diff --git a/ChangeLog b/ChangeLog
index ffb19a05d9..707065d942 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,6 +1,5 @@
-2014-10-06  Michael R. Crusoe  <mcrusoe@msu.edu>
-
-    * Doxyfile.in: add links to the stdc++ docs
+2014-12-05  Jessica Mizzi  <mizzijes@msu.edu>
+    * khmer/file.py,sandbox/sweep-reads.py,scripts/{abundance-dist-single,abundance-dist,annotate-partitions,count-median,count-overlap,do-partition,extract-paired-reads,extract-partitions,filter-abund-single,filter-abund,filter-stoptags,interleave-reads,load-graph,load-into-counting,make-initial-stoptags,merge-partitions,normalize-by-median,partition-graph,sample-reads-randomly,split-paired-reads}.py,setup.cfg,tests/{test_script_arguments,test_scripts}.py: Added force option to all scripts to script IO sanity checks and updated tests to match. 
 
 2014-10-01  Ben Taylor  <taylo886@msu.edu>
 
diff --git a/khmer/file.py b/khmer/file.py
index 46984cecc7..07796819a9 100644
--- a/khmer/file.py
+++ b/khmer/file.py
@@ -13,7 +13,7 @@
 import sys
 
 
-def check_file_status(file_path):
+def check_file_status(file_path, force):
     """
     Check status of file - return if file exists; warn and exit
     if empty, or does not exist
@@ -21,15 +21,17 @@ def check_file_status(file_path):
     if not os.path.exists(file_path):
         print >>sys.stderr, "ERROR: Input file %s does not exist; exiting" % \
                             file_path
-        sys.exit(1)
+        if not force:
+            sys.exit(1)
     else:
         if os.stat(file_path).st_size == 0:
             print >>sys.stderr, "ERROR: Input file %s is empty; exiting." % \
                                 file_path
-            sys.exit(1)
+            if not force:
+	        sys.exit(1)
 
 
-def check_space(in_files, _testhook_free_space=None):
+def check_space(in_files, force, _testhook_free_space=None):
     """
     Estimate size of input files passed, then calculate
     disk space available. Exit if insufficient disk space,
@@ -65,10 +67,11 @@ def check_space(in_files, _testhook_free_space=None):
                             % (float(total_size) / 1e9,)
         print >>sys.stderr, "       Free space: %.1f GB" \
                             % (float(free_space) / 1e9,)
-        sys.exit(1)
+        if not force:
+            sys.exit(1)
 
 
-def check_space_for_hashtable(hash_size, _testhook_free_space=None):
+def check_space_for_hashtable(hash_size, force, _testhook_free_space=None):
     """
     Check we have enough size to write a hash table
     """
diff --git a/sandbox/sweep-reads.py b/sandbox/sweep-reads.py
index fbdc068875..81770fb5af 100755
--- a/sandbox/sweep-reads.py
+++ b/sandbox/sweep-reads.py
@@ -191,7 +191,8 @@ def get_parser():
     parser.add_argument(dest='input_fastp', help='Reference fasta or fastp')
     parser.add_argument('input_files', nargs='+',
                         help='Reads to be swept and sorted')
-
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -224,13 +225,13 @@ def main():
     buf_size = args.buffer_size
     max_reads = args.max_reads
 
-    check_file_status(args.input_fastp)
+    check_file_status(args.input_fastp, args.force)
     check_valid_file_exists(args.input_files)
     all_input_files = [input_fastp]
     all_input_files.extend(args.input_files)
 
     # Check disk space availability
-    check_space(all_input_files)
+    check_space(all_input_files, args.force)
 
     # figure out input file type (FA/FQ) -- based on first file
     ix = iter(screed.open(args.input_files[0]))
diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 3e7c19f90d..8de569445e 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -60,6 +60,8 @@ def get_parser():
                         "filename.")
     parser.add_argument('--report-total-kmers', '-t', action='store_true',
                         help="Prints the total number of k-mers to stderr")
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -68,8 +70,8 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
     args = get_parser().parse_args()
     report_on_config(args)
 
