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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
126 stars 55 forks source link

unknown error <- the worst bug report. #55

Closed zeeev closed 7 years ago

zeeev commented 7 years ago

tabix -h ../ALL_Illumina_Integrate_20170206.vcf.gz chr4:140000000-150000000 | python ~/tools/svtyper/svtyper -B /net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00512.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00513.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00514.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00731.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00732.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/HG00733.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/NA19238.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/NA19239.bam,/net/eichler/vol24/projects/structural_variation/nobackups/bams/final/NA19240.bam -l lib.json 2> error

error

Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json...Reading library metrics from lib.json... done Traceback (most recent call last): File "/net/eichler/vol8/home/zevk/tools/svtyper/svtyper", line 1738, in sys.exit(main()) File "/net/eichler/vol8/home/zevk/tools/svtyper/svtyper", line 1733, in main args.alignment_outpath) File "/net/eichler/vol8/home/zevk/tools/svtyper/svtyper", line 1380, in sv_genotype vcf.add_header(header) File "/net/eichler/vol8/home/zevk/tools/svtyper/svtyper", line 70, in add_header self.add_info(*[b.split('=')[1] for b in r.findall(a)]) TypeError: add_info() takes exactly 5 arguments (4 given)

zeeev commented 7 years ago

Ok, just need error reporting, it's caused when SVTYPE isn't in the info field.

cc2qe commented 7 years ago

8637bc331085753b5a87afcd1503bd242b11eb39 throws a more informative error message if SVTYPE info field is missing