Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FilterFasta also need to adjust to new noncoding_peptides format? #675

Closed
lydiayliu opened this issue Feb 7, 2023 · 0 comments · Fixed by #677
Closed

FilterFasta also need to adjust to new noncoding_peptides format? #675

lydiayliu opened this issue Feb 7, 2023 · 0 comments · Fixed by #677
Labels
bug Something isn't working priority: now Issue to be fixed immediately

Comments

@lydiayliu
Copy link
Collaborator

lydiayliu commented Feb 7, 2023

Getting this error

      846c0b181fff: Download complete
      f96e9dd83687: Download complete
      846c0b181fff: Pull complete
      f96e9dd83687: Pull complete
      Digest: sha256:782a0162eae1a83cc4a16398c42b38a089b83b54a564db0fb394aa92656895e7
      Status: Image is up to date for ghcr.io/uclahs-cds/mopepgen:0.11.2
      [ 2023-02-07 21:49:31 ] moPepGen filterFasta started
      [ 2023-02-07 21:50:14 ] Peptide FASTA file loaded.
      [ 2023-02-07 21:50:15 ] Gene expression table loaded.
      Traceback (most recent call last):
        File "/usr/local/bin/moPepGen", line 8, in <module>
          sys.exit(main())
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 89, in main
          args.func(args)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/filter_fasta.py", line 193, in filter_fasta
          filtered_pool = pool.filter(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/VariantPeptidePool.py", line 103, in filter
          for x in entry.get_transcript_ids())
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/VariantPeptideLabel.py", line 261, in get_transcript_ids
          raise ValueError('Variant ID unrecognized')
      ValueError: Variant ID unrecognized
    
    Work dir:
      work/60/e26ee93d05c26e7a6e3631ba35d222
    
    Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
    
    
  
  Work dir:
    /scratch/a7/5482af9f3b5b4c44beed6d78aff0a3
  
  Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Maybe also worth double checking all the other steps LOL, like merge and split?

@lydiayliu lydiayliu added bug Something isn't working priority: now Issue to be fixed immediately labels Feb 7, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working priority: now Issue to be fixed immediately
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant