The Samtools sort command seems to have changed from earlier versions and now fails when using Samtools version 1.3+ with the following error message:
File specified as unsorted paired-end BAM file
Sorting BAM file 'test.bam' by read IDs ...
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
This probably just needs specifically specifying the outfile explicitly.
The Samtools sort command seems to have changed from earlier versions and now fails when using Samtools version 1.3+ with the following error message:
File specified as unsorted paired-end BAM file Sorting BAM file 'test.bam' by read IDs ...
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
This probably just needs specifically specifying the outfile explicitly.