diff --git a/python/LogisticRegressionByReadGroup.py b/python/LogisticRegressionByReadGroup.py
index b6299d3ab..f4389ea7f 100755
--- a/python/LogisticRegressionByReadGroup.py
+++ b/python/LogisticRegressionByReadGroup.py
@@ -44,8 +44,9 @@ def process_file(source_file,read_group,dinuc,target_file,R_exe,logistic_regress
     "Process the contents of an intermediate file.  An intermediate file is the specific data arranged per read group, per dinuc."
     base = source_file.name[:source_file.name.rfind('.csv')] + '.' + read_group
     regression_command = ' '.join((R_exe,logistic_regression_script,base,base,dinuc))
-    print "Running " + regression_command
-    os.system(regression_command)
+    result = os.system(regression_command)
+    if result != 0:
+        exit('Unable to run linear regression; command was %s, error code was %d' % (regression_command, result),1)
     parameters_filename = '.'.join((base,dinuc,'parameters'))
     if not os.access(parameters_filename,os.R_OK):
         exit("Unable to read output of R from file " + parameters_filename)
diff --git a/python/RecalQual.py b/python/RecalQual.py
index 1bfbc6ac2..20f5ea540 100755
--- a/python/RecalQual.py
+++ b/python/RecalQual.py
@@ -67,7 +67,7 @@ if not os.path.isdir('output'):
     os.mkdir('output')
 
 # assemble the required program arguments
-gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO','-L chrM'))
+gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))
 generate_covariates         = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',bam,'-mqs 40','--OUTPUT_FILEROOT output/initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
 apply_logistic_regression   = ' '.join((gatk_base_cmdline,'-T LogisticRecalibration','-I',bam,'-logisticParams output/linear_regression_results.out','-outputBAM',calibrated_bam))
 index_calibrated_bamfile    = ' '.join((samtools_exe,'index',calibrated_bam))