. 176s /usr/share/fasta3/scripts/ann_feats_up_sql.pl up|P09488|GSTM1_HUMAN 176s 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. 176s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN P09488 176s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN 176s 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. 176s 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. 176s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_sql.pl Thu Feb 5 02:54:35 UTC 2026 176s /usr/share/fasta3/scripts/ann_feats_up_www2.pl P09488 176s ==:Active site 176s =*:Modified 176s =#:Binding 176s =^:Metal binding 176s =@:Site 176s >P09488 176s /usr/share/fasta3/scripts/ann_feats_up_www2.pl sp|P09488 177s ==:Active site 177s =*:Modified 177s =#:Binding 177s =^:Metal binding 177s =@:Site 177s >sp|P09488 177s /usr/share/fasta3/scripts/ann_feats_up_www2.pl up|P09488|GSTM1_HUMAN 177s ==:Active site 177s =*:Modified 177s =#:Binding 177s =^:Metal binding 177s =@:Site 177s >up|P09488|GSTM1_HUMAN 177s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN P09488 177s ==:Active site 177s =*:Modified 177s =#:Binding 177s =^:Metal binding 177s =@:Site 177s >SP:GSTM1_HUMAN P09488 177s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN 177s *** /usr/share/fasta3/scripts/ann_feats_up_www2.pl accession required: SP:GSTM1_HUMAN 177s ==:Active site 177s =*:Modified 177s =#:Binding 177s =^:Metal binding 177s =@:Site 177s >SP:GSTM1_HUMAN 177s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_www2.pl Thu Feb 5 02:54:36 UTC 2026 177s /usr/share/fasta3/scripts/ann_ipr_www.pl P09488 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s >P09488 178s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 178s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 178s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 178s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 178s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 178s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 178s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 178s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 178s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 178s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 178s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 178s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 178s /usr/share/fasta3/scripts/ann_ipr_www.pl sp|P09488 178s >sp|P09488 178s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 178s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 178s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 178s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 178s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 178s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 178s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 178s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 178s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 178s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 178s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 178s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 178s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 178s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 178s /usr/share/fasta3/scripts/ann_ipr_www.pl up|P09488|GSTM1_HUMAN 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s >up|P09488|GSTM1_HUMAN 179s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 179s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 179s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 179s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 179s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 179s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 179s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 179s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 179s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 179s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 179s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 179s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 179s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN P09488 179s >SP:GSTM1_HUMAN P09488 179s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 179s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 179s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 179s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 179s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 179s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 179s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 179s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 179s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 179s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 179s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 179s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 179s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 179s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 179s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 180s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 180s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 180s >SP:GSTM1_HUMAN 180s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 180s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 180s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 180s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 180s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 180s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 180s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 180s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 180s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 180s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 180s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 180s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 180s ***DONE*** /usr/share/fasta3/scripts/ann_ipr_www.pl Thu Feb 5 02:54:39 UTC 2026 180s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl P09488 181s 181s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/arm-linux-gnueabihf/perl5/5.40/XML/Parser.pm line 187. 181s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 181s ==:Active site 181s =*:Modified 181s =#:Substrate binding 181s =^:Metal binding 181s =@:Site 181s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl sp|P09488 182s ==:Active site 182s =*:Modified 182s =#:Substrate binding 182s =^:Metal binding 182s =@:Site 182s 182s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/arm-linux-gnueabihf/perl5/5.40/XML/Parser.pm line 187. 182s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 182s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl up|P09488|GSTM1_HUMAN 183s ==:Active site 183s =*:Modified 183s =#:Substrate binding 183s =^:Metal binding 183s =@:Site 183s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN P09488 183s 183s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/arm-linux-gnueabihf/perl5/5.40/XML/Parser.pm line 187. 183s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 184s 184s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/arm-linux-gnueabihf/perl5/5.40/XML/Parser.pm line 187. 184s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 184s ==:Active site 184s =*:Modified 184s =#:Substrate binding 184s =^:Metal binding 184s =@:Site 184s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN 184s *** /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. 184s 184s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/arm-linux-gnueabihf/perl5/5.40/XML/Parser.pm line 187. 184s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 184s ==:Active site 184s =*:Modified 184s =#:Substrate binding 184s =^:Metal binding 184s =@:Site 184s ***DONE*** /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl Thu Feb 5 02:54:43 UTC 2026 184s get_protein.py 184s + /usr/share/fasta3/scripts/test_py.sh 185s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 185s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 185s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 185s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 185s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 185s 186s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 186s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 186s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 186s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 186s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 186s 194s >NP_000552.2 glutathione S-transferase Mu 1 isoform 1 [Homo sapiens] 194s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI 194s TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE 194s FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFS 194s KMAVWGNK 194s 194s 194s get_refseq.py 195s >NP_000552.2 glutathione S-transferase Mu 1 isoform 1 [Homo sapiens] 195s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI 195s TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE 195s FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFS 195s KMAVWGNK 195s 197s +Error%3A+CEFetchPApplication%3A%3Aproxy_stream()%3A+Error%3A+F+a+i+l+e+d++t+o++r+e+t+r+i+e+v+e++s+e+q+u+e+n+c+e+%3A++N+P+_+0+0+0+0+5+5+2+%0A%0A 197s get_uniprot.py 198s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 198s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 198s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 198s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 198s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 198s 199s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 199s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 199s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 199s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 199s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 199s 199s ################################################################ 199s map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output 201s 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. 201s *** ERROR [compacc2e.c:2269] -- get_annot() - premature annotation file end () 201s 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. 201s *** ERROR [compacc2e.c:1873] - premature annotation file end (annot_bline_KTjW4f.annot) 201s *** 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 201s #/usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL 201s # 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 201s # FASTA 36.3.8i Nov, 2022 201s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 201s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 201s # 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 201s # 1 hits found 201s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 2.1e-58 207.5 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 201s # FASTA processed 1 queries 201s rename_exons.py -- look for exon_X in output 201s # 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 201s # FASTA 36.3.8i Nov, 2022 201s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 201s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 201s # 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 201s # 1 hits found 201s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 2.1e-58 207.5 15ASVI4KRKT1DN4LFRKIH1DE1IF1-D-S-V-L-G-K-K-P-A-A-A-S-G-A-E-R-P-R-T1QPHSLN1DEAGFDAGQKVINSPL5AV8TA1SCVT6TS3KNVT2YH3QS1LIQKAK2RQ5AS1QH1TATNLI1RASNCALPRKATLM1HI2MLFI1VL1LT1EQ1VQSPPSQETK1AQAETVLMAEEG1DSVTTS1QKLQLF1DEKR3ND3LITI1PSHE9TV3HQ3AV2QDVI2GD2KR1AMTE2QR3AE3EKDE2QFEQ3VM2KNAI1DEFLPS-N-IPQAI2TQIL1QEKH1MA1WVVLLMAK1ILRK 201s # FASTA processed 1 queries 201s + fasta36 -q mgstm1.aa prot_test.lseg 201s # fasta36 -q mgstm1.aa prot_test.lseg 201s FASTA searches a protein or DNA sequence data bank 201s version 36.3.8i Nov, 2022 201s Please cite: 201s W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 201s 201s Query: mgstm1.aa 201s 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 201s Library: prot_test.lseg 201s 2267 residues in 12 sequences 201s 201s Statistics: (shuffled [451]) MLE statistics: Lambda= 0.1565; K=0.003778 201s statistics sampled from 4 (4) to 451 sequences 201s Algorithm: FASTA (3.8 Nov 2011) [optimized] 201s Parameters: BL50 matrix (15:-5), open/ext: -10/-2 201s ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 201s Scan time: 0.010 201s 201s The best scores are: opt bits E(12) 201s sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 290.4 2.2e-82 201s sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 63.4 4.8e-14 201s sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.4 0.13 201s sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.6 1.1 201s sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.0 1.3 201s sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.9 2.1 201s sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.7 2.4 201s sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.7 3.4 201s sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.7 3.8 201s sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.8 4 201s sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.2 4 201s sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.1 5.9 201s 201s >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) 201s initn: 1242 init1: 1242 opt: 1242 Z-score: 1530.7 bits: 290.4 E(12): 2.2e-82 201s Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 201s 201s 10 20 30 40 50 60 201s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNL 201s ::::::::..:::.: ::.:::::::::.::.::::::::.::::::::::::::::::: 201s sp|P09 MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 201s 10 20 30 40 50 60 201s 201s 70 80 90 100 110 120 201s sp|P10 PYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDF 201s ::::::.:::::::::: :.::::.: ::::::.::.::.:::.::..::: :.::::.: 201s sp|P09 PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 201s 70 80 90 100 110 120 201s 201s 130 140 150 160 170 180 201s sp|P10 EKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPN 201s :: ::..:. .:::.:::::::::::::::.:.:.::::.::.:: .:.::::::::::: 201s sp|P09 EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 201s 130 140 150 160 170 180 201s 201s 190 200 210 201s sp|P10 LRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 201s :.::..:::::.::::::::::.. :.::::: :.:: 201s sp|P09 LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 201s 190 200 210 201s 201s >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) 201s initn: 204 init1: 73 opt: 237 Z-score: 304.0 bits: 63.4 E(12): 4.8e-14 201s Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 201s 201s 10 20 30 40 50 201s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLD 201s .: :.:.:: . :: :: . .::: : .: ::.: .: 201s sp|P00 MSGKPVLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLM 201s 10 20 30 40 50 201s 201s 60 70 80 90 100 110 201s sp|P10 FPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIML 201s : ..:.. ::: :..:. ::: :.: :. : :. .:: :. . ..: :.: . .. 201s sp|P00 FDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLV 201s 60 70 80 90 100 110 201s 201s 120 130 140 150 160 170 201s sp|P10 CYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMF 201s :: .. : . : : . . . . : . . ...:...: ::. ..: . : 201s sp|P00 ICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEF 201s 120 130 140 150 160 170 201s 201s 180 190 200 210 201s sp|P10 EPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 201s . . : .:: :. : .:. .: ... ... . :. .:. . . : 201s sp|P00 DASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARKIFKF 201s 180 190 200 210 220 201s 201s >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) 201s initn: 40 init1: 40 opt: 51 Z-score: 80.5 bits: 21.4 E(12): 0.13 201s Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 201s 201s 150 160 170 180 190 200 201s sp|P10 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA 201s .::. . .. .:. :.. :: .:. .. .: 201s sp|P69 ADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFD-LSHGSAQVKGHGKKVA 201s 10 20 30 40 50 60 201s 201s 210 201s sp|P10 TPIFSKMAHWSNK 201s . . .:: 201s sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 201s 70 80 90 100 110 120 201s 201s >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) 201s initn: 43 init1: 43 opt: 43 Z-score: 63.7 bits: 19.6 E(12): 1.1 201s Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 201s 201s 110 120 130 140 150 160 201s sp|P10 TRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQ 201s .: : :.:: . . . .. . 