ERROR with Bowtie2 install and running

Question

[tianhan313]

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.

[Devon Ryan]

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

[tianhan313]

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

[syxbestmayer]

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

[tianhan313]

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.