diff --git a/CHEWBBACA/tests/data/allelecall_data/test_invalid_input_names/pdb_prefix/5454.fasta b/CHEWBBACA/tests/data/allelecall_data/test_invalid_input_names/pdb_prefix/5454.fasta
new file mode 100644
index 00000000..1fc8a190
--- /dev/null
+++ b/CHEWBBACA/tests/data/allelecall_data/test_invalid_input_names/pdb_prefix/5454.fasta
@@ -0,0 +1,2 @@
+>GCA_000007265-protein1
+ATGGTACAATATAACAATAATTATCCACAAGACAATAAGGAAGAAGCTATGACGGAAAACGAACAACTATTTTGGAATAGAGTACTAGAGCTATCTCGTTCTCAAATAGCACCAGCAGCTTATGAATTTTTTGTTCTAGAGGCTAGACTCCTCAAAATTGAACATCAAACTGCAGTTATTACTTTAGATAACATTGAAATGAAAAAGCTATTCTGGGAACAAAATTTGGGGCCTGTTATCCTAACAGCTGGTTTTGAAATTTTCAATGCTGAAATTACAGCTAACTATGTCTCAAACGATTTACATTTACAAGAAACTAGTTTTTCTAACTACCAGCAATCTAGCAATGAAGTAAATACTTTACCAATTAGAAAAATCGACTCTAACCTTAAAGAGAAATATACTTTTGCTAATTTTGTTCAAGGAGATGAAAATAGATGGGCTGTTTCAGCATCAATTGCTGTAGCTGATAGTCCTGGCACGACTTATAATCCTCTATTTATCTGGGGGGGACCTGGTCTAGGAAAGACGCATCTACTAAATGCTATTGGAAATCAAGTCTTAAGAGATAATCCAAACGCGAGGGTTTTATACATCACTGCTGAGAATTTTATTAATGAATTTGTCAGTCATATTCGTTTAGATTCGATGGAAGAATTAAAAGAAAAGTTTCGCAACTTAGACTTACTCCTGATTGATGATATTCAGTCGCTTGCTAAGAAAACCTTAGGGGGGACCCAAGAGGAGTTCTTCAATACTTTCAATGCTTTACATACAAACGATAAACAAATCGTATTGACCAGTGACCGAAATCCAAATCAATTAAATGATCTAGAAGAACGTCTAGTCACGCGCTTTAGTTGGGGACTCCCAGTAAATATCACACCACCTGATTTTGAAACACGAGTTGCTATTTTAACCAATAAAATTCAAGAATATCCTTATGATTTTCCTCAAGATACCATTGAATACTTAGCAGGAGAATTTGATTCCAACGTACGTGAATTAGAAGGAGCCTTGAAAAATATTAGTCTAGTTGCTGACTTTAAGCATGCTAAAACTATTACAGTAGATATAGCTGCAGAAGCTATCAGAGCACGTAAAAATGATGGTCCTATTGTTACTGTCATTCCTATAGAAGAAATTCAAATACAAGTTGGTAAATTCTATGGCGTAACTGTAAAAGAGATAAAAGCAACTAAAAGAACACAAGATATTGTCCTTGCAAGACAGGTAGCCATGTACTTAGCTCGTGAGATGACAGATAACAGTCTCCCAAAAATAGGTAAAGAATTTGGGGGACGAGATCACTCAACTGTTCTCCACGCTTATAATAAAATAAAAAATATGGTTGCTCAAGATGACAACTTACGAATTGAGATAGAAACTATCAAAAATAAAATCAGATAG
diff --git a/CHEWBBACA/tests/test_allelecall.py b/CHEWBBACA/tests/test_allelecall.py
index b38008f8..50da5dbb 100644
--- a/CHEWBBACA/tests/test_allelecall.py
+++ b/CHEWBBACA/tests/test_allelecall.py
@@ -85,7 +85,8 @@ def test_allelecall_valid_input(monkeypatch, args_fixture):
 	 (ta.ALLELECALL_TEST_FAKE_PATH, ct.INVALID_INPUT_PATH),
 	 (ta.ALLELECALL_TEST_BLANK_SPACE, ct.INPUTS_INCLUDE_BLANKS[:46]),
 	 (ta.ALLELECALL_TEST_LONG_PREFIX, ct.INPUTS_LONG_PREFIX[:65]),
-	 (ta.ALLELECALL_TEST_SAME_PREFIX, ct.INPUTS_SHARE_PREFIX[:56])
+	 (ta.ALLELECALL_TEST_SAME_PREFIX, ct.INPUTS_SHARE_PREFIX[:56]),
+	 (ta.ALLELECALL_TEST_PDB_CHAIN, ct.INPUTS_PDB_PREFIX[:70]),
 	],
 	indirect=True
 )
diff --git a/CHEWBBACA/tests/test_arguments.py b/CHEWBBACA/tests/test_arguments.py
index abeb81b0..23e6a5f5 100644
--- a/CHEWBBACA/tests/test_arguments.py
+++ b/CHEWBBACA/tests/test_arguments.py
@@ -130,6 +130,12 @@
 		   					   '-g', 'data/allelecall_data/sagalactiae_schema',
 		   					   '-o', 'allelecall_results']
 
