nohup: ignoring input
I0112 23:31:35.316951 140633533384512 af.py:89] Mounting /home/goddard/ucsf -> /mnt/fasta_path_0
I0112 23:31:35.317038 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/uniref90 -> /mnt/uniref90_database_path
I0112 23:31:35.317081 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/mgnify -> /mnt/mgnify_database_path
I0112 23:31:35.317119 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases -> /mnt/data_dir
I0112 23:31:35.317154 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb_mmcif -> /mnt/template_mmcif_dir
I0112 23:31:35.317188 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0112 23:31:35.317221 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/pdb70 -> /mnt/pdb70_database_path
I0112 23:31:35.317254 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path
I0112 23:31:35.317300 140633533384512 af.py:89] Mounting /home/goddard/ucsf/databases/alphafold21/bfd -> /mnt/bfd_database_path
I0112 23:31:39.072877 140633533384512 af.py:224] I0113 07:31:39.072357 140580048105664 templates.py:857] Using precomputed obsolete pdbs /mnt/obsolete_pdbs_path/obsolete.dat.
I0112 23:31:39.798019 140633533384512 af.py:224] I0113 07:31:39.797696 140580048105664 xla_bridge.py:244] Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker:
I0112 23:31:39.890583 140633533384512 af.py:224] I0113 07:31:39.890058 140580048105664 xla_bridge.py:244] Unable to initialize backend 'tpu': INVALID_ARGUMENT: TpuPlatform is not available.
I0112 23:31:45.472911 140633533384512 af.py:224] I0113 07:31:45.472380 140580048105664 run_alphafold.py:385] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5']
I0112 23:31:45.473024 140633533384512 af.py:224] I0113 07:31:45.472488 140580048105664 run_alphafold.py:397] Using random seed 4173000136169150 for the data pipeline
I0112 23:31:45.473077 140633533384512 af.py:224] I0113 07:31:45.472657 140580048105664 run_alphafold.py:150] Predicting seq_7ban
I0112 23:31:45.473345 140633533384512 af.py:224] I0113 07:31:45.473045 140580048105664 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmppkwai312/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /mnt/fasta_path_0/seq_7ban.fasta /mnt/uniref90_database_path/uniref90.fasta"
I0112 23:31:45.562041 140633533384512 af.py:224] I0113 07:31:45.561512 140580048105664 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0112 23:36:24.477283 140633533384512 af.py:224] I0113 07:36:24.476834 140580048105664 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 278.915 seconds
I0112 23:36:24.930766 140633533384512 af.py:224] I0113 07:36:24.930332 140580048105664 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmp1n77x1io/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /mnt/fasta_path_0/seq_7ban.fasta /mnt/mgnify_database_path/mgy_clusters_2018_12.fa"
I0112 23:36:25.028505 140633533384512 af.py:224] I0113 07:36:25.028039 140580048105664 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I0112 23:41:58.632245 140633533384512 af.py:224] I0113 07:41:58.631802 140580048105664 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 333.604 seconds
I0112 23:42:15.129762 140633533384512 af.py:224] I0113 07:42:15.129251 140580048105664 hhsearch.py:85] Launching subprocess "/usr/bin/hhsearch -i /tmp/tmpyi9uedo0/query.a3m -o /tmp/tmpyi9uedo0/output.hhr -maxseq 1000000 -d /mnt/pdb70_database_path/pdb70"
I0112 23:42:15.240598 140633533384512 af.py:224] I0113 07:42:15.239508 140580048105664 utils.py:36] Started HHsearch query
I0112 23:44:11.624128 140633533384512 af.py:224] I0113 07:44:11.623614 140580048105664 utils.py:40] Finished HHsearch query in 116.384 seconds
I0112 23:44:36.811607 140633533384512 af.py:224] I0113 07:44:36.811084 140580048105664 hhblits.py:128] Launching subprocess "/usr/bin/hhblits -i /mnt/fasta_path_0/seq_7ban.fasta -cpu 4 -oa3m /tmp/tmpv8mg4wff/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"
I0112 23:44:36.927299 140633533384512 af.py:224] I0113 07:44:36.926743 140580048105664 utils.py:36] Started HHblits query
I0113 00:54:21.082471 140633533384512 af.py:224] I0113 08:54:21.006307 140580048105664 utils.py:40] Finished HHblits query in 4184.059 seconds
I0113 00:54:21.089764 140633533384512 af.py:224] E0113 08:54:21.048157 140580048105664 hhblits.py:138] HHblits failed. HHblits stderr begin:
I0113 00:54:21.089822 140633533384512 af.py:224] E0113 08:54:21.052109 140580048105664 hhblits.py:141] - 07:44:53.961 INFO: Searching 65983866 column state sequences.
I0113 00:54:21.089902 140633533384512 af.py:224] E0113 08:54:21.052663 140580048105664 hhblits.py:141] - 07:44:54.430 INFO: Searching 15161831 column state sequences.
I0113 00:54:21.089949 140633533384512 af.py:224] E0113 08:54:21.052698 140580048105664 hhblits.py:141] - 07:44:54.470 INFO: /mnt/fasta_path_0/seq_7ban.fasta is in A2M, A3M or FASTA format
I0113 00:54:21.089993 140633533384512 af.py:224] E0113 08:54:21.053173 140580048105664 hhblits.py:141] - 07:44:54.471 INFO: Iteration 1
I0113 00:54:21.090035 140633533384512 af.py:224] E0113 08:54:21.053205 140580048105664 hhblits.py:141] - 07:44:54.964 INFO: Prefiltering database
I0113 00:54:21.090077 140633533384512 af.py:224] E0113 08:54:21.053235 140580048105664 hhblits.py:141] - 07:52:13.326 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 2518416
I0113 00:54:21.090119 140633533384512 af.py:224] E0113 08:54:21.053292 140580048105664 hhblits.py:141] - 07:54:08.742 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 506022
I0113 00:54:21.090160 140633533384512 af.py:224] E0113 08:54:21.053336 140580048105664 hhblits.py:141] - 07:54:13.543 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment)   : 63157
I0113 00:54:21.090201 140633533384512 af.py:224] E0113 08:54:21.053366 140580048105664 hhblits.py:141] - 07:54:13.543 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 63157
I0113 00:54:21.090242 140633533384512 af.py:224] E0113 08:54:21.053422 140580048105664 hhblits.py:141] - 07:54:13.543 INFO: Scoring 63157 HMMs using HMM-HMM Viterbi alignment
I0113 00:54:21.090282 140633533384512 af.py:224] E0113 08:54:21.053466 140580048105664 hhblits.py:141] - 07:54:13.688 INFO: Alternative alignment: 0
I0113 00:54:21.090322 140633533384512 af.py:224] E0113 08:54:21.053494 140580048105664 hhblits.py:141] - 07:54:16.541 INFO: 2000 alignments done
I0113 00:54:21.090363 140633533384512 af.py:224] E0113 08:54:21.053550 140580048105664 hhblits.py:141] - 07:54:19.346 INFO: 4000 alignments done
I0113 00:54:21.090404 140633533384512 af.py:224] E0113 08:54:21.053596 140580048105664 hhblits.py:141] - 07:54:22.323 INFO: 6000 alignments done
