Question: Optimize AUGUSTUS Segmentation Fault
0
gravatar for gtasource
2 days ago by
gtasource20
gtasource20 wrote:

Not sure if anybody will be able to help, but I've been using the BRAKER2 pipeline and everything has been running fine, up until I reach the optimize AUGUSTUS step. Here's how it's failing:

Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Could not read the accuracy values out of predictions.txt when processing bucket 1. at /home/Aug/scripts/optimize_augustus.pl line 1224.

I'm on a high performance HPC with 8 cores, 56GB memory, so I'm not entirely sure why it's now giving me the segmentation fault. Again, not sure if anybody will be able to help, but thought I'd get this posted here while I continue to troubleshoot.

braker augustus • 88 views
ADD COMMENTlink modified 2 days ago • written 2 days ago by gtasource20

Can you get any job resource usage from your cluster job? I know that BRAKER tend to use quite some resources for certain steps

ADD REPLYlink written 2 days ago by lieven.sterck3.3k

I have the CPU average chart in front of me. I started BRAKER2 around 10PM last night, and CPU usage hovered around 97%. Right before the Optimize Augustus step (that keeps failing) it went down to 80%. Here's the full command that keeps failing:

perl /home/Aug/scripts/optimize_augustus.pl --rounds=5 --species=XVF9 --kfold=4 --AUGUSTUS_CONFIG_PATH=/home/Aug/config --onlytrain=/home/BRAKER-/scripts/braker/XVF9/train.gb.train.train /home/BRAKER/scripts/braker/XVF9/train.gb.train.test 1>/home/BRAKER/scripts/braker/XVF9/optimize_augustus.stdout 2>/home/BRAKER/scripts/braker/XVF9/errors/optimize_augustus.stderr!
ADD REPLYlink modified 2 days ago by genomax59k • written 2 days ago by gtasource20

Are there any useful messages in the stderr and stdout file?

ADD REPLYlink written 2 days ago by genomax59k

Unfortunately no, besides the:

Segmentation fault (core dumped)
Could not read the accuracy values out of predictions.txt when processing bucket 1. at /home/Aug/scripts/optimize_augustus.pl line 1224.

And then also a failed to execute braker.pl error.

ADD REPLYlink modified 2 days ago • written 2 days ago by gtasource20

ok, thanks, any info on the memory-usage of the job?

ADD REPLYlink written 2 days ago by lieven.sterck3.3k
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