bowtie2-align exited with value 139

[Anupriya014]

aj_R1_aj_edi.fq.gz
aj_R2_aj_edi.fq.gz

Hi all,

I've been using bowtie2 for a long time now. But there are times I get error such as :
Segmentation fault (core dumped)
(ERR): bowtie2-align exited with value 139

I've search many issues like this, but everyone tells first to check my bowtie2 version. So I changed from version from 2.2.6 to 2.3.3.1 ,which is the latest version. (I tried running bowtie2 from pre-complied binaries from sourceforge too)

Then I've tried to find error in my files itself by segmenting down them to 25 reads. Still couldn't find any error in them.

I've tried running BWA-mem too on these files. Surprisingly, it ran.

Please help me fix this problem.

Command used : /home/softwares/bowtie2-2.3.3.1-linux-x86_64/bowtie2 -p 20 --phred33 --local --sensitive -x /media/bowtie2_index/human_grch38/ref_index -1 /home/error/aj_R1_aj_edi.fq -2 /home/error/aj_R2_aj_edi.fq -S out_trail1.sam

Hereby, I'm attaching my 25 reads file. Thanks in advance.

[BenLangmead]

This may be related to #158 and #155. You might try to confirm this by re-trying with -p 1 and seeing if the problem goes away. Either way, we have an alpha build with a potential fix which you can find in the comments for issue #158. If you have a chance, try that (with -p 20 or the like) and let us know if the problem remains. Either way, there will be a new release very soon with that fix.

[ch4rr0]

A fix for this has been released as of v2.3.4.