Added alternative base config #24
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
resource limits and larger resource classes.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Dear maintainers,
I have run FastOMA on about 2200 genomes and in order to make the run smoother I have created a customised base config.
The most important change is that I have removed the checking for maximum resource limits from the resource classes. The reson for this that our SLURM cluster has multiple partitions with different resource limits (e.g. bigmem) and the jobs are dynamically allocated to the appropriate queue. I found that with the current base config the jobs are always allocated to the default partition and hence some of them eventually run out of resources, crashing the pipeline.
Also, this config has resource classes with higher memory which can be specified for the processes in the main Nextflow file.
I would like to contribute this alterantive base config to the FastOMA repo in the hope that it will be useful for us and other users.
Best,
Botond