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Open source code for AlphaFold 2.
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RuntimeError: HHblits failed #97

Closed huangjk1103 closed 2 years ago

huangjk1103 commented 3 years ago

I had try to predict a protein's stucture, but it failed, can you help me?

/data/apps/alphafold/alphafold200_1/lib/python3.7/site-packages/absl/flags/_validators.py:206: UserWarning: Flag --preset has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! 'command line!' % flag_name) I0803 23:01:13.789970 139723086509888 templates.py:837] Using precomputed obsolete pdbs /data/public/pdb_mmcif/obsolete.dat. I0803 23:01:14.698018 139723086509888 tpu_client.py:54] Starting the local TPU driver. I0803 23:01:14.719603 139723086509888 xla_bridge.py:214] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local:// I0803 23:01:14.966662 139723086509888 xla_bridge.py:214] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available. I0803 23:01:23.010689 139723086509888 run_alphafold.py:261] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5'] I0803 23:01:23.010993 139723086509888 run_alphafold.py:273] Using random seed 1376016366686354143 for the data pipeline I0803 23:01:23.035536 139723086509888 jackhmmer.py:130] Launching subprocess "/data/apps/alphafold/alphafold200/bin/jackhmmer -o /dev/null -A /tmp/tmp1o0pnq_t/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 ./data/22007.fasta /data/public/uniref90/uniref90.fasta" I0803 23:01:23.066604 139723086509888 utils.py:36] Started Jackhmmer (uniref90.fasta) query I0803 23:15:18.661020 139723086509888 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 835.594 seconds I0803 23:15:21.842122 139723086509888 jackhmmer.py:130] Launching subprocess "/data/apps/alphafold/alphafold200/bin/jackhmmer -o /dev/null -A /tmp/tmpegmh9ytz/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 ./data/22007.fasta /data/public/mgnify/mgy_clusters.fa" I0803 23:15:21.911606 139723086509888 utils.py:36] Started Jackhmmer (mgy_clusters.fa) query I0803 23:28:52.221145 139723086509888 utils.py:40] Finished Jackhmmer (mgy_clusters.fa) query in 810.309 seconds I0803 23:29:15.419130 139723086509888 hhsearch.py:76] Launching subprocess "/data/apps/alphafold/alphafold200/bin/hhsearch -i /tmp/tmpd2kes4s2/query.a3m -o /tmp/tmpd2kes4s2/output.hhr -maxseq 1000000 -d /data/public/pdb70/pdb70" I0803 23:29:15.580710 139723086509888 utils.py:36] Started HHsearch query I0803 23:33:59.937626 139723086509888 utils.py:40] Finished HHsearch query in 284.356 seconds I0803 23:37:12.944531 139723086509888 hhblits.py:128] Launching subprocess "/data/apps/alphafold/alphafold200/bin/hhblits -i ./data/22007.fasta -cpu 4 -oa3m /tmp/tmpg957yehn/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data/public/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data/public/uniclust30/uniclust30_2018_08/uniclust30_2018_08" I0803 23:37:13.247214 139723086509888 utils.py:36] Started HHblits query I0804 00:46:09.004908 139723086509888 utils.py:40] Finished HHblits query in 4135.755 seconds E0804 00:46:09.019532 139723086509888 hhblits.py:138] HHblits failed. HHblits stderr begin: E0804 00:46:09.021161 139723086509888 hhblits.py:141] - 23:37:48.447 INFO: Searching 65983866 column state sequences. E0804 00:46:09.021250 139723086509888 hhblits.py:141] - 23:37:49.637 INFO: Searching 15161831 column state sequences. E0804 00:46:09.021305 139723086509888 hhblits.py:141] - 23:37:49.720 INFO: ./data/22007.fasta is in A2M, A3M or FASTA format E0804 00:46:09.021353 139723086509888 hhblits.py:141] - 23:37:49.721 INFO: Iteration 1 E0804 00:46:09.021399 139723086509888 hhblits.py:141] - 23:37:50.452 INFO: Prefiltering database E0804 00:46:09.021443 139723086509888 hhblits.py:141] - 23:55:52.099 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 6905944 E0804 00:46:09.021486 139723086509888 hhblits.py:141] - 00:03:15.552 WARNING: Number of hits passing 2nd prefilter (reduced from 319529 to allowed maximum of 100000). E0804 00:46:09.021530 139723086509888 hhblits.py:141] You can increase the allowed maximum using the -maxfilt option. E0804 00:46:09.021573 139723086509888 hhblits.py:141] - 00:07:13.586 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1127018 E0804 00:46:09.021616 139723086509888 hhblits.py:141] - 00:07:44.644 WARNING: database