Bowtie2 for macintosh

MariaGeorge61 · 04-09-2014, 06:52 PM

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 · 04-09-2014, 06:55 PM

What was your command line ?

MariaGeorge61 · 04-09-2014, 08:18 PM

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 · 04-09-2014, 08:42 PM

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 · 04-10-2014, 01:23 AM

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.

MariaGeorge61 · 04-10-2014, 07:38 AM

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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04-09-2014, 06:52 PM	#1
MariaGeorge61 Junior Member Location: Puebla Mexico Join Date: Apr 2014 Posts: 5	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

04-10-2014, 01:23 AM	#5
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.

04-10-2014, 07:38 AM	#6
MariaGeorge61 Junior Member Location: Puebla Mexico Join Date: Apr 2014 Posts: 5	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!

04-09-2014, 06:55 PM	#2
yueluo Member Location: Guangzhou China Join Date: Aug 2013 Posts: 82	What was your command line ?

04-09-2014, 08:18 PM	#3
MariaGeorge61 Junior Member Location: Puebla Mexico Join Date: Apr 2014 Posts: 5	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

04-09-2014, 08:42 PM	#4
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.