Bowtie2 for macintosh

[MariaGeorge61]

Hi forum members:
I tried to work with bowtie2 in macintosh OS X 10.8.5, however, bowtie2 is not working. After following step by step the example with lambda_virus from Bowtie 2 Manual the following message does appear:

Warning: Could not open read file "/example/reads/reads_1.fq" for reading; skipping...
Error: No input read files were valid
bowtie2-align exited with value 1

Could anybody help me please?

MariaGeorge

[yueluo]

What was your command line ?

[MariaGeorge61]

Thank you very much.

$bowtie2 -x lambda_virus -1 /example/reads/reads_1.fq -2 /example/reads/reads_2.fq -S eg2.sam

I tried writting the entire path but also failed, other basenames and local alignment also gave identical results.

Sorry for the trouble.

MariaGeorge

[Brian Bushnell]

Maria,

I can't help you with bowtie2, but BBMap will work on OSX, if you have Java installed.

java -ea -Xmx1g -cp path/to/current align2.BBMap ref=reference.fa in1=reads1.fq in2=reads2.fq out=mapped.sam

You have to replace "path/to/current" with the actual path to the directory "current" from the unzipped package.

[dpryan]

The error is due to you specifying:

... /example/reads/reads_1.fq ...

which is very unlikely to exist on your computer unless you happened to make a /example directory. Normally you'd just "cd" to the directory containing the bowtie2 executable and type:

./bowtie2 -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq -S eg2.sam

Note the usage of relative paths above. You might want to pick up a book on basic linux/mac command line usage. That'll save you a lot of headaches.

[MariaGeorge61]

Thank you very much

It works well. Now I realize what is going on with macintosh comand line.
I will read, and also try with BBMap it also seems a good option.

Thanks everybody and good day!