diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.genes_list b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.genes_list
index c5842dc1..b7d81c5f 100644
Binary files a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.genes_list and b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.genes_list differ
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.schema_config b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.schema_config
index 67200c76..45bd4248 100644
Binary files a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.schema_config and b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/.schema_config differ
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1208.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1208.fasta
deleted file mode 100644
index aef76bdd..00000000
--- a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1208.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->GCA-000007265-protein1208_1
-ATGTCAACATTTAAACGCTATGATGAAGAATTCAAACAATCTCTTGTTAACCTTTATCAAACTGGAAAAACTCAGTCTGAACTCTGTAAAGACTATGGGGTATCCACTTCTACGCTTGCAAAATGGATCAAACAGTATTCCCAAGTCAAACTCGAAGATAATTCTGTACTTACTGCCAAGCAAATACAAGAGTTACAAAAACGTAATGCGCAGCTTGAAGAGGAGAACCTTATCCTAAAAAAAGCAAGTGCCATATTCATGCAAAACTTAAAGTAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1312.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1312.fasta
deleted file mode 100644
index 1ddec209..00000000
--- a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein1312.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->GCA-000007265-protein1312_1
-ATGACGCTTCGAGAATTAACAATAGAAGAATTTAAAGAACATTCAGGAAATTATGATTCACAATCATTTTTACAAACACCTGAGATGGCTAAACTTTTAGAAAAACGCGGCTATGATGTTAGGTATTTGGGATATCAAGTAGAAAATAAACTAGAGATAATCAGTTTATCTTATATTATGCCAGTCACTGGTGGTTTTCAAATGAAAATTGATTCAGGACCAGTTCATTCAAATTCTAAGTATCTAAAACAATTTTATAAAGCATTGCAAGGCTATGCCAAATCCAACGGTGTTCTAGAATTAATAGTTGAGCCTTATGATGATTACCAATTATTCACTAGTTCGGGAGTTCCTAGTAATCAGGGAAATGATAATCTGATTGAAGATTTTACCAGTTCAGGTTATCACCATGATGGTTTAACAACTGGTTTTACTGGTAAATATTTATCTTGGCACTATGTTAAAAATTTAGAAGGTGTCACTTCTGAAACGTTACTATCTTCATTCTCTAAGACAGGACGAGCTTTGGTTAAGAAAGCAATGTCTTTTGGAATCAAGGTTCGCGTTCTTAAACGTGATGAGCTACATTTATTTAAAGAGATAACAACTTCTACGTCAAATAGACGTGATTATATGGATAAGTCCTTAGATTATTATCAAGATTTTTACGATAGCTTTGAAGGCAAGGCTGAATTTGTGATTGCCACTTTAAATTTTAGAGAATACGACCATAACTTGCAAATAAAAGCTGAAGCATTGGAAAATAAGCTTAAATTGCTTGATGAACGTTTTAGGGAAAATGCAGACTCTCCTAAGTATCATAGGCAACGCTCTGAAATAATTAATCAACTGGCTAGTTTTGAAACACGACGACAAGAAGTTCAGTCATTTATTCAAAAGTATGATAACCAAGACGTTGTTTTAGCTGGTAGTCTATTTGTTTATAGTCTTAAGGAGACAGTTTATTTCTTTTCAGGATCCTACACAGAATTTAATAAATTTTATGCACCAGCAGTTCTTCAGGAATATGTTATGCAAGAGGCTCTCAAAAGAGGTTCTACTTTCTATAACCTCCTAGGTATTCAGGGAACTTTTGATGGTTCAGATAGTATTCTTCGCTTTAAACAGAATTTTAATGGTTGTATCATTCGTAAAATGGGAACTTTTAACTATTATCCAAGTCCTTTTAAATACAAAGGAATTCAGCTTCTTAAAAAGGTTTTGAAGAGAAATTAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein495.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein495.fasta