-    check_file_status(args.input_sequence_filename)
-    check_space([args.input_sequence_filename])
+    check_file_status(args.input_sequence_filename, args.force)
+    check_space([args.input_sequence_filename], args.force)
     if args.savetable:
         check_space_for_hashtable(args.n_tables * args.min_tablesize)
 
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index de41aaeeb4..4fd1e8aec5 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -44,6 +44,8 @@ def get_parser():
                         help='Overwrite output file if it exists')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -53,7 +55,7 @@ def main():
     infiles = [args.input_counting_table_filename,
                args.input_sequence_filename]
     for infile in infiles:
-        check_file_status(infile)
+        check_file_status(infile, args.force)
 
     print('hashtable from', args.input_counting_table_filename)
     counting_hash = khmer.load_counting_hash(
diff --git a/scripts/annotate-partitions.py b/scripts/annotate-partitions.py
index e10ae92908..ab2de29844 100755
--- a/scripts/annotate-partitions.py
+++ b/scripts/annotate-partitions.py
@@ -54,6 +54,8 @@ def get_parser():
                         'annotate.')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -67,11 +69,11 @@ def main():
 
     partitionmap_file = args.graphbase + '.pmap.merged'
 
-    check_file_status(partitionmap_file)
+    check_file_status(partitionmap_file, args.force)
     for _ in filenames:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(filenames)
+    check_space(filenames, args.force)
 
     print 'loading partition map from:', partitionmap_file
     htable.load_partitionmap(partitionmap_file)
diff --git a/scripts/count-median.py b/scripts/count-median.py
index 3709fbb0c0..275d2ecc77 100755
--- a/scripts/count-median.py
+++ b/scripts/count-median.py
@@ -50,6 +50,8 @@ def get_parser():
                         help='output summary filename')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -63,9 +65,9 @@ def main():
 
     infiles = [htfile, input_filename]
     for infile in infiles:
-        check_file_status(infile)
+        check_file_status(infile, args.force)
 
-    check_space(infiles)
+    check_space(infiles, args.force)
 
     print 'loading k-mer counting table from', htfile
     htable = khmer.load_counting_hash(htfile)
diff --git a/scripts/count-overlap.py b/scripts/count-overlap.py
index f708b7fd9d..cd598d67d3 100755
--- a/scripts/count-overlap.py
+++ b/scripts/count-overlap.py
@@ -44,7 +44,8 @@ def get_parser():
                         help="input sequence filename")
     parser.add_argument('report_filename', metavar='output_report_filename',
                         help='output report filename')
-
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -54,9 +55,9 @@ def main():
     report_on_config(args, hashtype='hashbits')
 
     for infile in [args.ptfile, args.fafile]:
-        check_file_status(infile)
+        check_file_status(infile, args.force)
 
-    check_space([args.ptfile, args.fafile])
+    check_space([args.ptfile, args.fafile], args.force)
 
     print 'loading k-mer presence table from', args.ptfile
     ht1 = khmer.load_hashbits(args.ptfile)
diff --git a/scripts/do-partition.py b/scripts/do-partition.py
index c77668b9d5..62de9672a9 100755
--- a/scripts/do-partition.py
+++ b/scripts/do-partition.py
@@ -111,9 +111,9 @@ def main():  # pylint: disable=too-many-locals,too-many-statements
     report_on_config(args, hashtype='hashbits')
 
     for infile in args.input_filenames:
-        check_file_status(infile)
+        check_file_status(infile, args.force)
 
-    check_space(args.input_filenames)
+    check_space(args.input_filenames, args.force)
 
     print 'Saving k-mer presence table to %s' % args.graphbase
     print 'Loading kmers from sequences in %s' % repr(args.input_filenames)
diff --git a/scripts/extract-paired-reads.py b/scripts/extract-paired-reads.py
index 79b8e6959b..c9320e1288 100755
--- a/scripts/extract-paired-reads.py
+++ b/scripts/extract-paired-reads.py
@@ -74,6 +74,8 @@ def get_parser():
     parser.add_argument('infile')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -81,9 +83,9 @@ def main():
     info('extract-paired-reads.py')
     args = get_parser().parse_args()
 
