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When the allele discovery stage runs on large WGS/WES cohorts, the discovered_alleles data structures use a considerable amount of memory not currently accounted for in the --mem-gbytes budget. This can cause an OOM problem trying to run everything in one shot (as opposed to splitting up chromosomes or such into separate runs).
The text was updated successfully, but these errors were encountered:
9185487 ameliorates this by running allele dsicovery while RocksKeyValue is still open in BULK_LOAD mode, during which it has a much smaller LRU block cache (1/4 of memory budget instead of 3/4)
When the allele discovery stage runs on large WGS/WES cohorts, the discovered_alleles data structures use a considerable amount of memory not currently accounted for in the
--mem-gbytes
budget. This can cause an OOM problem trying to run everything in one shot (as opposed to splitting up chromosomes or such into separate runs).The text was updated successfully, but these errors were encountered: