This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bowtie2 error while mapping the fastq files ?

I am trying to map fastq files by using bowtie2 and the command i am using is: bowtie2 -q -x ./Index/genome -U 114_1.fastq -S 2> 114.out > 114.sam

but getting error every time: Error: Encountered internal Bowtie 2 exception (#1) Command: /opt/bowtie2/bowtie2-align-s --wrapper basic-0 -x ./Index/genome -q 114_1.fastq -S (ERR): bowtie2-align exited with value 1

Could any body help me whats this problem is?

software error
• 3,798 views • link
updated by mastal511 mastal511 • written by ahsan.raza.rana • ahsan.raza.rana

Try

bowtie2 -q -x ./Index/genome -U 114_1.fastq -S 114.sam 2> 114.out

Since bowtie2 is capable of writing alignments to a file with -S option you do not need to try to capture that stream from stdout. That was not the right of way of doing it anyway (based on the command you have provided).

• 2 views • link
written by GenoMax GenoMax

1 answer

It looks like your command should be rearranged as:

bowtie2 -q -x ./Index/genome -U 114_1.fastq -S 114.sam 2> 114.out

See the Getting Started section from the Bowtie2 web page,

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example

• 2 views • link
written by mastal511 mastal511

Log in to answer this question.

More posts like this