total=ERROR: could not find sequence of contig '20' mouse genome (mm39)

[SimJohal]

Hi,

I am trying to use Arriba on some mouse samples and using the appropriate files provided in download_references.sh but I am repeatedly getting the error 'total=ERROR: could not find sequence of contig '20'

I am running STAR piped into Arriba as in the demo script. I am including a blacklist and protein domains

I'd be grateful for any help provided!

[suhrig]

This error occurs when the BAM file contains alignments on chromosome 20, but the FastA file does not contain a sequence for this chromosome. Did you align this using a STAR index from human by any chance? Mouse only has 19 autosomes.

What command did you use to run download-references.sh?