Hisat2 computing efficiency too low

Question

[ianlee96]

I use wsl(ubuntu) to run Hisat2, it covers >30% cpu and >=0.1 memory while cpu and memory went very high at the time I use hisat2-build how can I improve the computing efficiency？ thanks！

[ianlee96]

this is the script I use

 #!/bin/bash
    for i in {LbG1,LbG2,LbG3,LbT1,LbT2,LbT3,LbR1,LbR2,LbR3,LrG1,LrG2,LrG3,LrT1,LrT2,LrT3,LrR1,LrR2,LrR3}
    do echo $i
        hisat2 -x index_build -1 /mnt/c/SCIProgram/trans/01clean_data/${i}_1.clean.gz -2 /mnt/c/SCIProgram/trans/01clean_data/${i}_2.clean.gz -S /mnt/c/SCIProgram/trans/02hisat2/hisat2_output/${i}_hisat2_output -p 11
    done

and this is the code

bash run.sh

[ATpoint]

What machine are you running on, how many cores and memory total, and is this SSD or spinning disks?

[ianlee96]

6cores, 12 threads, 8 mem, ssd, windows11(wsl/Ubuntu)

Answer 1

[ianlee96]

I solved the problem by rebuilding index