diff --git a/downloads-generation/data_mass_spec_benchmark/GENERATE.sh b/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
index 474768ea9ad7d93187bddb8fb37b012393f63bf6..3328779eeddae01f2764315ea3ada9312e0df301 100755
--- a/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
+++ b/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
@@ -96,8 +96,7 @@ else
 fi
 
 # Write out and process peptides.
-#for subset in all
-for subset in chr1
+for subset in all
 do
     if [ "$2" == "reuse-all" ]
     then
@@ -126,7 +125,7 @@ do
     fi
 
     python run_predictors.py \
-        proteome_peptides.$subset.csv.bz2 \
+        "$(pwd)/proteome_peptides.$subset.csv.bz2" \
         --result-dtype "float16" \
         --predictor mixmhcpred \
         --chunk-size 500000 \
@@ -134,7 +133,6 @@ do
         --out "$OUT_DIR" \
         --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
         --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.nogpu.lsf \
-	--max-peptides 1000 \
         --reuse-predictions "$REUSE" $EXTRA_ARGS
 
     # Run netmhcpan4
@@ -148,7 +146,7 @@ do
         fi
 
         python run_predictors.py \
-            proteome_peptides.$subset.csv.bz2 \
+            "$(pwd)/proteome_peptides.$subset.csv.bz2" \
             --result-dtype "float16" \
             --predictor netmhcpan4-$kind \
             --chunk-size 1000 \
@@ -171,7 +169,7 @@ do
         fi
 
         python run_predictors.py \
-            proteome_peptides.${subset}.csv.bz2 \
+            "$(pwd)/proteome_peptides.$subset.csv.bz2" \
             --result-dtype "float16" \
             --predictor mhcflurry \
             --chunk-size 500000 \
diff --git a/downloads-generation/data_mass_spec_benchmark/run_predictors.py b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
index 5bdd02db8a4d2d3486f613e5b9dafb6c2bc6f820..d0e5637967883baac7b9d03460c565bfc4c90fa2 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_predictors.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
@@ -89,8 +89,8 @@ add_cluster_parallelism_args(parser)
 PREDICTOR_TO_COLS = {
     "mhcflurry": ["affinity"],
     "netmhcpan4-ba": ["affinity", "percentile_rank"],
-    "netmhcpan4-el": ["elution_score"],
-    "mixmhcpred": ["elution_score"],
+    "netmhcpan4-el": ["score"],
+    "mixmhcpred": ["score"],
 }
 
 
@@ -405,7 +405,7 @@ def do_predictions_mhctools(work_item_dicts, constant_data=None):
                 # to execute.
                 empty_results = pandas.Series(index=peptides,
                     dtype=numpy.float16)
-                empty_results[:] = numpy.inf
+                empty_results[:] = float('-inf')
                 try:
                     predictor.predict_peptides_dataframe(["PEPTIDESS"])
                     mixmhcpred_usable_alleles.append(allele)
@@ -416,9 +416,8 @@ def do_predictions_mhctools(work_item_dicts, constant_data=None):
 
             print("MixMHCpred usable alleles: ", *mixmhcpred_usable_alleles)
             print("MixMHCpred unusable alleles: ", *unusable_alleles)
-            predictor = mhctools.MixMHCpred(alleles=alleles)
+            predictor = mhctools.MixMHCpred(alleles=mixmhcpred_usable_alleles)
             assert mixmhcpred_usable_alleles, mixmhcpred_usable_alleles
-            alleles = mixmhcpred_usable_alleles
         else:
             raise ValueError("Unsupported", predictor_name)
 
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index 585fd8197d26eb5cc32b2bcb98c0fb74db0a1512..76737300a498b4b9fd6f0d93fecc2a7fa3b234dd 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -68,7 +68,7 @@ then
     python generate_hyperparameters.py hyperparameters.production.yaml compact_peptide > hyperparameters.compact_peptide.yaml
 fi
 
-for kind in 34mer_sequence single_hidden_no_pretrain no_pretrain compact_peptide no_additional_ms ms_only affinity_only
+for kind in no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only
 do
     CONTINUE_INCOMPLETE_ARGS=""
     if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
@@ -116,7 +116,7 @@ done
 
 echo "Done training. Beginning model selection."
 
-for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence compact_peptide no_additional_ms ms_only affinity_only
+for kind in no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only
 do
     MODELS_DIR="models.unselected.${kind}"
     mhcflurry-class1-select-pan-allele-models \
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index bc8accf0054b2f6df1b33536cbdc30d25d22fbb3..f3d0160fc1cd594ebf112b0a2bcb98dd1daf6169 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -21,11 +21,11 @@ releases:
         compatibility-version: 2
         downloads:
             - name: models_class1_pan
-              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.selected.20200102.tar.bz2
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.selected.20200104.tar.bz2
               default: false
 
             - name: models_class1_pan_unselected
-              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.20200102.tar.bz2
+              url: https://github.com/openvax/mhcflurry/releases/download/1.6.0/models_class1_pan.20200104.tar.bz2
               default: false
 
             - name: models_class1_pan_refined