201s sp|P00 LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF 201s 200 210 220 230 240 250 201s 201s 170 180 190 200 210 201s sp|P10 YRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 201s : : . :: :. :: .::. .:. ...:: 201s sp|P00 PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK 201s 260 270 280 290 300 310 201s 201s sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 201s 320 330 340 350 201s 201s >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) 201s initn: 56 init1: 36 opt: 36 Z-score: 62.4 bits: 18.0 E(12): 1.3 201s Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 201s 201s 10 20 30 201s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG 201s ::.. :: 201s sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP 201s 20 30 40 50 60 70 201s 201s 40 50 60 70 80 90 201s sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR 201s 201s sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG 201s 80 90 100 110 120 130 201s 201s >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) 201s initn: 31 init1: 31 opt: 31 Z-score: 58.2 bits: 16.9 E(12): 2.1 201s Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 201s 201s 120 130 140 150 160 170 201s sp|P10 FEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDI---LDQYRMFE---PK 201s ::.:: . . :: :. :.. :: 201s sp|P01 DIQMTQSPSSLSASVGDRVTITCQASQDINHYLNWYQQGPKKAPK 201s 10 20 30 40 201s 201s 180 190 200 210 201s sp|P10 CL--DAFPNLRDFL-ARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 201s : :: ::. . .:: : 201s sp|P01 ILIYDA-SNLETGVPSRFSGSGFGTDFTFTISGLQPEDIATYYCQQYDTLPRTFGQGTKL 201s 50 60 70 80 90 100 201s 201s >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) 201s initn: 30 init1: 30 opt: 30 Z-score: 57.2 bits: 16.7 E(12): 2.4 201s Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 201s 201s 100 110 120 130 140 150 201s sp|P10 IVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWF---AGDKVTY 201s :: :. :... :. : . :..: 201s sp|P99 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKG 201s 10 20 30 40 50 201s 201s 160 170 180 190 200 210 201s sp|P10 VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW 201s . . . : : .: . .:: .:. . . : :.:: 201s sp|P99 I-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKKKEERADLIAYLKKATNE 201s 60 70 80 90 100 201s 201s 201s sp|P10 SNK 201s 201s >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) 201s initn: 30 init1: 30 opt: 30 Z-score: 53.9 bits: 16.7 E(12): 3.4 201s Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 201s 201s 20 30 40 50 60 70 201s sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- 201s :. . .:: ..:. . ::. :. 201s sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK 201s 10 20 30 201s 201s 80 90 100 110 120 201s sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL 201s . ....:.:.. :..::. :: 201s sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 201s 40 50 60 70 80 90 201s 201s >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) 201s initn: 26 init1: 26 opt: 26 Z-score: 53.1 bits: 15.7 E(12): 3.8 201s Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 201s 201s 90 100 110 120 130 140 201s sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK 201s : :: ::.: 201s sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG 201s 60 70 80 90 201s 201s 150 160 170 180 190 200 201s sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI 201s 201s >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) 201s initn: 22 init1: 22 opt: 22 Z-score: 52.6 bits: 14.8 E(12): 4 201s Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 201s 201s 150 160 170 180 190 200 201s sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS 201s .:.: 201s sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV 201s 10 20 30 40 201s 201s 210 201s sp|P10 SRYIATPIFSKMAHWSNK 201s 201s sp|P00 CPVGAPNPED 201s 50 201s 201s >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) 201s initn: 37 init1: 37 opt: 37 Z-score: 52.6 bits: 18.2 E(12): 4 201s Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 201s 201s 50 60 70 80 90 100 201s sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN 201s : ... .: :... : : . : . .:. 201s sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK 201s 370 380 390 400 410 420 201s 201s 110 120 130 140 150 160 201s sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD 201s : ::...: 201s sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 201s 430 440 450 460 470 480 201s 201s >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) 201s initn: 23 init1: 23 opt: 23 Z-score: 48.6 bits: 15.1 E(12): 5.9 201s Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 201s 201s 30 40 50 60 70 80 201s sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH 201s :. : .:. ... .: : . . 201s sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK 201s 10 20 30 40 201s 201s 90 100 110 120 130 140 201s sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG 201s .:. . . ...:.. :. ..: . . :.::.: 201s sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 201s 50 60 70 80 90 100 201s 201s 150 160 170 180 190 200 201s sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY 201s 201s sp|P01 NRGEC 201s 201s 201s 201s 201s 218 residues in 1 query sequences 201s 2267 residues in 12 library sequences 201s Tcomplib [36.3.8i Nov, 2022] (8 proc in memory [0G]) 201s start: Thu Feb 5 02:55:00 2026 done: Thu Feb 5 02:55:00 2026 201s Total Scan time: 0.010 Total Display time: 0.000 201s 201s Function used was FASTA [36.3.8i Nov, 2022] 202s autopkgtest [02:55:01]: test run-unit-test: -----------------------] 206s run-unit-test PASS 206s autopkgtest [02:55:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 210s autopkgtest [02:55:09]: @@@@@@@@@@@@@@@@@@@@ summary 210s run-unit-test PASS