Question: bowtie2-align exited with value 139
0
gravatar for anu014
7 months ago by
anu014140
India
anu014140 wrote:

Hi Biostars,

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.

https://www.dropbox.com/s/39mgsuauoabdf2w/aj_R1_aj_edi.fq.gz?dl=0 https://www.dropbox.com/s/kgndmhcfeuf9zgn/aj_R2_aj_edi.fq.gz?dl=0

ADD COMMENTlink modified 7 months ago • written 7 months ago by anu014140
1

This is a memory issue. Are you sure that the 256GB memory is not shared by anyone else. Use free -g to check the memory currently available.

ADD REPLYlink written 6 months ago by ashish200

This is what it's showing with 'free -g' command :

              total        used        free      shared  buff/cache   available
Mem:            251          57          20           0         173         192
Swap:           255           0         255

But the files I was running bowtie2 on were just in kilobytes, how it's even possible..

ADD REPLYlink modified 6 months ago • written 6 months ago by anu014140
1

The error (segmentation fault) is a memory issue. It means you are trying to access memory you don't have access to. However, bowtie2 works fine on a laptop with only 4Gb RAM. I've seen that if the free memory is less than 50gb, jobs do not run. Maybe the cluster itself requires more than 20gb to work properly.

ADD REPLYlink written 6 months ago by ashish200

Thanks Ashish.. So what to do now? Can I ask you a favour? Please run the attached files on your computer..

ADD REPLYlink written 6 months ago by anu014140

Use top to see all the running processes, see which process is using maximum memory, kill it or wait for it to finish and then run bowtie2. I work on plants and use different tools. To run your job on my system I'll have to setup many things.

ADD REPLYlink written 6 months ago by ashish200

Okay. Thanks for the support :)

ADD REPLYlink written 6 months ago by anu014140

How much memory is available on the machine that you use?

ADD REPLYlink written 7 months ago by ATpoint3.9k

It has 256GB memory. 32 cores.

ADD REPLYlink written 7 months ago by anu014140
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