bowtie2-align died with signal 11 (SEGV) (core dumped)

Question

[cvu]

Hi all,

I'm using bowtie2(version 2.1.0) to map two paired end fastq files, each ~13GB in size.

commandline arguments:

bowtie2 -p 30 --phred33 --local --sensitive -x ref_index -1 forward_reads.fastq -2 reverse_reads.fastq -S out.sam

It's running fine until it generates out.sam file 13.2GB and then throwing error bowtie2-align died with signal 11 (SEGV) (core dumped).

Is this some memory problem? I am running on system with 32cores and 256GB of RAM.

Any help would be appreciated

Thanks!!

Answer 1

[sushuaikun]

Maybe because you typed the wrong input file name, so bowtie2 can not find the file. You can check them again. I met this error when I typed the wrong fastq file name. Then when the file name was correct, the error was gone. Good luck!

Answer 2

[Devon Ryan]

It's likely that one of the reads is ever so slightly corrupt. You can use the -u and -s options to find out approximately where the offending read(s) is/are and then have a look in that area.

Answer 3

[Santosh Anand]

Usually, SEGV means that the program is trying to access some 'protected' part of memory (protected by OS). So in a way, the problem is related to memory, but I don't think think this is due to insufficiency of memory and the SEGV error is so generic that it is impossible to understand what specific thing went wrong. That said, It might be possible that you have hit a Ubuntu specific bug in Bowtie2 https://sourceforge.net/p/bowtie-bio/bugs/339/

Could you try upgrading bowtie to latest version, or on a different OS (e.g. inside a VM running SUSE)?