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ISUgenomics / SequelTools

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QC samtools and awk steps run on 1 thread? #10

Open KristinaGagalova opened 3 years ago

KristinaGagalova commented 3 years ago

Hi, I had several files and I've noticed that it took quite a lot of time to run the QC even with -n 24 option. Looks like the awk and samtools stages are single thread? That can be easily run in parallel for multiple files Thank you in advance

DavidEHufnagel commented 3 years ago

Samtools does indeed use multiple threads when you specify -n 24. Samtools is the only part of SequelTools that takes advantage of this argument, but it will speed up the process.

Good luck with your research! Best, Dr. David E. Hufnagel

On Tue, Nov 10, 2020 at 12:52 PM Kristina Gagalova notifications@github.com wrote:

Hi, I had several files and I've noticed that it took quite a lot of time to run the QC even with -n 24 option. Looks like the awk and samtools stages are single thread? That can be easily run in parallel for multiple files Thank you in advance

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KristinaGagalova commented 3 years ago

I am giving a list of bam files and it looks like its running them one at the time. I believe that one can be multi-threaded as well. Just a suggestion of course. Thank you again