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
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