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Old 12-12-2012, 09:42 AM   #1
Location: Madrid

Join Date: Jun 2012
Posts: 16
Default Basic problem while using BWA

I have other recent post asking for the convenience of using BWA-SW for some kind of database.

While I am waiting for your great help, I tried to get into the algorithm. But I have not be able.

I work with mac, and I was trying to work BWA in the terminal window.
First, I unzipped the .tar file that I have downloaded from the BWA webpage and copy all its content to a folder.
Then, I opened 'Terminal' and in the prompt I got into that folder. Once there, I wrote the following:

bwa index -p unite -a bwtsw -c unite.fungal.fasta

And after that a message appeared, saying:

-bash: bwa: command not found

What am I doing wrong??

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Old 12-12-2012, 10:15 AM   #2
Location: Germany

Join Date: Oct 2012
Posts: 48

If I am not mistaken (been a while since I installed BWA); you have to compile it first.

Try typing make while being in the bwa directory.

And if you are working on mac; you may wanna read this:

Last edited by TabeaK; 12-12-2012 at 10:19 AM.
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Old 12-13-2012, 12:31 AM   #3
Location: Madrid

Join Date: Jun 2012
Posts: 16

Thanks a lot.

I'll try what you say and read that page inmediatly and I'll write back then.
miguelangel is offline   Reply With Quote

bwa-sw, index command, mac

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