(ERR): bowtie2-align exited with value 1

Question

[biostarsb]

Hello

I have a problem with bowtie2 tools

When I type the command bowtie2 -h It shows me the help but with an error message at the end

(ERR): bowtie2-align exited with value 1

Can someone help me solve the problem?

thank you in advance

[GenoMax]

How did you acquire bowtie2? Did you install it yourself or are you using it on a server?

[biostarsb]

i installed it myself

[amoltej]

I am having same problem? did you find out the reason and how to resolve the issue?

[valengo]

Which version of bowtie2 are you using? I was using bowtie2-2.1.0 and then I noticed that there was a new version (bowtie2-2.3.0), so I've updated it and bowtie2 started giving me this very same error when trying to align sequences to the reference. I went back to bowtie2-2.1.0 and it's working again. I understand that this is not the best solution, but it's still better than no solution at all.

[KHP]

I Have the same error since 2 weeks ago but until now I could not find a way to resolve the error "Bowtie2 (ERR): bowtie2-align exited with value 1" when using tophat2. Please help

[mikoliu798]

I'm having the same problem. I installed the legacy version bowtie2-2.3.2-legacy. It worked fine before, but not now...

[xk995]

I'm having the same problem,and I installed the bowtie2-2.3.4.3 by conda. Did you find out the reason and how to resolve the issue?

[GenoMax]

Did you download or make your own bowtie2 indexes?

[xk995]

I installed the bowtie2-2.3.4.3 by conda using "conda install -c bioconda bowtie2". When I type the command bowtie2, an error message is at the end "(ERR): bowtie2-align exited with value 1". but I type the ommand bowtie2 -h, it's ok.

[GenoMax]

You should enter the complete bowtie2command you want to execute. Since bowtie2 -h is working the programs is properly installed.

[basucsmcri]

I am having the same problem- Ubuntu 14.04 virtual box, mac

manager@bl8vbox[Bowtie] which bowtie2                                 [ 8:41PM]
/usr/bin/bowtie2
manager@bl8vbox[Bowtie] which bowtie2-align                           [ 8:46PM]
bowtie2-align not found
manager@bl8vbox[Bowtie]

Can anyone help, it will be much appreciated

[GenoMax]

This seems to be a simple issue of bowtie2-align not being in the $PATH. Should be easily fixable by doing export PATH=$PATH:/path_to_bowtie2_executables.

BTW: Why are you using a VM if you are working on a Mac? macOS is a real unix OS and you can compile/run most bioinformatics programs natively. Bowtie2 macOS binaries available here.

[e.rempel]

Or use Homebrew to install Bowtie2.