Question: bowtie2 error while mapping the fastq files ?
0
gravatar for ahsan.raza.rana
3.4 years ago by
ahsan.raza.rana40 wrote:

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 • 1.5k views
ADD COMMENTlink modified 3.4 years ago by mastal5112.0k • written 3.4 years ago by ahsan.raza.rana40
1

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).

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax70k
0
gravatar for mastal511
3.4 years ago by
mastal5112.0k
mastal5112.0k wrote:

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

ADD COMMENTlink written 3.4 years ago by mastal5112.0k
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