nohup: ignoring input I1220 10:33:51.625877 139721917527872 af.py:89] Mounting /home/goddard/ucsf -> /mnt/fasta_path_0 I1220 10:33:51.625961 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/uniref90 -> /mnt/uniref90_database_path I1220 10:33:51.626003 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/mgnify -> /mnt/mgnify_database_path I1220 10:33:51.626040 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases -> /mnt/data_dir I1220 10:33:51.626075 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb_mmcif -> /mnt/template_mmcif_dir I1220 10:33:51.626108 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb_mmcif -> /mnt/obsolete_pdbs_path I1220 10:33:51.626141 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/uniprot -> /mnt/uniprot_database_path I1220 10:33:51.626174 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb_seqres -> /mnt/pdb_seqres_database_path I1220 10:33:51.626216 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path I1220 10:33:51.626256 139721917527872 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/bfd -> /mnt/bfd_database_path I1220 10:33:55.596843 139721917527872 af.py:224] I1220 18:33:55.595563 140435568107712 templates.py:857] Using precomputed obsolete pdbs /mnt/obsolete_pdbs_path/obsolete.dat. I1220 10:33:56.299760 139721917527872 af.py:224] I1220 18:33:56.299397 140435568107712 xla_bridge.py:244] Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker: I1220 10:33:56.382674 139721917527872 af.py:224] I1220 18:33:56.382184 140435568107712 xla_bridge.py:244] Unable to initialize backend 'tpu': INVALID_ARGUMENT: TpuPlatform is not available. I1220 10:34:02.061077 139721917527872 af.py:224] I1220 18:34:02.060597 140435568107712 run_alphafold.py:385] Have 5 models: ['model_1_multimer', 'model_2_multimer', 'model_3_multimer', 'model_4_multimer', 'model_5_multimer'] I1220 10:34:02.061189 139721917527872 af.py:224] I1220 18:34:02.060706 140435568107712 run_alphafold.py:397] Using random seed 1001085691971862205 for the data pipeline I1220 10:34:02.061245 139721917527872 af.py:224] I1220 18:34:02.060833 140435568107712 run_alphafold.py:150] Predicting seq_7e5n I1220 10:34:02.061731 139721917527872 af.py:224] I1220 18:34:02.061424 140435568107712 pipeline_multimer.py:211] Running monomer pipeline on chain A: 7E5N_A|Chains A, B, C, D|Tumor-associated calcium signal transducer 2|Homo sapiens (9606) I1220 10:34:02.061806 139721917527872 af.py:224] I1220 18:34:02.061589 140435568107712 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmpw0mqf2l2/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmp1v8tsant.fasta /mnt/uniref90_database_path/uniref90.fasta" I1220 10:34:02.131336 139721917527872 af.py:224] I1220 18:34:02.130793 140435568107712 utils.py:36] Started Jackhmmer (uniref90.fasta) query I1220 10:36:53.431310 139721917527872 af.py:224] I1220 18:36:53.430812 140435568107712 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 171.300 seconds I1220 10:36:53.434583 139721917527872 af.py:224] I1220 18:36:53.434250 140435568107712 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmp5wctmy0h/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmp1v8tsant.fasta /mnt/mgnify_database_path/mgy_clusters_2018_12.fa" I1220 10:36:53.507682 139721917527872 af.py:224] I1220 18:36:53.507148 140435568107712 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query I1220 10:40:01.582996 139721917527872 af.py:224] I1220 18:40:01.582513 140435568107712 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 188.075 seconds I1220 10:40:01.729228 139721917527872 af.py:224] I1220 18:40:01.728729 140435568107712 hmmbuild.py:121] Launching subprocess ['/usr/bin/hmmbuild', '--hand', '--amino', '/tmp/tmpajd92z8p/output.hmm', '/tmp/tmpajd92z8p/query.msa'] I1220 10:40:01.802624 139721917527872 af.py:224] I1220 18:40:01.801113 140435568107712 utils.py:36] Started hmmbuild query I1220 10:40:02.071395 139721917527872 af.py:224] I1220 18:40:02.070914 140435568107712 hmmbuild.py:129] hmmbuild stdout: I1220 10:40:02.071483 139721917527872 af.py:224] # hmmbuild :: profile HMM construction from multiple sequence alignments I1220 10:40:02.071534 139721917527872 af.py:224] # HMMER 3.1b2 (February 2015); http://hmmer.org/ I1220 10:40:02.071580 139721917527872 af.py:224] # Copyright (C) 2015 Howard Hughes Medical Institute. I1220 10:40:02.071625 139721917527872 af.py:224] # Freely distributed under the GNU General Public License (GPLv3). I1220 10:40:02.071668 139721917527872 af.py:224] # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I1220 10:40:02.071710 139721917527872 af.py:224] # input alignment file: /tmp/tmpajd92z8p/query.msa I1220 10:40:02.071752 139721917527872 af.py:224] # output HMM file: /tmp/tmpajd92z8p/output.hmm I1220 10:40:02.071794 139721917527872 af.py:224] # input alignment is asserted as: protein I1220 10:40:02.071836 139721917527872 af.py:224] # model architecture construction: hand-specified by RF annotation I1220 10:40:02.071878 139721917527872 af.py:224] # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I1220 10:40:02.071945 139721917527872 af.py:224] I1220 10:40:02.071993 139721917527872 af.py:224] # idx name nseq alen mlen eff_nseq re/pos description I1220 10:40:02.072053 139721917527872 af.py:224] #---- -------------------- ----- ----- ----- -------- ------ ----------- I1220 10:40:02.072095 139721917527872 af.py:224] 1 query 1769 728 323 6.08 0.590 I1220 10:40:02.072149 139721917527872 af.py:224] I1220 10:40:02.072192 139721917527872 af.py:224] # CPU time: 0.26u 0.00s 00:00:00.26 Elapsed: 00:00:00.27 I1220 10:40:02.072235 139721917527872 af.py:224] I1220 10:40:02.072276 139721917527872 af.py:224] I1220 10:40:02.072318 139721917527872 af.py:224] stderr: I1220 10:40:02.072360 139721917527872 af.py:224] I1220 10:40:02.072402 139721917527872 af.py:224] I1220 