sokrypton / sokrypton/ColabFold

In colabfold_search GPU mmseqs not compatible with `--use-templates 1`

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Description

In this line:
https://github.com/sokrypton/ColabFold/blob/406d4c6cf25a0755f61b3adac7c5d47d3025f42c/colabfold/mmseqs/search.py#L171

The --gpu 1 parameter is not propagated from the command line.

I built the local databases with:
GPU=1 ./setup_databases.sh /path/to/db_folder
as in the documentation.

When my run gets to the template search, it runs the command:

mmseqs search msas/prof_res /mnt/rbg/sequence_databases/colabfold_db/pdb100_230517 msas/res_pdb msas/tmp2 --db-load-mode 1 --threads 64 -s 7.5 -a -e 0.1 --prefilter-mode 0

and crashes with this error:

Index version: 16
Generated by:  8ef870f95af2a3ee474c2cdbb845f5f007fe5be6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Profile
Estimated memory consumption: 1G
Target database size: 329605 type: Aminoacid
Invalid database read for database data file=/mnt/rbg/sequence_databases/colabfold_db/pdb100_230517.idx, database index=/mnt/rbg/sequence_databases/colabfold_db/pdb100_230517.idx.index
getData: local id (4294967295) >= db size (17)
Error: Prefilter died

I can get the search to complete by modifying the command to:

mmseqs search msas/prof_res /mnt/rbg/sequence_databases/colabfold_db/pdb100_230517 msas/res_pdb msas/tmp2 --db-load-mode 1 --threads 64 -s 7.5 -a -e 0.1 --prefilter-mode 1 --gpu 1

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First steps

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Research direction

Start at colabfold/mmseqs/search.py line 171 and inspect how the template-search command is assembled from command-line options. Reproduce the local-database search with GPU-enabled mmseqs and verify that the generated command includes the required GPU settings and completes without the reported prefilter error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
55/100

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