contains sequences that exceed maximum allowed size (maxres = 20001). Max sequence length can be increased with parameter -maxres. E0804 00:46:09.021663 139723086509888 hhblits.py:141] - 00:07:45.136 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 178190 E0804 00:46:09.021706 139723086509888 hhblits.py:141] - 00:07:45.137 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 178190 E0804 00:46:09.021749 139723086509888 hhblits.py:141] - 00:07:45.137 INFO: Scoring 178190 HMMs using HMM-HMM Viterbi alignment E0804 00:46:09.021792 139723086509888 hhblits.py:141] - 00:07:45.366 INFO: Alternative alignment: 0 E0804 00:46:09.021835 139723086509888 hhblits.py:141] - 00:07:58.684 INFO: 2000 alignments done E0804 00:46:09.021913 139723086509888 hhblits.py:141] - 00:08:14.142 INFO: 4000 alignments done E0804 00:46:09.021959 139723086509888 hhblits.py:141] - 00:08:28.631 INFO: 6000 alignments done E0804 00:46:09.022015 139723086509888 hhblits.py:141] - 00:08:42.732 INFO: 8000 alignments done E0804 00:46:09.022057 139723086509888 hhblits.py:141] - 00:08:55.653 INFO: 10000 alignments done E0804 00:46:09.022100 139723086509888 hhblits.py:141] - 00:09:06.817 INFO: 12000 alignments done E0804 00:46:09.022142 139723086509888 hhblits.py:141] - 00:09:18.051 INFO: 14000 alignments done E0804 00:46:09.022186 139723086509888 hhblits.py:141] - 00:09:33.523 INFO: 16000 alignments done E0804 00:46:09.022228 139723086509888 hhblits.py:141] - 00:09:43.505 INFO: 18000 alignments done E0804 00:46:09.022271 139723086509888 hhblits.py:141] - 00:09:53.848 INFO: 20000 alignments done E0804 00:46:09.022314 139723086509888 hhblits.py:141] - 00:10:11.309 INFO: 22000 alignments done E0804 00:46:09.022356 139723086509888 hhblits.py:141] - 00:10:21.097 INFO: 24000 alignments done E0804 00:46:09.022399 139723086509888 hhblits.py:141] - 00:10:30.242 INFO: 26000 alignments done E0804 00:46:09.022442 139723086509888 hhblits.py:141] - 00:10:39.877 INFO: 28000 alignments done E0804 00:46:09.022485 139723086509888 hhblits.py:141] - 00:10:49.706 INFO: 30000 alignments done E0804 00:46:09.022527 139723086509888 hhblits.py:141] - 00:11:02.306 INFO: 32000 alignments done E0804 00:46:09.022569 139723086509888 hhblits.py:141] - 00:11:14.206 INFO: 34000 alignments done E0804 00:46:09.022611 139723086509888 hhblits.py:141] - 00:11:24.107 INFO: 36000 alignments done E0804 00:46:09.022654 139723086509888 hhblits.py:141] - 00:11:34.196 INFO: 38000 alignments done E0804 00:46:09.022696 139723086509888 hhblits.py:141] - 00:11:43.886 INFO: 40000 alignments done E0804 00:46:09.022738 139723086509888 hhblits.py:141] - 00:11:54.462 INFO: 42000 alignments done E0804 00:46:09.022781 139723086509888 hhblits.py:141] - 00:12:06.316 INFO: 44000 alignments done E0804 00:46:09.022823 139723086509888 hhblits.py:141] - 00:12:16.029 INFO: 46000 alignments done E0804 00:46:09.022878 139723086509888 hhblits.py:141] - 00:12:25.527 INFO: 48000 alignments done E0804 00:46:09.022922 139723086509888 hhblits.py:141] - 00:12:34.905 INFO: 50000 alignments done E0804 00:46:09.022972 139723086509888 hhblits.py:141] - 00:12:44.296 INFO: 52000 alignments done E0804 00:46:09.023016 139723086509888 hhblits.py:141] - 00:12:54.272 INFO: 54000 alignments done E0804 00:46:09.023058 139723086509888 hhblits.py:141] - 00:13:05.223 INFO: 56000 alignments done E0804 00:46:09.023101 139723086509888 hhblits.py:141] - 00:13:23.589 INFO: 58000 alignments done E0804 00:46:09.023143 139723086509888 hhblits.py:141] - 00:13:34.849 INFO: 60000 alignments done E0804 00:46:09.023186 139723086509888 hhblits.py:141] - 00:13:46.660 INFO: 62000 alignments done E0804 00:46:09.023228 139723086509888 hhblits.py:141] - 00:13:59.061 INFO: 64000 alignments done E0804 00:46:09.023270 139723086509888 hhblits.py:141] - 00:14:11.361 INFO: 66000 alignments done E0804 00:46:09.023312 139723086509888 hhblits.py:141] - 00:14:23.280 INFO: 68000 alignments done E0804 00:46:09.023355 139723086509888 hhblits.py:141] - 00:14:35.515 INFO: 70000 alignments done E0804 00:46:09.023397 139723086509888 hhblits.py:141] - 00:14:47.450 INFO: 72000 alignments done E0804 00:46:09.023440 139723086509888 hhblits.py:141] - 00:15:00.765 INFO: 74000 alignments done E0804 00:46:09.023482 139723086509888 hhblits.py:141] - 00:15:14.500 INFO: 76000 alignments done E0804 00:46:09.023525 139723086509888 hhblits.py:141] - 