From 4f43911bcc43fcadf25af5b5637c64e4536fd809 Mon Sep 17 00:00:00 2001 From: Rebecca Asch Date: Tue, 8 Feb 2022 13:39:52 -0500 Subject: [PATCH 1/3] removed retries and updated error message --- scripts/variantstore/wdl/GvsImportGenomes.wdl | 1 - .../hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl index 72b13fbe16b..ddc49db3724 100644 --- a/scripts/variantstore/wdl/GvsImportGenomes.wdl +++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl @@ -292,7 +292,6 @@ task LoadData { >>> runtime { docker: docker - maxRetries: 3 memory: "3.75 GB" disks: "local-disk 50 HDD" preemptible: select_first([preemptible_tries, 5]) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java index 9454fd21071..54c3bb34d26 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java @@ -229,7 +229,7 @@ public void onTraversalStart() { logger.info("Sample id " + sampleId + " was detected as already loaded, exiting successfully."); System.exit(0); } else if (state == LoadStatus.LoadState.PARTIAL) { - throw new GATKException("Sample Id " + sampleId + " has already been partially loaded!"); + throw new GATKException("The loading for sample id " + sampleId + " was interrupted before it was able to complete successfully."); } } From 1df4cd97b0da61b7a4136c3f681df6b935bed623 Mon Sep 17 00:00:00 2001 From: Rebecca Asch Date: Wed, 16 Feb 2022 16:38:38 -0500 Subject: [PATCH 2/3] added table number to message to help with next steps --- .../hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java index 54c3bb34d26..5501af02854 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java @@ -229,7 +229,7 @@ public void onTraversalStart() { logger.info("Sample id " + sampleId + " was detected as already loaded, exiting successfully."); System.exit(0); } else if (state == LoadStatus.LoadState.PARTIAL) { - throw new GATKException("The loading for sample id " + sampleId + " was interrupted before it was able to complete successfully."); + throw new GATKException("The loading for sample id " + sampleId + " into the _" + tableNumber + " table(s) was interrupted before it was able to complete successfully."); } } From f95ed4a0560867feab445d1dd8421f31db7a122c Mon Sep 17 00:00:00 2001 From: Rebecca Asch Date: Thu, 17 Feb 2022 09:43:26 -0500 Subject: [PATCH 3/3] PR feedback --- scripts/variantstore/wdl/GvsImportGenomes.wdl | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl index 5f1fceda012..6cc53a679a3 100644 --- a/scripts/variantstore/wdl/GvsImportGenomes.wdl +++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl @@ -293,6 +293,7 @@ task LoadData { >>> runtime { docker: docker + maxRetries: 1 memory: "3.75 GB" disks: "local-disk 50 HDD" preemptible: select_first([preemptible_tries, 5])