0s autopkgtest [01:45:03]: starting date and time: 2026-02-05 01:45:03+0000 0s autopkgtest [01:45:03]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:45:03]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tmguhm6a/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade fasta3 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-22.secgroup --name adt-resolute-arm64-fasta3-20260205-014502-juju-7f2275-prod-proposed-migration-environment-20-f268ebf1-c64c-4c88-9b0d-c676cff60d8b --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-arm64-fasta3-20260205-014502-juju-7f2275-prod-proposed-migration-environment-20-f268ebf1-c64c-4c88-9b0d-c676cff60d8b from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 72s autopkgtest [01:46:15]: testbed dpkg architecture: arm64 72s autopkgtest [01:46:15]: testbed apt version: 3.1.14 72s autopkgtest [01:46:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [01:46:19]: testbed release detected to be: None 76s autopkgtest [01:46:19]: updating testbed package index (apt update) 77s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 78s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 78s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1768 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 78s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [262 kB] 78s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7248 B] 78s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 78s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 78s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1540 kB] 78s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 78s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 82s Fetched 4091 kB in 1s (3441 kB/s) 83s Reading package lists... 84s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 84s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 85s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade... 86s The following packages will be upgraded: 86s libc-bin libc-gconv-modules-extra libc6 locales python3-linkify-it 86s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 7881 kB of archives. 86s After this operation, 0 B of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 86s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 86s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 86s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 86s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 87s dpkg-preconfigure: unable to re-open stdin: No such file or directory 87s Fetched 7881 kB in 0s (16.4 MB/s) 87s (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 ... 89360 files and directories currently installed.) 87s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 87s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 87s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 87s (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 ... 89360 files and directories currently installed.) 87s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 87s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 88s Setting up libc6:arm64 (2.42-2ubuntu5) ... 88s (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 ... 89360 files and directories currently installed.) 88s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 88s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 88s Setting up libc-bin (2.42-2ubuntu5) ... 88s (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 ... 89360 files and directories currently installed.) 88s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 88s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 89s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 89s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 89s Setting up locales (2.42-2ubuntu5) ... 89s Generating locales (this might take a while)... 92s en_US.UTF-8... done 92s Generation complete. 92s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 92s Processing triggers for man-db (2.13.1-1) ... 93s Processing triggers for systemd (259-1ubuntu3) ... 95s autopkgtest [01:46:38]: upgrading testbed (apt dist-upgrade and autopurge) 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Calculating upgrade... 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Solving dependencies... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [01:46:43]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 100s autopkgtest [01:46:43]: @@@@@@@@@@@@@@@@@@@@ apt-source fasta3 102s Get:1 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (dsc) [2248 B] 102s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (tar) [1403 kB] 102s Get:3 http://ftpmaster.internal/ubuntu resolute/multiverse fasta3 36.3.8i.14-Nov-2020-4 (diff) [14.8 kB] 103s gpgv: Signature made Wed Sep 24 06:35:50 2025 UTC 103s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 103s gpgv: issuer "tillea@rki.de" 103s gpgv: Can't check signature: No public key 103s dpkg-source: warning: cannot verify inline signature for ./fasta3_36.3.8i.14-Nov-2020-4.dsc: no acceptable signature found 103s autopkgtest [01:46:46]: testing package fasta3 version 36.3.8i.14-Nov-2020-4 104s autopkgtest [01:46:47]: build not needed 106s autopkgtest [01:46:49]: test run-unit-test: preparing testbed 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Solving dependencies... 