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 bfcb1d14a616015b049d52d6d518c7d5ac93e5eb..74de35464282d94610f2fc19190a05ada11aa4ae 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" \