I0113 00:54:21.090444 140633533384512 af.py:224] E0113 08:54:21.053653 140580048105664 hhblits.py:141] - 07:54:24.822 INFO: 8000 alignments done
I0113 00:54:21.090484 140633533384512 af.py:224] E0113 08:54:21.053717 140580048105664 hhblits.py:141] - 07:54:27.308 INFO: 10000 alignments done
I0113 00:54:21.090524 140633533384512 af.py:224] E0113 08:54:21.053762 140580048105664 hhblits.py:141] - 07:54:29.755 INFO: 12000 alignments done
I0113 00:54:21.090564 140633533384512 af.py:224] E0113 08:54:21.053810 140580048105664 hhblits.py:141] - 07:54:32.278 INFO: 14000 alignments done
I0113 00:54:21.090605 140633533384512 af.py:224] E0113 08:54:21.053839 140580048105664 hhblits.py:141] - 07:54:34.754 INFO: 16000 alignments done
I0113 00:54:21.090645 140633533384512 af.py:224] E0113 08:54:21.053868 140580048105664 hhblits.py:141] - 07:54:37.809 INFO: 18000 alignments done
I0113 00:54:21.090685 140633533384512 af.py:224] E0113 08:54:21.053897 140580048105664 hhblits.py:141] - 07:54:41.142 INFO: 20000 alignments done
I0113 00:54:21.090733 140633533384512 af.py:224] E0113 08:54:21.053926 140580048105664 hhblits.py:141] - 07:54:44.248 INFO: 22000 alignments done
I0113 00:54:21.090775 140633533384512 af.py:224] E0113 08:54:21.053955 140580048105664 hhblits.py:141] - 07:54:47.578 INFO: 24000 alignments done
I0113 00:54:21.090815 140633533384512 af.py:224] E0113 08:54:21.053983 140580048105664 hhblits.py:141] - 07:54:50.568 INFO: 26000 alignments done
I0113 00:54:21.090855 140633533384512 af.py:224] E0113 08:54:21.054012 140580048105664 hhblits.py:141] - 07:54:52.994 INFO: 28000 alignments done
I0113 00:54:21.090895 140633533384512 af.py:224] E0113 08:54:21.054041 140580048105664 hhblits.py:141] - 07:54:55.432 INFO: 30000 alignments done
I0113 00:54:21.090934 140633533384512 af.py:224] E0113 08:54:21.054104 140580048105664 hhblits.py:141] - 07:54:57.690 INFO: 32000 alignments done
I0113 00:54:21.090975 140633533384512 af.py:224] E0113 08:54:21.054133 140580048105664 hhblits.py:141] - 07:55:00.026 INFO: 34000 alignments done
I0113 00:54:21.091015 140633533384512 af.py:224] E0113 08:54:21.054162 140580048105664 hhblits.py:141] - 07:55:02.325 INFO: 36000 alignments done
I0113 00:54:21.091055 140633533384512 af.py:224] E0113 08:54:21.054208 140580048105664 hhblits.py:141] - 07:55:04.583 INFO: 38000 alignments done
I0113 00:54:21.091095 140633533384512 af.py:224] E0113 08:54:21.054255 140580048105664 hhblits.py:141] - 07:55:06.826 INFO: 40000 alignments done
I0113 00:54:21.091136 140633533384512 af.py:224] E0113 08:54:21.054284 140580048105664 hhblits.py:141] - 07:55:09.027 INFO: 42000 alignments done
I0113 00:54:21.091177 140633533384512 af.py:224] E0113 08:54:21.054312 140580048105664 hhblits.py:141] - 07:55:11.177 INFO: 44000 alignments done
I0113 00:54:21.091217 140633533384512 af.py:224] E0113 08:54:21.054341 140580048105664 hhblits.py:141] - 07:55:13.525 INFO: 46000 alignments done
I0113 00:54:21.091257 140633533384512 af.py:224] E0113 08:54:21.054369 140580048105664 hhblits.py:141] - 07:55:15.504 INFO: 48000 alignments done
I0113 00:54:21.091297 140633533384512 af.py:224] E0113 08:54:21.054398 140580048105664 hhblits.py:141] - 07:55:17.628 INFO: 50000 alignments done
I0113 00:54:21.091337 140633533384512 af.py:224] E0113 08:54:21.054462 140580048105664 hhblits.py:141] - 07:55:19.522 INFO: 52000 alignments done
I0113 00:54:21.091376 140633533384512 af.py:224] E0113 08:54:21.054490 140580048105664 hhblits.py:141] - 07:55:21.763 INFO: 54000 alignments done
I0113 00:54:21.091416 140633533384512 af.py:224] E0113 08:54:21.054519 140580048105664 hhblits.py:141] - 07:55:25.150 INFO: 56000 alignments done
I0113 00:54:21.091456 140633533384512 af.py:224] E0113 08:54:21.054548 140580048105664 hhblits.py:141] - 07:55:29.459 INFO: 58000 alignments done
I0113 00:54:21.091496 140633533384512 af.py:224] E0113 08:54:21.054576 140580048105664 hhblits.py:141] - 07:55:32.713 INFO: 60000 alignments done
I0113 00:54:21.091536 140633533384512 af.py:224] E0113 08:54:21.054605 140580048105664 hhblits.py:141] - 07:55:35.850 INFO: 62000 alignments done
I0113 00:54:21.091576 140633533384512 af.py:224] E0113 08:54:21.054633 140580048105664 hhblits.py:141] - 07:55:37.490 INFO: 63157 alignments done
I0113 00:54:21.091616 140633533384512 af.py:224] E0113 08:54:21.054662 140580048105664 hhblits.py:141] - 07:55:37.491 INFO: Alternative alignment: 1
I0113 00:54:21.091656 140633533384512 af.py:224] E0113 08:54:21.054690 140580048105664 hhblits.py:141] - 07:56:47.902 INFO: 62359 alignments done
I0113 00:54:21.091696 140633533384512 af.py:224] E0113 08:54:21.054718 140580048105664 hhblits.py:141] - 07:56:47.994 INFO: Alternative alignment: 2
I0113 00:54:21.091737 140633533384512 af.py:224] E0113 08:54:21.054783 140580048105664 hhblits.py:141] - 07:57:55.303 INFO: 54967 alignments done
I0113 00:54:21.091777 140633533384512 af.py:224] E0113 08:54:21.054812 140580048105664 hhblits.py:141] - 07:57:55.419 INFO: Alternative alignment: 3
I0113 00:54:21.091816 140633533384512 af.py:224] E0113 08:54:21.054840 140580048105664 hhblits.py:141] - 07:59:00.246 INFO: 50910 alignments done
I0113 00:54:21.091861 140633533384512 af.py:224] E0113 08:54:21.054886 140580048105664 hhblits.py:141] - 07:59:03.775 INFO: Premerge done
I0113 00:54:21.091902 140633533384512 af.py:224] E0113 08:54:21.054934 140580048105664 hhblits.py:141] - 07:59:03.789 INFO: Realigning 19887 HMM-HMM alignments using Maximum Accuracy algorithm
I0113 00:54:21.091942 140633533384512 af.py:224] E0113 08:54:21.054963 140580048105664 hhblits.py:141] - 08:17:09.949 INFO: 19890 sequences belonging to 19890 database HMMs found with an E-value < 0.001
I0113 00:54:21.091986 140633533384512 af.py:224] E0113 08:54:21.054991 140580048105664 hhblits.py:141] - 08:17:09.949 INFO: Number of effective sequences of resulting query HMM: Neff = 9.05164
I0113 00:54:21.092028 140633533384512 af.py:224] E0113 08:54:21.055020 140580048105664 hhblits.py:141] - 08:17:10.488 INFO: Iteration 2
I0113 00:54:21.092069 140633533384512 af.py:224] E0113 08:54:21.055048 140580048105664 hhblits.py:141] - 08:17:10.488 INFO: Set premerge to 0! (premerge: 3 iteration: 2 hits.Size: 19887)
I0113 00:54:21.092109 140633533384512 af.py:224] E0113 08:54:21.055077 140580048105664 hhblits.py:141] - 08:17:11.039 INFO: Prefiltering database
I0113 00:54:21.092149 140633533384512 af.py:224] E0113 08:54:21.055106 140580048105664 hhblits.py:141] - 08:24:30.340 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 5852176
I0113 00:54:21.092189 140633533384512 af.py:224] E0113 08:54:21.055134 140580048105664 hhblits.py:141] - 08:25:09.936 WARNING: Number of hits passing 2nd prefilter (reduced from 261479 to allowed maximum of 100000).
