Hi everyone! I'm having some issues running AFmultimer:

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  I0327 20:46:14.864375 139900343002944 templates.py:857] Using precomputed obsolete pdbs ./obsolete_pdb/obsolete.dat.
  E0327 20:46:14.875260 139900343002944 jackhmmer.py:75] Could not find Jackhmmer database ./uniref90/uniref90.fasta
  Traceback (most recent call last):
    File "/app/alphafold/run_alphafold.py", line 570, in <module>
      app.run(main)
    File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 312, in run
      _run_main(main, args)
    File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
      sys.exit(main(argv))
               ^^^^^^^^^^
    File "/app/alphafold/run_alphafold.py", line 486, in main
      monomer_data_pipeline = pipeline.DataPipeline(
                              ^^^^^^^^^^^^^^^^^^^^^^
    File "/app/alphafold/alphafold/data/pipeline.py", line 130, in __init__
      self.jackhmmer_uniref90_runner = jackhmmer.Jackhmmer(
                                       ^^^^^^^^^^^^^^^^^^^^
    File "/app/alphafold/alphafold/data/tools/jackhmmer.py", line 76, in __init__
      raise ValueError(f'Could not find Jackhmmer database {database_path}')
  ValueError: Could not find Jackhmmer database ./uniref90/uniref90.fasta

I have the following structure in the

full_dbs

:

├── bfd
├── mgnify
├── params
├── pdb70
├── pdb_mmcif
│   └── mmcif_files
├── pdb_seqres
├── small_bfd
├── uniprot
├── uniref30
└── uniref90

All the files that were .gz are not longer compressed. If I check the directory of

Uniref90

that is related with the error message:

├── nohup.out
├── uniref90.fasta
└── uniref90.fasta.gz

I have both files

fasta

and

fasta.gz

I'm not completely sure why is this issue, looks that I'm missing something here, Please feel free to comment! All comments are greatly appreciated! Thank you

hi, would you mind posting the command you used to run the pipeline

Sorry, I totally forgot that. Here the command:

nextflow run nf-core/proteinfold -r dev -resume --input '/users/mmora30/mmora30/workspace/alphafold/alphafold2/alphafold-2.3.1/run_01_h5n1/input/testing_files/samplesheet.csv' --outdir '/users/mmora30/mmora30/workspace/alphafold/alphafold2/alphafold-2.3.1/run_01_h5n1/output/testing_files_out' --mode alphafold2 --alphafold2_db '/users/mmora30/mmora30/workspace/alphafold/full_dbs' --full_dbs true --alphafold2_model_preset multimer --use_gpu true -profile singularity

I am trying to reproduce the error and I can not, the permission on my case are:

ll ~/db/alphafold/uniref90/
total 76G
-rwxr-xr-x 1 user foo 63G Apr 24  2024 uniref90.fasta

I will try to add the same permission and see what happens, I will let you know the results

maybe you can try to use the dbs that we made available at s3 by adding to your command

--uniref90_path <s3://proteinfold-dataset/db/alphafold/uniref90/uniref90.fasta|s3://proteinfold-dataset/db/alphafold/uniref90/uniref90.fasta>

My job is in

PD

stage so I do not know if the permission changes is working. > made available at s3 That sounds like a good alternative, do I need to perform any pre-installation to make that resource available in my HPC? Sorry for the question, I can not find documentation in the GitHub repository related to

s3

Thanks for reporting back!