Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

LearnReadOrientationModel is a Memory Hog #7948

Open
DarioS opened this issue Jul 16, 2022 · 0 comments · May be fixed by #8639
Open

LearnReadOrientationModel is a Memory Hog #7948

DarioS opened this issue Jul 16, 2022 · 0 comments · May be fixed by #8639
Assignees
@davidbenjamin
Labels
Mutect performance

Comments

@DarioS
Copy link

DarioS commented Jul 16, 2022

I am doing somatic variant calling for whole genome sequencing. This tool could be improved to have reasonable RAM demands.

#PBS -l walltime=05:00:00,ncpus=26,mem=750GB
#PBS -q hugemem

Fails after almost two hours.

   NCPUs Requested:    26                     NCPUs Used: 26
                                           CPU Time Used: 28:09:38
   Memory Requested:   750.0GB               Memory Used: 749.95GB
   Walltime requested: 05:00:00            Walltime Used: 01:54:14

The reason is that the RAM allowance was exceeded.

Job 51320644 has exceeded memory allocation on node gadi-hmem-clx-0005.gadi.nci.org.au
Process "bash", pid 742028, rss 3346432, vmem 21680128
Process "51320644.gadi-p", pid 742086, rss 3059712, vmem 10174464
Process "mpirun", pid 742112, rss 6406144, vmem 220180480
Process "nci-parallel", pid 742118, rss 266031104, vmem 1423237120
    ...        ...

Normals about 30 times coverage, tumours about 60 times coverage, 26 patients in total. It should be made more efficient.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@davidbenjamin davidbenjamin

Labels
Mutect performance
Projects
None yet
Milestone
No milestone
3 participants
@DarioS @droazen @davidbenjamin