#356 bowtie2 Segmentation fault: 11

[Javier Diaz]

Hello,

I was being able to run bowtie2 v2.2.8 as a part of of a package called miARma, which contained bowtie1, bowtie2 and other aligners.

For a different purpose I had to install gfortran (requirement for other package) and after that bowtie2 is no longer working. I'm suspicious that gfortran messed up something because until before it was working, but I'm not certain on this.

if I just type ./bowtie2 or ./bowtie2 -h
I get this error:

bowtie2 Segmentation fault: 11

Same error if I provide parameters for an alignment run.

I've tried the following with no success (same error was produced on each attempt):
1) re-installed miARma package
2) removed miARma and installed bowtie2 itself (v2.3.4.1)
for this I've tried:
a) downloading and installing bowtie2 from Sourceforge
b) using Homebrew to get dependencies too (Mac software installer - no errors were produced)
c) removed any executable matching bowtie2 (previous installations) and tried a) and b) again
d) tried installing from bowtie2-2.3.4.1-source.zip

I read over reported Segmentation error tickets here, but they don't seem to be quite the same, since they seem to occurr when bowtie2 is already running (reading/writing files?) whereas in my case I can't even get the -h option to work.

Both bowtie1 and bowtie2-built are working fine.

Any idea what may be happening?

Thanks.

Javier.