Ticket #6105: 7m1p_wynton.log

File 7m1p_wynton.log, 21.7 KB (added by Tom Goddard, 4 years ago)

AlphaFold log with sequence alignment failure

Line 
1mkdir: cannot create directory '/tmp/lock-gpu1': File exists
2/sbin/ldconfig.real: Can't create temporary cache file /etc/ld.so.cache~: Read-only file system
3I0115 01:07:18.061003 47353884217536 templates.py:857] Using precomputed obsolete pdbs /wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_mmcif/obsolete.dat.
4I0115 01:07:18.933793 47353884217536 xla_bridge.py:231] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker:
5I0115 01:07:19.081084 47353884217536 xla_bridge.py:231] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available.
6I0115 01:07:26.657055 47353884217536 run_alphafold.py:385] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5']
7I0115 01:07:26.657800 47353884217536 run_alphafold.py:397] Using random seed 346610710325312215 for the data pipeline
8I0115 01:07:26.658504 47353884217536 run_alphafold.py:150] Predicting seq_7m1p
9I0115 01:07:26.665186 47353884217536 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /scratch/518064.1.gpu.q/tmpbcxbe7ax/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 seq_7m1p.fasta /wynton/group/databases/alphafold_CASP14_v2.1.1/uniref90/uniref90.fasta"
10I0115 01:07:26.811553 47353884217536 utils.py:36] Started Jackhmmer (uniref90.fasta) query
11I0115 01:45:44.363026 47353884217536 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 2297.551 seconds
12I0115 01:48:04.852845 47353884217536 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /scratch/518064.1.gpu.q/tmppvmkyxfc/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 seq_7m1p.fasta /wynton/group/databases/alphafold_CASP14_v2.1.1/mgnify/mgy_clusters_2018_12.fa"
13I0115 01:48:05.637711 47353884217536 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
14I0115 02:35:01.477145 47353884217536 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 2815.839 seconds
15I0115 02:42:27.145391 47353884217536 hhsearch.py:85] Launching subprocess "/usr/bin/hhsearch -i /scratch/518064.1.gpu.q/tmpamnodot7/query.a3m -o /scratch/518064.1.gpu.q/tmpamnodot7/output.hhr -maxseq 1000000 -d /wynton/group/databases/alphafold_CASP14_v2.1.1/pdb70/pdb70"
16I0115 02:42:28.451507 47353884217536 utils.py:36] Started HHsearch query
17I0115 02:45:23.178210 47353884217536 utils.py:40] Finished HHsearch query in 174.726 seconds
18I0115 03:41:12.708372 47353884217536 hhblits.py:128] Launching subprocess "/usr/bin/hhblits -i seq_7m1p.fasta -cpu 4 -oa3m /scratch/518064.1.gpu.q/tmp_vlzcise/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /wynton/group/databases/alphafold_CASP14_v2.1.1/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /wynton/group/databases/alphafold_CASP14_v2.1.1/uniclust30/uniclust30_2018_08/uniclust30_2018_08"
19I0115 03:41:14.390513 47353884217536 utils.py:36] Started HHblits query
20I0115 04:51:06.449815 47353884217536 utils.py:40] Finished HHblits query in 4192.059 seconds
21E0115 04:51:06.467852 47353884217536 hhblits.py:138] HHblits failed. HHblits stderr begin:
22E0115 04:51:06.468421 47353884217536 hhblits.py:141] - 03:42:45.354 INFO: Searching 65983866 column state sequences.
23E0115 04:51:06.468819 47353884217536 hhblits.py:141] - 03:42:45.987 INFO: Searching 15161831 column state sequences.
24E0115 04:51:06.469182 47353884217536 hhblits.py:141] - 03:42:46.064 INFO: seq_7m1p.fasta is in A2M, A3M or FASTA format
25E0115 04:51:06.469511 47353884217536 hhblits.py:141] - 03:42:46.065 INFO: Iteration 1
26E0115 04:51:06.469897 47353884217536 hhblits.py:141] - 03:42:46.808 INFO: Prefiltering database
27E0115 04:51:06.470251 47353884217536 hhblits.py:141] - 04:05:18.207 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 5035442
28E0115 04:51:06.470614 47353884217536 hhblits.py:141] - 04:05:57.154 WARNING: Number of hits passing 2nd prefilter (reduced from 236543 to allowed maximum of 100000).