I0113 00:54:21.092230 140633533384512 af.py:224] E0113 08:54:21.055164 140580048105664 hhblits.py:141] You can increase the allowed maximum using the -maxfilt <max> option.
I0113 00:54:21.092270 140633533384512 af.py:224] E0113 08:54:21.055193 140580048105664 hhblits.py:141] - 08:26:49.170 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 976618
I0113 00:54:21.092311 140633533384512 af.py:224] E0113 08:54:21.055222 140580048105664 hhblits.py:141] - 08:26:58.095 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment)   : 146928
I0113 00:54:21.092350 140633533384512 af.py:224] E0113 08:54:21.055251 140580048105664 hhblits.py:141] - 08:26:58.095 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 139250
I0113 00:54:21.092391 140633533384512 af.py:224] E0113 08:54:21.055280 140580048105664 hhblits.py:141] - 08:26:58.095 INFO: Scoring 139250 HMMs using HMM-HMM Viterbi alignment
I0113 00:54:21.092431 140633533384512 af.py:224] E0113 08:54:21.055309 140580048105664 hhblits.py:141] - 08:26:58.216 INFO: Alternative alignment: 0
I0113 00:54:21.092471 140633533384512 af.py:224] E0113 08:54:21.055337 140580048105664 hhblits.py:141] - 08:27:00.526 INFO: 2000 alignments done
I0113 00:54:21.092511 140633533384512 af.py:224] E0113 08:54:21.055366 140580048105664 hhblits.py:141] - 08:27:02.810 INFO: 4000 alignments done
I0113 00:54:21.092551 140633533384512 af.py:224] E0113 08:54:21.055395 140580048105664 hhblits.py:141] - 08:27:04.981 INFO: 6000 alignments done
I0113 00:54:21.092616 140633533384512 af.py:224] E0113 08:54:21.055423 140580048105664 hhblits.py:141] - 08:27:07.238 INFO: 8000 alignments done
I0113 00:54:21.092658 140633533384512 af.py:224] E0113 08:54:21.055451 140580048105664 hhblits.py:141] - 08:27:09.394 INFO: 10000 alignments done
I0113 00:54:21.092698 140633533384512 af.py:224] E0113 08:54:21.055480 140580048105664 hhblits.py:141] - 08:27:11.621 INFO: 12000 alignments done
I0113 00:54:21.092738 140633533384512 af.py:224] E0113 08:54:21.055509 140580048105664 hhblits.py:141] - 08:27:13.960 INFO: 14000 alignments done
I0113 00:54:21.092778 140633533384512 af.py:224] E0113 08:54:21.055537 140580048105664 hhblits.py:141] - 08:27:16.135 INFO: 16000 alignments done
I0113 00:54:21.092819 140633533384512 af.py:224] E0113 08:54:21.055566 140580048105664 hhblits.py:141] - 08:27:18.283 INFO: 18000 alignments done
I0113 00:54:21.092863 140633533384512 af.py:224] E0113 08:54:21.055595 140580048105664 hhblits.py:141] - 08:27:20.429 INFO: 20000 alignments done
I0113 00:54:21.092903 140633533384512 af.py:224] E0113 08:54:21.055623 140580048105664 hhblits.py:141] - 08:27:22.847 INFO: 22000 alignments done
I0113 00:54:21.092944 140633533384512 af.py:224] E0113 08:54:21.055651 140580048105664 hhblits.py:141] - 08:27:24.990 INFO: 24000 alignments done
I0113 00:54:21.092983 140633533384512 af.py:224] E0113 08:54:21.055680 140580048105664 hhblits.py:141] - 08:27:27.098 INFO: 26000 alignments done
I0113 00:54:21.093024 140633533384512 af.py:224] E0113 08:54:21.055708 140580048105664 hhblits.py:141] - 08:27:29.186 INFO: 28000 alignments done
I0113 00:54:21.093064 140633533384512 af.py:224] E0113 08:54:21.055736 140580048105664 hhblits.py:141] - 08:27:31.198 INFO: 30000 alignments done
I0113 00:54:21.093104 140633533384512 af.py:224] E0113 08:54:21.055764 140580048105664 hhblits.py:141] - 08:27:33.352 INFO: 32000 alignments done
I0113 00:54:21.093144 140633533384512 af.py:224] E0113 08:54:21.055792 140580048105664 hhblits.py:141] - 08:27:35.386 INFO: 34000 alignments done
I0113 00:54:21.093184 140633533384512 af.py:224] E0113 08:54:21.055820 140580048105664 hhblits.py:141] - 08:27:37.153 INFO: 36000 alignments done
I0113 00:54:21.093224 140633533384512 af.py:224] E0113 08:54:21.055849 140580048105664 hhblits.py:141] - 08:27:39.041 INFO: 38000 alignments done
I0113 00:54:21.093263 140633533384512 af.py:224] E0113 08:54:21.055876 140580048105664 hhblits.py:141] - 08:27:40.963 INFO: 40000 alignments done
I0113 00:54:21.093303 140633533384512 af.py:224] E0113 08:54:21.055905 140580048105664 hhblits.py:141] - 08:27:42.885 INFO: 42000 alignments done
I0113 00:54:21.093343 140633533384512 af.py:224] E0113 08:54:21.055933 140580048105664 hhblits.py:141] - 08:27:44.792 INFO: 44000 alignments done
I0113 00:54:21.093384 140633533384512 af.py:224] E0113 08:54:21.055961 140580048105664 hhblits.py:141] - 08:27:46.810 INFO: 46000 alignments done
I0113 00:54:21.093424 140633533384512 af.py:224] E0113 08:54:21.055995 140580048105664 hhblits.py:141] - 08:27:48.706 INFO: 48000 alignments done
I0113 00:54:21.093464 140633533384512 af.py:224] E0113 08:54:21.056023 140580048105664 hhblits.py:141] - 08:27:50.722 INFO: 50000 alignments done
I0113 00:54:21.093504 140633533384512 af.py:224] E0113 08:54:21.056051 140580048105664 hhblits.py:141] - 08:27:52.696 INFO: 52000 alignments done
I0113 00:54:21.093544 140633533384512 af.py:224] E0113 08:54:21.056079 140580048105664 hhblits.py:141] - 08:27:54.754 INFO: 54000 alignments done
I0113 00:54:21.093585 140633533384512 af.py:224] E0113 08:54:21.056106 140580048105664 hhblits.py:141] - 08:27:56.716 INFO: 56000 alignments done
I0113 00:54:21.093625 140633533384512 af.py:224] E0113 08:54:21.056134 140580048105664 hhblits.py:141] - 08:27:58.716 INFO: 58000 alignments done
I0113 00:54:21.093665 140633533384512 af.py:224] E0113 08:54:21.056161 140580048105664 hhblits.py:141] - 08:28:00.726 INFO: 60000 alignments done
I0113 00:54:21.093706 140633533384512 af.py:224] E0113 08:54:21.056188 140580048105664 hhblits.py:141] - 08:28:02.782 INFO: 62000 alignments done
