gemini query error

Question

[krismopolitan]

Hi,

I'm trying to query a gemini database made from a merged vcf file and a ped file.

The vcf was made from WGS reads by using speedseq i.e. FreeBayes caller.

The PED file looks like this:

3 Sample_6-F3S4-77749 -9 -9 -9 ALL
3 Sample_7-F3S5-77750 -9 -9 -9 ALL

I have tried running several queries, but every single one gives me this error:

  File "/services/tools/anaconda2/4.0.0/bin/gemini", line 6, in <module>
    gemini.gemini_main.main()
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_main.py", line 1227, in main
    args.func(parser, args)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_main.py", line 422, in query_fn
    gemini_query.query(parser, args)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_query.py", line 167, in query
    run_query(args)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_query.py", line 122, in run_query
    subjects = get_subjects(args)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_subjects.py", line 136, in get_subjects
    gq = GeminiQuery.GeminiQuery(args.db)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/GeminiQuery.py", line 550, in __init__
    self.idx_to_sample_object = {s['sample_id'] -1: Subject(s) for s in samples}
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/GeminiQuery.py", line 550, in <dictcomp>
    self.idx_to_sample_object = {s['sample_id'] -1: Subject(s) for s in samples}
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_subjects.py", line 63, in __init__
    self._set_fields_from_row(row)
  File "/services/tools/anaconda2/4.0.0/lib/python2.7/site-packages/gemini/gemini_subjects.py", line 79, in _set_fields_from_row
    self.phenotype = int(self.phenotype) if self._has_phenotype() else None
ValueError: invalid literal for int() with base 10: 'ALL'

Anyone have an idea of how to fix this?

Thank you,

Answer 1

[krismopolitan]

HI again,

Just in case anyone with a similar problem stumbles upon this thread; I managed to run without problems simply by not specifying the phenotype, i.e. changed the .ped file to

3 Sample_6-F3S4-77749 -9 -9 -9 -9
3 Sample_7-F3S5-77750 -9 -9 -9 -9

and reloaded the gemini database.

Bw.