29E0115 04:51:06.470940 47353884217536 hhblits.py:141] You can increase the allowed maximum using the -maxfilt <max> option.
30E0115 04:51:06.471340 47353884217536 hhblits.py:141] - 04:10:44.198 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 860407
31E0115 04:51:06.471716 47353884217536 hhblits.py:141] - 04:10:53.348 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 162981
32E0115 04:51:06.472154 47353884217536 hhblits.py:141] - 04:10:53.348 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 162981
33E0115 04:51:06.472554 47353884217536 hhblits.py:141] - 04:10:53.348 INFO: Scoring 162981 HMMs using HMM-HMM Viterbi alignment
34E0115 04:51:06.472904 47353884217536 hhblits.py:141] - 04:10:53.485 INFO: Alternative alignment: 0
35E0115 04:51:06.473242 47353884217536 hhblits.py:141] - 04:11:04.095 INFO: 2000 alignments done
36E0115 04:51:06.473594 47353884217536 hhblits.py:141] - 04:11:14.589 INFO: 4000 alignments done
37E0115 04:51:06.473946 47353884217536 hhblits.py:141] - 04:11:23.662 INFO: 6000 alignments done
38E0115 04:51:06.474278 47353884217536 hhblits.py:141] - 04:11:33.379 INFO: 8000 alignments done
39E0115 04:51:06.474568 47353884217536 hhblits.py:141] - 04:11:43.330 INFO: 10000 alignments done
40E0115 04:51:06.474884 47353884217536 hhblits.py:141] - 04:11:54.851 INFO: 12000 alignments done
41E0115 04:51:06.475270 47353884217536 hhblits.py:141] - 04:12:04.765 INFO: 14000 alignments done
42E0115 04:51:06.475602 47353884217536 hhblits.py:141] - 04:12:14.374 INFO: 16000 alignments done
43E0115 04:51:06.475970 47353884217536 hhblits.py:141] - 04:12:23.697 INFO: 18000 alignments done
44E0115 04:51:06.476334 47353884217536 hhblits.py:141] - 04:12:33.272 INFO: 20000 alignments done
45E0115 04:51:06.476711 47353884217536 hhblits.py:141] - 04:12:42.972 INFO: 22000 alignments done
46E0115 04:51:06.477035 47353884217536 hhblits.py:141] - 04:12:53.043 INFO: 24000 alignments done
47E0115 04:51:06.477371 47353884217536 hhblits.py:141] - 04:13:02.917 INFO: 26000 alignments done
48E0115 04:51:06.477760 47353884217536 hhblits.py:141] - 04:13:12.316 INFO: 28000 alignments done
49E0115 04:51:06.478098 47353884217536 hhblits.py:141] - 04:13:22.139 INFO: 30000 alignments done
50E0115 04:51:06.478441 47353884217536 hhblits.py:141] - 04:13:32.176 INFO: 32000 alignments done
51E0115 04:51:06.478789 47353884217536 hhblits.py:141] - 04:13:42.948 INFO: 34000 alignments done
52E0115 04:51:06.479081 47353884217536 hhblits.py:141] - 04:13:53.368 INFO: 36000 alignments done
53E0115 04:51:06.479404 47353884217536 hhblits.py:141] - 04:14:03.074 INFO: 38000 alignments done
54E0115 04:51:06.479757 47353884217536 hhblits.py:141] - 04:14:13.288 INFO: 40000 alignments done
55E0115 04:51:06.480093 47353884217536 hhblits.py:141] - 04:14:25.179 INFO: 42000 alignments done
56E0115 04:51:06.480478 47353884217536 hhblits.py:141] - 04:14:35.547 INFO: 44000 alignments done