new file mode 100644
index 00000000..2bbf79a7
--- /dev/null
+++ b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein495.fasta
@@ -0,0 +1,2 @@
+>GCA-000007265-protein495_1
+ATGGCGCTTAAAGAATTAACAGCTAAAGAGTTCGAAAGTTATTCAGGAAATTACGATTTACAATCGTTTATGCAAACCCCTGAGATGGCAAAGCTTCTAAAAAAACGTGGGTATGACATTACCTACATGGGCTACCAAATCGATGGGAAAATGGAAATCATCAGTATTGTTTATACCATCCCAATGACTGGTGGACTTCATATGGAAGTCAATTCTGGTCCAGCCCATTCCAATTCTAAATATCTGAAACATTTTTATAAAGAACTACAGAACTATGCCAAATCTCAGGGCGCTTTAGAATTATTAATTAAACCTTATGATACCTACCAAGAGTTTACTGGTGAAGGTAAGCCTAAAGGTGCACCGAACACCTATCTTATTGATGACCTGACTAGTATAGGTTATCACCACGATGGGCTTCATATTGGTTATCCTGGCGGTGAACCTGATTGGCATTATGTTAAAAATCTAGAAGGTATCACTCCTCAAAATCTTCTTAAATCTTTCTCTAAAAAAGGACGCCCCTTGGTTAAAAAAGCCATGTCTTTTGGTATAAAAATACGTGTCCTCAAGCGGGAAGAACTACATATCTTTAAGGATATTACTTCTTCTACTTCTGATCGCCGGGACTATATGGATAAATCTCTAGATTATTATCAAGATTTTTATGATAGTTTCGGAGATAAGGCGGAATTTGTCATTGCAACTCTAAACTTTAGGGAATATGATCATAACCTACAATTAAATGCAAAGAAATTGGAAGAACAGATTACAGTCCTTGATAATCGCCATCAAAATAATACAGATTCTGCCAAATACCATCGTCAACGTACTGAGCTTGTCAATCAACTAGCTAGTTTAGATAAACGTCGCAAAGAAGTCGAACCTTTTATTCAAAAATTTGGAAATCAAGATGTTGTTTTAGCTGGTAGCCTCTTTATTTATAGCCCGAAAGAAACTGTCTATCTTTTCTCTGGCTCATACACAGAATTTAATAAATTTTATGCGCCTGCAGTTCTTCAAGAATATGTTATGCAAGAGGCTTTAAAGCGTCAATCAACTTTCTATAATTTTTTAGGTATTCAAGGAAATTTTGATGGTTCAGATGGCGTACTTCGCTTTAAACAGAATTTTAATGGTTACATTGTTCGTAAAATGGGTACTTTCCGCTACTATCCAAATCCATTAAAATATAAGAGTATTCAATTACTAAAGAAAATCTTACGCCGAACATAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein625.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein625.fasta
new file mode 100644
index 00000000..1e5dc0e7
--- /dev/null
+++ b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/GCA-000007265-protein625.fasta
@@ -0,0 +1,2 @@
+>GCA-000007265-protein625_1
+ATGTCAACATTTAAACGCTATGATGAAGAATTCAAACAATCTCTTGTTAACCTTTATCAAACTGGAAAAACTCAGTCTGAACTCTGTAAAGACTATAGGGTATCCACTTCTGCGCTTGCAAAATGGATCAAACAGTACTCTCAATTCAAACTCGAAGATAATTCTGTACTTACTGCCAAGCAAATACAAGAGTTACAAAAACGTAATGCGCAGCTTGAAGAGGAGAACCTTATCCTAAAAAAAGCAAGTGCCATATTCATGCAAAACTTAAAGTAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1208_short.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1208_short.fasta
deleted file mode 100644
index aef76bdd..00000000
