bowtie2 error while mapping the fastq files ?

Question

[ahsan.raza.rana]

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?

[GenoMax]

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).

Answer 1

[mastal511]

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