57E0115 04:51:06.480877 47353884217536 hhblits.py:141] - 04:14:46.119 INFO: 46000 alignments done
58E0115 04:51:06.481276 47353884217536 hhblits.py:141] - 04:14:56.649 INFO: 48000 alignments done
59E0115 04:51:06.481677 47353884217536 hhblits.py:141] - 04:15:07.097 INFO: 50000 alignments done
60E0115 04:51:06.482140 47353884217536 hhblits.py:141] - 04:15:17.084 INFO: 52000 alignments done
61E0115 04:51:06.482582 47353884217536 hhblits.py:141] - 04:15:26.732 INFO: 54000 alignments done
62E0115 04:51:06.483014 47353884217536 hhblits.py:141] - 04:15:36.062 INFO: 56000 alignments done
63E0115 04:51:06.483347 47353884217536 hhblits.py:141] - 04:15:45.789 INFO: 58000 alignments done
64E0115 04:51:06.483776 47353884217536 hhblits.py:141] - 04:15:55.489 INFO: 60000 alignments done
65E0115 04:51:06.484205 47353884217536 hhblits.py:141] - 04:16:09.424 INFO: 62000 alignments done
66E0115 04:51:06.484536 47353884217536 hhblits.py:141] - 04:16:25.977 INFO: 64000 alignments done
67E0115 04:51:06.484962 47353884217536 hhblits.py:141] - 04:16:42.054 INFO: 66000 alignments done
68E0115 04:51:06.485280 47353884217536 hhblits.py:141] - 04:16:55.757 INFO: 68000 alignments done
69E0115 04:51:06.485720 47353884217536 hhblits.py:141] - 04:17:07.988 INFO: 70000 alignments done
70E0115 04:51:06.486065 47353884217536 hhblits.py:141] - 04:17:19.378 INFO: 72000 alignments done
71E0115 04:51:06.486390 47353884217536 hhblits.py:141] - 04:17:31.320 INFO: 74000 alignments done
72E0115 04:51:06.486781 47353884217536 hhblits.py:141] - 04:17:42.428 INFO: 76000 alignments done
73E0115 04:51:06.487091 47353884217536 hhblits.py:141] - 04:17:54.177 INFO: 78000 alignments done
74E0115 04:51:06.487500 47353884217536 hhblits.py:141] - 04:18:06.698 INFO: 80000 alignments done
75E0115 04:51:06.487841 47353884217536 hhblits.py:141] - 04:18:22.296 INFO: 82000 alignments done
76E0115 04:51:06.488200 47353884217536 hhblits.py:141] - 04:18:37.983 INFO: 84000 alignments done
77E0115 04:51:06.488520 47353884217536 hhblits.py:141] - 04:18:50.290 INFO: 86000 alignments done
78E0115 04:51:06.488862 47353884217536 hhblits.py:141] - 04:19:01.109 INFO: 88000 alignments done
79E0115 04:51:06.489234 47353884217536 hhblits.py:141] - 04:19:11.623 INFO: 90000 alignments done
80E0115 04:51:06.489561 47353884217536 hhblits.py:141] - 04:19:22.533 INFO: 92000 alignments done
81E0115 04:51:06.489879 47353884217536 hhblits.py:141] - 04:19:33.271 INFO: 94000 alignments done
82E0115 04:51:06.490222 47353884217536 hhblits.py:141] - 04:19:43.786 INFO: 96000 alignments done
83E0115 04:51:06.490561 47353884217536 hhblits.py:141] - 04:19:54.736 INFO: 98000 alignments done
84E0115 04:51:06.490920 47353884217536 hhblits.py:141] - 04:20:04.706 INFO: 100000 alignments done
85E0115 04:51:06.491394 47353884217536 hhblits.py:141] - 04:20:13.425 INFO: 102000 alignments done
86E0115 04:51:06.491738 47353884217536 hhblits.py:141] - 04:20:21.517 INFO: 104000 alignments done
