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Old 09-09-2017, 11:53 PM   #1
tirohia
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Location: Auckland, NZ

Join Date: Nov 2011
Posts: 45
Default Hisat2 multithreading not working.

As best I can see, this should be working. I've got 16 cores:

Code:
$ grep -c ^processor /proc/cpuinfo     
16
I then attempt to use hisat2 with multiple threads. I've tried using both --threads -p
Code:
hisat2 --threads 15 -x ../genome/genome -1 fq1.fq -2 fq2.fq -S aligned.sam
Neither works. If I flick to another screen and run top, it looks like:
Code:
top - 07:29:52 up  4:17,  2 users,  load average: 0.61, 0.34, 0.44
Tasks: 164 total,   2 running, 162 sleeping,   0 stopped,   0 zombie
%Cpu(s):  2.3 us,  4.0 sy,  0.0 ni, 93.7 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:  61976884 total, 61398192 used,   578692 free,    35588 buffers
KiB Swap:        0 total,        0 used,        0 free. 59440624 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND         
10666 tirohia   20   0  982432   3984   3700 R 100.0  0.0   3:28.93 hisat2-align-s  
10667 tirohia   20   0   25740   2948   2440 R   0.3  0.0   0:00.28 top             
    1 root      20   0   28564   4744   3120 S   0.0  0.0   0:01.46 systemd
    2 root      20   0       0      0      0 S   0.0  0.0   0:00.00 kthreadd
hisat2 isn't getting past 100% - my understanding of top is that it's percentage is based of the usage of a single cpu - so it should be showing 1500%.

What am I missing?

Cheers
Ben.
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