samtools view run into "uninterruptible sleep" status
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6.9 years ago
Pei ▴ 140

Hi all:

I try to run ten samtools view jobs simultaneously, and found that most of them usually change from "R" to "D" when examined by the top cmd. Do you think it is nothing strange since I submit too much jobs? The %cpu and %mem seemed to be quite normal.

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linux • 1.2k views
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That won't be CPU or memory bound, it's IO limited. Unless you have only solid state hard drives it's unlikely that you can effectively use more than a few instances at once. Note also that the compression part can be multithreaded (the -@ option).

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Thanks you!