87E0115 04:51:06.492124 47353884217536 hhblits.py:141] - 04:20:29.802 INFO: 106000 alignments done
88E0115 04:51:06.492489 47353884217536 hhblits.py:141] - 04:20:38.238 INFO: 108000 alignments done
89E0115 04:51:06.492836 47353884217536 hhblits.py:141] - 04:20:46.637 INFO: 110000 alignments done
90E0115 04:51:06.493178 47353884217536 hhblits.py:141] - 04:20:55.013 INFO: 112000 alignments done
91E0115 04:51:06.493501 47353884217536 hhblits.py:141] - 04:21:03.504 INFO: 114000 alignments done
92E0115 04:51:06.493851 47353884217536 hhblits.py:141] - 04:21:12.254 INFO: 116000 alignments done
93E0115 04:51:06.494201 47353884217536 hhblits.py:141] - 04:21:20.595 INFO: 118000 alignments done
94E0115 04:51:06.494522 47353884217536 hhblits.py:141] - 04:21:29.638 INFO: 120000 alignments done
95E0115 04:51:06.494868 47353884217536 hhblits.py:141] - 04:21:37.943 INFO: 122000 alignments done
96E0115 04:51:06.495212 47353884217536 hhblits.py:141] - 04:21:46.835 INFO: 124000 alignments done
97E0115 04:51:06.495555 47353884217536 hhblits.py:141] - 04:21:54.710 INFO: 126000 alignments done
98E0115 04:51:06.495910 47353884217536 hhblits.py:141] - 04:22:03.177 INFO: 128000 alignments done
99E0115 04:51:06.496214 47353884217536 hhblits.py:141] - 04:22:11.309 INFO: 130000 alignments done
100E0115 04:51:06.496512 47353884217536 hhblits.py:141] - 04:22:19.856 INFO: 132000 alignments done
101E0115 04:51:06.496835 47353884217536 hhblits.py:141] - 04:22:29.624 INFO: 134000 alignments done
102E0115 04:51:06.497166 47353884217536 hhblits.py:141] - 04:22:39.789 INFO: 136000 alignments done
103E0115 04:51:06.497474 47353884217536 hhblits.py:141] - 04:22:48.545 INFO: 138000 alignments done
104E0115 04:51:06.497776 47353884217536 hhblits.py:141] - 04:22:55.806 INFO: 140000 alignments done
105E0115 04:51:06.498127 47353884217536 hhblits.py:141] - 04:23:03.013 INFO: 142000 alignments done
106E0115 04:51:06.498444 47353884217536 hhblits.py:141] - 04:23:10.106 INFO: 144000 alignments done
107E0115 04:51:06.498780 47353884217536 hhblits.py:141] - 04:23:18.559 INFO: 146000 alignments done
108E0115 04:51:06.499123 47353884217536 hhblits.py:141] - 04:23:26.489 INFO: 148000 alignments done
109E0115 04:51:06.499448 47353884217536 hhblits.py:141] - 04:23:33.882 INFO: 150000 alignments done
110E0115 04:51:06.499833 47353884217536 hhblits.py:141] - 04:23:41.137 INFO: 152000 alignments done
111E0115 04:51:06.500292 47353884217536 hhblits.py:141] - 04:23:48.837 INFO: 154000 alignments done
112E0115 04:51:06.500634 47353884217536 hhblits.py:141] - 04:23:56.690 INFO: 156000 alignments done
113E0115 04:51:06.500982 47353884217536 hhblits.py:141] - 04:23:56.697 INFO: Stop after DB-HHM: 156000 because early stop 19.1439 < filter cutoff 20
114E0115 04:51:06.501358 47353884217536 hhblits.py:141] - 04:23:56.697 INFO: Alternative alignment: 1
115E0115 04:51:06.501697 47353884217536 hhblits.py:141] - 04:25:42.790 INFO: 154498 alignments done
