(ERR): bowtie2-align exited with value 1

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7.8 years ago

biostarsb ▴ 30

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

software error RNA-Seq • 13k views

ADD COMMENT • link updated 6.8 years ago by basucsmcri • 0 • written 7.8 years ago by biostarsb ▴ 30

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

ADD REPLY • link 7.8 years ago by GenoMax 147k

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i installed it myself

ADD REPLY • link 7.8 years ago by biostarsb ▴ 30

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

ADD REPLY • link 7.8 years ago by amoltej ▴ 100

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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.

ADD REPLY • link 7.7 years ago by valengo • 0

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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

ADD REPLY • link 7.7 years ago by KHP • 0

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

ADD REPLY • link 7.3 years ago by mikoliu798 • 0

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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?

ADD REPLY • link 5.5 years ago by xk995 • 0

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Did you download or make your own bowtie2 indexes?

ADD REPLY • link 5.5 years ago by GenoMax 147k

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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.

ADD REPLY • link 5.5 years ago by xk995 • 0

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

ADD REPLY • link 5.5 years ago by GenoMax 147k

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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

ADD REPLY • link updated 6.8 years ago by GenoMax 147k • written 6.8 years ago by basucsmcri • 0

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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.