-
Notifications
You must be signed in to change notification settings - Fork 144
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
Pipeline requires 72GB of RAM, even to test. #408
Comments
its true that it requires 72.GB mem as the process is labelled with I can limit the max mem for the test_full profile but, if any other changes you have to make as per your resource availability by setting institutional cluster specific config settings. Does that sound ok to you ? |
Hi @mpiersonsmela, it’s true that the If convinced with the answer, kindly close this issue. Thank you! |
Description of the bug
On my university's cluster, users are penalized (with priority reduction) for requesting more RAM than they actually use. So the fact that the pipeline requires at least 72GB of RAM to run is an issue for me, given than I'm just trying to test it with the example samplesheet.csv from https://nf-co.re/methylseq/2.6.0/
This is the relevant portion of the output. Does bismark genome preparation really need so much RAM?
`ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION (BismarkIndex/grch38_core+bs_controls.fa)'
Caused by:
Process requirement exceeds available memory -- req: 72 GB; avail: 32 GB
Command executed:
bismark_genome_preparation
--bowtie2
BismarkIndex`
Command used and terminal output
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: