diff --git a/R/exomePreQC.R b/R/exomePreQC.R
index 8d04ea99c..ce37477a2 100644
--- a/R/exomePreQC.R
+++ b/R/exomePreQC.R
@@ -3,8 +3,8 @@ onCMDLine = ! is.na(args[1])
 
 if ( onCMDLine ) {
   reference_dataset = '/Users/mhanna/metrics.perSample.formatted.table'
-  inputTSV = args[2]
-  outputPDF = args[3]
+  inputTSV = args[1]
+  outputPDF = args[2]
 } else {
   reference_dataset = '/Users/mhanna/metrics.perSample.formatted.table'
   inputTSV = 'GoT2D_exomes_batch_005.tsv'
@@ -13,7 +13,6 @@ if ( onCMDLine ) {
 
 require('ggplot2')
 
-inputTSV = "GoT2D_exomes_batch_005.tsv"
 data <- read.table(inputTSV,header=T)
 
 complete <- read.table(reference_dataset,header=T)
diff --git a/python/generate_per_sample_metrics.py b/python/generate_per_sample_metrics.py
index e59badd1d..4092f711e 100644
--- a/python/generate_per_sample_metrics.py
+++ b/python/generate_per_sample_metrics.py
@@ -90,19 +90,17 @@ for sample_id,filename in samples.items():
     if fingerprinting_summary_metrics != None:
         haplotypes_confidently_matching = [str(metric.HAPLOTYPES_CONFIDENTLY_MATCHING) for metric in fingerprinting_summary_metrics]
         fingerprint_lods = [str(metric.LOD_EXPECTED_SAMPLE) for metric in fingerprinting_summary_metrics]
-#        min_haplotypes_confidently_matching = str(min(haplotypes_confidently_matching))
-#        max_haplotypes_confidently_matching = str(max(haplotypes_confidently_matching))
-#        median_haplotypes_confidently_matching = str(median(haplotypes_confidently_matching))
     else:
         haplotypes_confidently_matching = []
         fingerprint_lods = []
-#        min_haplotypes_confidently_matching = 'NA'
-#        max_haplotypes_confidently_matching = 'NA'
-#        median_haplotypes_confidently_matching = 'NA'
 
     data = [sample_id,'c('+string.join(fingerprint_lods,',')+')','c('+string.join(haplotypes_confidently_matching,',')+')']
 
     for metrics_type,metrics_extension in sample_summary_metrics_types:
-        metrics = get_sample_summary_metrics('%s.%s' % (basepath,metrics_extension))
-        data.extend([getattr(metrics, metrics_field_name) for metrics_field_name in get_sample_summary_metrics_fields(metrics_type)])
+        metrics_pathname = '%s.%s' % (basepath,metrics_extension)
+        if os.path.exists(metrics_pathname):
+            metrics = get_sample_summary_metrics(metrics_pathname)
+            data.extend([getattr(metrics, metrics_field_name) for metrics_field_name in get_sample_summary_metrics_fields(metrics_type)])
+        else:
+            data.extend(['NA' for metrics_field_name in get_sample_summary_metrics_fields(metrics_type)])
     print string.join(['%s']*len(header),'\t')%tuple(data)
diff --git a/python/parse_pm_input.py b/python/parse_pm_input.py
index 13c82076c..d6239aba4 100644
--- a/python/parse_pm_input.py
+++ b/python/parse_pm_input.py
@@ -50,7 +50,7 @@ def create_reader(filename):
     extension = os.path.splitext(filename)[1]
     if extension == '.xls' or extension == '.xlsx':
         return excel_reader(filename)
-    elif extensions == '.tsv' or extension == '.txt':
+    elif extension == '.tsv' or extension == '.txt':
         return tsv_reader(filename)
     else:
         print 'Unrecognized file extension',extension
@@ -73,6 +73,8 @@ for project,sample in create_reader(input_filename):
             print 'Hit a path name that cannot be parsed: ',version_path
             sys.exit(1)
         versions.append(int(version_path[1:]))
+    if len(versions) == 0:
+        continue
     versions = sorted(versions)
     bam_file = '%s/v%d/%s.bam' % (sample_path,versions[-1],sample)
     if not os.path.exists(bam_file):