From 83fc6e6bfb1ef3718b08621cee3212ee58d6de86 Mon Sep 17 00:00:00 2001 From: Jover Date: Wed, 9 Aug 2023 16:14:06 -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 22.0.2¹ ¹ https://github.com/nextstrain/seasonal-flu/blob/65df51732abcad6480239fb0c7e76e47ae5c9723/workflow/envs/nextstrain.yaml#L7 --- Snakefile | 4 ---- profiles/scicore/submit.sh | 3 --- 2 files changed, 7 deletions(-) diff --git a/Snakefile b/Snakefile index 20a882e8..4ab9f54a 100644 --- a/Snakefile +++ b/Snakefile @@ -2,10 +2,6 @@ import datetime import pandas as pd from treetime.utils import numeric_date -# 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; ") wildcard_constraints: segment = r'pb2|pb1|pa|ha|np|na|ma', diff --git a/profiles/scicore/submit.sh b/profiles/scicore/submit.sh index 7a94007e..4f9b1e21 100644 --- a/profiles/scicore/submit.sh +++ b/profiles/scicore/submit.sh @@ -8,8 +8,5 @@ source ~/miniconda3/etc/profile.d/conda.sh conda activate nextstrain #Test export AUGUR_MINIFY_JSON=1 -export AUGUR_RECURSION_LIMIT=10000 {exec_job} - -