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

SeqSero2 1.0.2 fails on salmonella with O antigen 13 #24

Open
crashfrog opened this issue Nov 15, 2019 · 0 comments
Open

SeqSero2 1.0.2 fails on salmonella with O antigen 13 #24

crashfrog opened this issue Nov 15, 2019 · 0 comments

Comments

@crashfrog
Copy link

Doesn't correctly resolve paths to special database files:

Traceback (most recent call last):
  File "/tool/shed_tools/toolrepo.galaxytrakr.org/repos/estrain/ss2v102/558823a8c53a/ss2v102/SeqSero2_package.py", line 1473, in <module>
    main()
  File "/tool/shed_tools/toolrepo.galaxytrakr.org/repos/estrain/ss2v102/558823a8c53a/ss2v102/SeqSero2_package.py", line 1310, in main
    predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies)
  File "/tool/shed_tools/toolrepo.galaxytrakr.org/repos/estrain/ss2v102/558823a8c53a/ss2v102/SeqSero2_package.py", line 461, in seqsero_from_formula_to_serotypes
    f = open(ex_dir + '/special.pickle', 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tool/shed_tools/toolrepo.galaxytrakr.org/repos/estrain/ss2v102/558823a8c53a/seqsero2_db/special.pickle'

This error can be replicated using sequencing data available at the SRA under accession SRR9326726.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant