java.lang.IllegalArgumentException: Invalid reference index -1

[ianaebutler]

I am getting the following error message when trying to run the variant caller tool. I saw someone had a similar error in another thread, which was solved by removing spaces from the reference title #43. There are no spaces in the reference title in my sample, but I think the problem must be with the format of either the reference or the index file. Any other ideas about what could be causing the error?

call, --reference=sample72mtassembly.fasta, --output, sample72out.txt, --threads, 4, sample72_sorted_mappedreadsonly.bam]
❌ sample72_sorted_mappedreadsonly.bam[>-------------------------------------][00:00:00]
java.lang.IllegalArgumentException: Invalid reference index -1
at htsjdk.samtools.QueryInterval.(QueryInterval.java:24)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538)
at genepi.mut.tasks.VariantCallingTask.run(VariantCallingTask.java:129)
at lukfor.progress.tasks.Task.call(Task.java:39)
at lukfor.progress.tasks.Task.call(Task.java:1)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
java.lang.Exception: Invalid reference index -1
at genepi.mut.tasks.VariantCallingTask.run(VariantCallingTask.java:133)
at lukfor.progress.tasks.Task.call(Task.java:39)
at lukfor.progress.tasks.Task.call(Task.java:1)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
Variant Calling failed. Mutserve terminated.

[izu0421]

I got the same problem... do you have any progress on this? thanks!

[haansi]

Sorry for the delay - could you try to set the parameter "--contig-name" to the respective name in the fasta reference? Is the reference length equal to 16569 (i.e. length of rCRS/chrM in GRCh38)?

[izu0421]

This worked fine, thanks a lot! I was using mutserve for my own sample and specifying contig-name solved the issue.