Qualimap fails due to out of memory

uab-cgds-worthey / quac

🦆 Quality Control of WGS and exome samples 🦆

https://quac.readthedocs.io

GNU General Public License v3.0

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Qualimap fails due to out of memory #48

Closed ManavalanG closed 1 year ago

ManavalanG commented 2 years ago

Qualimap failed with the following error for a WGS sample with unusual high coverage of ~90x.

WARNING: out of memory!
Qualimap allows to set RAM size using special argument: --java-mem-size
Check more details using --help command or read the manual.

ManavalanG commented 2 years ago

--java-mem-size for qualimap was hardcoded in the workflow and therefore couldn't be modified by user via configuration.
So, refactoring was performed to resolve the issue.
- Attempts were first done to provide this capability via modifying cluster config.
- But this attempt failed due to several difficulties.
- So workflow was refactored to instead use configs/workflow.yaml for user configuration.

ManavalanG commented 2 years ago

mentioned in commit df9cde51060991beadd5bb7e966ae19b18116369