(ERR): bowtie2-align exited with value 141

Question

[jh]

Hi!

I am running bowtie2 with the command

bowtie2 --maxins 2000 -p 16 -1 sample.r1.fq.gz -2 sample.r2.fq.gz -x indexfile 2> sample.bowtie2.log

and get the following error perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = "en_US:en", LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to a fallback locale ("en_US.UTF-8"). (ERR): bowtie2-align exited with value 141

Is the problem locale settings? Or value 141, if so what is that?

Thanks!

[Medhat]

I will assume that you are working on linux so the fix for the warning is http://askubuntu.com/questions/162391/how-do-i-fix-my-locale-issue but that does not interfere with running your Bowtie2

I do not know what bowtie2 version you use or your OS

[jh]

Hi!

Thanks for fixing locale advice. (i'm working on linux yes)

I'm running Bowtie2 2.2.8

[Medhat]

there is another post saying that 141 was a bug and it was fixed already, can you please update your bowtie2 and see if it is still exists ?

[jh]

Thanks Medhat! Can you please post the link where it says that 141 was a bug? I installed Bowtie2 2.2.8 as a conda package and the next release 2.2.9 doesn't exist as a conda package :(

[Medhat]

not directly connected to bowtie2 page

https://github.com/bowhan/piPipes/issues/11

https://github.com/FelixKrueger/Bismark/issues/64

also try to use --verbose for debugging

[jh]

I installed a previous version, bowtie2 2.2.6 and then it worked! So the 141 error seems to be a bug in the 2.2.8 release. Thanks!