00:15:28.118 INFO: 78000 alignments done E0804 00:46:09.023567 139723086509888 hhblits.py:141] - 00:15:41.805 INFO: 80000 alignments done E0804 00:46:09.023609 139723086509888 hhblits.py:141] - 00:15:55.681 INFO: 82000 alignments done E0804 00:46:09.023651 139723086509888 hhblits.py:141] - 00:16:09.212 INFO: 84000 alignments done E0804 00:46:09.023693 139723086509888 hhblits.py:141] - 00:16:22.941 INFO: 86000 alignments done E0804 00:46:09.023748 139723086509888 hhblits.py:141] - 00:16:34.996 INFO: 88000 alignments done E0804 00:46:09.023792 139723086509888 hhblits.py:141] - 00:16:47.443 INFO: 90000 alignments done E0804 00:46:09.023835 139723086509888 hhblits.py:141] - 00:16:58.603 INFO: 92000 alignments done E0804 00:46:09.023892 139723086509888 hhblits.py:141] - 00:17:10.273 INFO: 94000 alignments done E0804 00:46:09.023935 139723086509888 hhblits.py:141] - 00:17:21.990 INFO: 96000 alignments done E0804 00:46:09.023984 139723086509888 hhblits.py:141] - 00:17:36.342 INFO: 98000 alignments done E0804 00:46:09.024028 139723086509888 hhblits.py:141] - 00:17:51.060 INFO: 100000 alignments done E0804 00:46:09.024070 139723086509888 hhblits.py:141] - 00:17:59.710 INFO: 102000 alignments done E0804 00:46:09.024112 139723086509888 hhblits.py:141] - 00:18:07.873 INFO: 104000 alignments done E0804 00:46:09.024154 139723086509888 hhblits.py:141] - 00:18:16.130 INFO: 106000 alignments done E0804 00:46:09.024196 139723086509888 hhblits.py:141] - 00:18:24.375 INFO: 108000 alignments done E0804 00:46:09.024238 139723086509888 hhblits.py:141] - 00:18:32.424 INFO: 110000 alignments done E0804 00:46:09.024280 139723086509888 hhblits.py:141] - 00:18:42.069 INFO: 112000 alignments done E0804 00:46:09.024322 139723086509888 hhblits.py:141] - 00:18:49.615 INFO: 114000 alignments done E0804 00:46:09.024364 139723086509888 hhblits.py:141] - 00:18:58.052 INFO: 116000 alignments done E0804 00:46:09.024406 139723086509888 hhblits.py:141] - 00:19:06.386 INFO: 118000 alignments done E0804 00:46:09.024449 139723086509888 hhblits.py:141] - 00:19:14.232 INFO: 120000 alignments done E0804 00:46:09.024490 139723086509888 hhblits.py:141] - 00:19:22.616 INFO: 122000 alignments done E0804 00:46:09.024533 139723086509888 hhblits.py:141] - 00:19:30.370 INFO: 124000 alignments done E0804 00:46:09.024574 139723086509888 hhblits.py:141] - 00:19:38.019 INFO: 126000 alignments done E0804 00:46:09.024617 139723086509888 hhblits.py:141] - 00:19:45.593 INFO: 128000 alignments done E0804 00:46:09.024659 139723086509888 hhblits.py:141] - 00:19:45.601 INFO: Stop after DB-HHM: 128000 because early stop 19.5091 < filter cutoff 20 E0804 00:46:09.024701 139723086509888 hhblits.py:141] - 00:19:45.610 INFO: Alternative alignment: 1 E0804 00:46:09.024743 139723086509888 hhblits.py:141] - 00:25:51.603 INFO: 106040 alignments done E0804 00:46:09.024785 139723086509888 hhblits.py:141] - 00:25:52.034 INFO: Alternative alignment: 2 E0804 00:46:09.024827 139723086509888 hhblits.py:141] - 00:30:34.459 INFO: 81231 alignments done E0804 00:46:09.024880 139723086509888 hhblits.py:141] - 00:30:35.078 INFO: Alternative alignment: 3 E0804 00:46:09.024923 139723086509888 hhblits.py:141] - 00:34:38.509 INFO: 68285 alignments done E0804 00:46:09.024972 139723086509888 hhblits.py:141] - 00:34:44.972 INFO: Premerge done E0804 00:46:09.025016 139723086509888 hhblits.py:141] - 00:34:45.002 INFO: Realigning 89456 HMM-HMM alignments using Maximum Accuracy algorithm E0804 00:46:09.025061 139723086509888 hhblits.py:142] HHblits stderr end Traceback (most recent call last): File "/data/public/alphafold2/alphafold/run_alphafold.py", line 303, in app.run(main) File "/data/apps/alphafold/alphafold200_1/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/data/apps/alphafold/alphafold200_1/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/data/public/alphafold2/alphafold/run_alphafold.py", line 285, in main random_seed=random_seed) File "/data/public/alphafold2/alphafold/run_alphafold.py", line 129, in predict_structure msa_output_dir=msa_output_dir) File "/data/public/alphafold2/alphafold/alphafold/data/pipeline.py", line 171, in process input_fasta_path) File "/data/public/alphafold2/alphafold/alphafold/data/tools/hhblits.py", line 144, in query stdout.decode('utf-8'), stderr[:500_000].decode('utf-8'))) RuntimeError: HHblits failed stdout:

