Realigned BAM output producing an error

[poxon]

Hello,

I tried running the latest version with option for outputting realigned BAM set to 1 but sadly there is an error in the samtools command:

2017-10-09T14:41:23.315974622Z [2017-10-09T14:41:23.315688] [beb8080319ee] [13_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'CallGenome+sortRealignedSegment_normal_chromId_080_GL000193_1_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '"/opt/strelka-2.8.3/libexec/samtools" sort "StrelkaSomaticWorkflow/workspace/genomeSegment.tmpdir/normal.chromId_080_GL000193_1_0000.unsorted.realigned.bam" "StrelkaSomaticWorkflow/workspace/genomeSegment.tmpdir/normal.chromId_080_GL000193_1_0000.realigned" && rm -f "StrelkaSomaticWorkflow/workspace/genomeSegment.tmpdir/normal.chromId_080_GL000193_1_0000.unsorted.realigned.bam"'
...Some lines omitted...
[CallGenome+sortRealignedSegment_normal_chromId_080_GL000193_1_0000] Usage: samtools sort [options...] [in.bam]
...

As far as I can see the command line for samtools is not correct. Could it be that the -o argument is missing for the output filename or at least a redirection >?

Thank you in advance.

[ctsa]

Sorry I believe the realigned BAM option has escaped our test attention for a while now. I confirm this is not working. We will fix or withdraw this feature in the next patch update.

[ctsa]

I've just pushed the v2.8.4 release which should fix this issue. Please re-open this ticket if you are still experiencing problems.

https://github.com/Illumina/strelka/releases/tag/v2.8.4