116E0115 04:51:06.502066 47353884217536 hhblits.py:141] - 04:25:43.184 INFO: Alternative alignment: 2
117E0115 04:51:06.502401 47353884217536 hhblits.py:141] - 04:27:30.977 INFO: 152236 alignments done
118E0115 04:51:06.502739 47353884217536 hhblits.py:141] - 04:27:31.114 INFO: Alternative alignment: 3
119E0115 04:51:06.503082 47353884217536 hhblits.py:141] - 04:28:22.650 INFO: 45837 alignments done
120E0115 04:51:06.503445 47353884217536 hhblits.py:141] - 04:28:28.176 INFO: Premerge done
121E0115 04:51:06.503825 47353884217536 hhblits.py:141] - 04:28:28.178 INFO: Realigning 100001 HMM-HMM alignments using Maximum Accuracy algorithm
122E0115 04:51:06.504233 47353884217536 hhblits.py:141] - 04:51:01.543 ERROR: Error in /tmp/hh-suite/src/hhalignment.cpp:3539: MergeMasterSlave:
123E0115 04:51:06.504605 47353884217536 hhblits.py:141] - 04:51:01.543 ERROR: did not find 569 match states in sequence 1 of tr|A0A1H9CGJ3|A0A1H9CGJ3_9FIRM. Sequence:
124E0115 04:51:06.505017 47353884217536 hhblits.py:141] MVKVNGIRKTFGANEVLKGVSFEIEEGTIYGLIGRNGAGKTTLMNIMSGLLKADSGTFDMGTGKGSGKTQVGYLPDLPNFYDYLTTDEYLDFLLMESNPVRRDALLETVGLGKGLRIKTMSRGMKQRLGIAAVLVNDPKIILLDEPTSALDPAGRADVRSILMKLKSEGKTIILSTHILADMDSICDKAGFLAKGVIAREVNIAESRESASIMTISFASEPDLPTLHKYAPEIYIMDKCTIKIVLDKSDIITSQQKALQGLSQLPQEITSISSAALSLDNIFQEVCL
125E0115 04:51:06.505381 47353884217536 hhblits.py:142] HHblits stderr end
126Traceback (most recent call last):
127 File "/app/alphafold/run_alphafold.py", line 427, in <module>
128 app.run(main)
129 File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
130 _run_main(main, args)
131 File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
132 sys.exit(main(argv))
133 File "/app/alphafold/run_alphafold.py", line 412, in main
134 is_prokaryote=is_prokaryote)
135 File "/app/alphafold/run_alphafold.py", line 164, in predict_structure
136 msa_output_dir=msa_output_dir)
137 File "/app/alphafold/alphafold/data/pipeline.py", line 207, in process
138 'a3m', self.use_precomputed_msas)
139 File "/app/alphafold/alphafold/data/pipeline.py", line 97, in run_msa_tool
140 result = msa_runner.query(input_fasta_path)[0]
141 File "/app/alphafold/alphafold/data/tools/hhblits.py", line 144, in query
142 stdout.decode('utf-8'), stderr[:500_000].decode('utf-8')))
143RuntimeError: HHblits failed
144stdout:
145
146
147stderr:
148- 03:42:45.354 INFO: Searching 65983866 column state sequences.
149
150- 03:42:45.987 INFO: Searching 15161831 column state sequences.
151
152- 03:42:46.064 INFO: seq_7m1p.fasta is in A2M, A3M or FASTA format
153
154- 03:42:46.065 INFO: Iteration 1
155
156- 03:42:46.808 INFO: Prefiltering database
157
158- 04:05:18.207 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 5035442
159
160- 04:05:57.154 WARNING: Number of hits passing 2nd prefilter (reduced from 236543 to allowed maximum of 100000).
161You can increase the allowed maximum using the -maxfilt <max> option.
162
163- 04:10:44.198 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 860407
164
165- 04:10:53.348 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 162981
166
167- 04:10:53.348 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 162981
168
169- 04:10:53.348 INFO: Scoring 162981 HMMs using HMM-HMM Viterbi alignment
170
171- 04:10:53.485 INFO: Alternative alignment: 0
172
173- 04:11:04.095 INFO: 2000 alignments done
174
175- 04:11:14.589 INFO: 4000 alignments done
176
177- 04:11:23.662 INFO: 6000 alignments done
178
179- 04:11:33.379 INFO: 8000 alignments done
180
181- 04:11:43.330 INFO: 10000 alignments done
182
183- 04:11:54.851 INFO: 12000 alignments done
184
185- 04:12:04.765 INFO: 14000 alignments done
186
187- 04:12:14.374 INFO: 16000 alignments done
188
189- 04:12:23.697 INFO: 18000 alignments done
190
191- 04:12:33.272 INFO: 20000 alignments done
192
193- 04:12:42.972 INFO: 22000 alignments done
194
195- 04:12:53.043 INFO: 24000 alignments done
196
197- 04:13:02.917 INFO: 26000 alignments done
198
199- 04:13:12.316 INFO: 28000 alignments done
200
201- 04:13:22.139 INFO: 30000 alignments done
202
203- 04:13:32.176 INFO: 32000 alignments done
204
205- 04:13:42.948 INFO: 34000 alignments done
206
207- 04:13:53.368 INFO: 36000 alignments done
208
209- 04:14:03.074 INFO: 38000 alignments done
210
211- 04:14:13.288 INFO: 40000 alignments done
212
213- 04:14:25.179 INFO: 42000 alignments done
214
215- 04:14:35.547 INFO: 44000 alignments done
216
217- 04:14:46.119 INFO: 46000 alignments done
218
219- 04:14:56.649 INFO: 48000 alignments done
220
221- 04:15:07.097 INFO: 50000 alignments done
222
223- 04:15:17.084 INFO: 52000 alignments done
224
225- 04:15:26.732 INFO: 54000 alignments done
226
227- 04:15:36.062 INFO: 56000 alignments done
228
229- 04:15:45.789 INFO: 58000 alignments done
230
231- 04:15:55.489 INFO: 60000 alignments done
232
233- 04:16:09.424 INFO: 62000 alignments done
234
235- 04:16:25.977 INFO: 64000 alignments done
236
237- 04:16:42.054 INFO: 66000 alignments done
238
239- 04:16:55.757 INFO: 68000 alignments done
240
241- 04:17:07.988 INFO: 70000 alignments done
242
243- 04:17:19.378 INFO: 72000 alignments done
244
245- 04:17:31.320 INFO: 74000 alignments done
246
247- 04:17:42.428 INFO: 76000 alignments done
248
249- 04:17:54.177 INFO: 78000 alignments done
250
251- 04:18:06.698 INFO: 80000 alignments done
252
253- 04:18:22.296 INFO: 82000 alignments done
254
255- 04:18:37.983 INFO: 84000 alignments done
256
257- 04:18:50.290 INFO: 86000 alignments done
258
259- 04:19:01.109 INFO: 88000 alignments done
260
261- 04:19:11.623 INFO: 90000 alignments done
262
263- 04:19:22.533 INFO: 92000 alignments done
264
265- 04:19:33.271 INFO: 94000 alignments done
266
267- 04:19:43.786 INFO: 96000 alignments done
268
269- 04:19:54.736 INFO: 98000 alignments done
270
271- 04:20:04.706 INFO: 100000 alignments done
272
273- 04:20:13.425 INFO: 102000 alignments done
274
275- 04:20:21.517 INFO: 104000 alignments done
276
277- 04:20:29.802 INFO: 106000 alignments done
278
279- 04:20:38.238 INFO: 108000 alignments done
280
281- 04:20:46.637 INFO: 110000 alignments done
282
283- 04:20:55.013 INFO: 112000 alignments done
284
285- 04:21:03.504 INFO: 114000 alignments done
286
287- 04:21:12.254 INFO: 116000 alignments done
288
289- 04:21:20.595 INFO: 118000 alignments done
290
291- 04:21:29.638 INFO: 120000 alignments done
292
293- 04:21:37.943 INFO: 122000 alignments done
294
295- 04:21:46.835 INFO: 124000 alignments done
296
297- 04:21:54.710 INFO: 126000 alignments done
298