I0113 00:54:21.093746 140633533384512 af.py:224] E0113 08:54:21.056216 140580048105664 hhblits.py:141] - 08:28:04.799 INFO: 64000 alignments done
I0113 00:54:21.093785 140633533384512 af.py:224] E0113 08:54:21.056243 140580048105664 hhblits.py:141] - 08:28:06.715 INFO: 66000 alignments done
I0113 00:54:21.093825 140633533384512 af.py:224] E0113 08:54:21.056270 140580048105664 hhblits.py:141] - 08:28:08.554 INFO: 68000 alignments done
I0113 00:54:21.093864 140633533384512 af.py:224] E0113 08:54:21.056298 140580048105664 hhblits.py:141] - 08:28:10.501 INFO: 70000 alignments done
I0113 00:54:21.093904 140633533384512 af.py:224] E0113 08:54:21.056325 140580048105664 hhblits.py:141] - 08:28:12.306 INFO: 72000 alignments done
I0113 00:54:21.093944 140633533384512 af.py:224] E0113 08:54:21.056353 140580048105664 hhblits.py:141] - 08:28:14.311 INFO: 74000 alignments done
I0113 00:54:21.093989 140633533384512 af.py:224] E0113 08:54:21.056381 140580048105664 hhblits.py:141] - 08:28:16.209 INFO: 76000 alignments done
I0113 00:54:21.094030 140633533384512 af.py:224] E0113 08:54:21.056409 140580048105664 hhblits.py:141] - 08:28:18.050 INFO: 78000 alignments done
I0113 00:54:21.094069 140633533384512 af.py:224] E0113 08:54:21.056437 140580048105664 hhblits.py:141] - 08:28:20.027 INFO: 80000 alignments done
I0113 00:54:21.094109 140633533384512 af.py:224] E0113 08:54:21.056465 140580048105664 hhblits.py:141] - 08:28:21.873 INFO: 82000 alignments done
I0113 00:54:21.094149 140633533384512 af.py:224] E0113 08:54:21.056493 140580048105664 hhblits.py:141] - 08:28:23.764 INFO: 84000 alignments done
I0113 00:54:21.094189 140633533384512 af.py:224] E0113 08:54:21.056522 140580048105664 hhblits.py:141] - 08:28:25.654 INFO: 86000 alignments done
I0113 00:54:21.094229 140633533384512 af.py:224] E0113 08:54:21.056550 140580048105664 hhblits.py:141] - 08:28:28.987 INFO: 88000 alignments done
I0113 00:54:21.094270 140633533384512 af.py:224] E0113 08:54:21.056578 140580048105664 hhblits.py:141] - 08:28:32.323 INFO: 90000 alignments done
I0113 00:54:21.094310 140633533384512 af.py:224] E0113 08:54:21.056607 140580048105664 hhblits.py:141] - 08:28:34.536 INFO: 92000 alignments done
I0113 00:54:21.094350 140633533384512 af.py:224] E0113 08:54:21.056635 140580048105664 hhblits.py:141] - 08:28:36.898 INFO: 94000 alignments done
I0113 00:54:21.094389 140633533384512 af.py:224] E0113 08:54:21.056663 140580048105664 hhblits.py:141] - 08:28:39.775 INFO: 96000 alignments done
I0113 00:54:21.094429 140633533384512 af.py:224] E0113 08:54:21.056692 140580048105664 hhblits.py:141] - 08:28:42.509 INFO: 98000 alignments done
I0113 00:54:21.094469 140633533384512 af.py:224] E0113 08:54:21.056720 140580048105664 hhblits.py:141] - 08:28:45.280 INFO: 100000 alignments done
I0113 00:54:21.094509 140633533384512 af.py:224] E0113 08:54:21.056748 140580048105664 hhblits.py:141] - 08:28:47.967 INFO: 102000 alignments done
I0113 00:54:21.094549 140633533384512 af.py:224] E0113 08:54:21.056777 140580048105664 hhblits.py:141] - 08:28:50.860 INFO: 104000 alignments done
I0113 00:54:21.094589 140633533384512 af.py:224] E0113 08:54:21.056805 140580048105664 hhblits.py:141] - 08:28:53.597 INFO: 106000 alignments done
I0113 00:54:21.094629 140633533384512 af.py:224] E0113 08:54:21.056833 140580048105664 hhblits.py:141] - 08:28:56.413 INFO: 108000 alignments done
I0113 00:54:21.094669 140633533384512 af.py:224] E0113 08:54:21.056862 140580048105664 hhblits.py:141] - 08:28:59.309 INFO: 110000 alignments done
I0113 00:54:21.094709 140633533384512 af.py:224] E0113 08:54:21.056890 140580048105664 hhblits.py:141] - 08:29:02.132 INFO: 112000 alignments done
I0113 00:54:21.094748 140633533384512 af.py:224] E0113 08:54:21.056918 140580048105664 hhblits.py:141] - 08:29:04.580 INFO: 114000 alignments done
I0113 00:54:21.094789 140633533384512 af.py:224] E0113 08:54:21.056946 140580048105664 hhblits.py:141] - 08:29:06.996 INFO: 116000 alignments done
I0113 00:54:21.094828 140633533384512 af.py:224] E0113 08:54:21.056975 140580048105664 hhblits.py:141] - 08:29:09.950 INFO: 118000 alignments done
I0113 00:54:21.094869 140633533384512 af.py:224] E0113 08:54:21.057003 140580048105664 hhblits.py:141] - 08:29:12.541 INFO: 120000 alignments done
I0113 00:54:21.094909 140633533384512 af.py:224] E0113 08:54:21.057031 140580048105664 hhblits.py:141] - 08:29:14.780 INFO: 122000 alignments done
I0113 00:54:21.094950 140633533384512 af.py:224] E0113 08:54:21.057060 140580048105664 hhblits.py:141] - 08:29:17.316 INFO: 124000 alignments done
I0113 00:54:21.094990 140633533384512 af.py:224] E0113 08:54:21.057088 140580048105664 hhblits.py:141] - 08:29:19.861 INFO: 126000 alignments done
I0113 00:54:21.095030 140633533384512 af.py:224] E0113 08:54:21.057116 140580048105664 hhblits.py:141] - 08:29:19.863 INFO: Stop after DB-HHM: 126000 because early stop  18.0788 < filter cutoff 20
I0113 00:54:21.095071 140633533384512 af.py:224] E0113 08:54:21.057145 140580048105664 hhblits.py:141] - 08:29:19.866 INFO: Alternative alignment: 1
I0113 00:54:21.095114 140633533384512 af.py:224] E0113 08:54:21.057173 140580048105664 hhblits.py:141] - 08:31:12.480 INFO: 120453 alignments done
I0113 00:54:21.095155 140633533384512 af.py:224] E0113 08:54:21.057201 140580048105664 hhblits.py:141] - 08:31:12.616 INFO: Alternative alignment: 2
I0113 00:54:21.095196 140633533384512 af.py:224] E0113 08:54:21.057229 140580048105664 hhblits.py:141] - 08:32:53.814 INFO: 97154 alignments done
I0113 00:54:21.095235 140633533384512 af.py:224] E0113 08:54:21.057258 140580048105664 hhblits.py:141] - 08:32:54.033 INFO: Alternative alignment: 3
