Hello, I run the monomer prediction without any problems, but in the compound prediction, there was a mistake, I have checked my directory structure is consistent with the official. However, I made an error when downloading to the uniprot file when using download all data.sh, so I later downloaded uniprot and pdb _ seqres separately. Don 't know if there is a reason for this?
The following is the error content.
(alphafold) bash run_alphafold.sh -d /home/fsd/afdata/ -o /home/fsd/afoutput/ -f /h
I1023 16:33:13.358484 47290920877760 templates.py:857] Using precomputed obsolete pd
I1023 16:33:14.708593 47290920877760 tpu_client.py:54] Starting the local TPU driver
I1023 16:33:14.709099 47290920877760 xla_bridge.py:212] Unable to initialize backend
I1023 16:33:15.603161 47290920877760 xla_bridge.py:212] Unable to initialize backend
I1023 16:33:23.785693 47290920877760 run_alphafold.py:376] Have 25 models: ['model_1pred_3', 'model_1_multimer_v2_pred_4', 'model_2_multimer_v2_pred_0', 'model_2_multim, 'model_3_multimer_v2_pred_0', 'model_3_multimer_v2_pred_1', 'model_3_multimer_v2_pl_4_multimer_v2_pred_1', 'model_4_multimer_v2_pred_2', 'model_4_multimer_v2_pred_3',timer_v2_pred_2', 'model_5_multimer_v2_pred_3', 'model_5_multimer_v2_pred_4']
I1023 16:33:23.785909 47290920877760 run_alphafold.py:393] Using random seed 2717477
I1023 16:33:23.786309 47290920877760 run_alphafold.py:161] Predicting multimer
I1023 16:33:23.959514 47290920877760 pipeline_multimer.py:210] Running monomer pipel
I1023 16:33:23.960077 47290920877760 jackhmmer.py:133] Launching subprocess "/home/f05 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmpmu_z1046.fasta
I1023 16:33:23.991682 47290920877760 utils.py:36] Started Jackhmmer (uniref90.fasta)
I1023 16:39:41.744481 47290920877760 utils.py:40] Finished Jackhmmer (uniref90.fasta
I1023 16:39:42.184468 47290920877760 jackhmmer.py:133] Launching subprocess "/home/f05 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmpmu_z1046.fasta
I1023 16:39:42.207394 47290920877760 utils.py:36] Started Jackhmmer (mgy_clusters_20
I1023 16:46:42.247396 47290920877760 utils.py:40] Finished Jackhmmer (mgy_clusters_2
I1023 16:46:43.379640 47290920877760 hmmbuild.py:121] Launching subprocess ['/home/fpjatb3j5u/query.msa']
I1023 16:46:43.421558 47290920877760 utils.py:36] Started hmmbuild query
I1023 16:46:44.075075 47290920877760 hmmbuild.py:128] hmmbuild stdout:
# hmmbuild :: profile HMM construction from multiple sequence alignments
# HMMER 3.3.2 (Nov 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# input alignment file: /tmp/tmpjatb3j5u/query.msa
# output HMM file: /tmp/tmpjatb3j5u/output.hmm
# input alignment is asserted as: protein
# model architecture construction: hand-specified by RF annotation
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# idx name nseq alen mlen eff_nseq re/pos description
#---- -------------------- ----- ----- ----- -------- ------ -----------
1 query 9218 799 191 7.65 0.590
# CPU time: 0.58u 0.07s 00:00:00.64 Elapsed: 00:00:00.64
stderr:
I1023 16:46:44.075536 47290920877760 utils.py:40] Finished hmmbuild query in 0.654 s
I1023 16:46:44.081163 47290920877760 hmmsearch.py:103] Launching sub-process ['/home-F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A'.txt']
I1023 16:46:44.144675 47290920877760 utils.py:36] Started hmmsearch (pdb_seqres.txt)
I1023 16:46:49.798766 47290920877760 utils.py:40] Finished hmmsearch (pdb_seqres.txt
Traceback (most recent call last):
File "/home/fsd/alphafold-2.2.0/run_alphafold.py", line 422, in <module>
app.run(main)
File "/home/fsd/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py",
_run_main(main, args)
File "/home/fsd/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py",
sys.exit(main(argv))
File "/home/fsd/alphafold-2.2.0/run_alphafold.py", line 398, in main
predict_structure(
File "/home/fsd/alphafold-2.2.0/run_alphafold.py", line 172, in predict_structure
feature_dict = data_pipeline.process(
File "/home/fsd/alphafold-2.2.0/alphafold/data/pipeline_multimer.py", line 264, in
chain_features = self._process_single_chain(
File "/home/fsd/alphafold-2.2.0/alphafold/data/pipeline_multimer.py", line 212, in
chain_features = self._monomer_data_pipeline.process(
File "/home/fsd/alphafold-2.2.0/alphafold/data/pipeline.py", line 185, in process
pdb_templates_result = self.template_searcher.query(msa_for_templates)
File "/home/fsd/alphafold-2.2.0/alphafold/data/tools/hmmsearch.py", line 79, in qu
return self.query_with_hmm(hmm)
File "/home/fsd/alphafold-2.2.0/alphafold/data/tools/hmmsearch.py", line 112, in q
raise RuntimeError(
RuntimeError: hmmsearch failed:
stdout:
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.2 (Nov 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: /tmp/tmp2_sps4u7/query.hmm
# target sequence database: /home/fsd/afdata//pdb_seqres/pdb_seqres.txt
# MSA of all hits saved to file: /tmp/tmp2_sps4u7/output.sto
# show alignments in output: no
# sequence reporting threshold: E-value <= 100
# domain reporting threshold: E-value <= 100
# sequence inclusion threshold: E-value <= 100
# domain inclusion threshold: E-value <= 100
# MSV filter P threshold: <= 0.1
# Vit filter P threshold: <= 0.1
# Fwd filter P threshold: <= 0.1
# number of worker threads: 8
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: query [M=191]
stderr:
Parse failed (sequence file /home/fsd/afdata//pdb_seqres/pdb_seqres.txt):
Line 1364572: illegal character 0
Hello, I run the monomer prediction without any problems, but in the compound prediction, there was a mistake, I have checked my directory structure is consistent with the official. However, I made an error when downloading to the uniprot file when using download all data.sh, so I later downloaded uniprot and pdb _ seqres separately. Don 't know if there is a reason for this?
The following is the error content.