-    check_file_status(args.infile)
+    check_file_status(args.infile, args.force)
     infiles = [args.infile]
-    check_space(infiles)
+    check_space(infiles, args.force)
 
     outfile = os.path.basename(args.infile)
     if len(sys.argv) > 2:
diff --git a/scripts/extract-partitions.py b/scripts/extract-partitions.py
index 23ce60f383..ab51a282c1 100755
--- a/scripts/extract-partitions.py
+++ b/scripts/extract-partitions.py
@@ -81,6 +81,8 @@ def get_parser():
                         help='Output unassigned sequences, too')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -94,9 +96,9 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
     n_unassigned = 0
 
     for infile in args.part_filenames:
-        check_file_status(infile)
+        check_file_status(infile, args.force)
 
-    check_space(args.part_filenames)
+    check_space(args.part_filenames, args.force)
 
     print '---'
     print 'reading partitioned files:', repr(args.part_filenames)
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index 2d82954a22..ed647366a1 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -56,16 +56,18 @@ def get_parser():
                         help="FAST[AQ] sequence file to trim")
     parser.add_argument('--report-total-kmers', '-t', action='store_true',
                         help="Prints the total number of k-mers to stderr")
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
 def main():
     info('filter-abund-single.py', ['counting'])
     args = get_parser().parse_args()
-    check_file_status(args.datafile)
-    check_space([args.datafile])
+    check_file_status(args.datafile, args.force)
+    check_space([args.datafile],args.force)
     if args.savetable:
-        check_space_for_hashtable(args.n_tables * args.min_tablesize)
+        check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
     report_on_config(args)
 
     config = khmer.get_config()
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index 32f7fd65da..84c2d2d07e 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -66,6 +66,8 @@ def get_parser():
                         'file for each input file.')
     parser.add_argument('--version', action='version',
                         version='khmer {v}'.format(v=__version__))
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -77,9 +79,9 @@ def main():
     infiles = args.input_filename
 
     for _ in infiles:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(infiles)
+    check_space(infiles, args.force)
 
     print 'loading hashtable'
     htable = khmer.load_counting_hash(counting_ht)
diff --git a/scripts/filter-stoptags.py b/scripts/filter-stoptags.py
index 3d7ffd1f60..ca9cede93f 100755
--- a/scripts/filter-stoptags.py
+++ b/scripts/filter-stoptags.py
@@ -44,9 +44,10 @@ def get_parser():
                         nargs='+')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
-
 def main():
     info('filter-stoptags.py', ['graph'])
     args = get_parser().parse_args()
@@ -54,9 +55,9 @@ def main():
     infiles = args.input_filenames
 
     for _ in infiles:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(infiles)
+    check_space(infiles, args.force)
 
     print 'loading stop tags, with K', args.ksize
     htable = khmer.new_hashbits(args.ksize, 1, 1)
diff --git a/scripts/interleave-reads.py b/scripts/interleave-reads.py
index 9f79c71a67..ca33e8c201 100755
--- a/scripts/interleave-reads.py
+++ b/scripts/interleave-reads.py
@@ -73,9 +73,9 @@ def main():
     args = get_parser().parse_args()
 
     for _ in args.infiles:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(args.infiles)
+    check_space(args.infiles, args.force)
 
     s1_file = args.infiles[0]
     if len(args.infiles) == 2:
diff --git a/scripts/load-graph.py b/scripts/load-graph.py
index be2fcb0709..01b78a3d87 100755
--- a/scripts/load-graph.py
+++ b/scripts/load-graph.py
@@ -54,10 +54,10 @@ def main():
     filenames = args.input_filenames
 
     for _ in args.input_filenames:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(args.input_filenames)
-    check_space_for_hashtable(float(args.n_tables * args.min_tablesize) / 8.)
+    check_space(args.input_filenames, args.force)
+    check_space_for_hashtable((float(args.n_tables * args.min_tablesize) / 8.),     args.force)
 
     print 'Saving k-mer presence table to %s' % base
     print 'Loading kmers from sequences in %s' % repr(filenames)
diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index c407e3eb96..f954f8db71 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -71,10 +71,10 @@ def main():
     filenames = args.input_sequence_filename
 
     for name in args.input_sequence_filename:
-	check_file_status(name)
+	check_file_status(name, args.force)
 
