MarkDups takes much longer than expected???
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18 months ago

In the past, my 40x WGS BAMs take about 2-6 hours to run sambamba markdups with 12-24 threads. I have received a batch of BAMs that are taking over 7 days to run. The file size is the same, and so is the sequencing center.

Any ideas what could cause this step to take much longer than expected?

MarkDup Sambamba • 313 views
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Check with top if the tool is really running or if some I/O bottlenecks or a malfunction in the file servers reduces performance.