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
How did you acquire bowtie2? Did you install it yourself or are you using it on a server?
i installed it myself
I am having same problem? did you find out the reason and how to resolve the issue?
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.
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
I'm having the same problem. I installed the legacy version bowtie2-2.3.2-legacy. It worked fine before, but not now...
I'm having the same problem,and I installed the bowtie2-18.104.22.168 by conda. Did you find out the reason and how to resolve the issue?
Did you download or make your own bowtie2 indexes?
I installed the bowtie2-22.214.171.124 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.
You should enter the complete bowtie2command you want to execute. Since bowtie2 -h is working the programs is properly installed.
I am having the same problem- Ubuntu 14.04 virtual box, mac
manager@bl8vbox[Bowtie] which bowtie2 [ 8:41PM]
manager@bl8vbox[Bowtie] which bowtie2-align [ 8:46PM]
bowtie2-align not found
Can anyone help, it will be much appreciated
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.
Or use Homebrew to install Bowtie2.
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