107s The following NEW packages will be installed: 107s bedtools fasta3 libclone-perl libdbd-mysql-perl libdbi-perl 107s libencode-locale-perl libfile-listing-perl libhtml-parser-perl 107s libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl 107s libhttp-message-perl libhttp-negotiate-perl libio-html-perl 107s libio-socket-ssl-perl libjson-perl liblwp-mediatypes-perl 107s liblwp-protocol-https-perl libmysqlclient24 libnet-http-perl 107s libnet-ssleay-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl 107s libwww-robotrules-perl libxml-parser-perl libxml-twig-perl mysql-common 107s perl-openssl-defaults python3-mysqldb 107s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 5522 kB of archives. 107s After this operation, 24.9 MB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedtools arm64 2.31.1+dfsg-3 [531 kB] 107s Get:2 http://ftpmaster.internal/ubuntu resolute/multiverse arm64 fasta3 arm64 36.3.8i.14-Nov-2020-4 [993 kB] 107s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libclone-perl arm64 0.47-1 [10.4 kB] 107s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libdbi-perl arm64 1.647-1build1 [827 kB] 107s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 107s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libmysqlclient24 arm64 8.4.8-0ubuntu1 [1244 kB] 108s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libdbd-mysql-perl arm64 4.053-1ubuntu1 [83.6 kB] 108s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libencode-locale-perl all 1.05-3 [11.6 kB] 108s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libtimedate-perl all 2.3300-2 [34.0 kB] 108s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-date-perl all 6.06-1 [10.2 kB] 108s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-listing-perl all 6.16-1 [11.3 kB] 108s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-tagset-perl all 3.24-1 [14.1 kB] 108s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liburi-perl all 5.34-2build1 [100 kB] 108s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-parser-perl arm64 3.83-1build1 [85.3 kB] 108s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libhtml-tree-perl all 5.07-3 [200 kB] 108s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libio-html-perl all 1.004-3 [15.9 kB] 108s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 108s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-message-perl all 7.01-1ubuntu1 [76.1 kB] 108s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-cookies-perl all 6.11-1 [18.2 kB] 108s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libhttp-negotiate-perl all 6.01-2 [12.4 kB] 108s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 perl-openssl-defaults arm64 7build4 [6710 B] 108s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libnet-ssleay-perl arm64 1.94-3 [307 kB] 108s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libio-socket-ssl-perl all 2.098-1 [205 kB] 108s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 108s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libnet-http-perl all 6.24-1build1 [21.7 kB] 108s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libtry-tiny-perl all 0.32-1 [21.2 kB] 108s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libwww-robotrules-perl all 6.02-1build1 [12.4 kB] 108s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libwww-perl all 6.81-1build1 [141 kB] 108s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblwp-protocol-https-perl all 6.14-1 [9040 B] 108s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libxml-parser-perl arm64 2.47-1build4 [201 kB] 108s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libxml-twig-perl all 1:3.54-1build1 [157 kB] 108s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-mysqldb arm64 1.4.6-2build7 [52.8 kB] 108s Fetched 5522 kB in 1s (8460 kB/s) 108s Selecting previously unselected package bedtools. 108s (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 ... 89360 files and directories currently installed.) 108s Preparing to unpack .../00-bedtools_2.31.1+dfsg-3_arm64.deb ... 108s Unpacking bedtools (2.31.1+dfsg-3) ... 108s Selecting previously unselected package fasta3. 108s Preparing to unpack .../01-fasta3_36.3.8i.14-Nov-2020-4_arm64.deb ... 108s Unpacking fasta3 (36.3.8i.14-Nov-2020-4) ... 108s Selecting previously unselected package libclone-perl:arm64. 108s Preparing to unpack .../02-libclone-perl_0.47-1_arm64.deb ... 108s Unpacking libclone-perl:arm64 (0.47-1) ... 108s Selecting previously unselected package libdbi-perl:arm64. 108s Preparing to unpack .../03-libdbi-perl_1.647-1build1_arm64.deb ... 108s Unpacking libdbi-perl:arm64 (1.647-1build1) ... 108s Selecting previously unselected package mysql-common. 108s Preparing to unpack .../04-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 108s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 108s Selecting previously unselected package libmysqlclient24:arm64. 108s Preparing to unpack .../05-libmysqlclient24_8.4.8-0ubuntu1_arm64.deb ... 108s Unpacking libmysqlclient24:arm64 (8.4.8-0ubuntu1) ... 108s Selecting previously unselected package libdbd-mysql-perl:arm64. 108s Preparing to unpack .../06-libdbd-mysql-perl_4.053-1ubuntu1_arm64.deb ... 108s Unpacking libdbd-mysql-perl:arm64 (4.053-1ubuntu1) ... 108s Selecting previously unselected package libencode-locale-perl. 108s Preparing to unpack .../07-libencode-locale-perl_1.05-3_all.deb ... 108s Unpacking libencode-locale-perl (1.05-3) ... 108s Selecting previously unselected package libtimedate-perl. 108s Preparing to unpack .../08-libtimedate-perl_2.3300-2_all.deb ... 108s Unpacking libtimedate-perl (2.3300-2) ... 