I0113 00:54:21.095275 140633533384512 af.py:224] E0113 08:54:21.057287 140580048105664 hhblits.py:141] - 08:34:34.185 INFO: 93115 alignments done
I0113 00:54:21.095315 140633533384512 af.py:224] E0113 08:54:21.057315 140580048105664 hhblits.py:141] - 08:34:36.393 INFO: Realigning 100008 HMM-HMM alignments using Maximum Accuracy algorithm
I0113 00:54:21.095355 140633533384512 af.py:224] E0113 08:54:21.057812 140580048105664 hhblits.py:142] HHblits stderr end
I0113 00:54:21.170309 140633533384512 af.py:224] Traceback (most recent call last):
I0113 00:54:21.170372 140633533384512 af.py:224] File "/app/alphafold/run_alphafold.py", line 427, in <module>
I0113 00:54:21.170421 140633533384512 af.py:224] app.run(main)
I0113 00:54:21.170467 140633533384512 af.py:224] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
I0113 00:54:21.170511 140633533384512 af.py:224] _run_main(main, args)
I0113 00:54:21.170554 140633533384512 af.py:224] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
I0113 00:54:21.170596 140633533384512 af.py:224] sys.exit(main(argv))
I0113 00:54:21.170638 140633533384512 af.py:224] File "/app/alphafold/run_alphafold.py", line 412, in main
I0113 00:54:21.170680 140633533384512 af.py:224] is_prokaryote=is_prokaryote)
I0113 00:54:21.170736 140633533384512 af.py:224] File "/app/alphafold/run_alphafold.py", line 164, in predict_structure
I0113 00:54:21.170775 140633533384512 af.py:224] msa_output_dir=msa_output_dir)
I0113 00:54:21.170816 140633533384512 af.py:224] File "/app/alphafold/alphafold/data/pipeline.py", line 207, in process
I0113 00:54:21.170909 140633533384512 af.py:224] 'a3m', self.use_precomputed_msas)
I0113 00:54:21.170951 140633533384512 af.py:224] File "/app/alphafold/alphafold/data/pipeline.py", line 97, in run_msa_tool
I0113 00:54:21.170992 140633533384512 af.py:224] result = msa_runner.query(input_fasta_path)[0]
I0113 00:54:21.171033 140633533384512 af.py:224] File "/app/alphafold/alphafold/data/tools/hhblits.py", line 144, in query
I0113 00:54:21.171073 140633533384512 af.py:224] stdout.decode('utf-8'), stderr[:500_000].decode('utf-8')))
I0113 00:54:21.171114 140633533384512 af.py:224] RuntimeError: HHblits failed
I0113 00:54:21.171154 140633533384512 af.py:224] stdout:
I0113 00:54:21.171195 140633533384512 af.py:224] 
I0113 00:54:21.171236 140633533384512 af.py:224] 
I0113 00:54:21.171277 140633533384512 af.py:224] stderr:
I0113 00:54:21.171317 140633533384512 af.py:224] - 07:44:53.961 INFO: Searching 65983866 column state sequences.
I0113 00:54:21.171357 140633533384512 af.py:224] 
I0113 00:54:21.171397 140633533384512 af.py:224] - 07:44:54.430 INFO: Searching 15161831 column state sequences.
I0113 00:54:21.171437 140633533384512 af.py:224] 
I0113 00:54:21.171478 140633533384512 af.py:224] - 07:44:54.470 INFO: /mnt/fasta_path_0/seq_7ban.fasta is in A2M, A3M or FASTA format
I0113 00:54:21.171518 140633533384512 af.py:224] 
I0113 00:54:21.171559 140633533384512 af.py:224] - 07:44:54.471 INFO: Iteration 1
I0113 00:54:21.171599 140633533384512 af.py:224] 
I0113 00:54:21.171639 140633533384512 af.py:224] - 07:44:54.964 INFO: Prefiltering database
I0113 00:54:21.171679 140633533384512 af.py:224] 
I0113 00:54:21.171720 140633533384512 af.py:224] - 07:52:13.326 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 2518416
I0113 00:54:21.171760 140633533384512 af.py:224] 
I0113 00:54:21.171800 140633533384512 af.py:224] - 07:54:08.742 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 506022
I0113 00:54:21.171846 140633533384512 af.py:224] 
I0113 00:54:21.171887 140633533384512 af.py:224] - 07:54:13.543 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment)   : 63157
I0113 00:54:21.171927 140633533384512 af.py:224] 
I0113 00:54:21.171967 140633533384512 af.py:224] - 07:54:13.543 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 63157
I0113 00:54:21.172013 140633533384512 af.py:224] 
I0113 00:54:21.172054 140633533384512 af.py:224] - 07:54:13.543 INFO: Scoring 63157 HMMs using HMM-HMM Viterbi alignment
I0113 00:54:21.172095 140633533384512 af.py:224] 
I0113 00:54:21.172136 140633533384512 af.py:224] - 07:54:13.688 INFO: Alternative alignment: 0
I0113 00:54:21.172176 140633533384512 af.py:224] 
I0113 00:54:21.172217 140633533384512 af.py:224] - 07:54:16.541 INFO: 2000 alignments done
I0113 00:54:21.172257 140633533384512 af.py:224] 
I0113 00:54:21.172297 140633533384512 af.py:224] - 07:54:19.346 INFO: 4000 alignments done
I0113 00:54:21.172336 140633533384512 af.py:224] 
I0113 00:54:21.172376 140633533384512 af.py:224] - 07:54:22.323 INFO: 6000 alignments done
I0113 00:54:21.172416 140633533384512 af.py:224] 
I0113 00:54:21.172456 140633533384512 af.py:224] - 07:54:24.822 INFO: 8000 alignments done
I0113 00:54:21.172496 140633533384512 af.py:224] 
I0113 00:54:21.172536 140633533384512 af.py:224] - 07:54:27.308 INFO: 10000 alignments done
I0113 00:54:21.172575 140633533384512 af.py:224] 
I0113 00:54:21.172615 140633533384512 af.py:224] - 07:54:29.755 INFO: 12000 alignments done
I0113 00:54:21.172655 140633533384512 af.py:224] 
I0113 00:54:21.172694 140633533384512 af.py:224] - 07:54:32.278 INFO: 14000 alignments done
I0113 00:54:21.172735 140633533384512 af.py:224] 
I0113 00:54:21.172775 140633533384512 af.py:224] - 07:54:34.754 INFO: 16000 alignments done
I0113 00:54:21.172815 140633533384512 af.py:224] 
I0113 00:54:21.172855 140633533384512 af.py:224] - 07:54:37.809 INFO: 18000 alignments done
I0113 00:54:21.172894 140633533384512 af.py:224] 
I0113 00:54:21.172934 140633533384512 af.py:224] - 07:54:41.142 INFO: 20000 alignments done
