Open nick-youngblut opened 2 years ago
@nick-youngblut Excuse me! have you solved your problem? I encountered the same problem, but I don't how to deal with it.
`I0525 17:37:18.623581 47755692236224 utils.py:36] Started HHsearch query
I0525 17:37:51.544831 47755692236224 utils.py:40] Finished HHsearch query in 32.921 seconds
I0525 17:37:51.552284 47755692236224 hhblits.py:128] Launching subprocess "/usr/bin/hhblits -i test.fasta -cpu 4 -oa3m /tmp/tmp8y6hhyho/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /home/lijundi/protein/alphafold/database/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /home/lijundi/protein/alphafold/database/uniref30/UniRef30_2021_03"
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
stderr:
17:38:15.391 INFO: Searching 65983866 column state sequences.
17:38:16.778 INFO: Searching 29291635 column state sequences.
17:38:16.886 INFO: test.fasta is in A2M, A3M or FASTA format
17:38:16.886 INFO: Iteration 1
17:38:16.952 INFO: Prefiltering database
17:41:26.216 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 968028
17:42:06.654 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 323631
17:42:08.259 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2630
17:42:08.259 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2630
17:42:08.259 INFO: Scoring 2630 HMMs using HMM-HMM Viterbi alignment
17:42:08.330 INFO: Alternative alignment: 0
`
I've tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at https://github.com/kalininalab/alphafold_non_docker, and both result in the following error:
The error occurs both via
run_alphafold.py
and when just running thehhblits
command. Based on https://github.com/soedinglab/hh-suite/issues/279, it seems to be a memory issue, but I've used up to 504 Gb of memory, and I still get the error.Typical stats for the cluster jobs:
I've also tried compiling hh-suite for the cluster nodes, and that didn't help.
My conda env based on https://github.com/kalininalab/alphafold_non_docker (only one setup that I've tried):