Comments (2)
alexdobin
commented on June 26, 2024
Hi Rory,
this is very strange, I cannot imagine how STAR would use 60GB for this genome. Your parameters look OK.
It also looks like the mapping speed goes down significantly, though this may be caused by RAM swapping. I do not think that short reads would cause this. Do you expect that sequencing quality decreases towards the end of the file? If you take 1M reads from the end of the file, map them with 1 thread, do you see slow mapping and high memory usage?
It would be nice if you could get me a portion of the file that still exhibits the problem, so that I can try it on my system.
Cheers
Alex
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roryk
commented on June 26, 2024
Hi Alex,
We tracked this down to a memory leak in sambamba, which we were piping the output of STAR to. Sorry to waste your time. Thanks so much.
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Related Issues (20)
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