I0113 00:54:21.172973 140633533384512 af.py:224] 
I0113 00:54:21.173013 140633533384512 af.py:224] - 07:54:44.248 INFO: 22000 alignments done
I0113 00:54:21.173053 140633533384512 af.py:224] 
I0113 00:54:21.173094 140633533384512 af.py:224] - 07:54:47.578 INFO: 24000 alignments done
I0113 00:54:21.173133 140633533384512 af.py:224] 
I0113 00:54:21.173173 140633533384512 af.py:224] - 07:54:50.568 INFO: 26000 alignments done
I0113 00:54:21.173213 140633533384512 af.py:224] 
I0113 00:54:21.173253 140633533384512 af.py:224] - 07:54:52.994 INFO: 28000 alignments done
I0113 00:54:21.173293 140633533384512 af.py:224] 
I0113 00:54:21.173333 140633533384512 af.py:224] - 07:54:55.432 INFO: 30000 alignments done
I0113 00:54:21.173373 140633533384512 af.py:224] 
I0113 00:54:21.173413 140633533384512 af.py:224] - 07:54:57.690 INFO: 32000 alignments done
I0113 00:54:21.173453 140633533384512 af.py:224] 
I0113 00:54:21.173492 140633533384512 af.py:224] - 07:55:00.026 INFO: 34000 alignments done
I0113 00:54:21.173532 140633533384512 af.py:224] 
I0113 00:54:21.173572 140633533384512 af.py:224] - 07:55:02.325 INFO: 36000 alignments done
I0113 00:54:21.173613 140633533384512 af.py:224] 
I0113 00:54:21.173652 140633533384512 af.py:224] - 07:55:04.583 INFO: 38000 alignments done
I0113 00:54:21.173692 140633533384512 af.py:224] 
I0113 00:54:21.173733 140633533384512 af.py:224] - 07:55:06.826 INFO: 40000 alignments done
I0113 00:54:21.173773 140633533384512 af.py:224] 
I0113 00:54:21.173813 140633533384512 af.py:224] - 07:55:09.027 INFO: 42000 alignments done
I0113 00:54:21.173853 140633533384512 af.py:224] 
I0113 00:54:21.173893 140633533384512 af.py:224] - 07:55:11.177 INFO: 44000 alignments done
I0113 00:54:21.173933 140633533384512 af.py:224] 
I0113 00:54:21.173973 140633533384512 af.py:224] - 07:55:13.525 INFO: 46000 alignments done
I0113 00:54:21.174018 140633533384512 af.py:224] 
I0113 00:54:21.174058 140633533384512 af.py:224] - 07:55:15.504 INFO: 48000 alignments done
I0113 00:54:21.174099 140633533384512 af.py:224] 
I0113 00:54:21.174139 140633533384512 af.py:224] - 07:55:17.628 INFO: 50000 alignments done
I0113 00:54:21.174179 140633533384512 af.py:224] 
I0113 00:54:21.174219 140633533384512 af.py:224] - 07:55:19.522 INFO: 52000 alignments done
I0113 00:54:21.174258 140633533384512 af.py:224] 
I0113 00:54:21.174299 140633533384512 af.py:224] - 07:55:21.763 INFO: 54000 alignments done
I0113 00:54:21.174339 140633533384512 af.py:224] 
I0113 00:54:21.174380 140633533384512 af.py:224] - 07:55:25.150 INFO: 56000 alignments done
I0113 00:54:21.174420 140633533384512 af.py:224] 
I0113 00:54:21.174461 140633533384512 af.py:224] - 07:55:29.459 INFO: 58000 alignments done
I0113 00:54:21.174501 140633533384512 af.py:224] 
I0113 00:54:21.174541 140633533384512 af.py:224] - 07:55:32.713 INFO: 60000 alignments done
I0113 00:54:21.174581 140633533384512 af.py:224] 
I0113 00:54:21.174621 140633533384512 af.py:224] - 07:55:35.850 INFO: 62000 alignments done
I0113 00:54:21.174661 140633533384512 af.py:224] 
I0113 00:54:21.174701 140633533384512 af.py:224] - 07:55:37.490 INFO: 63157 alignments done
I0113 00:54:21.174741 140633533384512 af.py:224] 
I0113 00:54:21.174781 140633533384512 af.py:224] - 07:55:37.491 INFO: Alternative alignment: 1
I0113 00:54:21.174820 140633533384512 af.py:224] 
I0113 00:54:21.174860 140633533384512 af.py:224] - 07:56:47.902 INFO: 62359 alignments done
I0113 00:54:21.174901 140633533384512 af.py:224] 
I0113 00:54:21.174941 140633533384512 af.py:224] - 07:56:47.994 INFO: Alternative alignment: 2
I0113 00:54:21.174981 140633533384512 af.py:224] 
I0113 00:54:21.175021 140633533384512 af.py:224] - 07:57:55.303 INFO: 54967 alignments done
I0113 00:54:21.175060 140633533384512 af.py:224] 
I0113 00:54:21.175101 140633533384512 af.py:224] - 07:57:55.419 INFO: Alternative alignment: 3
I0113 00:54:21.175140 140633533384512 af.py:224] 
I0113 00:54:21.175180 140633533384512 af.py:224] - 07:59:00.246 INFO: 50910 alignments done
I0113 00:54:21.175220 140633533384512 af.py:224] 
I0113 00:54:21.175260 140633533384512 af.py:224] - 07:59:03.775 INFO: Premerge done
I0113 00:54:21.175300 140633533384512 af.py:224] 
I0113 00:54:21.175340 140633533384512 af.py:224] - 07:59:03.789 INFO: Realigning 19887 HMM-HMM alignments using Maximum Accuracy algorithm
I0113 00:54:21.175380 140633533384512 af.py:224] 
I0113 00:54:21.175420 140633533384512 af.py:224] - 08:17:09.949 INFO: 19890 sequences belonging to 19890 database HMMs found with an E-value < 0.001
I0113 00:54:21.175460 140633533384512 af.py:224] 
I0113 00:54:21.175501 140633533384512 af.py:224] - 08:17:09.949 INFO: Number of effective sequences of resulting query HMM: Neff = 9.05164
I0113 00:54:21.175540 140633533384512 af.py:224] 
I0113 00:54:21.175580 140633533384512 af.py:224] - 08:17:10.488 INFO: Iteration 2
I0113 00:54:21.175620 140633533384512 af.py:224] 
I0113 00:54:21.175661 140633533384512 af.py:224] - 08:17:10.488 INFO: Set premerge to 0! (premerge: 3 iteration: 2 hits.Size: 19887)
I0113 00:54:21.175700 140633533384512 af.py:224] 
I0113 00:54:21.175741 140633533384512 af.py:224] - 08:17:11.039 INFO: Prefiltering database
I0113 00:54:21.175781 140633533384512 af.py:224] 
I0113 00:54:21.175821 140633533384512 af.py:224] - 08:24:30.340 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 5852176
I0113 00:54:21.175862 140633533384512 af.py:224] 
I0113 00:54:21.175901 140633533384512 af.py:224] - 08:25:09.936 WARNING: Number of hits passing 2nd prefilter (reduced from 261479 to allowed maximum of 100000).