109s Selecting previously unselected package libhttp-date-perl. 109s Preparing to unpack .../09-libhttp-date-perl_6.06-1_all.deb ... 109s Unpacking libhttp-date-perl (6.06-1) ... 109s Selecting previously unselected package libfile-listing-perl. 109s Preparing to unpack .../10-libfile-listing-perl_6.16-1_all.deb ... 109s Unpacking libfile-listing-perl (6.16-1) ... 109s Selecting previously unselected package libhtml-tagset-perl. 109s Preparing to unpack .../11-libhtml-tagset-perl_3.24-1_all.deb ... 109s Unpacking libhtml-tagset-perl (3.24-1) ... 109s Selecting previously unselected package liburi-perl. 109s Preparing to unpack .../12-liburi-perl_5.34-2build1_all.deb ... 109s Unpacking liburi-perl (5.34-2build1) ... 109s Selecting previously unselected package libhtml-parser-perl:arm64. 109s Preparing to unpack .../13-libhtml-parser-perl_3.83-1build1_arm64.deb ... 109s Unpacking libhtml-parser-perl:arm64 (3.83-1build1) ... 109s Selecting previously unselected package libhtml-tree-perl. 109s Preparing to unpack .../14-libhtml-tree-perl_5.07-3_all.deb ... 109s Unpacking libhtml-tree-perl (5.07-3) ... 109s Selecting previously unselected package libio-html-perl. 109s Preparing to unpack .../15-libio-html-perl_1.004-3_all.deb ... 109s Unpacking libio-html-perl (1.004-3) ... 109s Selecting previously unselected package liblwp-mediatypes-perl. 109s Preparing to unpack .../16-liblwp-mediatypes-perl_6.04-2_all.deb ... 109s Unpacking liblwp-mediatypes-perl (6.04-2) ... 109s Selecting previously unselected package libhttp-message-perl. 109s Preparing to unpack .../17-libhttp-message-perl_7.01-1ubuntu1_all.deb ... 109s Unpacking libhttp-message-perl (7.01-1ubuntu1) ... 109s Selecting previously unselected package libhttp-cookies-perl. 109s Preparing to unpack .../18-libhttp-cookies-perl_6.11-1_all.deb ... 109s Unpacking libhttp-cookies-perl (6.11-1) ... 109s Selecting previously unselected package libhttp-negotiate-perl. 109s Preparing to unpack .../19-libhttp-negotiate-perl_6.01-2_all.deb ... 109s Unpacking libhttp-negotiate-perl (6.01-2) ... 109s Selecting previously unselected package perl-openssl-defaults:arm64. 109s Preparing to unpack .../20-perl-openssl-defaults_7build4_arm64.deb ... 109s Unpacking perl-openssl-defaults:arm64 (7build4) ... 109s Selecting previously unselected package libnet-ssleay-perl:arm64. 109s Preparing to unpack .../21-libnet-ssleay-perl_1.94-3_arm64.deb ... 109s Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... 109s Selecting previously unselected package libio-socket-ssl-perl. 109s Preparing to unpack .../22-libio-socket-ssl-perl_2.098-1_all.deb ... 109s Unpacking libio-socket-ssl-perl (2.098-1) ... 109s Selecting previously unselected package libjson-perl. 109s Preparing to unpack .../23-libjson-perl_4.10000-1_all.deb ... 109s Unpacking libjson-perl (4.10000-1) ... 109s Selecting previously unselected package libnet-http-perl. 109s Preparing to unpack .../24-libnet-http-perl_6.24-1build1_all.deb ... 109s Unpacking libnet-http-perl (6.24-1build1) ... 109s Selecting previously unselected package libtry-tiny-perl. 109s Preparing to unpack .../25-libtry-tiny-perl_0.32-1_all.deb ... 109s Unpacking libtry-tiny-perl (0.32-1) ... 109s Selecting previously unselected package libwww-robotrules-perl. 109s Preparing to unpack .../26-libwww-robotrules-perl_6.02-1build1_all.deb ... 109s Unpacking libwww-robotrules-perl (6.02-1build1) ... 109s Selecting previously unselected package libwww-perl. 109s Preparing to unpack .../27-libwww-perl_6.81-1build1_all.deb ... 109s Unpacking libwww-perl (6.81-1build1) ... 109s Selecting previously unselected package liblwp-protocol-https-perl. 109s Preparing to unpack .../28-liblwp-protocol-https-perl_6.14-1_all.deb ... 109s Unpacking liblwp-protocol-https-perl (6.14-1) ... 109s Selecting previously unselected package libxml-parser-perl. 109s Preparing to unpack .../29-libxml-parser-perl_2.47-1build4_arm64.deb ... 109s Unpacking libxml-parser-perl (2.47-1build4) ... 109s Selecting previously unselected package libxml-twig-perl. 109s Preparing to unpack .../30-libxml-twig-perl_1%3a3.54-1build1_all.deb ... 109s Unpacking libxml-twig-perl (1:3.54-1build1) ... 109s Selecting previously unselected package python3-mysqldb. 110s Preparing to unpack .../31-python3-mysqldb_1.4.6-2build7_arm64.deb ... 110s Unpacking python3-mysqldb (1.4.6-2build7) ... 110s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 110s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 110s Setting up libclone-perl:arm64 (0.47-1) ... 110s Setting up libhtml-tagset-perl (3.24-1) ... 110s Setting up liblwp-mediatypes-perl (6.04-2) ... 110s Setting up fasta3 (36.3.8i.14-Nov-2020-4) ... 110s Setting up libtry-tiny-perl (0.32-1) ... 110s Setting up perl-openssl-defaults:arm64 (7build4) ... 110s Setting up libencode-locale-perl (1.05-3) ... 110s Setting up libmysqlclient24:arm64 (8.4.8-0ubuntu1) ... 110s Setting up python3-mysqldb (1.4.6-2build7) ... 110s Setting up libio-html-perl (1.004-3) ... 110s Setting up libtimedate-perl (2.3300-2) ... 110s Setting up libjson-perl (4.10000-1) ... 110s Setting up bedtools (2.31.1+dfsg-3) ... 110s Setting up liburi-perl (5.34-2build1) ... 110s Setting up libdbi-perl:arm64 (1.647-1build1) ... 110s Setting up libnet-ssleay-perl:arm64 (1.94-3) ... 110s Setting up libhttp-date-perl (6.06-1) ... 110s Setting up libfile-listing-perl (6.16-1) ... 110s Setting up libnet-http-perl (6.24-1build1) ... 110s Setting up libdbd-mysql-perl:arm64 (4.053-1ubuntu1) ... 110s Setting up libwww-robotrules-perl (6.02-1build1) ... 