--- a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1208_short.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->GCA-000007265-protein1208_1
-ATGTCAACATTTAAACGCTATGATGAAGAATTCAAACAATCTCTTGTTAACCTTTATCAAACTGGAAAAACTCAGTCTGAACTCTGTAAAGACTATGGGGTATCCACTTCTACGCTTGCAAAATGGATCAAACAGTATTCCCAAGTCAAACTCGAAGATAATTCTGTACTTACTGCCAAGCAAATACAAGAGTTACAAAAACGTAATGCGCAGCTTGAAGAGGAGAACCTTATCCTAAAAAAAGCAAGTGCCATATTCATGCAAAACTTAAAGTAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1312_short.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1312_short.fasta
deleted file mode 100644
index 1ddec209..00000000
--- a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein1312_short.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->GCA-000007265-protein1312_1
-ATGACGCTTCGAGAATTAACAATAGAAGAATTTAAAGAACATTCAGGAAATTATGATTCACAATCATTTTTACAAACACCTGAGATGGCTAAACTTTTAGAAAAACGCGGCTATGATGTTAGGTATTTGGGATATCAAGTAGAAAATAAACTAGAGATAATCAGTTTATCTTATATTATGCCAGTCACTGGTGGTTTTCAAATGAAAATTGATTCAGGACCAGTTCATTCAAATTCTAAGTATCTAAAACAATTTTATAAAGCATTGCAAGGCTATGCCAAATCCAACGGTGTTCTAGAATTAATAGTTGAGCCTTATGATGATTACCAATTATTCACTAGTTCGGGAGTTCCTAGTAATCAGGGAAATGATAATCTGATTGAAGATTTTACCAGTTCAGGTTATCACCATGATGGTTTAACAACTGGTTTTACTGGTAAATATTTATCTTGGCACTATGTTAAAAATTTAGAAGGTGTCACTTCTGAAACGTTACTATCTTCATTCTCTAAGACAGGACGAGCTTTGGTTAAGAAAGCAATGTCTTTTGGAATCAAGGTTCGCGTTCTTAAACGTGATGAGCTACATTTATTTAAAGAGATAACAACTTCTACGTCAAATAGACGTGATTATATGGATAAGTCCTTAGATTATTATCAAGATTTTTACGATAGCTTTGAAGGCAAGGCTGAATTTGTGATTGCCACTTTAAATTTTAGAGAATACGACCATAACTTGCAAATAAAAGCTGAAGCATTGGAAAATAAGCTTAAATTGCTTGATGAACGTTTTAGGGAAAATGCAGACTCTCCTAAGTATCATAGGCAACGCTCTGAAATAATTAATCAACTGGCTAGTTTTGAAACACGACGACAAGAAGTTCAGTCATTTATTCAAAAGTATGATAACCAAGACGTTGTTTTAGCTGGTAGTCTATTTGTTTATAGTCTTAAGGAGACAGTTTATTTCTTTTCAGGATCCTACACAGAATTTAATAAATTTTATGCACCAGCAGTTCTTCAGGAATATGTTATGCAAGAGGCTCTCAAAAGAGGTTCTACTTTCTATAACCTCCTAGGTATTCAGGGAACTTTTGATGGTTCAGATAGTATTCTTCGCTTTAAACAGAATTTTAATGGTTGTATCATTCGTAAAATGGGAACTTTTAACTATTATCCAAGTCCTTTTAAATACAAAGGAATTCAGCTTCTTAAAAAGGTTTTGAAGAGAAATTAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein495_short.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein495_short.fasta
new file mode 100644
index 00000000..2bbf79a7
--- /dev/null
+++ b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein495_short.fasta
@@ -0,0 +1,2 @@
+>GCA-000007265-protein495_1
