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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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HHblits failed #14

Closed lugoly closed 2 years ago

lugoly commented 2 years ago

Who could do me a favor? when I run AF2, came up with HHblits error. script: python ./run_alphafold.py --fasta_paths=XXX.fas

results: /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --output_dir has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --model_names has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --data_dir has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: 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! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --uniref90_database_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --mgnify_database_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --uniclust30_database_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --bfd_database_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --pdb70_database_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --template_mmcif_dir has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --max_template_date has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( /home/linlab/.local/lib/python3.8/site-packages/absl/flags/_validators.py:203: UserWarning: Flag --obsolete_pdbs_path has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line! warnings.warn( I0827 14:21:24.269093 140066848117952 templates.py:880] Using precomputed obsolete pdbs /data1/AF2_Database/pdb_mmcif/obsolete.dat. I0827 14:21:26.650146 140066848117952 xla_bridge.py:236] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: I0827 14:21:27.050851 140066848117952 xla_bridge.py:236] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available. I0827 14:21:38.779491 140066848117952 run_alphafold.py:293] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5'] I0827 14:21:38.779775 140066848117952 run_alphafold.py:306] Using random seed 8466485706823161682 for the data pipeline I0827 14:21:38.780414 140066848117952 pipeline.py:130] query uniref90 I0827 14:21:38.780694 140066848117952 jackhmmer.py:119] Launching subprocess "jackhmmer -o /dev/null -A /tmp/tmpng40rd11/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 GARS_insertion.fas /data1/AF2_Database/uniref90/uniref90.fasta" I0827 14:21:38.840389 140066848117952 utils.py:36] Started Jackhmmer (uniref90.fasta) query I0827 14:28:35.052657 140066848117952 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 416.212 seconds I0827 14:28:35.053834 140066848117952 pipeline.py:141] query mgnify I0827 14:28:35.054065 140066848117952 jackhmmer.py:119] Launching subprocess "jackhmmer -o /dev/null -A /tmp/tmp48u78l3n/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 GARS_insertion.fas /data1/AF2_Database/mgnify/mgy_clusters.fa" I0827 14:28:35.103244 140066848117952 utils.py:36] Started Jackhmmer (mgy_clusters.fa) query I0827 14:36:06.724052 140066848117952 utils.py:40] Finished Jackhmmer (mgy_clusters.fa) query in 451.621 seconds I0827 14:36:06.727063 140066848117952 pipeline.py:153] query mgnify I0827 14:36:06.727788 140066848117952 hhblits.py:128] Launching subprocess "hhblits -i GARS_insertion.fas -cpu 4 -oa3m /tmp/tmptyl5pi44/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data1/AF2_Database/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data1/AF2_Database/uniclust30/uniclust30_2018_08/uniclust30_2018_08" I0827 14:36:06.858779 140066848117952 utils.py:36] Started HHblits query I0827 14:38:43.267431 140066848117952 utils.py:40] Finished HHblits query in 156.408 seconds E0827 14:38:43.267613 140066848117952 hhblits.py:138] HHblits failed. HHblits stderr begin: E0827 14:38:43.267664 140066848117952 hhblits.py:141] - 14:36:31.573 INFO: Searching 65983866 column state sequences. E0827 14:38:43.267698 140066848117952 hhblits.py:141] - 14:36:32.498 INFO: Searching 15161831 column state sequences. E0827 14:38:43.267728 140066848117952 hhblits.py:141] - 14:36:32.569 INFO: GARS_insertion.fas is in A2M, A3M or FASTA format E0827 14:38:43.267756 140066848117952 hhblits.py:141] - 14:36:32.569 INFO: Iteration 1 E0827 14:38:43.267784 140066848117952 hhblits.py:141] - 14:36:32.607 INFO: Prefiltering database E0827 14:38:43.267811 140066848117952 hhblits.py:141] - 14:37:27.399 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 735240 E0827 14:38:43.267838 140066848117952 hhblits.py:141] - 14:38:40.391 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 198439 E0827 14:38:43.267866 140066848117952 hhblits.py:141] - 14:38:41.184 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2000 E0827 14:38:43.267893 140066848117952 hhblits.py:141] - 14:38:41.184 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2000 E0827 14:38:43.267920 140066848117952 hhblits.py:141] - 14:38:41.184 INFO: Scoring 2000 HMMs using HMM-HMM Viterbi alignment E0827 14:38:43.267946 140066848117952 hhblits.py:141] - 14:38:41.286 INFO: Alternative alignment: 0 E0827 14:38:43.267974 140066848117952 hhblits.py:142] HHblits stderr end Traceback (most recent call last): File "../run_alphafold.py", line 338, in app.run(main) File "/home/linlab/.local/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/home/linlab/.local/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "../run_alphafold.py", line 310, in main predict_structure( File "../run_alphafold.py", line 170, in predict_structure feature_dict = data_pipeline.process( File "/home/linlab/Applications/alphafold/alphafold/data/pipeline.py", line 154, in process hhblits_bfd_uniclust_result = self.hhblits_bfd_uniclust_runner.query( File "/home/linlab/Applications/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:

lugoly commented 2 years ago

I have fixed the error.

Firstly, I run the script hhblits -i GARS_insertion.fas -cpu 4 -oa3m /tmp/tmptyl5pi44/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data1/AF2_Database/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data1/AF2_Database/uniclust30/uniclust30_2018_08/uniclust30_2018_08

It turned out that the files in bfd cannot open. may be broken in tar process.

Then, I replaced the bfd folder by re-download the bfd database.

sanjaysrikakulam commented 2 years ago

Thank you for sharing the solution.

xianyu-123 commented 3 months ago

i have the same error, but my error line in 94

File "/home/wgj/wanggj/MyWorkSpace/tools/alphafold-2.3.1/alphafold/data/tools/hhsearch.py", line 94, in query raise RuntimeError( RuntimeError: HHSearch failed: stdout:

stderr: