Optimize AUGUSTUS Segmentation Fault
0
0
Entering edit mode
5.5 years ago
gtasource ▴ 60

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.

AUGUSTUS BRAKER • 3.2k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 3312 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6