fix(k8s/prepro): reducem pox batch size to 5 to not use more than 1GB…

… of memory (#1878) Use one processing thread to reduce memory consumption
loculus-project · May 11, 2024 · 2d73e4c · 2d73e4c
1 parent 7e27daf
commit 2d73e4c
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diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -392,7 +392,7 @@ defaultOrganisms:
           nextclade_dataset_tag: 2024-04-19--07-50-39Z
           genes:
             - OPG001
-          batch_size: 20
+          batch_size: 5
           processing_spec:
             total_snps:
               function: identity

diff --git a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
@@ -109,6 +109,7 @@ def enrich_with_nextclade(
             f"--output-all={result_dir}",
             f"--input-dataset={dataset_dir}",
             f"--output-translations={result_dir}/nextclade.cds_translation.{{cds}}.fasta",
+            "--jobs=1",
             "--",
             f"{input_file}",
         ]