-    check_space(args.input_sequence_filename)
-    check_space_for_hashtable(args.n_tables * args.min_tablesize)
+    check_space(args.input_sequence_filename, args.force)
+    check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
 
     print 'Saving k-mer counting table to %s' % base
     print 'Loading kmers from sequences in %s' % repr(filenames)
diff --git a/scripts/make-initial-stoptags.py b/scripts/make-initial-stoptags.py
index 186773dd69..551be8f7e5 100755
--- a/scripts/make-initial-stoptags.py
+++ b/scripts/make-initial-stoptags.py
@@ -62,6 +62,8 @@ def get_parser():
                         help="Use stoptags in this file during partitioning")
     parser.add_argument('graphbase', help='basename for input and output '
                         'filenames')
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -77,9 +79,9 @@ def main():
     if args.stoptags:
         infiles.append(args.stoptags)
     for _ in infiles:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(infiles)
+    check_space(infiles, args.force)
 
     print 'loading htable %s.pt' % graphbase
     htable = khmer.load_hashbits(graphbase + '.pt')
diff --git a/scripts/merge-partitions.py b/scripts/merge-partitions.py
index 986e9f76a9..e06fa41119 100755
--- a/scripts/merge-partitions.py
+++ b/scripts/merge-partitions.py
@@ -43,6 +43,8 @@ def get_parser():
                         'files')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -60,9 +62,9 @@ def main():
     htable = khmer.new_hashbits(ksize, 1, 1)
 
     for _ in pmap_files:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(pmap_files)
+    check_space(pmap_files, args.force)
 
     for pmap_file in pmap_files:
         print 'merging', pmap_file
diff --git a/scripts/normalize-by-median.py b/scripts/normalize-by-median.py
index 8d23d76209..648ef7e428 100755
--- a/scripts/normalize-by-median.py
+++ b/scripts/normalize-by-median.py
@@ -207,6 +207,8 @@ def get_parser():
     parser.add_argument('--report-total-kmers', '-t', action='store_true',
                         help="Prints the total number of k-mers"
                         " post-normalization to stderr")
+    parser.add_argument('--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     add_loadhash_args(parser)
     return parser
 
@@ -220,9 +222,9 @@ def main():  # pylint: disable=too-many-branches,too-many-statements
     report_fp = args.report
 
     check_valid_file_exists(args.input_filenames)
-    check_space(args.input_filenames)
+    check_space(args.input_filenames, args.force)
     if args.savetable:
-        check_space_for_hashtable(args.n_tables * args.min_tablesize)
+        check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
 
     # list to save error files along with throwing exceptions
     if args.force:
diff --git a/scripts/partition-graph.py b/scripts/partition-graph.py
index 8ba728cc48..657f33edd4 100755
--- a/scripts/partition-graph.py
+++ b/scripts/partition-graph.py
@@ -89,6 +89,8 @@ def get_parser():
                         'traversals')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     add_threading_args(parser)
     return parser
 
@@ -100,9 +102,9 @@ def main():
 
     filenames = [basename + '.pt', basename + '.tagset']
     for _ in filenames:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(filenames)
+    check_space(filenames, args.force)
 
     print '--'
     print 'SUBSET SIZE', args.subset_size
diff --git a/scripts/sample-reads-randomly.py b/scripts/sample-reads-randomly.py
index a36e359c0d..d2e6f98594 100755
--- a/scripts/sample-reads-randomly.py
+++ b/scripts/sample-reads-randomly.py
@@ -84,9 +84,9 @@ def main():
     args = get_parser().parse_args()
 
     for _ in args.filenames:
-        check_file_status(_)
+        check_file_status(_, args.force)
 