stderr:

Alfatlawi commented 3 years ago

I have the same error! Any suggestion, please?

ww2283 commented 3 years ago

Same error here. Ubuntu 20.04+CUDA11.4.

I seem to have solved the problem. Here are the steps I think may play a role:

  1. better install cuda-11-2 by sudo apt install cuda-11-2;
  2. then use the Dockerfile as described here, because this modified file took care of the CUDA ARG issue: https://github.com/deepmind/alphafold/pull/36/commits/c1bf7af1730785cd243179706500edf38c206eb6
  3. in that Dockerfile, you should modify the "Install Miniconda package manger" section. The most recent miniconda has python3.9, which may cause problem for later patching. I suggest use the miniconda version that still has python3.8 (e.g. https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh).
  4. After above modifications you should be ready to get the right docker built. Happy folding!
huangjk1103 commented 3 years ago

Increase the GPU number and increase the memory can solve this problem!!

I did it!

On 8/5/2021 @.***> wrote：

I have the same error! Any suggestion, please?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

Davidswang commented 3 years ago

@huangjk1103 increase GPU number and memory？parameters of -cpu and -n in hhbits？

andreybespalov89 commented 3 years ago

I have the same problem. No one response from this topic don`t help me to solve this problem. Please help me.

yamule commented 3 years ago

If the problem is caused by RAM issue (I'm not 100 % sure but if you have so many XXXX alignments done ~ lines like the top comment), possibly you can run successfully with --preset=reduced_dbs option with reduced db listed in https://github.com/deepmind/alphafold#genetic-databases .

andreybespalov89 commented 3 years ago

If the problem is caused by RAM issue (I'm not 100 % sure but if you have so many XXXX alignments done ~ lines like the top comment), possibly you can run successfully with --preset=reduced_dbs option with reduced db listed in https://github.com/deepmind/alphafold#genetic-databases .

thank you for reply, but unfortunately it isn`t work. I have 64 GB RAM 3200MHz, AMD Ryzen 3900X 12 cores and 24 threads. I suggest that main problem is not memory insufficient

