openfold-multimer branch ：Error: Oops. Wait. I need name annotation on each alignment in a multi MSA file; failed on #3

[liweiqing1997]

When I ran the openfold-multimer branch code to infer the multi-chain amino acid sequence, I encountered the following error. Can someone tell me the solution.

(openfold_venv) [lwq@alphafold2-1 openfold-multimer]$ cd /data/lwq/openfold-multimer ; /usr/bin/env /data/lwq/openfold-multimer/lib/conda/envs/openfold_venv/bin/python /data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher 37577 -- /data/lwq/openfold-multimer/run_pretrained_openfold.py alignments begin. Traceback (most recent call last): File "/data/lwq/openfold-multimer/lib/conda/envs/openfold_venv/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/data/lwq/openfold-multimer/lib/conda/envs/openfold_venv/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher/../../debugpy/main.py", line 39, in cli.main() File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher/../../debugpy/../debugpy/server/cli.py", line 430, in main run() File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher/../../debugpy/../debugpy/server/cli.py", line 284, in run_file runpy.run_path(target, run_name="main") File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 322, in run_path pkg_name=pkg_name, script_name=fname) File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 136, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "/data/lwq/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/python/debugpy/_vendored/pydevd/_pydevd_bundle/pydevd_runpy.py", line 124, in _run_code exec(code, run_globals) File "/data/lwq/openfold-multimer/run_pretrained_openfold.py", line 355, in main(args) File "/data/lwq/openfold-multimer/run_pretrained_openfold.py", line 168, in main fasta_path, local_alignment_dir File "/data/lwq/openfold-multimer/openfold/data/data_pipeline.py", line 414, in run output_dir=output_dir File "/data/lwq/openfold-multimer/openfold/data/tools/hmmsearch.py", line 79, in query model_construction='hand' File "/data/lwq/openfold-multimer/openfold/data/tools/hmmbuild.py", line 59, in build_profile_from_sto return self._build_profile(sto, model_construction=model_construction) File "/data/lwq/openfold-multimer/openfold/data/tools/hmmbuild.py", line 132, in _build_profile % (stdout.decode('utf-8'), stderr.decode('utf-8'))) RuntimeError: hmmbuild failed

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.

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input alignment file: /tmp/tmp52zxvifp/query.msa

output HMM file: /tmp/tmp52zxvifp/output.hmm

input alignment is asserted as: protein

model architecture construction: hand-specified by RF annotation

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idx name nseq alen mlen eff_nseq re/pos description

#---- -------------------- ----- ----- ----- -------- ------ -----------

stderr:

Error: Oops. Wait. I need name annotation on each alignment in a multi MSA file; failed on #3