Reduce filter resources requests
Reduces memory requests for augur filter commands from 12GB to 4GB to
account for lower requirements of the latest augur filter and to allow
more subsample jobs to run simultaneously on AWS Batch jobs for
Nextstrain builds.
@@ -296,8 +296,9 @@ rule subsample:
max_date = _get_specific_subsampling_setting("max_date", optional=True),
priority_argument = get_priority_argument
resources:
- # Memory use scales primarily with the size of the metadata file.
- mem_mb=12000
+ # Memory use scales with the number of sequences per group * number of groups.
+ # We pin this to a reasonably high value based on Nextstrain production builds.
+ mem_mb=4000
conda: config["conda_environment"]
shell:
"""
@@ -332,8 +333,9 @@ rule extract_subsampled_sequences:
benchmark:
"benchmarks/extract_subsampled_sequences_{build_name}_{subsample}.txt"
resources:
- # Memory use scales primarily with the size of the metadata file.
- mem_mb=12000
+ # Memory use scales with the number of sequences per group * number of groups.
+ # We pin this to a reasonably high value based on Nextstrain production builds.
+ mem_mb=4000
conda: config["conda_environment"]
shell:
"""