10:40:02.072443 139721917527872 af.py:224] I1220 18:40:02.071012 140435568107712 utils.py:40] Finished hmmbuild query in 0.269 seconds I1220 10:40:02.072486 139721917527872 af.py:224] I1220 18:40:02.071822 140435568107712 hmmsearch.py:103] Launching sub-process ['/usr/bin/hmmsearch', '--noali', '--cpu', '8', '--F1', '0.1', '--F2', '0.1', '--F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A', '/tmp/tmpopslbh9y/output.sto', '/tmp/tmpopslbh9y/query.hmm', '/mnt/pdb_seqres_database_path/pdb_seqres.txt'] I1220 10:40:02.148610 139721917527872 af.py:224] I1220 18:40:02.148133 140435568107712 utils.py:36] Started hmmsearch (pdb_seqres.txt) query I1220 10:40:07.192434 139721917527872 af.py:224] I1220 18:40:07.192034 140435568107712 utils.py:40] Finished hmmsearch (pdb_seqres.txt) query in 5.044 seconds I1220 10:40:07.402552 139721917527872 af.py:224] I1220 18:40:07.402206 140435568107712 hhblits.py:128] Launching subprocess "/usr/bin/hhblits -i /tmp/tmp1v8tsant.fasta -cpu 4 -oa3m /tmp/tmpw14y_efr/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /mnt/bfd_database_path/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /mnt/uniclust30_database_path/uniclust30_2018_08" I1220 10:40:07.475600 139721917527872 af.py:224] I1220 18:40:07.474538 140435568107712 utils.py:36] Started HHblits query I1220 10:47:36.005775 139721917527872 af.py:224] I1220 18:47:36.005272 140435568107712 utils.py:40] Finished HHblits query in 448.530 seconds I1220 10:47:36.063973 139721917527872 af.py:224] I1220 18:47:36.063612 140435568107712 templates.py:940] Searching for template for: MARGPGLAPPPLRLPLLLLVLAAVTGHTAAQDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCNQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQNTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTAGLIAVIVVVVVALVAGMAVLVITNRRKSGKYKKVEIKELGELRKEPSL I1220 10:47:36.422907 139721917527872 af.py:224] W1220 18:47:36.422333 140435568107712 templates.py:547] The exact sequence QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT was not found in 7pee_A. Realigning the template to the actual sequence. I1220 10:47:36.423012 139721917527872 af.py:224] I1220 18:47:36.422444 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:36.423076 139721917527872 af.py:224] I1220 18:47:36.422697 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmpo_bu6a_m/input.fasta -o /tmp/tmpo_bu6a_m/output.a3m -format fasta" I1220 10:47:36.496323 139721917527872 af.py:224] I1220 18:47:36.495762 140435568107712 utils.py:36] Started Kalign query I1220 10:47:36.497460 139721917527872 af.py:224] I1220 18:47:36.497104 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:36.497542 139721917527872 af.py:224] I1220 10:47:36.497593 139721917527872 af.py:224] I1220 10:47:36.497653 139721917527872 af.py:224] stderr: I1220 10:47:36.497699 139721917527872 af.py:224] I1220 10:47:36.497784 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:36.497835 139721917527872 af.py:224] I1220 10:47:36.497904 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:36.498006 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:36.498054 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:36.498101 139721917527872 af.py:224] I1220 10:47:36.498144 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:36.498187 139721917527872 af.py:224] reading from /tmp/tmpo_bu6a_m/input.fasta: found 2 sequences I1220 10:47:36.498229 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:36.498270 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:36.498312 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:36.498354 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:36.498395 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:36.498437 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmpo_bu6a_m/output.a3m'. I1220 10:47:36.498479 139721917527872 af.py:224] I1220 10:47:36.498520 139721917527872 af.py:224] Distance Calculation: I1220 10:47:36.498561 139721917527872 af.py:224] 100 percent done I1220 10:47:36.498603 139721917527872 af.py:224] Alignment: I1220 10:47:36.498645 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:36.498686 139721917527872 af.py:224] I1220 10:47:36.498727 139721917527872 af.py:224] I1220 10:47:36.498769 139721917527872 af.py:224] I1220 18:47:36.497184 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:36.498820 139721917527872 af.py:224] I1220 18:47:36.497601 140435568107712 templates.py:371] Old aligned template: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT------ I1220 10:47:36.498864 139721917527872 af.py:224] New aligned template: EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.498909 139721917527872 af.py:224] I1220 18:47:36.497788 140435568107712 templates.py:556] Sequence in 7pee_A: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT successfully realigned to EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.507353 139721917527872 af.py:224] W1220 18:47:36.507110 140435568107712 templates.py:547] The exact sequence QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT was not found in 7pee_B. Realigning the template to the actual sequence. I1220 10:47:36.507419 139721917527872 af.py:224] I1220 18:47:36.507179 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:36.507561 139721917527872 af.py:224] I1220 18:47:36.507355 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmpfgtww9oq/input.fasta -o /tmp/tmpfgtww9oq/output.a3m -format fasta" I1220 10:47:36.580863 139721917527872 af.py:224] I1220 18:47:36.580295 140435568107712 utils.py:36] Started Kalign query I1220 10:47:36.581321 139721917527872 af.py:224] I1220 18:47:36.580980 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:36.581386 139721917527872 af.py:224] I1220 10:47:36.581437 139721917527872 af.py:224] I1220 10:47:36.581483 139721917527872 af.py:224] stderr: I1220 10:47:36.581558 139721917527872 af.py:224] I1220 10:47:36.581667 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:36.581712 139721917527872 af.py:224] I1220 10:47:36.581782 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:36.581842 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:36.581884 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:36.581926 139721917527872 af.py:224] I1220 10:47:36.581968 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:36.582011 139721917527872 af.py:224] reading from /tmp/tmpfgtww9oq/input.fasta: found 2 sequences I1220 10:47:36.582052 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:36.582094 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:36.582135 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:36.582177 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:36.582219 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:36.582260 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmpfgtww9oq/output.a3m'. I1220 10:47:36.582301 139721917527872 af.py:224] I1220 10:47:36.582342 139721917527872 af.py:224] Distance Calculation: I1220 10:47:36.582384 139721917527872 af.py:224] 100 percent done I1220 10:47:36.582425 139721917527872 af.py:224] Alignment: I1220 10:47:36.582467 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:36.582509 139721917527872 af.py:224] I1220 10:47:36.582550 139721917527872 af.py:224] I1220 10:47:36.582591 139721917527872 af.py:224] I1220 18:47:36.581040 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:36.582646 139721917527872 af.py:224] I1220 18:47:36.581399 140435568107712 templates.py:371] Old aligned template: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT------ I1220 10:47:36.582691 139721917527872 af.py:224] New aligned template: EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.582742 139721917527872 af.py:224] I1220 18:47:36.581567 140435568107712 templates.py:556] Sequence in 7pee_B: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT successfully realigned to EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.591280 139721917527872 af.py:224] W1220 18:47:36.590983 140435568107712 templates.py:547] The exact sequence QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT was not found in 7pee_C. Realigning the template to the actual sequence. I1220 10:47:36.591343 139721917527872 af.py:224] I1220 18:47:36.591055 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:36.591607 139721917527872 af.py:224] I1220 18:47:36.591271 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmp16_6h7rd/input.fasta -o /tmp/tmp16_6h7rd/output.a3m -format fasta" I1220 10:47:36.664654 139721917527872 af.py:224] I1220 18:47:36.664137 140435568107712 utils.py:36] Started Kalign query I1220 10:47:36.665207 139721917527872 af.py:224] I1220 18:47:36.664822 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:36.665271 139721917527872 af.py:224] I1220 10:47:36.665320 139721917527872 af.py:224] I1220 10:47:36.665366 139721917527872 af.py:224] stderr: I1220 10:47:36.665430 139721917527872 af.py:224] I1220 10:47:36.665494 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:36.665540 139721917527872 af.py:224] I1220 10:47:36.665622 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:36.665698 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:36.665740 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:36.665782 139721917527872 af.py:224] I1220 10:47:36.665825 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:36.665867 139721917527872 af.py:224] reading from /tmp/tmp16_6h7rd/input.fasta: found 2 sequences I1220 10:47:36.665910 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:36.665952 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:36.665993 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:36.666034 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:36.666076 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:36.666118 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmp16_6h7rd/output.a3m'. I1220 10:47:36.666159 139721917527872 af.py:224] I1220 10:47:36.666202 139721917527872 af.py:224] Distance Calculation: I1220 10:47:36.666244 139721917527872 af.py:224] 100 percent done I1220 10:47:36.666285 139721917527872 af.py:224] Alignment: I1220 10:47:36.666327 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:36.666369 139721917527872 af.py:224] I1220 10:47:36.666410 139721917527872 af.py:224] I1220 10:47:36.666452 139721917527872 af.py:224] I1220 18:47:36.664882 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:36.666507 139721917527872 af.py:224] I1220 18:47:36.665277 140435568107712 templates.py:371] Old aligned template: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT------ I1220 10:47:36.666560 139721917527872 af.py:224] New aligned template: EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.666604 139721917527872 af.py:224] I1220 18:47:36.665461 140435568107712 templates.py:556] Sequence in 7pee_C: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT successfully realigned to EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.675070 139721917527872 af.py:224] W1220 18:47:36.674760 140435568107712 templates.py:547] The exact sequence QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT was not found in 7pee_D. Realigning the template to the actual sequence. I1220 10:47:36.675142 139721917527872 af.py:224] I1220 18:47:36.674831 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:36.675204 139721917527872 af.py:224] I1220 18:47:36.675007 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmp020e9p43/input.fasta -o /tmp/tmp020e9p43/output.a3m -format fasta" I1220 10:47:36.748422 139721917527872 af.py:224] I1220 18:47:36.747860 140435568107712 utils.py:36] Started Kalign query I1220 10:47:36.748915 139721917527872 af.py:224] I1220 18:47:36.748556 