diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 6ede4c2614f..1fa6bd500a0 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -33,6 +33,9 @@ from galaxy.util.checkers import is_bz2, is_gzip
 from . import data, dataproviders
 
 log = logging.getLogger(__name__)
+# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
+# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
+pysam.set_verbosity(0)
 
 # Currently these supported binary data types must be manually set on upload
 
@@ -489,9 +492,9 @@ class Bam(BamNative):
             # we start another process and discard stderr.
             if index_flag == '-b':
                 # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-                cmd = ['python', '-c', "import pysam; pysam.index('%s', '%s')" % (file_name, index_name)]
+                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}')".format(file_name, index_name)]
             else:
-                cmd = ['python', '-c', "import pysam; pysam.index('%s', '%s', '%s')" % (index_flag, file_name, index_name)]
+                cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}', '{}')".format(index_flag, file_name, index_name)]
             with open(os.devnull, 'w') as devnull:
                 subprocess.check_call(cmd, stderr=devnull, shell=False)
             needs_sorting = False
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index 1e06e82bcab..c9c1a82b2c2 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -27,6 +27,9 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
 # Utility functions.
 #
 
+# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
+# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
+pysam.set_verbosity(0)
 PYSAM_INDEX_SYMLINK_NECESSARY = packaging.version.parse(pysam.__version__) <= packaging.version.parse('0.13.0')