110s Setting up libhtml-parser-perl:arm64 (3.83-1build1) ... 110s Setting up libio-socket-ssl-perl (2.098-1) ... 110s Setting up libhttp-message-perl (7.01-1ubuntu1) ... 110s Setting up libhttp-negotiate-perl (6.01-2) ... 110s Setting up libhttp-cookies-perl (6.11-1) ... 110s Setting up libhtml-tree-perl (5.07-3) ... 110s Setting up liblwp-protocol-https-perl (6.14-1) ... 110s Setting up libwww-perl (6.81-1build1) ... 110s Setting up libxml-parser-perl (2.47-1build4) ... 110s Setting up libxml-twig-perl (1:3.54-1build1) ... 110s Processing triggers for man-db (2.13.1-1) ... 110s Processing triggers for libc-bin (2.42-2ubuntu5) ... 111s autopkgtest [01:46:54]: test run-unit-test: [----------------------- 111s + pkg=fasta3 111s + export LC_ALL=C.UTF-8 111s + LC_ALL=C.UTF-8 111s + '[' /tmp/autopkgtest.ZMMtDM/autopkgtest_tmp = '' ']' 111s + 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.ZMMtDM/autopkgtest_tmp 111s + cd /tmp/autopkgtest.ZMMtDM/autopkgtest_tmp 111s + /usr/share/fasta3/scripts/test_ann_scripts.sh 111s /usr/share/fasta3/scripts/ann_exons_up_www.pl P09488 112s >P09488 112s 1 - 12 exon_1~1 112s 13 - 37 exon_2~2 112s 38 - 59 exon_3~3 112s 60 - 86 exon_4~4 112s 87 - 120 exon_5~5 112s 121 - 152 exon_6~6 112s 153 - 189 exon_7~7 112s 190 - 218 exon_8~8 112s /usr/share/fasta3/scripts/ann_exons_up_www.pl sp|P09488 113s >sp|P09488 113s 1 - 12 exon_1~1 113s 13 - 37 exon_2~2 113s 38 - 59 exon_3~3 113s 60 - 86 exon_4~4 113s 87 - 120 exon_5~5 113s 121 - 152 exon_6~6 113s 153 - 189 exon_7~7 113s 190 - 218 exon_8~8 113s /usr/share/fasta3/scripts/ann_exons_up_www.pl up|P09488|GSTM1_HUMAN 114s >up|P09488|GSTM1_HUMAN 114s 1 - 12 exon_1~1 114s 13 - 37 exon_2~2 114s 38 - 59 exon_3~3 114s 60 - 86 exon_4~4 114s 87 - 120 exon_5~5 114s 121 - 152 exon_6~6 114s 153 - 189 exon_7~7 114s 190 - 218 exon_8~8 114s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN P09488 114s >SP:GSTM1_HUMAN P09488 114s 1 - 12 exon_1~1 114s 13 - 37 exon_2~2 114s 38 - 59 exon_3~3 114s 60 - 86 exon_4~4 114s 87 - 120 exon_5~5 114s 121 - 152 exon_6~6 114s 153 - 189 exon_7~7 114s 190 - 218 exon_8~8 114s /usr/share/fasta3/scripts/ann_exons_up_www.pl SP:GSTM1_HUMAN 114s *** /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. 115s >SP:GSTM1_HUMAN 115s 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. 115s ***DONE*** /usr/share/fasta3/scripts/ann_exons_up_www.pl Thu Feb 5 01:46:58 UTC 2026 115s /usr/share/fasta3/scripts/ann_feats_up_sql.pl P09488 115s /usr/share/fasta3/scripts/ann_feats_up_sql.pl sp|P09488 115s /usr/share/fasta3/scripts/ann_feats_up_sql.pl up|P09488|GSTM1_HUMAN 115s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN P09488 115s /usr/share/fasta3/scripts/ann_feats_up_sql.pl SP:GSTM1_HUMAN 115s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_sql.pl Thu Feb 5 01:46:58 UTC 2026 115s /usr/share/fasta3/scripts/ann_feats_up_www2.pl P09488 115s 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. 115s 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. 115s 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. 115s 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. 250s ==:Active site 250s =*:Modified 250s =#:Binding 250s =^:Metal binding 250s =@:Site 250s >P09488 250s /usr/share/fasta3/scripts/ann_feats_up_www2.pl sp|P09488 385s ==:Active site 385s =*:Modified 385s =#:Binding 385s =^:Metal binding 385s =@:Site 385s >sp|P09488 385s /usr/share/fasta3/scripts/ann_feats_up_www2.pl up|P09488|GSTM1_HUMAN 520s ==:Active site 520s =*:Modified 520s =#:Binding 520s =^:Metal binding 520s =@:Site 520s >up|P09488|GSTM1_HUMAN 520s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN P09488 656s ==:Active site 656s =*:Modified 656s =#:Binding 656s =^:Metal binding 656s =@:Site 656s >SP:GSTM1_HUMAN P09488 656s /usr/share/fasta3/scripts/ann_feats_up_www2.pl SP:GSTM1_HUMAN 656s ==:Active site 656s =*:Modified 656s =#:Binding 656s =^:Metal binding 656s =@:Site 656s >SP:GSTM1_HUMAN 656s *** /usr/share/fasta3/scripts/ann_feats_up_www2.pl accession required: SP:GSTM1_HUMAN 656s ***DONE*** /usr/share/fasta3/scripts/ann_feats_up_www2.pl Thu Feb 5 01:55:59 UTC 2026 656s /usr/share/fasta3/scripts/ann_ipr_www.pl P09488 656s >P09488 656s /usr/share/fasta3/scripts/ann_ipr_www.pl sp|P09488 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $primary_acc in concatenation (.) or string at /usr/share/fasta3/scripts/ann_ipr_www.pl line 380. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s Use of uninitialized value $ipr_data{"db"} in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 371. 657s Use of uninitialized value $ipr_data{"descr"} in substitution (s///) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 372. 657s Use of uninitialized value in pattern match (m//) at /usr/share/fasta3/scripts/ann_ipr_www.pl line 379. 