diff --git a/script/hatchet.ini b/script/hatchet.ini
index 1a3dcde3..0cead1f2 100644
--- a/script/hatchet.ini
+++ b/script/hatchet.ini
@@ -64,7 +64,7 @@ msr = 5000
 # Minimum number of total reads per bin and sample
 mtr = 5000
 
-[cluster_bins_loc]
+[cluster_bins]
 diploidbaf = 0.08
 # Minimum and maximum number of clusters to infer
 # (using silhouette score for model selection)
diff --git a/src/hatchet/utils/count_alleles.py b/src/hatchet/utils/count_alleles.py
index 25a4d97f..41ff6bef 100644
--- a/src/hatchet/utils/count_alleles.py
+++ b/src/hatchet/utils/count_alleles.py
@@ -264,7 +264,7 @@ def countAlleles(self, bamfile, samplename, chromosome):
             self.dp,
             self.snplist[chromosome],
         )
-        cmd_query = "{} query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(AD)<={} & SUM(AD)>={}'".format(
+        cmd_query = "{} query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(INFO/AD)<={} & SUM(INFO/AD)>={}'".format(
             self.bcftools, self.dp, self.mincov
         )
         if self.E:
@@ -287,6 +287,8 @@ def countAlleles(self, bamfile, samplename, chromosome):
                 stderr=err,
                 universal_newlines=True,
             )
+            # Allow sp mpileup to receive a SIGPIPE if p2 exits. avoid deadlock
+            mpileup.stdout.close()
             stdout, _ = query.communicate()
             codes = map(lambda p: p.wait(), [mpileup, query])
         if any(c != 0 for c in codes):