From 8a347f497ef07fc942128cf04b1c662ea70f2cd6 Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Tue, 1 Oct 2019 10:14:35 -0400
Subject: [PATCH] fix
---
.../data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh | 2 ++
1 file changed, 2 insertions(+)
diff --git a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
index bfcb1d14..74de3546 100755
--- a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
@@ -47,6 +47,8 @@ for kind in with_mass_spec no_mass_spec
do
python run_mhcflurry.py \
proteome_peptides.csv.bz2 \
+ --chunk-size 1000000 \
+ --batch-size 65536 \
--models-dir "$(mhcflurry-downloads path models_class1_pan)/models.$kind" \
--allele $(cat alleles.txt) \
--out "predictions/mhcflurry.$kind" \
--
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