I am using stampy for aligning against a reference genome but it seems to get stuck during the alignment process. For a single sorted.bam file, it will produce alignments for ~ 3mn and then does not produce anything. It says it is aligning but no more data are being produced, even after running my script for 12 hours. Here is what I tried:
- Reinstall stampy and reindex the genome
- Tried with different genome versions
- Tried with different sorted.bam files (including some that previously worked to align with stampy)
None of this helped.
Maybe it needs more time but I find it strange it is taking so long particularly for a sorted.bam file that is just 10MB. My sorted.bam files are from a BWA alignment, samtools view to create the .bam files and samtools sort to sort them.
Any thoughts or ideas are welcome!