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4.7 years ago
QVINTVS_FABIVS_MAXIMVS
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2.6k
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?
Check with
topif the tool is really running or if some I/O bottlenecks or a malfunction in the file servers reduces performance.