From cc134afa390f55437d4f208d60d459f0b91e74e9 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 0636e776..acf217ce 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -61,7 +61,7 @@ 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 a88fe947..b6b3939d 100644 --- a/phylogenetic/rules/prepare_sequences_E.smk +++ b/phylogenetic/rules/prepare_sequences_E.smk @@ -51,7 +51,7 @@ rule align_and_extract_E: shell: """ nextclade run \ - -j 2 \ + -j 1 \ --input-ref {input.reference} \ --output-fasta {output.sequences} \ --min-seed-cover 0.01 \