From 220ae2efdea048048f1625c0f1241fba3bdb8817 Mon Sep 17 00:00:00 2001 From: Jover Date: Wed, 9 Aug 2023 15:57:42 -0700 Subject: [PATCH] Remove AUGUR_RECURSION_LIMIT MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The AUGUR_RECURSION_LIMIT is set to 10,000 by default since Augur 22.0.0 and the workflow's minimum required Augur version is now 22.0.1¹ ¹ https://github.com/nextstrain/ncov/blob/d34a0cf67890fc6b33e003247b90e900ac02c80c/workflow/envs/nextstrain.yaml#L7 --- Snakefile | 4 ---- nextstrain_profiles/nextstrain-scicore/submit.sh | 5 +---- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/Snakefile b/Snakefile index df097ff9d..e51496819 100644 --- a/Snakefile +++ b/Snakefile @@ -12,10 +12,6 @@ from collections import OrderedDict import textwrap import time -# Set the maximum recursion limit globally for all shell commands, to avoid -# issues with large trees crashing the workflow. Preserve Snakemake's default -# use of Bash's "strict mode", as we rely on that behaviour. -shell.prefix("set -euo pipefail; export AUGUR_RECURSION_LIMIT=10000; ") # Store the user's configuration prior to loading defaults, so we can check for # reused subsampling scheme names in the user's config. We need to make a deep diff --git a/nextstrain_profiles/nextstrain-scicore/submit.sh b/nextstrain_profiles/nextstrain-scicore/submit.sh index 4358225da..8b372f427 100644 --- a/nextstrain_profiles/nextstrain-scicore/submit.sh +++ b/nextstrain_profiles/nextstrain-scicore/submit.sh @@ -1,5 +1,5 @@ #!/bin/sh - + #SBATCH --output=log/%j.out # where to store the output ( %j is the JOBID ) #SBATCH --error=log/%j.err # where to store error messages @@ -7,8 +7,5 @@ source /scicore/home/neher/neher/miniconda3/etc/profile.d/conda.sh conda activate nextstrain export AUGUR_MINIFY_JSON=1 -export AUGUR_RECURSION_LIMIT=10000 {exec_job} - -