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:36.748984 139721917527872 af.py:224] I1220 10:47:36.749033 139721917527872 af.py:224] I1220 10:47:36.749119 139721917527872 af.py:224] stderr: I1220 10:47:36.749181 139721917527872 af.py:224] I1220 10:47:36.749312 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:36.749375 139721917527872 af.py:224] I1220 10:47:36.749418 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:36.749462 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:36.749505 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:36.749547 139721917527872 af.py:224] I1220 10:47:36.749589 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:36.749631 139721917527872 af.py:224] reading from /tmp/tmp020e9p43/input.fasta: found 2 sequences I1220 10:47:36.749673 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:36.749714 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:36.749756 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:36.749797 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:36.749839 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:36.749880 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmp020e9p43/output.a3m'. I1220 10:47:36.749922 139721917527872 af.py:224] I1220 10:47:36.749963 139721917527872 af.py:224] Distance Calculation: I1220 10:47:36.750005 139721917527872 af.py:224] 100 percent done I1220 10:47:36.750046 139721917527872 af.py:224] Alignment: I1220 10:47:36.750088 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:36.750129 139721917527872 af.py:224] I1220 10:47:36.750171 139721917527872 af.py:224] I1220 10:47:36.750213 139721917527872 af.py:224] I1220 18:47:36.748618 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:36.750256 139721917527872 af.py:224] I1220 18:47:36.748975 140435568107712 templates.py:371] Old aligned template: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT------ I1220 10:47:36.750306 139721917527872 af.py:224] New aligned template: EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:36.750361 139721917527872 af.py:224] I1220 18:47:36.749169 140435568107712 templates.py:556] Sequence in 7pee_D: QDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLT successfully realigned to EDNCTCPTNKMTVCSPDGPGGRCQCRALGSGMAVDCSTLTSKCLLLKARMSAPKNARTLVRPSEHALVDNDGLYDPDCDPEGRFKARQCQQTSVCWCVNSVGVRRTDKGDLSLRCDELVRTHHILIDLRHRPTAGAFNHSDLDAELRRLFRERYRLHPKFVAAVHYEQPTIQIELRQQTSQKAAGDVDIGDAAYYFERDIKGESLFQGRGGLDLRVRGEPLQVERTLIYYLDEIPPKFSMKRLTHHHHHH I1220 10:47:37.055964 139721917527872 af.py:224] W1220 18:47:37.055440 140435568107712 templates.py:547] The exact sequence QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG was not found in 6i07_C. Realigning the template to the actual sequence. I1220 10:47:37.056090 139721917527872 af.py:224] I1220 18:47:37.055553 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:37.056156 139721917527872 af.py:224] I1220 18:47:37.055829 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmpavp6vsn9/input.fasta -o /tmp/tmpavp6vsn9/output.a3m -format fasta" I1220 10:47:37.130565 139721917527872 af.py:224] I1220 18:47:37.130016 140435568107712 utils.py:36] Started Kalign query I1220 10:47:37.131077 139721917527872 af.py:224] I1220 18:47:37.130715 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:37.131144 139721917527872 af.py:224] I1220 10:47:37.131194 139721917527872 af.py:224] I1220 10:47:37.131240 139721917527872 af.py:224] stderr: I1220 10:47:37.131284 139721917527872 af.py:224] I1220 10:47:37.131367 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:37.131415 139721917527872 af.py:224] I1220 10:47:37.131517 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:37.131578 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:37.131621 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:37.131664 139721917527872 af.py:224] I1220 10:47:37.131705 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:37.131748 139721917527872 af.py:224] reading from /tmp/tmpavp6vsn9/input.fasta: found 2 sequences I1220 10:47:37.131790 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:37.131832 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:37.131873 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:37.131914 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:37.131956 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:37.132003 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmpavp6vsn9/output.a3m'. I1220 10:47:37.132087 139721917527872 af.py:224] I1220 10:47:37.132128 139721917527872 af.py:224] Distance Calculation: I1220 10:47:37.132170 139721917527872 af.py:224] 100 percent done I1220 10:47:37.132212 139721917527872 af.py:224] Alignment: I1220 10:47:37.132253 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:37.132302 139721917527872 af.py:224] I1220 10:47:37.132345 139721917527872 af.py:224] I1220 10:47:37.132387 139721917527872 af.py:224] I1220 18:47:37.130793 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:37.132443 139721917527872 af.py:224] I1220 18:47:37.131148 140435568107712 templates.py:371] Old aligned template: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG--------- I1220 10:47:37.132489 139721917527872 af.py:224] New aligned template: EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGGGGSHHHHHH I1220 10:47:37.132533 139721917527872 af.py:224] I1220 18:47:37.131321 140435568107712 templates.py:556] Sequence in 6i07_C: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG successfully realigned to EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGGGGSHHHHHH I1220 10:47:37.140438 139721917527872 af.py:224] W1220 18:47:37.140176 140435568107712 templates.py:547] The exact sequence QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG was not found in 6i07_D. Realigning the template to the actual sequence. I1220 10:47:37.140504 139721917527872 af.py:224] I1220 