From 48f4bf5a7f0892082fb2b6db1f5330e51aa2b1b9 Mon Sep 17 00:00:00 2001 From: Miguel Covarrubias Date: Mon, 19 Aug 2024 12:59:24 -0400 Subject: [PATCH] Slight AoU docs adjustment [VS-1366] (#8955) --- scripts/variantstore/docs/aou/AOU_DELIVERABLES.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md b/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md index c1ff184b282..d69edaf4136 100644 --- a/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md +++ b/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md @@ -128,9 +128,7 @@ The pipeline takes in the VDS and outputs a variant annotations table in BigQuer - For both PGEN and VCF extracts of ACAF only: - Specify an `extract_overhead_memory_override_gib` of 5 (GiB, up from the default of 3 GiB). - Specify a `y_bed_weight_scaling` of 8 (up from the default of 4). - - If re-running the extract workflow with call caching enabled, it may be necessary to increase memory in the `ExtractTask` / `PgenExtractTask` tasks. Due to the way call caching works in Cromwell (i.e. the `memory` attribute is not part of the call caching hashes), it is possible to edit the value of the `memory` runtime attribute of a task without breaking call caching. However, do *not* alter the value of the `memory_gib` input parameter as changing that absolutely will break call caching and will cause tens of thousands of shards to re-run needlessly! - - For Echo ACAF VCF extract, the VCF extract workflow was call-caching re-run with `ExtractTask` memory hard-coded to 100 GiB. 9/9 extract shards which did not complete on the initial run of the workflow succeeded on their first (non-preempted) attempt in the second run of the workflow. - - For Echo ACAF PGEN extract, the PGEN extract workflow was call-caching re-run with `PgenExtractTask` memory hard-coded to 50 GiB. 20/24 extract shards which did not complete on the initial run of the workflow succeeded on their first (non-preempted) attempt in the second run of the workflow. The remaining 4 shards hit `OutOfMemoryErrors` on their first attempt but succeeded on the second attempt with 50 GiB * 1.5 = 75 GiB of memory thanks to "retry with more memory". + - When re-running the extract workflow with call caching enabled, it will be necessary to increase memory in the `ExtractTask` / `PgenExtractTask` tasks. Due to the way call caching works in Cromwell (i.e. the `memory` runtime attribute is not part of the call caching hashes), it is possible to edit the value of the `memory` runtime attribute of a task _in the WDL_ without breaking call caching. However, do *not* alter the value of the `memory_gib` input parameter as changing that absolutely will break call caching and will cause tens of thousands of shards to re-run needlessly! Both VCF and PGEN extracts can have their memory set to `"50 GiB"` for the call-caching re-run. Most extract shards should finish on the first re-run attempt, but a few stragglers will likely OOM and automatically re-run with more memory. - If you want to collect the monitoring logs from a large number of `Extract` shards, the `summarize_task_monitor_logs.py` script will not work if the task is scattered too wide. Use the `summarize_task_monitor_logs_from_file.py` script, instead, which takes a FOFN of GCS paths instead of a space-separated series of localized files. - These workflows do not use the Terra Data Entity Model to run, so be sure to select the `Run workflow with inputs defined by file paths` workflow submission option.