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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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FILTER 'REJECT' is not defined in the header #1586

Closed JoKw closed 7 years ago

JoKw commented 7 years ago

Hi, I ran freebayes, scalpel, varscan and vardict for ensemble calling, but I ended up getting the error below. Is there any solution without rerunning the whole calling procedure from the beginning. Thanks

CalledProcessError: Command 'set -o pipefail; /usr/local/share/bcbio/anaconda/bin/bcftools concat --allow-overlaps -O z --file-list /test/work/scalpel/test-files.list -o /test/work/scalpel/tx/tmp8Vbs4E/NBvMB.vcf.gz [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header [W::vcf_parse] FILTER 'REJECT' is not defined in the header

chapmanb commented 7 years ago

Apologies about the problem and thanks for the report. Would you be able to paste the entire error message, including information up and downstream of this? Right now I can't tell why the concat command fails. We have warning messages from bcftools but those shouldn't trigger a failure. There are probably some useful error messages upstream indicating why the GATK attempt at CatVariants failed and we fell back to bcftools concat that might be diagnostic. Thanks much for the help debugging.

JoKw commented 7 years ago

Hi Brad, I have sent the log files to your fastmail.

chapmanb commented 7 years ago

Johnny; Thanks for the additional details, this helps a lot. scalpel is not supported as a standalone caller in bcbio, which is what triggers this error. It can only be used as a supplemental caller to add indels to SNP only callers (mutect currently). If you want to include it you could do with:

variantcaller: [freebayes, vardict, varscan, mutect]
indelcaller: scalpel

and that should work correctly. Alternatives you can remove scalpel from variantcaller and run with the other 3 callers.

Either way, you can edit your configuration and restart in place and it will pick up where it left off. Hope this helps.