18:47:37.140245 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:37.140650 139721917527872 af.py:224] I1220 18:47:37.140424 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmp3z5fh13u/input.fasta -o /tmp/tmp3z5fh13u/output.a3m -format fasta" I1220 10:47:37.214915 139721917527872 af.py:224] I1220 18:47:37.214372 140435568107712 utils.py:36] Started Kalign query I1220 10:47:37.215498 139721917527872 af.py:224] I1220 18:47:37.215076 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:37.215568 139721917527872 af.py:224] I1220 10:47:37.215617 139721917527872 af.py:224] I1220 10:47:37.215680 139721917527872 af.py:224] stderr: I1220 10:47:37.215725 139721917527872 af.py:224] I1220 10:47:37.215791 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:37.215852 139721917527872 af.py:224] I1220 10:47:37.215894 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:37.215937 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:37.215986 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:37.216045 139721917527872 af.py:224] I1220 10:47:37.216087 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:37.216129 139721917527872 af.py:224] reading from /tmp/tmp3z5fh13u/input.fasta: found 2 sequences I1220 10:47:37.216171 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:37.216212 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:37.216254 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:37.216295 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:37.216336 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:37.216377 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmp3z5fh13u/output.a3m'. I1220 10:47:37.216430 139721917527872 af.py:224] I1220 10:47:37.216480 139721917527872 af.py:224] Distance Calculation: I1220 10:47:37.216522 139721917527872 af.py:224] 100 percent done I1220 10:47:37.216564 139721917527872 af.py:224] Alignment: I1220 10:47:37.216606 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:37.216648 139721917527872 af.py:224] I1220 10:47:37.216689 139721917527872 af.py:224] I1220 10:47:37.216731 139721917527872 af.py:224] I1220 18:47:37.215137 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:37.216773 139721917527872 af.py:224] I1220 18:47:37.215570 140435568107712 templates.py:371] Old aligned template: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG--------- I1220 10:47:37.216817 139721917527872 af.py:224] New aligned template: EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGGGGSHHHHHH I1220 10:47:37.216859 139721917527872 af.py:224] I1220 18:47:37.215739 140435568107712 templates.py:556] Sequence in 6i07_D: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGG successfully realigned to EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSMCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKGGGGSHHHHHH I1220 10:47:37.381814 139721917527872 af.py:224] W1220 18:47:37.381414 140435568107712 templates.py:547] The exact sequence QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSTCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLK was not found in 4mzv_A. Realigning the template to the actual sequence. I1220 10:47:37.381928 139721917527872 af.py:224] I1220 18:47:37.381497 140435568107712 kalign.py:66] Aligning 2 sequences I1220 10:47:37.382091 139721917527872 af.py:224] I1220 18:47:37.381746 140435568107712 kalign.py:87] Launching subprocess "/usr/bin/kalign -i /tmp/tmpdmh92udu/input.fasta -o /tmp/tmpdmh92udu/output.a3m -format fasta" I1220 10:47:37.452390 139721917527872 af.py:224] I1220 18:47:37.451803 140435568107712 utils.py:36] Started Kalign query I1220 10:47:37.452939 139721917527872 af.py:224] I1220 18:47:37.452551 140435568107712 kalign.py:95] Kalign stdout: I1220 10:47:37.453008 139721917527872 af.py:224] I1220 10:47:37.453057 139721917527872 af.py:224] I1220 10:47:37.453105 139721917527872 af.py:224] stderr: I1220 10:47:37.453187 139721917527872 af.py:224] I1220 10:47:37.453258 139721917527872 af.py:224] Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann I1220 10:47:37.453351 139721917527872 af.py:224] I1220 10:47:37.453410 139721917527872 af.py:224] Kalign is free software. You can redistribute it and/or modify I1220 10:47:37.453452 139721917527872 af.py:224] it under the terms of the GNU General Public License as I1220 10:47:37.453495 139721917527872 af.py:224] published by the Free Software Foundation. I1220 10:47:37.453536 139721917527872 af.py:224] I1220 10:47:37.453578 139721917527872 af.py:224] reading from STDIN: found 0 sequences I1220 10:47:37.453620 139721917527872 af.py:224] reading from /tmp/tmpdmh92udu/input.fasta: found 2 sequences I1220 10:47:37.453662 139721917527872 af.py:224] Aligning 2 protein sequences with these parameters: I1220 10:47:37.453705 139721917527872 af.py:224] 54.94940948 gap open penalty I1220 10:47:37.453747 139721917527872 af.py:224] 8.52492046 gap extension I1220 10:47:37.453795 139721917527872 af.py:224] 4.42409992 terminal gap penalty I1220 10:47:37.453838 139721917527872 af.py:224] 0.20000000 bonus I1220 10:47:37.453880 139721917527872 af.py:224] Alignment will be written to file:'/tmp/tmpdmh92udu/output.a3m'. I1220 10:47:37.453921 139721917527872 af.py:224] I1220 10:47:37.453963 139721917527872 af.py:224] Distance Calculation: I1220 10:47:37.454004 139721917527872 af.py:224] 100 percent done I1220 10:47:37.454046 139721917527872 af.py:224] Alignment: I1220 10:47:37.454087 139721917527872 af.py:224] 0 percent done 100 percent done I1220 10:47:37.454129 139721917527872 af.py:224] I1220 10:47:37.454170 139721917527872 af.py:224] I1220 10:47:37.454212 139721917527872 af.py:224] I1220 18:47:37.452615 140435568107712 utils.py:40] Finished Kalign query in 0.001 seconds I1220 10:47:37.454267 139721917527872 af.py:224] I1220 18:47:37.452976 140435568107712 templates.py:371] Old aligned