RuntimeError: HHblits failed. Unrecognized HMM file format in '468479486'

[asmaali98]

Description of the bug

Hi,
We are trying to run the nfcore proteinfold pipeline in ec2. While running the alphafold, we are getting an error message saying HHblits failed. It comes from the python file "/app/alphafold/alphafold/data/tools/hhblits.py" which is in the nf-core / proteinfold_alphafold2_standard container. We are using the dev version of the container (https://quay.io/repository/nf-core/proteinfold_alphafold2_standard?tab=tags).

The error details :
Command error:
File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 264, in process
chain_features = self._process_single_chain(
File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 212, in _process_single_chain
chain_features = self._monomer_data_pipeline.process(
File "/app/alphafold/alphafold/data/pipeline.py", line 215, in process
hhblits_bfd_uniref_result = run_msa_tool(
File "/app/alphafold/alphafold/data/pipeline.py", line 96, in run_msa_tool
result = msa_runner.query(input_fasta_path)[0]
File "/app/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:

08:13:33.989 INFO: Searching 65983866 column state sequences.

08:13:35.413 INFO: Searching 29291635 column state sequences.

08:13:35.474 INFO: /tmp/tmppquf5va_.fasta is in A2M, A3M or FASTA format

08:13:35.474 INFO: Iteration 1

08:13:35.534 INFO: Prefiltering database

08:15:52.049 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1212889

08:19:04.295 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 497133

08:19:05.660 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 2000

08:19:05.660 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 2000

08:19:05.660 INFO: Scoring 2000 HMMs using HMM-HMM Viterbi alignment

08:19:05.838 INFO: Alternative alignment: 0

08:19:05.840 ERROR: In /tmp/hh-suite/src/hhdatabase.cpp:443: getTemplateHMM:

08:19:05.840 ERROR: Unrecognized HMM file format in '468479486'.

08:19:05.840 ERROR: Context:
'DEFGEARMVCGGVSADDFSLSADHSSAGEAAASGGWTVVPGGGFGAGGEKALTTGDTEVH-----------------RETSLCVIASE-----SSASKS---------------------------------

08:19:05.840 ERROR: >SRR5208283_2706711

08:19:05.840 ERROR: --------------------------------------------------------------VELHRMPLPRAGLPLAARAGAQLFRHLLQPSGRTHFADLFPAGRYAALRCSPLDDLGAAGLVCGGIPPDRLALSSDHSRAGAAAASAGWAVVPGGMPGAGGEEELTTGTPRNTG----------------IHRA---------------------------------------------------'

Please help us resolve this issue. Thanks in advance

Command used and terminal output

No response

Relevant files

nextflow.log.log

System information

Nextflow version: 23.10.1
Version of nf-core/proteinfold: dev
Container engine: Docker

[JoseEspinosa]

Thanks for reporting @asmaali98, could you try to add to your nextflow command --full_dbs false this way the reduced version of the bfd database will be used. In principle this shouldn't have any significant impact in the results while I think it will fixed the issue.

[JoseEspinosa]

Closed by inactivity