Question: ERROR with Bowtie2 install and running
0
gravatar for tianhan313
4.6 years ago by
tianhan3130
China
tianhan3130 wrote:

My computer has 32GB RAM, and I newly installed Ubuntu 14.04 LTS 64bit system. I downloaded bowtie2-2.2.4-linux-x86_64.zip file, unzip it, cd the document, I try to run bowtie2 with ./bowtie2 command, it shows the usage tips of bowtie2, but the last line shows "(err) bowtie2-align exited with value 1". After I index, I try to run bowtie2 processing my ChIP-seq data, it still shows the same error message. I have successfully running bowtie2 with this computer,but that system has broken down, so I re-install the system, I tried Ubuntu 14.04 and Ubuntu 12.04, the same ERROR shows after I run bowtie2. 

ADD COMMENTlink modified 4.2 years ago • written 4.6 years ago by tianhan3130
0
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

Can you post the exact command you ran? Usually errors like this happen with misformatted commands.

ADD COMMENTlink written 4.6 years ago by Devon Ryan90k

Yeah, you are right. The Bowtie2 program dosen't recognises index file correctly, after I change the index file path, Bowtie2 program is running succesfully.

ADD REPLYlink written 4.6 years ago by tianhan3130
0
gravatar for syxbestmayer
4.2 years ago by
syxbestmayer0 wrote:

can you tell me how to fix the index file path?

ADD COMMENTlink written 4.2 years ago by syxbestmayer0
0
gravatar for tianhan313
4.2 years ago by
tianhan3130
China
tianhan3130 wrote:
I think the problem may due to the incorrect environment PATH, if you put the index file in your install document, you could run bowtie2 in your install document path directly, a correct PATH may not be necessary.
ADD COMMENTlink written 4.2 years ago by tianhan3130
0
gravatar for tianhan313
4.2 years ago by
tianhan3130
China
tianhan3130 wrote:
think the problem may due to the incorrect environment PATH, if you put the index file in your install document, you could run bowtie2 in your install document path directly, a correct PATH may not be necessary.
ADD COMMENTlink written 4.2 years ago by tianhan3130
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