template: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSTCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLK------ I1220 10:47:37.454313 139721917527872 af.py:224] New aligned template: EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSTCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKHHHHHH I1220 10:47:37.454356 139721917527872 af.py:224] I1220 18:47:37.453151 140435568107712 templates.py:556] Sequence in 4mzv_A: QEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSTCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLK successfully realigned to EEECVCENYKLAVNCFVNNNRQCQCTSVGAQNTVICSKLAAKCLVMKAEMQGSKLGRRAKPEGALQNNDGLYDPDCDESGLFKAKQCQGTSTCWCVNTAGVRRTDKDTEITCSERVRTYWIIIELKHKAREKPYDSKSLRTALQKEITTRYQLDPKFITSILYENNVITIDLVQQSSQKTQNDVDIADVAYYFEKDVKGESLFHSKKMDLTVNGEQLDLDPGQTLIYYVDEKAPEFSMQGLKHHHHHH I1220 10:47:39.080803 139721917527872 af.py:224] I1220 18:47:39.077088 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.149123 139721917527872 af.py:224] I1220 18:47:39.148756 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.218539 139721917527872 af.py:224] I1220 18:47:39.218240 140435568107712 templates.py:718] hit 7n4y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.04643962848297214. I1220 10:47:39.218656 139721917527872 af.py:224] I1220 18:47:39.218337 140435568107712 templates.py:718] hit 7n4y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.05572755417956656. I1220 10:47:39.218815 139721917527872 af.py:224] I1220 18:47:39.218559 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.289198 139721917527872 af.py:224] I1220 18:47:39.288887 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.358673 139721917527872 af.py:224] I1220 18:47:39.358397 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.428225 139721917527872 af.py:224] I1220 18:47:39.427819 140435568107712 templates.py:718] hit 7n4y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.07739938080495357. I1220 10:47:39.428328 139721917527872 af.py:224] I1220 18:47:39.427909 140435568107712 templates.py:718] hit 7n4y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.06811145510835913. I1220 10:47:39.428454 139721917527872 af.py:224] I1220 18:47:39.428181 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.497534 139721917527872 af.py:224] I1220 18:47:39.497246 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.566562 139721917527872 af.py:224] I1220 18:47:39.566222 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.635312 139721917527872 af.py:224] I1220 18:47:39.634971 140435568107712 templates.py:718] hit 7n4y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.08978328173374613. I1220 10:47:39.635506 139721917527872 af.py:224] I1220 18:47:39.635231 140435568107712 templates.py:268] Found an exact template match 7n4y_A. I1220 10:47:39.704956 139721917527872 af.py:224] I1220 18:47:39.704636 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:39.776169 139721917527872 af.py:224] I1220 18:47:39.775826 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:39.846950 139721917527872 af.py:224] I1220 18:47:39.846550 140435568107712 templates.py:718] hit 7n4y_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.04643962848297214. I1220 10:47:39.847023 139721917527872 af.py:224] I1220 18:47:39.846645 140435568107712 templates.py:718] hit 7n4y_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.05572755417956656. I1220 10:47:39.847232 139721917527872 af.py:224] I1220 18:47:39.846921 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:39.917094 139721917527872 af.py:224] I1220 18:47:39.916760 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:39.986745 139721917527872 af.py:224] I1220 18:47:39.986409 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:40.055600 139721917527872 af.py:224] I1220 18:47:40.055270 140435568107712 templates.py:718] hit 7n4y_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.07739938080495357. I1220 10:47:40.055675 139721917527872 af.py:224] I1220 18:47:40.055363 140435568107712 templates.py:718] hit 7n4y_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.06811145510835913. I1220 10:47:40.055867 139721917527872 af.py:224] I1220 18:47:40.055622 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:40.124826 139721917527872 af.py:224] I1220 18:47:40.124525 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:40.194363 139721917527872 af.py:224] I1220 18:47:40.194016 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:40.263245 139721917527872 af.py:224] I1220 18:47:40.262909 140435568107712 templates.py:718] hit 7n4y_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.08978328173374613. I1220 10:47:40.263377 139721917527872 af.py:224] I1220 18:47:40.263147 140435568107712 templates.py:268] Found an exact template match 7n4y_B. I1220 10:47:42.098797 139721917527872 af.py:224] I1220 18:47:42.098309 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.172989 139721917527872 af.py:224] I1220 18:47:42.172639 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.246777 139721917527872 af.py:224] I1220 18:47:42.246384 140435568107712 templates.py:718] hit 6scj_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.04643962848297214. I1220 10:47:42.246849 139721917527872 af.py:224] I1220 18:47:42.246477 140435568107712 templates.py:718] hit 6scj_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.05572755417956656. I1220 10:47:42.247083 139721917527872 af.py:224] I1220 18:47:42.246778 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.319843 139721917527872 af.py:224] I1220 18:47:42.319503 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.392482 139721917527872 af.py:224] I1220 18:47:42.392169 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.465043 139721917527872 af.py:224] I1220 18:47:42.464720 140435568107712 templates.py:718] hit 6scj_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.06501547987616099. I1220 10:47:42.465120 139721917527872 af.py:224] I1220 18:47:42.464791 140435568107712 templates.py:718] hit 6scj_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.09597523219814241. I1220 10:47:42.465321 139721917527872 af.py:224] I1220 18:47:42.465008 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.538122 139721917527872 af.py:224] I1220 18:47:42.537791 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.610167 139721917527872 af.py:224] I1220 18:47:42.609832 140435568107712 templates.py:268] Found an exact template match 6scj_A. I1220 10:47:42.856586 139721917527872 af.py:224] I1220 18:47:42.855984 140435568107712 pipeline.py:221] Uniref90 MSA size: 2098 sequences. I1220 10:47:42.856689 139721917527872 af.py:224] I1220 18:47:42.856109 140435568107712 pipeline.py:222] BFD MSA size: 1761 sequences. I1220 10:47:42.856740 139721917527872 af.py:224] I1220 18:47:42.856150 140435568107712 pipeline.py:223] MGnify MSA size: 21 sequences. I1220 10:47:42.856797 139721917527872 af.py:224] I1220 18:47:42.856186 140435568107712 pipeline.py:225] Final (deduplicated) MSA size: 3548 sequences. I1220 10:47:42.856842 139721917527872 af.py:224] I1220 18:47:42.856380 140435568107712 pipeline.py:228] Total number of templates (NB: this can include bad templates and is later filtered to top 4): 20. I1220 10:47:42.949986 139721917527872 af.py:224] I1220 18:47:42.949533 140435568107712 run_alphafold.py:185] Running model model_1_multimer on seq_7e5n I1220 10:47:42.950213 139721917527872 af.py:224] I1220 18:47:42.949875 140435568107712 model.py:166] Running predict with shape(feat) = {'aatype': (1292,), 'residue_index': (1292,), 'seq_length': (), 'msa': (2048, 1292), 'num_alignments': (), 'template_aatype': (4, 1292), 'template_all_atom_mask': (4, 1292, 37), 'template_all_atom_positions': (4, 1292, 37, 3), 'asym_id': (1292,), 'sym_id': (1292,), 'entity_id': (1292,), 'deletion_matrix': (2048, 1292), 'deletion_mean': (1292,), 'all_atom_mask': (1292, 37), 'all_atom_positions': (1292, 37, 3), 'assembly_num_chains': (), 'entity_mask': (1292,), 'num_templates': (), 'cluster_bias_mask': (2048,), 'bert_mask': (2048, 1292), 'seq_mask': (1292,), 'msa_mask': (2048, 1292)} I1220 10:59:05.416298 139721917527872 af.py:224] I1220 18:59:05.415472 140435568107712 model.py:176] Output shape was {'distogram': {'bin_edges': (63,), 'logits': (1292, 1292, 64)}, 'experimentally_resolved': {'logits': (1292, 37)}, 'masked_msa': {'logits': (252, 1292, 22)}, 'predicted_aligned_error': (1292, 1292), 'predicted_lddt': {'logits': (1292, 50)}, 'structure_module': {'final_atom_mask': (1292, 37), 'final_atom_positions': (1292, 37, 3)}, 'plddt': (1292,), 'aligned_confidence_probs': (1292, 1292, 64), 'max_predicted_aligned_error': (), 'ptm': (), 'iptm': (), 'ranking_confidence': ()} I1220 10:59:05.416465 139721917527872 af.py:224] I1220 18:59:05.415599 140435568107712 run_alphafold.py:199] Total JAX model model_1_multimer on seq_7e5n predict time (includes compilation time, see --benchmark): 682.5s I1220 11:00:51.812956 139721917527872 af.py:224] I1220 19:00:51.812432 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {: ['OXT'], : ['OXT'], : ['OXT'], : ['OXT']}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 11:00:53.562399 139721917527872 af.py:224] I1220 19:00:53.561919 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 11:00:55.402789 139721917527872 af.py:224] I1220 19:00:55.402336 140435568107712 amber_minimize.py:69] Restraining 10000 / 20220 particles. I1220 11:38:12.143952 139721917527872 af.py:224] I1220 19:38:12.143367 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 11:38:21.956565 139721917527872 af.py:224] I1220 19:38:21.956200 140435568107712 amber_minimize.py:493] Iteration completed: Einit 7792932546498504704.00 Efinal 67393029847404298240.00 Time 2221.33 s num residue violations 750 num residue exclusions 0 I1220 11:38:21.994782 139721917527872 af.py:224] I1220 19:38:21.994303 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 11:38:23.949543 139721917527872 af.py:224] I1220 19:38:23.949066 140435568107712 amber_minimize.py:69] Restraining 4333 / 20220 particles. I1220 12:17:36.168163 139721917527872 af.py:224] I1220 20:17:36.167628 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 12:17:52.214557 139721917527872 af.py:224] I1220 20:17:52.214149 140435568107712 amber_minimize.py:493] Iteration completed: Einit 65316701477478907904.00 Efinal 460910.27 Time 2338.55 s num residue violations 624 num residue exclusions 750 I1220 12:17:52.214755 139721917527872 af.py:224] I1220 20:17:52.214620 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 12:17:53.905964 139721917527872 af.py:224] I1220 20:17:53.905510 140435568107712 amber_minimize.py:69] Restraining 3668 / 20220 particles. I1220 12:33:24.474288 139721917527872 af.py:224] I1220 20:33:24.473716 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 12:33:48.501600 139721917527872 af.py:224] I1220 20:33:48.501239 140435568107712 amber_minimize.py:493] Iteration completed: Einit 794952.01 Efinal 431981.99 Time 915.76 s num residue violations 606 num residue exclusions 828 I1220 12:34:48.050026 139721917527872 af.py:224] I1220 20:34:48.049511 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {: ['OXT'], : ['OXT'], : ['OXT'], : ['OXT']}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 12:34:51.615016 139721917527872 af.py:224] I1220 20:34:51.614561 140435568107712 run_alphafold.py:185] Running model model_2_multimer on seq_7e5n I1220 12:34:51.615216 139721917527872 af.py:224] I1220 20:34:51.614745 140435568107712 model.py:166] Running predict with shape(feat) = {'aatype': (1292,), 'residue_index': (1292,), 'seq_length': (), 'msa': (2048, 1292), 'num_alignments': (), 'template_aatype': (4, 1292), 