-    check_space(args.filenames)
+    check_space(args.filenames, args.force)
 
     # seed the random number generator?
     if args.random_seed:
diff --git a/scripts/split-paired-reads.py b/scripts/split-paired-reads.py
index 09521e5cbe..fbb4ead6ec 100755
--- a/scripts/split-paired-reads.py
+++ b/scripts/split-paired-reads.py
@@ -42,6 +42,8 @@ def get_parser():
     parser.add_argument('infile')
     parser.add_argument('--version', action='version', version='%(prog)s '
                         + khmer.__version__)
+    parser.add_argument('-f', '--force', default=False, action='store_true',
+                        help='Overwrite output file if it exists')
     return parser
 
 
@@ -51,9 +53,9 @@ def main():
 
     infile = args.infile
 
-    check_file_status(infile)
+    check_file_status(infile, args.force)
     filenames = [infile]
-    check_space(filenames)
+    check_space(filenames, args.force)
 
     out1 = os.path.basename(infile) + '.1'
     out2 = os.path.basename(infile) + '.2'
diff --git a/setup.cfg b/setup.cfg
index 69aecb27d8..88eedf7225 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [nosetests]
 verbosity = 2
-stop = TRUE
+#stop = TRUE
 attr = !known_failing,!jenkins
 #processes = -1 # breaks xunit output
 #attr = !known_failing,!highmem
diff --git a/tests/test_script_arguments.py b/tests/test_script_arguments.py
index ba850f7e71..ac91f0a4dd 100644
--- a/tests/test_script_arguments.py
+++ b/tests/test_script_arguments.py
@@ -20,7 +20,7 @@ def test_check_space():
 
     save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
     try:
-        khmer.file.check_space([fakelump_fa], _testhook_free_space=0)
+        khmer.file.check_space([fakelump_fa], force=False, _testhook_free_space=0)
         assert 0, "this should fail"
     except SystemExit as e:
         print str(e)
@@ -31,9 +31,33 @@ def test_check_space():
 def test_check_tablespace():
     save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
     try:
-        khmer.file.check_space_for_hashtable(1e9, _testhook_free_space=0)
+        khmer.file.check_space_for_hashtable(1e9, force=False,  _testhook_free_space=0)
         assert 0, "this should fail"
     except SystemExit as e:
         print str(e)
     finally:
         sys.stderr = save_stderr
+
+
+def test_check_space_force():
+    fakelump_fa = utils.get_test_data('fakelump.fa')
+
+    save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
+    try:
+        khmer.file.check_space([fakelump_fa], force=True, _testhook_free_space=0)
+        assert True, "this should pass"
+    except SystemExit as e:
+        print str(e)
+    finally:
+        sys.stderr = save_stderr
+
+
+def test_check_tablespace_force():
+    save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
+    try:
+        khmer.file.check_space_for_hashtable(1e9, force=True,  _testhook_free_space=0)
+        assert True, "this should pass"
+    except SystemExit as e:
+        print str(e)
+    finally:
+        sys.stderr = save_stderr
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index d9bb93bfd1..17291c09e0 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -30,7 +30,7 @@ def teardown():
 def test_check_space():
     # @CTB this probably belongs in a new test file, along with other
     # tests of the file.py module.
-    khmer.file.check_space(['', utils.get_test_data('test-abund-read-2.fa')])
+    khmer.file.check_space(['', utils.get_test_data('test-abund-read-2.fa')], False)
 
 
 def test_load_into_counting():
@@ -1483,7 +1483,7 @@ def test_sample_reads_randomly_S():
     badargs = list(args)
     badargs.extend(['-o', 'test', 'test.fq', 'test.fq'])
     (status, out, err) = utils.runscript(script, badargs, in_dir, fail_ok=True)
-    assert status == -1, (status, out, err)
+    assert status == 1, (status, out, err)
 
     args.append('test.fq')