I0113 00:54:21.175942 140633533384512 af.py:224] You can increase the allowed maximum using the -maxfilt <max> option.
I0113 00:54:21.175984 140633533384512 af.py:224] 
I0113 00:54:21.176025 140633533384512 af.py:224] - 08:26:49.170 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 976618
I0113 00:54:21.176065 140633533384512 af.py:224] 
I0113 00:54:21.176105 140633533384512 af.py:224] - 08:26:58.095 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment)   : 146928
I0113 00:54:21.176149 140633533384512 af.py:224] 
I0113 00:54:21.176189 140633533384512 af.py:224] - 08:26:58.095 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 139250
I0113 00:54:21.176229 140633533384512 af.py:224] 
I0113 00:54:21.176269 140633533384512 af.py:224] - 08:26:58.095 INFO: Scoring 139250 HMMs using HMM-HMM Viterbi alignment
I0113 00:54:21.176308 140633533384512 af.py:224] 
I0113 00:54:21.176348 140633533384512 af.py:224] - 08:26:58.216 INFO: Alternative alignment: 0
I0113 00:54:21.176388 140633533384512 af.py:224] 
I0113 00:54:21.176427 140633533384512 af.py:224] - 08:27:00.526 INFO: 2000 alignments done
I0113 00:54:21.176466 140633533384512 af.py:224] 
I0113 00:54:21.176507 140633533384512 af.py:224] - 08:27:02.810 INFO: 4000 alignments done
I0113 00:54:21.176547 140633533384512 af.py:224] 
I0113 00:54:21.176587 140633533384512 af.py:224] - 08:27:04.981 INFO: 6000 alignments done
I0113 00:54:21.176627 140633533384512 af.py:224] 
I0113 00:54:21.176667 140633533384512 af.py:224] - 08:27:07.238 INFO: 8000 alignments done
I0113 00:54:21.176706 140633533384512 af.py:224] 
I0113 00:54:21.176746 140633533384512 af.py:224] - 08:27:09.394 INFO: 10000 alignments done
I0113 00:54:21.176786 140633533384512 af.py:224] 
I0113 00:54:21.176826 140633533384512 af.py:224] - 08:27:11.621 INFO: 12000 alignments done
I0113 00:54:21.176866 140633533384512 af.py:224] 
I0113 00:54:21.176905 140633533384512 af.py:224] - 08:27:13.960 INFO: 14000 alignments done
I0113 00:54:21.176946 140633533384512 af.py:224] 
I0113 00:54:21.176985 140633533384512 af.py:224] - 08:27:16.135 INFO: 16000 alignments done
I0113 00:54:21.177025 140633533384512 af.py:224] 
I0113 00:54:21.177065 140633533384512 af.py:224] - 08:27:18.283 INFO: 18000 alignments done
I0113 00:54:21.177106 140633533384512 af.py:224] 
I0113 00:54:21.177146 140633533384512 af.py:224] - 08:27:20.429 INFO: 20000 alignments done
I0113 00:54:21.177186 140633533384512 af.py:224] 
I0113 00:54:21.177226 140633533384512 af.py:224] - 08:27:22.847 INFO: 22000 alignments done
I0113 00:54:21.177267 140633533384512 af.py:224] 
I0113 00:54:21.177307 140633533384512 af.py:224] - 08:27:24.990 INFO: 24000 alignments done
I0113 00:54:21.177346 140633533384512 af.py:224] 
I0113 00:54:21.177387 140633533384512 af.py:224] - 08:27:27.098 INFO: 26000 alignments done
I0113 00:54:21.177427 140633533384512 af.py:224] 
I0113 00:54:21.177466 140633533384512 af.py:224] - 08:27:29.186 INFO: 28000 alignments done
I0113 00:54:21.177505 140633533384512 af.py:224] 
I0113 00:54:21.177546 140633533384512 af.py:224] - 08:27:31.198 INFO: 30000 alignments done
I0113 00:54:21.177585 140633533384512 af.py:224] 
I0113 00:54:21.177626 140633533384512 af.py:224] - 08:27:33.352 INFO: 32000 alignments done
I0113 00:54:21.177666 140633533384512 af.py:224] 
I0113 00:54:21.177706 140633533384512 af.py:224] - 08:27:35.386 INFO: 34000 alignments done
I0113 00:54:21.177747 140633533384512 af.py:224] 
I0113 00:54:21.177786 140633533384512 af.py:224] - 08:27:37.153 INFO: 36000 alignments done
I0113 00:54:21.177826 140633533384512 af.py:224] 
I0113 00:54:21.177866 140633533384512 af.py:224] - 08:27:39.041 INFO: 38000 alignments done
I0113 00:54:21.177906 140633533384512 af.py:224] 
I0113 00:54:21.177946 140633533384512 af.py:224] - 08:27:40.963 INFO: 40000 alignments done
I0113 00:54:21.177986 140633533384512 af.py:224] 
I0113 00:54:21.178026 140633533384512 af.py:224] - 08:27:42.885 INFO: 42000 alignments done
I0113 00:54:21.178066 140633533384512 af.py:224] 
I0113 00:54:21.178106 140633533384512 af.py:224] - 08:27:44.792 INFO: 44000 alignments done
I0113 00:54:21.178146 140633533384512 af.py:224] 
I0113 00:54:21.178186 140633533384512 af.py:224] - 08:27:46.810 INFO: 46000 alignments done
I0113 00:54:21.178226 140633533384512 af.py:224] 
I0113 00:54:21.178266 140633533384512 af.py:224] - 08:27:48.706 INFO: 48000 alignments done
I0113 00:54:21.178306 140633533384512 af.py:224] 
I0113 00:54:21.178345 140633533384512 af.py:224] - 08:27:50.722 INFO: 50000 alignments done
I0113 00:54:21.178389 140633533384512 af.py:224] 
I0113 00:54:21.178429 140633533384512 af.py:224] - 08:27:52.696 INFO: 52000 alignments done
I0113 00:54:21.178469 140633533384512 af.py:224] 
I0113 00:54:21.178508 140633533384512 af.py:224] - 08:27:54.754 INFO: 54000 alignments done
I0113 00:54:21.178548 140633533384512 af.py:224] 
I0113 00:54:21.178588 140633533384512 af.py:224] - 08:27:56.716 INFO: 56000 alignments done
I0113 00:54:21.178628 140633533384512 af.py:224] 
I0113 00:54:21.178668 140633533384512 af.py:224] - 08:27:58.716 INFO: 58000 alignments done
I0113 00:54:21.178708 140633533384512 af.py:224] 
I0113 00:54:21.178749 140633533384512 af.py:224] - 08:28:00.726 INFO: 60000 alignments done
I0113 00:54:21.178789 140633533384512 af.py:224] 
I0113 00:54:21.178829 140633533384512 af.py:224] - 08:28:02.782 INFO: 62000 alignments done
I0113 00:54:21.178869 140633533384512 af.py:224] 
I0113 00:54:21.178910 140633533384512 af.py:224] - 08:28:04.799 INFO: 64000 alignments done
I0113 00:54:21.178950 140633533384512 af.py:224] 
I0113 00:54:21.178990 140633533384512 af.py:224] - 08:28:06.715 INFO: 66000 alignments done
