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Old 04-09-2014, 06:52 PM   #1
MariaGeorge61
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Location: Puebla Mexico

Join Date: Apr 2014
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Post Bowtie2 for macintosh

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
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Old 04-09-2014, 06:55 PM   #2
yueluo
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What was your command line ?
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Old 04-09-2014, 08:18 PM   #3
MariaGeorge61
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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
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Old 04-09-2014, 08:42 PM   #4
Brian Bushnell
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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.
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Old 04-10-2014, 01:23 AM   #5
dpryan
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Location: Freiburg, Germany

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The error is due to you specifying:

Code:
... /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:

Code:
./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.
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Old 04-10-2014, 07:38 AM   #6
MariaGeorge61
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Location: Puebla Mexico

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Default 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!
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