java.lang.IllegalArgumentException: Invalid reference index -1

[thesnakeguy]

Dear seppinho,

I am having trouble using mutserve call with whole mitogenome data. I get the following error when running the program:

File.bam[>-------------------------------------][00:00:00]
 null[>-------------------------------------][00:00:00]
java.lang.IllegalArgumentException: Invalid reference index -1
        at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
        at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538)
        at genepi.mut.tasks.VariantCallingTask.run(VariantCallingTask.java:129)
        at lukfor.progress.tasks.Task.call(Task.java:39)
        at lukfor.progress.tasks.Task.call(Task.java:8)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
java.lang.Exception: Invalid reference index -1
Variant Calling failed. Mutserve terminated.

This is my workflow:

samtools faidx $GENOME
bwa mem -t $THREADS -R $RG $GENOME $fq1 $fq2 > $sam
samtools view -@ $THREADS -b $sam > $bam     
samtools sort -@ $THREADS $bam > $sorted_bam 
samtools index $sorted_bam
$MUT/mutserve call $sorted_bam --baseQ 25 --level 0.05 --output $variants --write-fasta true --threads $THREADS --reference=$GENOME

What am I doing wrong here? Many thanks!

Kind regards

[thesnakeguy]

Solved! The refence title contained spaces