657s >sp|P09488 657s 1 - 88 PS50404:Glutathione_S-transferase,_N-terminal~1 657s 2 - 201 PTHR11571:Glutathione_S-transferase_superfamily~2 657s 3 - 200 SFLDS00019:Glutathione_transferase_family~3 657s 3 - 85 SSF52833:Thioredoxin-like_superfamily~4 657s 5 - 82 PF02798:Glutathione_S-transferase,_N-terminal~1 657s 31 - 43 :Glutathione_S-transferase,_Mu_class~5 657s 44 - 56 :Glutathione_S-transferase,_Mu_class~5 657s 86 - 217 SSF47616:Glutathione_S-transferase,_C-terminal_domain_superfamily~6 657s 87 - 98 :Glutathione_S-transferase,_Mu_class~5 657s 90 - 208 PS50405:Glutathione_S-transferase,_C-terminal-like~7 657s 105 - 191 PF00043:Glutathione_S-transferase,_C-terminal~8 657s 139 - 152 :Glutathione_S-transferase,_Mu_class~5 657s /usr/share/fasta3/scripts/ann_ipr_www.pl up|P09488|GSTM1_HUMAN 657s >up|P09488|GSTM1_HUMAN 657s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN P09488 657s >SP:GSTM1_HUMAN P09488 657s /usr/share/fasta3/scripts/ann_ipr_www.pl SP:GSTM1_HUMAN 658s >SP:GSTM1_HUMAN 658s ***DONE*** /usr/share/fasta3/scripts/ann_ipr_www.pl Thu Feb 5 01:56:01 UTC 2026 658s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl P09488 658s 658s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/aarch64-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 658s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 658s ==:Active site 658s =*:Modified 658s =#:Substrate binding 658s =^:Metal binding 658s =@:Site 658s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl sp|P09488 659s ==:Active site 659s =*:Modified 659s =#:Substrate binding 659s =^:Metal binding 659s =@:Site 659s 659s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/aarch64-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 659s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 659s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl up|P09488|GSTM1_HUMAN 659s 659s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/aarch64-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 659s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 659s ==:Active site 659s =*:Modified 659s =#:Substrate binding 659s =^:Metal binding 659s =@:Site 659s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN P09488 660s ==:Active site 660s =*:Modified 660s =#:Substrate binding 660s =^:Metal binding 660s =@:Site 660s 660s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/aarch64-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 660s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 660s /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl SP:GSTM1_HUMAN 660s *** /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. 660s ==:Active site 660s =*:Modified 660s =#:Substrate binding 660s =^:Metal binding 660s =@:Site 660s 660s not well-formed (invalid token) at line 1, column 237, byte 237 at /usr/lib/aarch64-linux-gnu/perl5/5.40/XML/Parser.pm line 187. 660s at /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl line 324. 660s + /usr/share/fasta3/scripts/test_py.sh 660s ***DONE*** /usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl Thu Feb 5 01:56:03 UTC 2026 660s get_protein.py 661s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 661s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 661s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 661s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 661s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 661s 661s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 661s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 661s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 661s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 661s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 661s 693s Traceback (most recent call last): 693s File "/usr/lib/python3.13/urllib/request.py", line 1319, in do_open 693s h.request(req.get_method(), req.selector, req.data, headers, 693s ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s encode_chunked=req.has_header('Transfer-encoding')) 693s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/http/client.py", line 1358, in request 693s self._send_request(method, url, body, headers, encode_chunked) 693s ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/http/client.py", line 1404, in _send_request 693s self.endheaders(body, encode_chunked=encode_chunked) 693s ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/http/client.py", line 1353, in endheaders 693s self._send_output(message_body, encode_chunked=encode_chunked) 693s ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/http/client.py", line 1113, in _send_output 693s self.send(msg) 693s ~~~~~~~~~^^^^^ 693s File "/usr/lib/python3.13/http/client.py", line 1057, in send 693s self.connect() 693s ~~~~~~~~~~~~^^ 693s File "/usr/lib/python3.13/http/client.py", line 1499, in connect 693s self.sock = self._context.wrap_socket(self.sock, 693s ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 693s server_hostname=server_hostname) 693s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/ssl.py", line 455, in wrap_socket 693s return self.sslsocket_class._create( 693s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 693s sock=sock, 693s ^^^^^^^^^^ 693s ...<5 lines>... 693s session=session 693s ^^^^^^^^^^^^^^^ 693s ) 693s ^ 693s File "/usr/lib/python3.13/ssl.py", line 1076, in _create 693s self.do_handshake() 693s ~~~~~~~~~~~~~~~~~^^ 693s File "/usr/lib/python3.13/ssl.py", line 1372, in do_handshake 693s self._sslobj.do_handshake() 693s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 693s ssl.SSLEOFError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033) 693s 693s During handling of the above exception, another exception occurred: 693s 693s Traceback (most recent call last): 693s File "/usr/share/fasta3/scripts/get_protein.py", line 43, in 693s req = urllib.request.urlopen(url_string) 693s File "/usr/lib/python3.13/urllib/request.py", line 189, in urlopen 693s return opener.open(url, data, timeout) 693s ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/urllib/request.py", line 489, in open 693s response = self._open(req, data) 693s File "/usr/lib/python3.13/urllib/request.py", line 506, in _open 