+ATGGCGCTTAAAGAATTAACAGCTAAAGAGTTCGAAAGTTATTCAGGAAATTACGATTTACAATCGTTTATGCAAACCCCTGAGATGGCAAAGCTTCTAAAAAAACGTGGGTATGACATTACCTACATGGGCTACCAAATCGATGGGAAAATGGAAATCATCAGTATTGTTTATACCATCCCAATGACTGGTGGACTTCATATGGAAGTCAATTCTGGTCCAGCCCATTCCAATTCTAAATATCTGAAACATTTTTATAAAGAACTACAGAACTATGCCAAATCTCAGGGCGCTTTAGAATTATTAATTAAACCTTATGATACCTACCAAGAGTTTACTGGTGAAGGTAAGCCTAAAGGTGCACCGAACACCTATCTTATTGATGACCTGACTAGTATAGGTTATCACCACGATGGGCTTCATATTGGTTATCCTGGCGGTGAACCTGATTGGCATTATGTTAAAAATCTAGAAGGTATCACTCCTCAAAATCTTCTTAAATCTTTCTCTAAAAAAGGACGCCCCTTGGTTAAAAAAGCCATGTCTTTTGGTATAAAAATACGTGTCCTCAAGCGGGAAGAACTACATATCTTTAAGGATATTACTTCTTCTACTTCTGATCGCCGGGACTATATGGATAAATCTCTAGATTATTATCAAGATTTTTATGATAGTTTCGGAGATAAGGCGGAATTTGTCATTGCAACTCTAAACTTTAGGGAATATGATCATAACCTACAATTAAATGCAAAGAAATTGGAAGAACAGATTACAGTCCTTGATAATCGCCATCAAAATAATACAGATTCTGCCAAATACCATCGTCAACGTACTGAGCTTGTCAATCAACTAGCTAGTTTAGATAAACGTCGCAAAGAAGTCGAACCTTTTATTCAAAAATTTGGAAATCAAGATGTTGTTTTAGCTGGTAGCCTCTTTATTTATAGCCCGAAAGAAACTGTCTATCTTTTCTCTGGCTCATACACAGAATTTAATAAATTTTATGCGCCTGCAGTTCTTCAAGAATATGTTATGCAAGAGGCTTTAAAGCGTCAATCAACTTTCTATAATTTTTTAGGTATTCAAGGAAATTTTGATGGTTCAGATGGCGTACTTCGCTTTAAACAGAATTTTAATGGTTACATTGTTCGTAAAATGGGTACTTTCCGCTACTATCCAAATCCATTAAAATATAAGAGTATTCAATTACTAAAGAAAATCTTACGCCGAACATAA
diff --git a/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein625_short.fasta b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein625_short.fasta
new file mode 100644
index 00000000..1e5dc0e7
--- /dev/null
+++ b/CHEWBBACA/tests/data/createschema_data/expected_results/schema_seed/short/GCA-000007265-protein625_short.fasta
@@ -0,0 +1,2 @@
+>GCA-000007265-protein625_1
+ATGTCAACATTTAAACGCTATGATGAAGAATTCAAACAATCTCTTGTTAACCTTTATCAAACTGGAAAAACTCAGTCTGAACTCTGTAAAGACTATAGGGTATCCACTTCTGCGCTTGCAAAATGGATCAAACAGTACTCTCAATTCAAACTCGAAGATAATTCTGTACTTACTGCCAAGCAAATACAAGAGTTACAAAAACGTAATGCGCAGCTTGAAGAGGAGAACCTTATCCTAAAAAAAGCAAGTGCCATATTCATGCAAAACTTAAAGTAA
diff --git a/CHEWBBACA/tests/test_create_schema_sanity.py b/CHEWBBACA/tests/test_create_schema_sanity.py
index fe83ae4b..ef779ac3 100644
--- a/CHEWBBACA/tests/test_create_schema_sanity.py
+++ b/CHEWBBACA/tests/test_create_schema_sanity.py
@@ -47,13 +47,13 @@ def test_createschema_valid(test_args, expected):
     schema_seed = os.path.join(test_args[5], 'schema_seed')
     output_files = [os.path.join(schema_seed, file)
                     for file in os.listdir(schema_seed)
-                    if 'short' != file]
+                    if 'short' not in file]
     output_files.sort()
 
     expected_seed = os.path.join(expected, 'schema_seed')
     expected_files = [os.path.join(expected_seed, file)
                       for file in os.listdir(expected_seed)
-                      if 'short' != file]
+                      if 'short' not in file]
     expected_files.sort()
 
     # get config files