QC samtools and awk steps run on 1 thread?

[KristinaGagalova]

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]

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

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On Tue, Nov 10, 2020 at 12:52 PM Kristina Gagalova ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQPE3O7R5J2KEGAHBBQT3DSPGDYHANCNFSM4TRA7RSQ> .

[KristinaGagalova]

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