I0830 23:21:40.646003 140225598170944 run_docker.py:193] E0830 16:21:40.645383 139881951138624 hhblits.py:140] HHblits failed. HHblits stderr begin: I0830 23:21:40.646096 140225598170944 run_docker.py:193] E0830 16:21:40.645464 139881951138624 hhblits.py:143] - 16:05:10.540 INFO: Searching 65983866 column state sequences. I0830 23:21:40.646206 140225598170944 run_docker.py:193] E0830 16:21:40.645519 139881951138624 hhblits.py:143] - 16:05:11.118 INFO: Searching 15161831 column state sequences. I0830 23:21:40.646292 140225598170944 run_docker.py:193] E0830 16:21:40.645567 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: /mnt/fasta_path_0/3rjp.fasta is in A2M, A3M or FASTA format I0830 23:21:40.646376 140225598170944 run_docker.py:193] E0830 16:21:40.645616 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: Iteration 1 I0830 23:21:40.646459 140225598170944 run_docker.py:193] E0830 16:21:40.645664 139881951138624 hhblits.py:143] - 16:05:11.174 INFO: Prefiltering database I0830 23:21:40.646543 140225598170944 run_docker.py:193] E0830 16:21:40.645712 139881951138624 hhblits.py:143] - 16:17:42.528 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 491795 I0830 23:21:40.646628 140225598170944 run_docker.py:193] E0830 16:21:40.645759 139881951138624 hhblits.py:143] - 16:21:38.774 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 162301 I0830 23:21:40.646712 140225598170944 run_docker.py:193] E0830 16:21:40.645806 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2000 I0830 23:21:40.646800 140225598170944 run_docker.py:193] E0830 16:21:40.645854 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2000 I0830 23:21:40.646885 140225598170944 run_docker.py:193] E0830 16:21:40.645902 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: Scoring 2000 HMMs using HMM-HMM Viterbi alignment I0830 23:21:40.646973 140225598170944 run_docker.py:193] E0830 16:21:40.645950 139881951138624 hhblits.py:143] - 16:21:39.195 INFO: Alternative alignment: 0 I0830 23:21:40.647056 140225598170944 run_docker.py:193] E0830 16:21:40.645997 139881951138624 hhblits.py:144] HHblits stderr end I0830 23:21:40.654336 140225598170944 run_docker.py:193] Traceback (most recent call last): I0830 23:21:40.654455 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 310, in I0830 23:21:40.655068 140225598170944 run_docker.py:193] app.run(main) I0830 23:21:40.655237 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 312, in run I0830 23:21:40.655341 140225598170944 run_docker.py:193] _run_main(main, args) I0830 23:21:40.655425 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main I0830 23:21:40.655524 140225598170944 run_docker.py:193] sys.exit(main(argv)) I0830 23:21:40.655606 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 284, in main I0830 23:21:40.655688 140225598170944 run_docker.py:193] predict_structure( I0830 23:21:40.655768 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 127, in predict_structure I0830 23:21:40.655848 140225598170944 run_docker.py:193] feature_dict = data_pipeline.process( I0830 23:21:40.655928 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/pipeline.py", line 173, in process I0830 23:21:40.656101 140225598170944 run_docker.py:193] hhblits_bfd_uniclust_result = self.hhblits_bfd_uniclust_runner.query( I0830 23:21:40.656203 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/tools/hhblits.py", line 145, in query I0830 23:21:40.656287 140225598170944 run_docker.py:193] raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( I0830 23:21:40.656370 140225598170944 run_docker.py:193] RuntimeError: HHblits failed I0830 23:21:40.656464 140225598170944 run_docker.py:193] stdout: I0830 23:21:40.656547 140225598170944 run_docker.py:193] I0830 23:21:40.656626 140225598170944 run_docker.py:193] I0830 23:21:40.656704 140225598170944 run_docker.py:193] stderr:

yamule commented 3 years ago

Hmmm, You are right. Your hits are not so large. It looks like that hhblits failed at the step producing MSA. Possibly, DB files are broken. Did you check MD5 of DBs? But I'm not 100% sure.

(However, reading the code, if you use the option --preset=reduced_dbs, it doesn't run hhblits. So I assume that your error logs are come from the one which did not use the option.)

Lsz-20 commented 2 years ago

If the problem is caused by RAM issue (I'm not 100 % sure but if you have so many XXXX alignments done ~ lines like the top comment), possibly you can run successfully with --preset=reduced_dbs option with reduced db listed in https://github.com/deepmind/alphafold#genetic-databases .

thank you for reply, but unfortunately it isn`t work. I have 64 GB RAM 3200MHz, AMD Ryzen 3900X 12 cores and 24 threads. I suggest that main problem is not memory insufficient

