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.

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

Revisit performance implications of commit 1eed8e8 #1923

heuermh opened this Issue Feb 26, 2018 · 0 comments


None yet
1 participant

heuermh commented Feb 26, 2018

Commit message for commit 1eed8e8 states

On a single node with 20 workers, BaseRecalibration time is reduced from 5.8 min to 1.7 min.

whereas now downstream we are seeing the opposite

Running the reads pipeline on latest master on GCP on an exome shows a major performance regression. At the end of last year this took 40 minutes for the whole job, now using master BQSR is taking 1.4 hours, and HC is taking well over an hour (it hasn't finished yet).
I tried reverting 1eed8e8 and the performance was back to normal!

@heuermh heuermh added this to the 0.24.0 milestone Feb 26, 2018

@heuermh heuermh closed this in #1926 Mar 1, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment