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Reduce VEP batch size (better to have more quicker ones)
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davmlaw committed Jul 29, 2024
1 parent 893cd26 commit a553d82
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2 changes: 1 addition & 1 deletion variantgrid/settings/components/default_settings.py
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@
# If it gets below min, it does a slower query to get range lock.
# The variant table is usually ~55% alt variants but may be different due to data or if you've deleted records
ANNOTATION_VEP_BATCH_MIN = 5000 # Dont' set too low due to overhead of running pipeline etc
ANNOTATION_VEP_BATCH_MAX = 100000 # Set to None to do all in 1 job (probably want to set FORK higher)
ANNOTATION_VEP_BATCH_MAX = 50_000 # Set to None to do all in 1 job (probably want to set FORK higher)
ANNOTATION_VEP_ARGS = [] # ["--buffer_size", "1000"] # default = 5000
ANNOTATION_VEP_VERSION = "110"
ANNOTATION_VEP_BASE_DIR = os.path.join(ANNOTATION_BASE_DIR, "VEP")
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