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No such file or directory: 'pdb100_2022Apr19/pdb100_2022Apr19_pdb.ffindex' #4

Closed blauemond closed 8 months ago

blauemond commented 8 months ago

When I run the followings: singularity run SE3nv-20240131.sif -m rf2aa.run_inference --config-name protein It reports this error:

Error executing job with overrides: [] 
Traceback (most recent call last): 
  File "/xcfhome/yzmeng/tools/fold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 205, in main
    runner = ModelRunner(config)
  File "/xcfhome/yzmeng/tools/fold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 27, in __init__
    self.ffdb = FFindexDB(read_index(config.database_params.hhdb+'_pdb.ffindex'),
  File "/xcfhome/yzmeng/tools/fold/RoseTTAFold-All-Atom/rf2aa/ffindex.py", line 21, in read_index
    fh = open(ffindex_filename, "r")
FileNotFoundError: [Errno 2] No such file or directory: 'pdb100_2022Apr19/pdb100_2022Apr19_pdb.ffindex''

But after I manually changed the PDB database path name in base.yaml, the error will still occur. How can I solve this problem, or is there any other way to use it.

Takk522 commented 8 months ago

老哥，你这个bug解决了吗，我也遇到这个问题了

Rolando-at-Arzeda commented 8 months ago

Hi If by any chance you are using a symlink instead of the real directory, it will not work well with the container, directories and files should be "real"

denizkavi commented 8 months ago

I am keeping my dbs in /data/ so I modified my config at "rf2aa/config/inference/base.yaml" to include that path:

job_name: "structure_prediction"
output_path: ""
checkpoint_path: RFAA_paper_weights.pt
database_params:
  sequencedb: ""
  hhdb: "/data/pdb100_2021Mar03/pdb100_2021Mar03"
  command: make_msa.sh
  num_cpus: 4
  mem: 64

Then, you can bind your path to the container to use: sudo /usr/bin/apptainer run --bind /data:/data SE3nv-20240131.sif -m rf2aa.run_inference --config-name protein

r-krishna commented 8 months ago

hello @amorehead has created a PR that installs dependencies using mamba (this is now merged in main). let me know if this solves your problem