Hi,

I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think  I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out.
Thanks in advance for any help.
Cheers
Mike
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