Bowtie: "Floating point exception: 8"

Question

[Marco Pannone]

Hello!

I am aligning some .fastq files from ChIP-seq experiment using bowtie(v1.2.3) and for only 5 out of 20 files in my dataset I get the following error message during the alignment process:

Floating point exception: 8

Consequenlty, the output .sam file gets truncated and bowtie stops running.

I did not manage to find any explanation for that, especially because everything works fine for the other .fastq files, except for 5 of them.

I wonder if any of you has faced the same problem before and managed to fix it.

Thanks!

Answer 1

[swbarnes2]

The obvious thing to troubleshoot is to cut the fastq file, and see if you can isolate a line in the fastq causing the problem.

[Marco Pannone]

Thanks for your answer, but I am not sure how I can find such line causing the issue. The error message does not indicate any line in the .fastq file causing the truncation. Also, the same .fastq files have been aligned also with bowtie2 and, in that case, everything was fine. Therefore, I was wondering if it was a bug specific of bowtie1 and especially for v1.2.3.