Mutserve crashes after incomplete analysis

[yganwork]

Hi,

I recently discovered your tool and I am using mutserve (v2.0.3) to detect variants in the mouse mitogenome. I am using the following command-line:

mutserve call --reference {mtFasta} --contig-name MT --output {vcfFile} {bamFile}

The tool seems to partially work, as it generates a {sampleName}_mutserve.txt file which lists detected variants in a tabular format. But before it can produce the output vcf file it stops with the following error:

✔️  Merge output files
htsjdk.samtools.SAMException: Sequence name 'MT dna:chromosome chromosome:GRCm39:MT:1:16299:1 REF' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*' 
	at htsjdk.samtools.SAMSequenceRecord.validateSequenceName(SAMSequenceRecord.java:336)

Is there a solution for this? Thank you for dealing with my question.

[seppinho]

Just rename the name of your contig (header line of your reference) to a simpler name