693s result = self._call_chain(self.handle_open, protocol, protocol + 693s '_open', req) 693s File "/usr/lib/python3.13/urllib/request.py", line 466, in _call_chain 693s result = func(*args) 693s File "/usr/lib/python3.13/urllib/request.py", line 1367, in https_open 693s return self.do_open(http.client.HTTPSConnection, req, 693s ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 693s context=self._context) 693s ^^^^^^^^^^^^^^^^^^^^^^ 693s File "/usr/lib/python3.13/urllib/request.py", line 1322, in do_open 693s raise URLError(err) 693s urllib.error.URLError: 693s 693s During handling of the above exception, another exception occurred: 693s 693s Traceback (most recent call last): 693s File "/usr/share/fasta3/scripts/get_protein.py", line 46, in 693s sys.stderr.write(e.read().decode('utf-8')+'\n') 693s ^^^^^^ 693s AttributeError: 'URLError' object has no attribute 'read' 693s get_refseq.py 699s >NP_000552.2 glutathione S-transferase Mu 1 isoform 1 [Homo sapiens] 699s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI 699s TQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSE 699s FLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFS 699s KMAVWGNK 699s 763s urllib3.exceptions.SSLError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1033) 763s 763s The above exception was the direct cause of the following exception: 763s 763s Traceback (most recent call last): 763s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 644, in send 763s resp = conn.urlopen( 763s method=request.method, 763s ...<9 lines>... 763s chunked=chunked, 763s ) 763s File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 841, in urlopen 763s retries = retries.increment( 763s method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2] 763s ) 763s File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 519, in increment 763s raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] 763s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 763s 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)'))) 763s 763s During handling of the above exception, another exception occurred: 763s 763s Traceback (most recent call last): 763s File "/usr/share/fasta3/scripts/get_refseq.py", line 19, in 763s req = requests.get(url_string) 763s File "/usr/lib/python3/dist-packages/requests/api.py", line 73, in get 763s return request("get", url, params=params, **kwargs) 763s File "/usr/lib/python3/dist-packages/requests/api.py", line 59, in request 763s return session.request(method=method, url=url, **kwargs) 763s ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 763s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 589, in request 763s resp = self.send(prep, **send_kwargs) 763s File "/usr/lib/python3/dist-packages/requests/sessions.py", line 703, in send 763s r = adapter.send(request, **kwargs) 763s File "/usr/lib/python3/dist-packages/requests/adapters.py", line 675, in send 763s raise SSLError(e, request=request) 763s 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)'))) 763s 763s During handling of the above exception, another exception occurred: 763s 763s Traceback (most recent call last): 763s File "/usr/share/fasta3/scripts/get_refseq.py", line 22, in 763s sys.stderr.print(e.response.text+'\n') 763s ^^^^^^^^^^^^^^^^ 763s AttributeError: '_io.TextIOWrapper' object has no attribute 'print' 763s get_uniprot.py 764s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 764s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 764s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 764s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 764s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 764s 764s >sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 OS=Homo sapiens OX=9606 GN=GSTM1 PE=1 SV=3 764s MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 764s PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 764s EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 764s LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 764s 764s ################################################################ 764s map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output 765s 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. 765s *** ERROR [compacc2e.c:2269] -- get_annot() - premature annotation file end () 766s 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. 766s *** ERROR [compacc2e.c:1873] - premature annotation file end (annot_bline_zqjNjk.annot) 766s *** 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 766s #/usr/share/fasta3/scripts/map_exon_coords.py hum_chk_map_test.m8CBL 766s # 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 766s # FASTA 36.3.8i Nov, 2022 766s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 766s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 766s # 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 766s # 1 hits found 766s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 1.2e-58 208.4 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 766s # FASTA processed 1 queries 766s rename_exons.py -- look for exon_X in output 766s # 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 766s # FASTA 36.3.8i Nov, 2022 766s # Query: sp|P30711|GSTT1_HUMAN Glutathione S-transferase theta-1 OS=Homo sapiens OX=9606 GN=GSTT1 PE=1 SV=4 - 240 aa 766s # Database: !