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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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vcfanno bug #3728

Open wangpenhok opened 1 year ago

wangpenhok commented 1 year ago

Version info

To Reproduce Exact bcbio command you have used:

Your yaml configuration file:

Log files (could be found in work/log) Please attach (10MB max): bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.

=============================================
vcfanno version 0.3.3 [built with go1.16.5]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:116: found 62 sources from 5 files
vcfanno.go:146: using 2 worker threads to decompress bgzip file
api.go:811: WARNING: using op 'self' when with Number='1' for 'CAF' from '/home/data/bcbio/genomes/Hsapiens/hg38/variation/dbsnp.vcf.gz' can result in out-of-order values when the query is multi-allelic
api.go:812:        : this is not an issue if the query has been decomposed.
api.go:811: WARNING: using op 'self' when with Number='1' for 'CLNDBN' from '/home/data/bcbio/genomes/Hsapiens/hg38/variation/clinvar.vcf.gz' can result in out-of-order values when the query is multi-allelic
api.go:812:        : this is not an issue if the query has been decomposed.
api.go:811: WARNING: using op 'self' when with Number='1' for 'GENEINFO' from '/home/data/bcbio/genomes/Hsapiens/hg38/variation/clinvar.vcf.gz' can result in out-of-order values when the query is multi-allelic
api.go:812:        : this is not an issue if the query has been decomposed.
panic: runtime error: slice bounds out of range [177:170]
goroutine 196 [running]:
github.com/brentp/bix.makeFields(0xc008dbc0b0, 0xaa, 0xab, 0x7f4e41, 0x2, 0xc008dbc0b0)
        /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/bix.go:291 +0x2db
github.com/brentp/bix.(*bixerator).inBounds(0xc007701d90, 0xc008dbc0b0, 0xaa, 0xab, 0xab, 0x0, 0x0, 0xc0003ec000, 0x7b30a0, 0x7dfc80)
        /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/bix.go:449 +0xab
github.com/brentp/bix.bixerator.Next(0x8732d0, 0xc003a63680, 0xc00202cf00, 0xc00202cd80, 0x875350, 0xc000b2fd60, 0xc001026240, 0x2, 0x0, 0x0)
        /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/bix.go:329 +0xf7
github.com/brentp/irelate.newMerger(0x812600, 0x0, 0xc001f71f20, 0x6, 0x6, 0x38d74cf8c39)
        /home/brentp/go/go/pkg/mod/github.com/brentp/irelate@v0.0.1/irelate.go:235 +0x142
github.com/brentp/irelate.IRelate(0x8125f8, 0x0, 0x812600, 0xc001f71f20, 0x6, 0x6, 0x38d74cfa809, 0x38d74cfa809)
        /home/brentp/go/go/pkg/mod/github.com/brentp/irelate@v0.0.1/irelate.go:143 +0x5d
github.com/brentp/irelate.PIRelate.func3.1(0xc00065d2c0, 0x8125c8, 0xc003a62c30, 0xc001f71f20, 0x6, 0x6)
        /home/brentp/go/go/pkg/mod/github.com/brentp/irelate@v0.0.1/parallel.go:245 +0x7b
created by github.com/brentp/irelate.PIRelate.func3
        /home/brentp/go/go/pkg/mod/github.com/brentp/irelate@v0.0.1/parallel.go:242 +0x10c
' returned non-zero exit status 2.