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PuffAligner significantly slower at mapping and thread usage is much less than specified when running with --compressedOutput #42

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hermidalc opened this issue Oct 24, 2022 · 1 comment
Open

PuffAligner significantly slower at mapping and thread usage is much less than specified when running with --compressedOutput #42

hermidalc opened this issue Oct 24, 2022 · 1 comment

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@hermidalc
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I've test both with --compressedOutput and without, and surprised how much slower align is when it is activated, writing of the compressed SAM file becomes a bottleneck to the entire command, and thread usage is much lower than what is specified. This is surprising as I haven't see writing to a compressed stream to cause such a bottleneck and change in performance with other tools.
@hermidalc
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It's much faster to not use --compressedOutput and pigz the SAM file afterwards. Then align uses all the threads that are specified and maps at a much faster speed

@hermidalc hermidalc changed the title Align significantly slower at mapping and thread usage much less than specified when running with --compressedOutput PuffAligner significantly slower at mapping and thread usage is much less than specified when running with --compressedOutput Oct 24, 2022
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@hermidalc