/usr/share/fasta3/scripts/get_protein.py+P20135 766s # 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 766s # 1 hits found 766s sp|P30711|GSTT1_HUMAN 240 sp|P20135|GSTT1_CHICK 261 54.17 240 110 21 1 240 1 261 1.2e-58 208.4 15ASVI4KRKT1DN4LFRKIH1DE1IF1-D-S-V-L-G-K-K-P-A-A-A-S-G-A-E-R-P-R-T1QPHSLN1DEAGFDAGQKVINSPL5AV8TA1SCVT6TS3KNVT2YH3QS1LIQKAK2RQ5AS1QH1TATNLI1RASNCALPRKATLM1HI2MLFI1VL1LT1EQ1VQSPPSQETK1AQAETVLMAEEG1DSVTTS1QKLQLF1DEKR3ND3LITI1PSHE9TV3HQ3AV2QDVI2GD2KR1AMTE2QR3AE3EKDE2QFEQ3VM2KNAI1DEFLPS-N-IPQAI2TQIL1QEKH1MA1WVVLLMAK1ILRK 766s # FASTA processed 1 queries 766s + fasta36 -q mgstm1.aa prot_test.lseg 766s # fasta36 -q mgstm1.aa prot_test.lseg 766s FASTA searches a protein or DNA sequence data bank 766s version 36.3.8i Nov, 2022 766s Please cite: 766s W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 766s 766s Query: mgstm1.aa 766s 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 766s Library: prot_test.lseg 766s 2267 residues in 12 sequences 766s 766s Statistics: (shuffled [495]) MLE statistics: Lambda= 0.1710; K=0.005911 766s statistics sampled from 4 (4) to 495 sequences 766s Algorithm: FASTA (3.8 Nov 2011) [optimized] 766s Parameters: BL50 matrix (15:-5), open/ext: -10/-2 766s ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 766s Scan time: 0.000 766s 766s The best scores are: opt bits E(12) 766s sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 315.6 5.6e-90 766s sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 67.7 2.5e-15 766s sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.8 0.1 766s sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.8 0.97 766s sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.1 1.3 766s sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.8 2.2 766s sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.6 2.5 766s sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.6 3.6 766s sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.3 3.8 766s sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.6 4.1 766s sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.6 4.5 766s sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.5 766s 766s >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) 766s initn: 1242 init1: 1242 opt: 1242 Z-score: 1667.3 bits: 315.6 E(12): 5.6e-90 766s Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 766s 766s 10 20 30 40 50 60 766s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNL 766s ::::::::..:::.: ::.:::::::::.::.::::::::.::::::::::::::::::: 766s sp|P09 MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 766s 10 20 30 40 50 60 766s 766s 70 80 90 100 110 120 766s sp|P10 PYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDF 766s ::::::.:::::::::: :.::::.: ::::::.::.::.:::.::..::: :.::::.: 766s sp|P09 PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 766s 70 80 90 100 110 120 766s 766s 130 140 150 160 170 180 766s sp|P10 EKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPN 766s :: ::..:. .:::.:::::::::::::::.:.:.::::.::.:: .:.::::::::::: 766s sp|P09 EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 766s 130 140 150 160 170 180 766s 766s 190 200 210 766s sp|P10 LRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 766s :.::..:::::.::::::::::.. :.::::: :.:: 766s sp|P09 LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 766s 190 200 210 766s 766s >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) 766s initn: 204 init1: 73 opt: 237 Z-score: 327.0 bits: 67.7 E(12): 2.5e-15 766s Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 766s 766s 10 20 30 40 50 766s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLD 766s .: :.:.:: . :: :: . .::: : .: ::.: .: 766s sp|P00 MSGKPVLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLM 766s 10 20 30 40 50 766s 766s 60 70 80 90 100 110 766s sp|P10 FPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIML 766s : ..:.. ::: :..:. ::: :.: :. : :. .:: :. . ..: :.: . .. 766s sp|P00 FDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLV 766s 60 70 80 90 100 110 766s 766s 120 130 140 150 160 170 766s sp|P10 CYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMF 766s :: .. : . : : . . . . : . . ...:...: ::. ..: . : 766s sp|P00 ICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEF 766s 120 130 140 150 160 170 766s 766s 180 190 200 210 766s sp|P10 EPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 766s . . : .:: :. : .:. .: ... ... . :. .:. . . : 766s sp|P00 DASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARKIFKF 766s 180 190 200 210 220 766s 766s >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) 766s initn: 40 init1: 40 opt: 51 Z-score: 82.5 bits: 21.8 E(12): 0.1 766s Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 766s 766s 150 160 170 180 190 200 766s sp|P10 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA 766s .::. . .. .:. :.. :: .:. .. .: 766s sp|P69 ADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFD-LSHGSAQVKGHGKKVA 766s 10 20 30 40 50 60 766s 766s 210 766s sp|P10 TPIFSKMAHWSNK 766s . . .:: 766s sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 766s 70 80 90 100 110 120 766s 766s >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) 766s initn: 43 init1: 43 opt: 43 Z-score: 64.8 bits: 19.8 E(12): 0.97 766s Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 766s 766s 110 120 130 140 150 160 766s sp|P10 TRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQ 766s .: : :.:: . . . .. . 