I0113 00:54:21.179031 140633533384512 af.py:224] 
I0113 00:54:21.179098 140633533384512 af.py:224] - 08:28:08.554 INFO: 68000 alignments done
I0113 00:54:21.179174 140633533384512 af.py:224] 
I0113 00:54:21.179215 140633533384512 af.py:224] - 08:28:10.501 INFO: 70000 alignments done
I0113 00:54:21.179255 140633533384512 af.py:224] 
I0113 00:54:21.179295 140633533384512 af.py:224] - 08:28:12.306 INFO: 72000 alignments done
I0113 00:54:21.179335 140633533384512 af.py:224] 
I0113 00:54:21.179375 140633533384512 af.py:224] - 08:28:14.311 INFO: 74000 alignments done
I0113 00:54:21.179415 140633533384512 af.py:224] 
I0113 00:54:21.179455 140633533384512 af.py:224] - 08:28:16.209 INFO: 76000 alignments done
I0113 00:54:21.179495 140633533384512 af.py:224] 
I0113 00:54:21.179536 140633533384512 af.py:224] - 08:28:18.050 INFO: 78000 alignments done
I0113 00:54:21.179578 140633533384512 af.py:224] 
I0113 00:54:21.179618 140633533384512 af.py:224] - 08:28:20.027 INFO: 80000 alignments done
I0113 00:54:21.179658 140633533384512 af.py:224] 
I0113 00:54:21.179699 140633533384512 af.py:224] - 08:28:21.873 INFO: 82000 alignments done
I0113 00:54:21.179739 140633533384512 af.py:224] 
I0113 00:54:21.179778 140633533384512 af.py:224] - 08:28:23.764 INFO: 84000 alignments done
I0113 00:54:21.179818 140633533384512 af.py:224] 
I0113 00:54:21.179859 140633533384512 af.py:224] - 08:28:25.654 INFO: 86000 alignments done
I0113 00:54:21.179899 140633533384512 af.py:224] 
I0113 00:54:21.179939 140633533384512 af.py:224] - 08:28:28.987 INFO: 88000 alignments done
I0113 00:54:21.179979 140633533384512 af.py:224] 
I0113 00:54:21.180023 140633533384512 af.py:224] - 08:28:32.323 INFO: 90000 alignments done
I0113 00:54:21.180063 140633533384512 af.py:224] 
I0113 00:54:21.180103 140633533384512 af.py:224] - 08:28:34.536 INFO: 92000 alignments done
I0113 00:54:21.180144 140633533384512 af.py:224] 
I0113 00:54:21.180184 140633533384512 af.py:224] - 08:28:36.898 INFO: 94000 alignments done
I0113 00:54:21.180224 140633533384512 af.py:224] 
I0113 00:54:21.180264 140633533384512 af.py:224] - 08:28:39.775 INFO: 96000 alignments done
I0113 00:54:21.180303 140633533384512 af.py:224] 
I0113 00:54:21.180343 140633533384512 af.py:224] - 08:28:42.509 INFO: 98000 alignments done
I0113 00:54:21.180383 140633533384512 af.py:224] 
I0113 00:54:21.180423 140633533384512 af.py:224] - 08:28:45.280 INFO: 100000 alignments done
I0113 00:54:21.180463 140633533384512 af.py:224] 
I0113 00:54:21.180504 140633533384512 af.py:224] - 08:28:47.967 INFO: 102000 alignments done
I0113 00:54:21.180544 140633533384512 af.py:224] 
I0113 00:54:21.180584 140633533384512 af.py:224] - 08:28:50.860 INFO: 104000 alignments done
I0113 00:54:21.180623 140633533384512 af.py:224] 
I0113 00:54:21.180663 140633533384512 af.py:224] - 08:28:53.597 INFO: 106000 alignments done
I0113 00:54:21.180703 140633533384512 af.py:224] 
I0113 00:54:21.180752 140633533384512 af.py:224] - 08:28:56.413 INFO: 108000 alignments done
I0113 00:54:21.180793 140633533384512 af.py:224] 
I0113 00:54:21.180833 140633533384512 af.py:224] - 08:28:59.309 INFO: 110000 alignments done
I0113 00:54:21.180872 140633533384512 af.py:224] 
I0113 00:54:21.180913 140633533384512 af.py:224] - 08:29:02.132 INFO: 112000 alignments done
I0113 00:54:21.180953 140633533384512 af.py:224] 
I0113 00:54:21.180994 140633533384512 af.py:224] - 08:29:04.580 INFO: 114000 alignments done
I0113 00:54:21.181034 140633533384512 af.py:224] 
I0113 00:54:21.181074 140633533384512 af.py:224] - 08:29:06.996 INFO: 116000 alignments done
I0113 00:54:21.181115 140633533384512 af.py:224] 
I0113 00:54:21.181155 140633533384512 af.py:224] - 08:29:09.950 INFO: 118000 alignments done
I0113 00:54:21.181195 140633533384512 af.py:224] 
I0113 00:54:21.181236 140633533384512 af.py:224] - 08:29:12.541 INFO: 120000 alignments done
I0113 00:54:21.181277 140633533384512 af.py:224] 
I0113 00:54:21.181317 140633533384512 af.py:224] - 08:29:14.780 INFO: 122000 alignments done
I0113 00:54:21.181357 140633533384512 af.py:224] 
I0113 00:54:21.181397 140633533384512 af.py:224] - 08:29:17.316 INFO: 124000 alignments done
I0113 00:54:21.181437 140633533384512 af.py:224] 
I0113 00:54:21.181477 140633533384512 af.py:224] - 08:29:19.861 INFO: 126000 alignments done
I0113 00:54:21.181517 140633533384512 af.py:224] 
I0113 00:54:21.181557 140633533384512 af.py:224] - 08:29:19.863 INFO: Stop after DB-HHM: 126000 because early stop  18.0788 < filter cutoff 20
I0113 00:54:21.181597 140633533384512 af.py:224] 
I0113 00:54:21.181637 140633533384512 af.py:224] - 08:29:19.866 INFO: Alternative alignment: 1
I0113 00:54:21.181678 140633533384512 af.py:224] 
I0113 00:54:21.181718 140633533384512 af.py:224] - 08:31:12.480 INFO: 120453 alignments done
I0113 00:54:21.181757 140633533384512 af.py:224] 
I0113 00:54:21.181797 140633533384512 af.py:224] - 08:31:12.616 INFO: Alternative alignment: 2
I0113 00:54:21.181837 140633533384512 af.py:224] 
I0113 00:54:21.181878 140633533384512 af.py:224] - 08:32:53.814 INFO: 97154 alignments done
I0113 00:54:21.181917 140633533384512 af.py:224] 
I0113 00:54:21.181957 140633533384512 af.py:224] - 08:32:54.033 INFO: Alternative alignment: 3
I0113 00:54:21.181998 140633533384512 af.py:224] 
I0113 00:54:21.182038 140633533384512 af.py:224] - 08:34:34.185 INFO: 93115 alignments done
I0113 00:54:21.182077 140633533384512 af.py:224] 
I0113 00:54:21.182117 140633533384512 af.py:224] - 08:34:36.393 INFO: Realigning 100008 HMM-HMM alignments using Maximum Accuracy algorithm
I0113 00:54:21.182164 140633533384512 af.py:224] 
I0113 00:54:21.182206 140633533384512 af.py:224] 
I0113 00:54:21.182246 140633533384512 af.py:224]