Sometimes hisat2 doesn't work.

Question

[aifiouap9q13]

When hisat2 is executed with the same command, the cpu usage rate increases, but there are times when the disk usage rate becomes 0% immediately and the result is not output forever, and when it works normally and the result is obtained.

I ran the following command on ubuntu on wsl on windows10.

hisat2 -x /mnt/f/ubuntu/hisat2_index/GRCm38/GRCm38_index -1 A_001_trimd.fastq -2 A_002_trimd.fastq -p 10 -S /mnt/d/ubuntu/hisat2_output/A_trimd.sam

Does anyone know the cause or solution to this problem?

I look forward to hearing from you.

Answer 1

[aifiouap9q13]

The problem has been resolved.

It turns out that it works only when I use the index file downloaded from the official site of hisat2 instead of the index I built by using the hisat2-build command.