bowtie2-align died with signal 2 (INT)

Question

[mailard]

Hi! I run bowtie2

bowtie2 -x human -U /home/user/h_1/tg8089.fastq -S wu_aligned.sam

And i have the error bowtie2-align died with signal 2 (INT) How can i fix it? Thanks for your time!

[GenoMax]

Are you using pre-compiled version of bowtie2 or did you compile it yourself? Is your install of bowtie2 known to work?

[mailard]

I installed pre-compiled version of bowtie2 Yup? it works

Answer 1

[Qiongyi]

Can't give you a very clear answer because I have never met this kind of error. I would 1) check if bowtie2 is really working using other fastq files and the same reference genome and 2) check if you fastq file is corrupted or incorrectly formatted.

If step 1 is working, you should definitely check your fastq file.