I0830 23:21:40.646003 140225598170944 run_docker.py:193] E0830 16:21:40.645383 139881951138624 hhblits.py:140] HHblits failed. HHblits stderr begin: I0830 23:21:40.646096 140225598170944 run_docker.py:193] E0830 16:21:40.645464 139881951138624 hhblits.py:143] - 16:05:10.540 INFO: Searching 65983866 column state sequences. I0830 23:21:40.646206 140225598170944 run_docker.py:193] E0830 16:21:40.645519 139881951138624 hhblits.py:143] - 16:05:11.118 INFO: Searching 15161831 column state sequences. I0830 23:21:40.646292 140225598170944 run_docker.py:193] E0830 16:21:40.645567 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: /mnt/fasta_path_0/3rjp.fasta is in A2M, A3M or FASTA format I0830 23:21:40.646376 140225598170944 run_docker.py:193] E0830 16:21:40.645616 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: Iteration 1 I0830 23:21:40.646459 140225598170944 run_docker.py:193] E0830 16:21:40.645664 139881951138624 hhblits.py:143] - 16:05:11.174 INFO: Prefiltering database I0830 23:21:40.646543 140225598170944 run_docker.py:193] E0830 16:21:40.645712 139881951138624 hhblits.py:143] - 16:17:42.528 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 491795 I0830 23:21:40.646628 140225598170944 run_docker.py:193] E0830 16:21:40.645759 139881951138624 hhblits.py:143] - 16:21:38.774 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 162301 I0830 23:21:40.646712 140225598170944 run_docker.py:193] E0830 16:21:40.645806 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2000 I0830 23:21:40.646800 140225598170944 run_docker.py:193] E0830 16:21:40.645854 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2000 I0830 23:21:40.646885 140225598170944 run_docker.py:193] E0830 16:21:40.645902 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: Scoring 2000 HMMs using HMM-HMM Viterbi alignment I0830 23:21:40.646973 140225598170944 run_docker.py:193] E0830 16:21:40.645950 139881951138624 hhblits.py:143] - 16:21:39.195 INFO: Alternative alignment: 0 I0830 23:21:40.647056 140225598170944 run_docker.py:193] E0830 16:21:40.645997 139881951138624 hhblits.py:144] HHblits stderr end I0830 23:21:40.654336 140225598170944 run_docker.py:193] Traceback (most recent call last): I0830 23:21:40.654455 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 310, in I0830 23:21:40.655068 140225598170944 run_docker.py:193] app.run(main) I0830 23:21:40.655237 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 312, in run I0830 23:21:40.655341 140225598170944 run_docker.py:193] _run_main(main, args) I0830 23:21:40.655425 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main I0830 23:21:40.655524 140225598170944 run_docker.py:193] sys.exit(main(argv)) I0830 23:21:40.655606 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 284, in main I0830 23:21:40.655688 140225598170944 run_docker.py:193] predict_structure( I0830 23:21:40.655768 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 127, in predict_structure I0830 23:21:40.655848 140225598170944 run_docker.py:193] feature_dict = data_pipeline.process( I0830 23:21:40.655928 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/pipeline.py", line 173, in process I0830 23:21:40.656101 140225598170944 run_docker.py:193] hhblits_bfd_uniclust_result = self.hhblits_bfd_uniclust_runner.query( I0830 23:21:40.656203 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/tools/hhblits.py", line 145, in query I0830 23:21:40.656287 140225598170944 run_docker.py:193] raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( I0830 23:21:40.656370 140225598170944 run_docker.py:193] RuntimeError: HHblits failed I0830 23:21:40.656464 140225598170944 run_docker.py:193] stdout: I0830 23:21:40.656547 140225598170944 run_docker.py:193] I0830 23:21:40.656626 140225598170944 run_docker.py:193] I0830 23:21:40.656704 140225598170944 run_docker.py:193] stderr:

Have you solved this problem right now? I have the same question

andreybespalov89 commented 2 years ago

If the problem is caused by RAM issue (I'm not 100 % sure but if you have so many XXXX alignments done ~ lines like the top comment), possibly you can run successfully with --preset=reduced_dbs option with reduced db listed in https://github.com/deepmind/alphafold#genetic-databases .

thank you for reply, but unfortunately it isn`t work. I have 64 GB RAM 3200MHz, AMD Ryzen 3900X 12 cores and 24 threads. I suggest that main problem is not memory insufficient I0830 23:21:40.646003 140225598170944 run_docker.py:193] E0830 16:21:40.645383 139881951138624 hhblits.py:140] HHblits failed. HHblits stderr begin: I0830 23:21:40.646096 140225598170944 run_docker.py:193] E0830 16:21:40.645464 139881951138624 hhblits.py:143] - 16:05:10.540 INFO: Searching 65983866 column state sequences. I0830 23:21:40.646206 140225598170944 run_docker.py:193] E0830 16:21:40.645519 139881951138624 hhblits.py:143] - 16:05:11.118 INFO: Searching 15161831 column state sequences. I0830 23:21:40.646292 140225598170944 run_docker.py:193] E0830 16:21:40.645567 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: /mnt/fasta_path_0/3rjp.fasta is in A2M, A3M or FASTA format I0830 23:21:40.646376 140225598170944 run_docker.py:193] E0830 16:21:40.645616 139881951138624 hhblits.py:143] - 16:05:11.160 INFO: Iteration 1 I0830 23:21:40.646459 140225598170944 run_docker.py:193] E0830 16:21:40.645664 139881951138624 hhblits.py:143] - 16:05:11.174 INFO: Prefiltering database I0830 23:21:40.646543 140225598170944 run_docker.py:193] E0830 16:21:40.645712 139881951138624 hhblits.py:143] - 16:17:42.528 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 491795 I0830 23:21:40.646628 140225598170944 run_docker.py:193] E0830 16:21:40.645759 139881951138624 hhblits.py:143] - 16:21:38.774 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 162301 I0830 23:21:40.646712 140225598170944 run_docker.py:193] E0830 16:21:40.645806 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2000 I0830 23:21:40.646800 140225598170944 run_docker.py:193] E0830 16:21:40.645854 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2000 I0830 23:21:40.646885 140225598170944 run_docker.py:193] E0830 16:21:40.645902 139881951138624 hhblits.py:143] - 16:21:38.845 INFO: Scoring 2000 HMMs using HMM-HMM Viterbi alignment I0830 23:21:40.646973 140225598170944 run_docker.py:193] E0830 16:21:40.645950 139881951138624 hhblits.py:143] - 16:21:39.195 INFO: Alternative alignment: 0 I0830 23:21:40.647056 140225598170944 run_docker.py:193] E0830 16:21:40.645997 139881951138624 hhblits.py:144] HHblits stderr end I0830 23:21:40.654336 140225598170944 run_docker.py:193] Traceback (most recent call last): I0830 23:21:40.654455 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 310, in I0830 23:21:40.655068 140225598170944 run_docker.py:193] app.run(main) I0830 23:21:40.655237 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 312, in run I0830 23:21:40.655341 140225598170944 run_docker.py:193] _run_main(main, args) I0830 23:21:40.655425 140225598170944 run_docker.py:193] File "/opt/conda/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main I0830 23:21:40.655524 140225598170944 run_docker.py:193] sys.exit(main(argv)) I0830 23:21:40.655606 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 284, in main I0830 23:21:40.655688 140225598170944 run_docker.py:193] predict_structure( I0830 23:21:40.655768 140225598170944 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 127, in predict_structure I0830 23:21:40.655848 140225598170944 run_docker.py:193] feature_dict = data_pipeline.process( I0830 23:21:40.655928 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/pipeline.py", line 173, in process I0830 23:21:40.656101 140225598170944 run_docker.py:193] hhblits_bfd_uniclust_result = self.hhblits_bfd_uniclust_runner.query( I0830 23:21:40.656203 140225598170944 run_docker.py:193] File "/app/alphafold/alphafold/data/tools/hhblits.py", line 145, in query I0830 23:21:40.656287 140225598170944 run_docker.py:193] raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( I0830 23:21:40.656370 140225598170944 run_docker.py:193] RuntimeError: HHblits failed I0830 23:21:40.656464 140225598170944 run_docker.py:193] stdout: I0830 23:21:40.656547 140225598170944 run_docker.py:193] I0830 23:21:40.656626 140225598170944 run_docker.py:193] I0830 23:21:40.656704 140225598170944 run_docker.py:193] stderr:

