From 32851955545fe3999c7723eeafa4278091ee45e8 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 28 Feb 2024 16:54:25 -0800 Subject: [PATCH] AWS cores --- phylogenetic/README.md | 2 +- phylogenetic/rules/prepare_sequences_E.smk | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/phylogenetic/README.md b/phylogenetic/README.md index d3942d66..f19b2311 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -62,7 +62,7 @@ example sequences into the `data/` directory like so: With access to AWS, this can be more quickly run as: - nextstrain build --aws-batch --aws-batch-cpus 4 --aws-batch-memory 7200 . --jobs 4 + nextstrain build --aws-batch --aws-batch-cpus 10 --aws-batch-memory 7200 . --jobs 10 [Nextstrain]: https://nextstrain.org [augur]: https://docs.nextstrain.org/projects/augur/en/stable/ diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/phylogenetic/rules/prepare_sequences_E.smk index 8c58cf55..a88fe947 100644 --- a/phylogenetic/rules/prepare_sequences_E.smk +++ b/phylogenetic/rules/prepare_sequences_E.smk @@ -50,7 +50,7 @@ rule align_and_extract_E: min_length = config['filter']['E_min_length'], shell: """ - nextclade3 run \ + nextclade run \ -j 2 \ --input-ref {input.reference} \ --output-fasta {output.sequences} \