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nf-core / proteinfold

Protein 3D structure prediction pipeline
https://nf-co.re/proteinfold
MIT License
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Database uniref30_2202_db does not exist while running colabfold local #121

Open nash73b91203005 opened 1 year ago

nash73b91203005 commented 1 year ago

Description of the bug

The python code search.py cannot find uniref30_2202_db even though I already specified the path. Maybe I lost something important? Thanks a lot in advance.

ERROR ~ Error executing process > 'NFCORE_PROTEINFOLD:COLABFOLD:MMSEQS_COLABFOLDSEARCH (T478K_T1)' Caused by: Process NFCORE_PROTEINFOLD:COLABFOLD:MMSEQS_COLABFOLDSEARCH (T478K_T1) terminated with an error exit status (1) Traceback (most recent call last): File "/colabfold_batch/colabfold-conda/bin/colabfold_search", line 8, in sys.exit(main()) File "/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/mmseqs/search.py", line 444, in main threads=args.threads, File "/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/mmseqs/search.py", line 66, in mmseqs_search_monomer raise FileNotFoundError(f"Database {db} does not exist") FileNotFoundError: Database uniref30_2202_db does not exist

Command used and terminal output

nextflow -bg run nf-core/proteinfold --input samplesheet.csv --outdir ./ --mode colabfold --colabfold_server local --num_recycle 3 --use_amber false --colabfold_model_preset AlphaFold2-ptm --use_gpu false --db_load_mode 0 -profile docker --colabfold_db_path ./colabfold_envdb_202108 --uniref30_path ./uniref30_2202_db --colabfold_alphafold2_params_path ./alphafold_params_2021-07-14 --max_memory 80.GB --colabfold_db ./

Relevant files

No response

System information

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JoseEspinosa commented 7 months ago

Hi @nash73b91203005 thanks for reporting. Are you sure you provided the correct path to uniref? I tried to reproduce your error and I can only do it when I provide a wrong path to the --uniref30_path parameter.

JoseEspinosa commented 5 months ago

Closed by inactivity, if you need any further assistance feel free to reopen it

vrennie commented 4 months ago

Hi @JoseEspinosa I have the same issue, directory looks like this, seems as though all files are there. Any ideas what might be going wrong?

Thanks

image
JoseEspinosa commented 4 months ago

Which version of the pipeline are you using? Could you also provide the command you used to run the pipeline and any config you are using?