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bowtie2-align exited with value 139 ?

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!

chip-seq rna-seq alignment bowtie2 software error
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written by star star

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?

• 1 views • link
written by Joe Joe

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

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written by star star

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).

• 1 views • link
written by Jeffin Rockey Jeffin Rockey

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