Entering edit mode
7.5 years ago
krismopolitan
•
0
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,