Have you solved this problem right now? I have the same question

Yes. I am solved this problem. It main reason is wrong database files downloading. I write myself script to download PDB database and then recursively ungzip all files in same directory. I am manually download obsolete.dat file. And I run alphafold without docker. If you need myself scripts, tell me know and I posted it on github, but it very easy. Rsync not able to download pdb database correctly

Lsz-20 commented 2 years ago

Yes. I am solved this problem. It main reason is wrong database files downloading. I write myself script to download PDB database and then recursively ungzip all files in same directory. I am manually download obsolete.dat file. And I run alphafold without docker. If you need myself scripts, tell me know and I posted it on github, but it very easy. Rsync not able to download pdb database correctly

oh,that's so greate! I also use conda (not docker) install . If convenient , please send me~Thanks!

Lsz-20 commented 2 years ago

Hello，I have tried monomer model and it can work well ,but if I use multimer , it shows me the same question like this QQ图片20211205232246 if you have any ideas to solve this? @huangjk1103 @Fundamentalistic @yamule Thanks!

Augustin-Zidek commented 2 years ago

The issue seems to be solved by re-downloading HH Suite databases.

@Lsz-20 I recommend trying either re-downloading the HHBlits databases or trying to run with --db_preset=reduced_dbs. Alternatively, you might be running on a system that doesn’t have enough RAM, upgrading to 32 GB might help with the issue.

Lsz-20 commented 2 years ago

The issue seems to be solved by re-downloading HH Suite databases.

@Lsz-20 I recommend trying either re-downloading the HHBlits databases or trying to run with --db_preset=reduced_dbs. Alternatively, you might be running on a system that doesn’t have enough RAM, upgrading to 32 GB might help with the issue.

Ok，thanks for your advice.

longerzone commented 2 years ago

blem. It main reason is wrong database files downloading. I write myself script to download PDB database and then recursively ungzip all files in same directory. I am manually download obsolete.dat file. And I run alphafold without docker. If you need myself scripts, tell me know and I posted it on github, but it very easy. Rsync not able to download pdb database correctly

sorry, It's a long time, hope you still remember the solution, Do you mean re-download the pdb70? And I checked the md5sum, all correct:

