Question: bowtie2-align exited with value 139 ?
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10 months ago by
star190
Netherlands
star190 wrote:

I have some data and I like to run bowtie2 for them, its version is 2.3.4.3. when I run it as loop for all samples I have faced with Segmentation fault (core dumped) (ERR): bowtie2-align exited with value 139, error, but when I run it for each sample separately it works. is there any solution for it?

$ free -g

              total        used        free      shared  buff/cache   available
Mem:             62           2          48           0          12          59
Swap:            63           0          63

Loop command:

for sample in `ls /home/Projects/ChIP-seq/Trim/*.gz`
do

dir="/home/Projects/ChIP-seq/Trim"
dir2="/home/Projects/ChIP-seq/Align"
base=$(basename $sample ".trim.fastq.gz")

bowtie2 --very-sensitive -x /home/Projects/Genome_Index/GRCH_37.91/GRCH- 37_RefGenome/Homo_sapiens_GRCh37 ${dir}/${base}.trim.fastq.gz > ${dir2}/${base}.bam

done

Single command:

bowtie2 --very-sensitive -p 8 -x /home/Projects/Genome_Index/GRCH_37.91/GRCH-37_RefGenome/Homo_sapiens_GRCh37 /home/Projects/ChIP-seq/Trim/L001_R1_001.trim.fastq.gz /home/Projects/ChIP-seq/Align/output.bam

Thanks in advance!

ADD COMMENTlink modified 10 months ago • written 10 months ago by star190

There must be some memory accumulation going on in your single loop command that isn't freed between iterations which is exceeding your available. Can you show us the 2 actual commands you are using?

ADD REPLYlink written 10 months ago by Joe14k

@ jrj.healey,Thanks for reply, I put the commands.

ADD REPLYlink modified 10 months ago • written 10 months ago by star190

The error 139 related bug that existed before is supposed to be fixed in the bowtie2 version 2.3.4.3 that you are using.

However, if you have time to try something which holds a very remote chance of being right, please go back three versions and rerun the same script with bowtie2 v2.3.4 in which a similar issue was specifically fixed (link).

ADD REPLYlink modified 10 months ago • written 10 months ago by Jeffin Rockey1.1k
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