sokrypton / sokrypton/ColabFold
fail in colabfold_search.sh with bfd_mgy_colabfold
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Description
I download uniref30_2103 and bfd_mgy_colabfold from https://colabfold.mmseqs.com/, following the steps to create the respective _db. Then run colabfold_search.sh against uniref30_2103_db and bfd_mgy_colabfold_db. I only got the alignment uniref.a3m. The profile search against bfd_mgy_colabfold_db failed with the following error (in the step of 'mmseqs expandaln'):
terminate called after throwing an instance of 'std::logic_error'
It seems that all intermediate files with res_env_exp* are empty.
PS: I am able to run through uniref30_2103_db+colabfold_envdb_202108. I guess there are some issue with the bfd_mgy_colabfold database?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with colabfold_search.sh and reproduce the search using uniref30_2103_db and bfd_mgy_colabfold_db. Inspect the mmseqs expandaln step and the res_env_exp* intermediate files, then compare the behavior with colabfold_envdb_202108. Done means identifying why the bfd_mgy_colabfold profile search fails and documenting or correcting the database-specific issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics, cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100