'template_all_atom_mask': (4, 1292, 37), 'template_all_atom_positions': (4, 1292, 37, 3), 'asym_id': (1292,), 'sym_id': (1292,), 'entity_id': (1292,), 'deletion_matrix': (2048, 1292), 'deletion_mean': (1292,), 'all_atom_mask': (1292, 37), 'all_atom_positions': (1292, 37, 3), 'assembly_num_chains': (), 'entity_mask': (1292,), 'num_templates': (), 'cluster_bias_mask': (2048,), 'bert_mask': (2048, 1292), 'seq_mask': (1292,), 'msa_mask': (2048, 1292)} I1220 12:44:49.762928 139721917527872 af.py:224] I1220 20:44:49.762377 140435568107712 model.py:176] Output shape was {'distogram': {'bin_edges': (63,), 'logits': (1292, 1292, 64)}, 'experimentally_resolved': {'logits': (1292, 37)}, 'masked_msa': {'logits': (252, 1292, 22)}, 'predicted_aligned_error': (1292, 1292), 'predicted_lddt': {'logits': (1292, 50)}, 'structure_module': {'final_atom_mask': (1292, 37), 'final_atom_positions': (1292, 37, 3)}, 'plddt': (1292,), 'aligned_confidence_probs': (1292, 1292, 64), 'max_predicted_aligned_error': (), 'ptm': (), 'iptm': (), 'ranking_confidence': ()} I1220 12:44:49.778264 139721917527872 af.py:224] I1220 20:44:49.777852 140435568107712 run_alphafold.py:199] Total JAX model model_2_multimer on seq_7e5n predict time (includes compilation time, see --benchmark): 598.2s I1220 12:46:35.595277 139721917527872 af.py:224] I1220 20:46:35.594717 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {: ['OXT'], : ['OXT'], : ['OXT'], : ['OXT']}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 12:46:37.469982 139721917527872 af.py:224] I1220 20:46:37.469545 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 12:46:39.422750 139721917527872 af.py:224] I1220 20:46:39.422327 140435568107712 amber_minimize.py:69] Restraining 10000 / 20220 particles. I1220 13:23:24.569057 139721917527872 af.py:224] I1220 21:23:24.568552 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 13:23:37.020151 139721917527872 af.py:224] I1220 21:23:37.019746 140435568107712 amber_minimize.py:493] Iteration completed: Einit 1366204665305568768.00 Efinal 863458396487459968.00 Time 2190.11 s num residue violations 776 num residue exclusions 0 I1220 13:23:37.020391 139721917527872 af.py:224] I1220 21:23:37.020233 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 13:23:38.408898 139721917527872 af.py:224] I1220 21:23:38.408473 140435568107712 amber_minimize.py:69] Restraining 4071 / 20220 particles. I1220 13:59:51.755321 139721917527872 af.py:224] I1220 21:59:51.754814 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 13:59:58.888464 139721917527872 af.py:224] I1220 21:59:58.888105 140435568107712 amber_minimize.py:493] Iteration completed: Einit 856547724696890624.00 Efinal 1188505.25 Time 2157.15 s num residue violations 740 num residue exclusions 776 I1220 13:59:58.888700 139721917527872 af.py:224] I1220 21:59:58.888580 140435568107712 amber_minimize.py:405] Minimizing protein, attempt 1 of 100. I1220 14:00:00.707838 139721917527872 af.py:224] I1220 22:00:00.707369 140435568107712 amber_minimize.py:69] Restraining 3265 / 20222 particles. I1220 14:07:59.371488 139721917527872 af.py:224] I1220 22:07:59.370978 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 14:08:05.484854 139721917527872 af.py:224] I1220 22:08:05.484436 140435568107712 amber_minimize.py:493] Iteration completed: Einit 1812795.98 Efinal 1638527.22 Time 464.14 s num residue violations 733 num residue exclusions 878 I1220 14:09:04.479464 139721917527872 af.py:224] I1220 22:09:04.478866 140435568107712 amber_minimize.py:176] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {: ['OXT'], : ['OXT'], : ['OXT'], : ['OXT']}, 'Se_in_MET': [], 'removed_chains': {0: []}} I1220 14:09:07.315768 139721917527872 af.py:224] Traceback (most recent call last): I1220 14:09:07.316015 139721917527872 af.py:224] File "/app/alphafold/run_alphafold.py", line 427, in I1220 14:09:07.316166 139721917527872 af.py:224] app.run(main) I1220 14:09:07.316290 139721917527872 af.py:224] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run I1220 14:09:07.316407 139721917527872 af.py:224] _run_main(main, args) I1220 14:09:07.316508 139721917527872 af.py:224] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main I1220 14:09:07.316633 139721917527872 af.py:224] sys.exit(main(argv)) I1220 14:09:07.316732 139721917527872 af.py:224] File "/app/alphafold/run_alphafold.py", line 412, in main I1220 14:09:07.316828 139721917527872 af.py:224] is_prokaryote=is_prokaryote) I1220 14:09:07.316923 139721917527872 af.py:224] File "/app/alphafold/run_alphafold.py", line 237, in predict_structure I1220 14:09:07.317018 139721917527872 af.py:224] relaxed_pdb_str, _, _ = amber_relaxer.process(prot=unrelaxed_protein) I1220 14:09:07.317114 139721917527872 af.py:224] File "/app/alphafold/alphafold/relax/relax.py", line 73, in process I1220 14:09:07.317208 139721917527872 af.py:224] min_pdb = utils.overwrite_pdb_coordinates(pdb_str, min_pos) I1220 14:09:07.317304 139721917527872 af.py:224] File "/app/alphafold/alphafold/relax/utils.py", line 29, in overwrite_pdb_coordinates I1220 14:09:07.317399 139721917527872 af.py:224] openmm_app.PDBFile.writeFile(topology, pos, f) I1220 14:09:07.317492 139721917527872 af.py:224] File "/opt/conda/lib/python3.7/site-packages/simtk/openmm/app/pdbfile.py", line 283, in writeFile I1220 14:09:07.317587 139721917527872 af.py:224] PDBFile.writeModel(topology, positions, file, keepIds=keepIds, extraParticleIdentifier=extraParticleIdentifier) I1220 14:09:07.317682 139721917527872 af.py:224] File "/opt/conda/lib/python3.7/site-packages/simtk/openmm/app/pdbfile.py", line 331, in writeModel I1220 14:09:07.317776 139721917527872 af.py:224] raise ValueError('The number of positions must match the number of atoms') I1220 14:09:07.317869 139721917527872 af.py:224] ValueError: The number of positions must match the number of atoms