Comments (4)
bozbezbozzel
commented on August 13, 2024
will try this suggestion: #678 and update
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bozbezbozzel
commented on August 13, 2024
My reference genome uses 1, 2, 3 etc... for the chromosomes and so do my sample bams:
less Homo_sapiens.GRCh38.dna.primary_assembly.fa | grep ">"
>1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
>10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF
>11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF
@HD VN:1.6 GO:none SO:coordinate
@SQ SN:1 LN:248956422 M5:2648ae1bacce4ec4b6cf337dcae37816
@SQ SN:10 LN:133797422 M5:907112d17fcb73bcab1ed1c72b97ce68
@SQ SN:11 LN:135086622 M5:1511375dc2dd1b633af8cf439ae90cec
I used the exact same reference genome file for every step and I'm coming from unmapped BAMs.
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bozbezbozzel
commented on August 13, 2024
Solved-- had to remove contigs from my antitarget and target input files.
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JiayangZhou
commented on August 13, 2024
got the same error, and my reference genome uses chr1, chr2..would you suggest I replace all with 1, 2, 3, and try again?
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