# cat /data1/dataset/pdb70/md5sum
1e4a67eb58df3885b1a161ca4ce8cc81  pdb70_hhm.ffindex
58043d1916b9bfeffde40da6b34c2981  pdb70_a3m.ffindex
65c38e47b7220bc12600c10ecf309faa  pdb70_cs219.ffindex
384772cb87c2be42ed92a6bd5bb91032  pdb70_clu.tsv
9bc7ffee558ff22d986baba054d85110  pdb70_cs219.ffdata
7211eb3fb092474b25dce825218077a5  pdb_filter.dat
16840ca77755b5666879ba38b848697b  pdb70_hhm.ffdata
563407f4b83831c6f222a68960c97ff3  pdb70_a3m.ffdata
# for i in `cat /data1/dataset/pdb70/md5sum |awk '{print $2}'` ; do md5sum /data1/dataset/pdb70/$i ;done
1e4a67eb58df3885b1a161ca4ce8cc81  /data1/dataset/pdb70/pdb70_hhm.ffindex
58043d1916b9bfeffde40da6b34c2981  /data1/dataset/pdb70/pdb70_a3m.ffindex
65c38e47b7220bc12600c10ecf309faa  /data1/dataset/pdb70/pdb70_cs219.ffindex
384772cb87c2be42ed92a6bd5bb91032  /data1/dataset/pdb70/pdb70_clu.tsv
9bc7ffee558ff22d986baba054d85110  /data1/dataset/pdb70/pdb70_cs219.ffdata
7211eb3fb092474b25dce825218077a5  /data1/dataset/pdb70/pdb_filter.dat
16840ca77755b5666879ba38b848697b  /data1/dataset/pdb70/pdb70_hhm.ffdata
563407f4b83831c6f222a68960c97ff3  /data1/dataset/pdb70/pdb70_a3m.ffdata

so I don't think re-download can resolve my problem.

josomir commented 2 years ago

Had the same error and tried all the solutions above with no success. The solution was to increase available RAM memory, from 64 GB to 256 GB in my case, after which no such error occurred.

Maiya19724 commented 2 years ago

@Augustin-Zidek I have the same error. alphafold2.2.0 My DBfiles are all correct, 256GB RAM. I tried all the solutions above, but none of them can solve the problem.

denizkavi commented 1 year ago

A reason for this problem could be wrong permissions. If you are storing the database files in external storage, you might want to make sure that root user has given you permission to execute/read etc. the required db files. Calling chmod 755/444 on each db file or asking the file owner to do so may resolve this problem.

donglianglxz commented 5 months ago

had the same error, and tried any possible solutions with no success.

`I0525 17:37:51.584613 47755692236224 utils.py:36] Started HHblits query I0525 17:42:09.718916 47755692236224 utils.py:40] Finished HHblits query in 258.134 seconds E0525 17:42:09.719525 47755692236224 hhblits.py:138] HHblits failed. HHblits stderr begin: E0525 17:42:09.719723 47755692236224 hhblits.py:141] - 17:38:15.391 INFO: Searching 65983866 column state sequences. E0525 17:42:09.719834 47755692236224 hhblits.py:141] - 17:38:16.778 INFO: Searching 29291635 column state sequences. E0525 17:42:09.719931 47755692236224 hhblits.py:141] - 17:38:16.886 INFO: test.fasta is in A2M, A3M or FASTA format E0525 17:42:09.720036 47755692236224 hhblits.py:141] - 17:38:16.886 INFO: Iteration 1 E0525 17:42:09.720133 47755692236224 hhblits.py:141] - 17:38:16.952 INFO: Prefiltering database E0525 17:42:09.720228 47755692236224 hhblits.py:141] - 17:41:26.216 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 968028 E0525 17:42:09.720326 47755692236224 hhblits.py:141] - 17:42:06.654 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 323631 E0525 17:42:09.720420 47755692236224 hhblits.py:141] - 17:42:08.259 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2630 E0525 17:42:09.720514 47755692236224 hhblits.py:141] - 17:42:08.259 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2630 E0525 17:42:09.720604 47755692236224 hhblits.py:141] - 17:42:08.259 INFO: Scoring 2630 HMMs using HMM-HMM Viterbi alignment E0525 17:42:09.720708 47755692236224 hhblits.py:141] - 17:42:08.330 INFO: Alternative alignment: 0 E0525 17:42:09.720803 47755692236224 hhblits.py:142] HHblits stderr end Traceback (most recent call last): File "/home/lijundi/protein/alphafold/run_alphafold.py", line 570, in app.run(main) File "/home/lijundi/miniconda3/envs/af2/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/home/lijundi/miniconda3/envs/af2/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/home/lijundi/protein/alphafold/run_alphafold.py", line 543, in main predict_structure( File "/home/lijundi/protein/alphafold/run_alphafold.py", line 256, in predict_structure feature_dict = data_pipeline.process( File "/home/lijundi/protein/alphafold/alphafold/data/pipeline.py", line 215, in process hhblits_bfd_uniref_result = run_msa_tool( File "/home/lijundi/protein/alphafold/alphafold/data/pipeline.py", line 96, in run_msa_tool result = msa_runner.query(input_fasta_path)[0] File "/home/lijundi/protein/alphafold/alphafold/data/tools/hhblits.py", line 143, in query raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( RuntimeError: HHblits failed stdout:

stderr:

yamule commented 5 months ago

If you are using non-docker version, you can run hhblits alone and it may give you some information. (Try the one with -oa3m option.) https://github.com/soedinglab/hh-suite?tab=readme-ov-file#usage Please provide DBs (uniref[clust]30 and BFD) separately as I think one of the DBs may have caused the error.