mutserve crashes before output gets generated

[suart-mvz]

Hi,

I downloaded mutserve via the downloader script from the repository.
Then I tried to execute mutserve with some bam files I downloaded from here: Heteroplasmy Benchmark Dataset
The command was ./mutserve call --reference <reference.fa> --output H1-mutserve.vcf.gz --thread 1 mito/*.bam
However when mutserve is about to finish the last bam file it throws this error:

java.lang.NullPointerException: Cannot invoke "java.lang.Throwable.printStackTrace()" because the return value of "lukfor.progress.tasks.TaskStatus.getThrowable()" is null
        at genepi.mut.commands.VariantCallingCommand.call(VariantCallingCommand.java:226)
        at genepi.mut.commands.VariantCallingCommand.call(VariantCallingCommand.java:35)
        at picocli.CommandLine.executeUserObject(CommandLine.java:1933)
        at picocli.CommandLine.access$1100(CommandLine.java:145)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2332)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2326)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2291)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2159)
        at picocli.CommandLine.execute(CommandLine.java:2058)
        at genepi.mut.App.main(App.java:62)

Is there something I can do to avoid this issue?

[rania-o]

Hello @suart-mvz

I have the same issue. But it's 5 seconds after starting to read the bam.
I don't have any issue when using it with the bam file provided for test.

Have you solved the problem?

Rania