sokrypton / sokrypton/ColabFold

terminate called after throwing an instance of 'std::logic_error'

Open
#732 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Jupyter Notebook
Stars
2.9k
Forks
747
PR merge metrics
No merged PRs in 30d

Description

This is my shell
(/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda) lyy@lyy-System-Product-Name:~/Desktop$ colabfold_search /home/lyy/Desktop/VenusREM/data/proteingym_v1/aa_seq/A0A1I9GEU1_NEIME_Kennouche_2019.fasta /home/lyy/data/db_folder msas

Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
Index version: 16
Generated by: 17.b804f
ScoreMatrix: VTML80.out
[=================================================================] 100.00% 1 eta -
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string: construction from null is not valid
Traceback (most recent call last):
File "/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda/bin/colabfold_search", line 8, in
sys.exit(main())
File "/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 319, in main
mmseqs_search_monomer(
File "/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 94, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["expandaln", base.joinpath("qdb"), dbbase.joinpath(f"{uniref_db}{dbSuffix1}"), base.joinpath("res"), dbbase.joinpath(f"{uniref_db}{dbSuffix2}"), base.joinpath("res_exp"), "--db-load-mode", str(db_load_mode), "--threads", str(threads)] + expand_param)
File "/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 25, in run_mmseqs
subprocess.check_call([mmseqs] + params)
File "/home/lyy/Desktop/ColabFold/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'expandaln', PosixPath('msas/qdb'), PosixPath('/home/lyy/data/db_folder/uniref30_2302_db.idx'), PosixPath('msas/res'), PosixPath('/home/lyy/data/db_folder/uniref30_2302_db.idx'), PosixPath('msas/res_exp'), '--db-load-mode', '0', '--threads', '64', '--expansion-mode', '0', '-e', 'inf', '--expand-filter-clusters', '1', '--max-seq-id', '0.95']' died with <Signals.SIGABRT: 6>.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the reported colabfold/mmseqs/search.py call at mmseqs_search_monomer line 94 and run_mmseqs line 25, then reproduce the colabfold_search command using the shown database paths. Inspect the mmseqs expandaln invocation and its SIGABRT output; done means the reported search completes without the basic_string null exception or the cause is documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.