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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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Empty line at the end of ped file breaks gemini load command #924

Closed mvelinder closed 5 years ago

mvelinder commented 5 years ago

$ gemini load -v platinum-exome.vcf.gz.vep.vcf.gz -t VEP -p platinum.ped --cores 40 platinum-exome.vcf.gz.vep.vcf.gz.gem.db

CADD scores are not being loaded because the annotation file could not be found. Run gemini update --dataonly --extra cadd_score to install the annotation file.

GERP per bp is not being loaded because the annotation file could not be found. Run gemini update --dataonly --extra gerp_bp to install the annotation file.

Loading 123078 variants. Breaking /scratch/ucgd/lustre-work/marth/u0691312/sandbox/bayesian_acmg/platinum-exome.vcf.gz.vep.vcf.gz into 40 chunks. Loading chunk 0. Loading chunk 1. Loading chunk 2. Loading chunk 3. Loading chunk 4. Loading chunk 5. Loading chunk 6. Loading chunk 7. Loading chunk 8. Loading chunk 9. Loading chunk 10. Loading chunk 11. Loading chunk 12. Loading chunk 13. Loading chunk 14. Loading chunk 15. Loading chunk 16. Loading chunk 17. Loading chunk 18. Loading chunk 19. Loading chunk 20. Loading chunk 21. Loading chunk 22. Loading chunk 23. Loading chunk 24. Loading chunk 25. Loading chunk 26. Loading chunk 27. Loading chunk 28. Loading chunk 29. Loading chunk 30. Loading chunk 31. Loading chunk 32. Loading chunk 33. Loading chunk 34. Loading chunk 35. Loading chunk 36. Loading chunk 37. Loading chunk 38. Loading chunk 39. Traceback (most recent call last): File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/tools/bin/gemini", line 7, in gemini_main.main() File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main args.func(parser, args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn gemini_load_chunk.load(parser, args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples Traceback (most recent call last): File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/tools/bin/gemini", line 7, in self.ped_hash = load_ped_file(self.args.ped_file) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 35, in load_ped_file gemini_main.main() File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main fields = [x.strip() for x in _fix_ped_family_fields(parts)] File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 58, in _fix_ped_family_fields args.func(parser, args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 311, in loadchunk_fn if fields[field] in missing_member: IndexError: list index out of range gemini_load_chunk.load(parser, args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 910, in load gemini_loader = GeminiLoader(args) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 132, in init self._prepare_samples() File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 770, in _prepare_samples self.ped_hash = load_ped_file(self.args.ped_file) File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 35, in load_ped_file fields = [x.strip() for x in _fix_ped_family_fields(parts)] File "/uufs/chpc.utah.edu/common/HIPAA/u0691312/bin/gemini/data/anaconda/lib/python2.7/site-packages/gemini/ped.py", line 58, in _fix_ped_family_fields if fields[field] in missing_member:

-- before ctrl+c killing it