766s sp|P00 LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF 766s 200 210 220 230 240 250 766s 766s 170 180 190 200 210 766s sp|P10 YRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 766s : : . :: :. :: .::. .:. ...:: 766s sp|P00 PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK 766s 260 270 280 290 300 310 766s 766s sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 766s 320 330 340 350 766s 766s >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) 766s initn: 56 init1: 36 opt: 36 Z-score: 62.7 bits: 18.1 E(12): 1.3 766s Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 766s 766s 10 20 30 766s sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG 766s ::.. :: 766s sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP 766s 20 30 40 50 60 70 766s 766s 40 50 60 70 80 90 766s sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR 766s 766s sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG 766s 80 90 100 110 120 130 766s 766s >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) 766s initn: 31 init1: 31 opt: 31 Z-score: 58.0 bits: 16.8 E(12): 2.2 766s Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 766s 766s 120 130 140 150 160 170 766s sp|P10 FEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDI---LDQYRMFE---PK 766s ::.:: . . :: :. :.. :: 766s sp|P01 DIQMTQSPSSLSASVGDRVTITCQASQDINHYLNWYQQGPKKAPK 766s 10 20 30 40 766s 766s 180 190 200 210 766s sp|P10 CL--DAFPNLRDFL-ARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK 766s : :: ::. . .:: : 766s sp|P01 ILIYDA-SNLETGVPSRFSGSGFGTDFTFTISGLQPEDIATYYCQQYDTLPRTFGQGTKL 766s 50 60 70 80 90 100 766s 766s >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) 766s initn: 30 init1: 30 opt: 30 Z-score: 56.9 bits: 16.6 E(12): 2.5 766s Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 766s 766s 100 110 120 130 140 150 766s sp|P10 IVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWF---AGDKVTY 766s :: :. :... :. : . :..: 766s sp|P99 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKG 766s 10 20 30 40 50 766s 766s 160 170 180 190 200 210 766s sp|P10 VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW 766s . . . : : .: . .:: .:. . . : :.:: 766s sp|P99 I-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKKKEERADLIAYLKKATNE 766s 60 70 80 90 100 766s 766s 766s sp|P10 SNK 766s 766s >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) 766s initn: 30 init1: 30 opt: 30 Z-score: 53.6 bits: 16.6 E(12): 3.6 766s Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 766s 766s 20 30 40 50 60 70 766s sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- 766s :. . .:: ..:. . ::. :. 766s sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK 766s 10 20 30 766s 766s 80 90 100 110 120 766s sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL 766s . ....:.:.. :..::. :: 766s sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 766s 40 50 60 70 80 90 766s 766s >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) 766s initn: 37 init1: 37 opt: 37 Z-score: 53.0 bits: 18.3 E(12): 3.8 766s Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 766s 766s 50 60 70 80 90 100 766s sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN 766s : ... .: :... : : . : . .:. 766s sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK 766s 370 380 390 400 410 420 766s 766s 110 120 130 140 150 160 766s sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD 766s : ::...: 766s sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 766s 430 440 450 460 470 480 766s 766s >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) 766s initn: 26 init1: 26 opt: 26 Z-score: 52.3 bits: 15.6 E(12): 4.1 766s Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 766s 766s 90 100 110 120 130 140 766s sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK 766s : :: ::.: 766s sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG 766s 60 70 80 90 766s 766s 150 160 170 180 190 200 766s sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI 766s 766s >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) 766s initn: 22 init1: 22 opt: 22 Z-score: 51.4 bits: 14.6 E(12): 4.5 766s Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 766s 766s 150 160 170 180 190 200 766s sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS 766s .:.: 766s sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV 766s 10 20 30 40 766s 766s 210 766s sp|P10 SRYIATPIFSKMAHWSNK 766s 766s sp|P00 CPVGAPNPED 766s 50 766s 766s >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) 766s initn: 23 init1: 23 opt: 23 Z-score: 47.4 bits: 14.9 E(12): 6.5 766s Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 766s 766s 30 40 50 60 70 80 766s sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH 766s :. : .:. ... .: : . . 766s sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK 766s 10 20 30 40 766s 766s 90 100 110 120 130 140 766s sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG 766s .:. . . ...:.. :. ..: . . :.::.: 766s sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 766s 50 60 70 80 90 100 766s 766s 150 160 170 180 190 200 766s sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY 766s 766s sp|P01 NRGEC 766s 766s 766s 766s 766s 218 residues in 1 query sequences 766s 2267 residues in 12 library sequences 766s Tcomplib [36.3.8i Nov, 2022] (2 proc in memory [0G]) 766s start: Thu Feb 5 01:57:49 2026 done: Thu Feb 5 01:57:49 2026 766s Total Scan time: 0.000 Total Display time: 0.000 766s 766s Function used was FASTA [36.3.8i Nov, 2022] 766s autopkgtest [01:57:49]: test run-unit-test: -----------------------] 766s autopkgtest [01:57:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 766s run-unit-test PASS 767s autopkgtest [01:57:50]: @@@@@@@@@@@@@@@@@@@@ summary 767s run-unit-test PASS