ref_map.pl: Aborted because the last command failed (128)

[Johanna]

Hi :) 

I'm having some trouble running the ref_map.pl. My command is:

ref_map.pl --samples samples_mapped/ -o refmap_output/ --popmap popmap184inds.txt -T 8

and I keep getting the error:

ref_map.pl: Aborted because the last command failed (128).

Last command executed by ref_map.pl was:
  /opt/nesi/CS400_centos7_bdw/Stacks/2.61-gimkl-2022a/bin/gstacks -I samples_mapped/ -M popmap184inds.txt -O refmap_output -t 8

(ref_map.log and gstacks.log are attached for more details). 

I'm not sure how to solves this issue. I ran the same command successfully a few month ago with the same dataset. The only difference now is that I'm using a masked reference genome when I mapping the reads. 

Any help would be much appreciated.

Thanks, 

Johanna 

[Catchen, Julian]

Hi Johanna,

 

Most likely you are running out of memory when gstacks runs. You could re-execute your gstacks command like this:

 

/usr/bin/time -v /opt/nesi/CS400_centos7_bdw/Stacks/2.61-gimkl-2022a/bin/gstacks -I samples_mapped/ -M popmap184inds.txt -O refmap_output -t 8

 

And it will tell you the maximum amount of memory your program consumed. Or, if this is a scheduled system, increase the amount of memory you requested from the scheduler.

 

julian

[Johanna Kann]

Hi Julian, 

That makes sense. I should have thought of it earlier. I increased the memory and it worked fine. 

Thanks a lot for your help!

Cheers, 

Johanna

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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