299- 04:22:03.177 INFO: 128000 alignments done
300
301- 04:22:11.309 INFO: 130000 alignments done
302
303- 04:22:19.856 INFO: 132000 alignments done
304
305- 04:22:29.624 INFO: 134000 alignments done
306
307- 04:22:39.789 INFO: 136000 alignments done
308
309- 04:22:48.545 INFO: 138000 alignments done
310
311- 04:22:55.806 INFO: 140000 alignments done
312
313- 04:23:03.013 INFO: 142000 alignments done
314
315- 04:23:10.106 INFO: 144000 alignments done
316
317- 04:23:18.559 INFO: 146000 alignments done
318
319- 04:23:26.489 INFO: 148000 alignments done
320
321- 04:23:33.882 INFO: 150000 alignments done
322
323- 04:23:41.137 INFO: 152000 alignments done
324
325- 04:23:48.837 INFO: 154000 alignments done
326
327- 04:23:56.690 INFO: 156000 alignments done
328
329- 04:23:56.697 INFO: Stop after DB-HHM: 156000 because early stop 19.1439 < filter cutoff 20
330
331- 04:23:56.697 INFO: Alternative alignment: 1
332
333- 04:25:42.790 INFO: 154498 alignments done
334
335- 04:25:43.184 INFO: Alternative alignment: 2
336
337- 04:27:30.977 INFO: 152236 alignments done
338
339- 04:27:31.114 INFO: Alternative alignment: 3
340
341- 04:28:22.650 INFO: 45837 alignments done
342
343- 04:28:28.176 INFO: Premerge done
344
345- 04:28:28.178 INFO: Realigning 100001 HMM-HMM alignments using Maximum Accuracy algorithm
346
347- 04:51:01.543 ERROR: Error in /tmp/hh-suite/src/hhalignment.cpp:3539: MergeMasterSlave:
348
349- 04:51:01.543 ERROR: did not find 569 match states in sequence 1 of tr|A0A1H9CGJ3|A0A1H9CGJ3_9FIRM. Sequence:
350 MVKVNGIRKTFGANEVLKGVSFEIEEGTIYGLIGRNGAGKTTLMNIMSGLLKADSGTFDMGTGKGSGKTQVGYLPDLPNFYDYLTTDEYLDFLLMESNPVRRDALLETVGLGKGLRIKTMSRGMKQRLGIAAVLVNDPKIILLDEPTSALDPAGRADVRSILMKLKSEGKTIILSTHILADMDSICDKAGFLAKGVIAREVNIAESRESASIMTISFASEPDLPTLHKYAPEIYIMDKCTIKIVLDKSDIITSQQKALQGLSQLPQEITSISSAALSLDNIFQEVCL
351
352
353
354Traceback (most recent call last):
355 File "/var/spool/sge/wynton/qb3-atgpu3/job_scripts/518064", line 230, in <module>
356 main()
357 File "/var/spool/sge/wynton/qb3-atgpu3/job_scripts/518064", line 227, in main
358 check = True)
359 File "/usr/lib64/python3.6/subprocess.py", line 438, in run
360 output=stdout, stderr=stderr)
361subprocess.CalledProcessError: Command 'module load cuda/11.0 ; singularity run --nv -B "/wynton/group/databases/alphafold_CASP14_v2.1.1" -B "/wynton/group/databases/alphafold_CASP14" -B "/wynton/home/ferrin/goddard/alphafold_singularity" -B "/scratch/518064.1.gpu.q" --env CUDA_VISIBLE_DEVICES=3,NVIDIA_VISIBLE_DEVICES=3,TF_FORCE_UNIFIED_MEMORY=1,XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 /wynton/home/ferrin/goddard/alphafold_singularity/alphafold21.sif --fasta_paths=seq_7m1p.fasta --uniref90_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniref90/uniref90.fasta --mgnify_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/mgnify/mgy_clusters_2018_12.fa --data_dir=/wynton/group/databases/alphafold_CASP14_v2.1.1 --template_mmcif_dir=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_mmcif/mmcif_files --obsolete_pdbs_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb_mmcif/obsolete.dat --pdb70_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/pdb70/pdb70 --uniclust30_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/uniclust30/uniclust30_2018_08/uniclust30_2018_08 --bfd_database_path=/wynton/group/databases/alphafold_CASP14_v2.1.1/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --output_dir=output --max_template_date=2100-01-01 --db_preset=full_dbs --model_preset=monomer --benchmark=False --use_precomputed_msas=False --logtostderr' returned non-zero exit status 1.