+# AlleleCall input prefix interpreted as PDB chain ID
+ALLELECALL_TEST_PDB_CHAIN = ['chewBBACA.py', 'AlleleCall',
+							 '-i', 'data/allelecall_data/test_invalid_input_names/pdb_prefix',
+							 '-g', 'data/allelecall_data/sagalactiae_schema',
+							 '-o', 'allelecall_results']
+
 # CreateSchema template command
 CREATESCHEMA_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'CreateSchema',
        								 '-i', 'data/createschema_data/mock_genome_dir',
@@ -179,6 +185,30 @@
 							   		'-o', 'createschema_results',
 							   		'--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn']
 
+# CreateSchema input name includes blank space
+CREATESCHEMA_TEST_BLANK_SPACE = ['chewBBACA.py', 'CreateSchema',
+		   					     '-i', 'data/allelecall_data/test_invalid_input_names/blank_spaces',
+		   					     '-o', 'createschema_results',
+							     '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn']
+
+# CreateSchema input file has unique prefix longer than 30 chars
+CREATESCHEMA_TEST_LONG_PREFIX = ['chewBBACA.py', 'CreateSchema',
+		   					     '-i', 'data/allelecall_data/test_invalid_input_names/long_prefix',
+		   					     '-o', 'createschema_results',
+							     '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn']
+
+# CreateSchema some input files have the same prefix
+CREATESCHEMA_TEST_SAME_PREFIX = ['chewBBACA.py', 'CreateSchema',
+		   					     '-i', 'data/allelecall_data/test_invalid_input_names/same_prefix',
+		   					     '-o', 'createschema_results',
+							     '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn']
+
+# CreateSchema input prefix interpreted as PDB chain ID
+CREATESCHEMA_TEST_PDB_CHAIN = ['chewBBACA.py', 'CreateSchema',
+							   '-i', 'data/allelecall_data/test_invalid_input_names/pdb_prefix',
+							   '-o', 'createschema_results',
+							   '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn']
+
 # AlleleCallEvaluator
 # AlleleCallEvaluator invalid path
 ALLELECALL_EVALUATOR_INVALID_PATH = ['chewBBACA.py', 'AlleleCallEvaluator',
@@ -229,6 +259,26 @@
 									 '-o', 'preped_schema',
 									 '--gl', 'data/prep_data/test_genes_list/test_genes_extension.txt']
 
+# PrepExternalSchema input name includes blank space
+PREPEXTERNALSCHEMA_TEST_BLANK_SPACE = ['chewBBACA.py', 'PrepExternalSchema',
+									 '-g', 'data/allelecall_data/test_invalid_input_names/blank_spaces',
+									 '-o', 'preped_schema']
+
+# PrepExternalSchema input file has unique prefix longer than 30 chars
+PREPEXTERNALSCHEMA_TEST_LONG_PREFIX = ['chewBBACA.py', 'PrepExternalSchema',
+									 '-g', 'data/allelecall_data/test_invalid_input_names/long_prefix',
+									 '-o', 'preped_schema']
+
+# PrepExternalSchema some input files have the same prefix
+PREPEXTERNALSCHEMA_TEST_SAME_PREFIX = ['chewBBACA.py', 'PrepExternalSchema',
+									 '-g', 'data/allelecall_data/test_invalid_input_names/same_prefix',
+									 '-o', 'preped_schema']
+
+# PrepExternalSchema input prefix interpreted as PDB chain ID
+PREPEXTERNALSCHEMA_TEST_PDB_CHAIN = ['chewBBACA.py', 'PrepExternalSchema',
+									 '-g', 'data/allelecall_data/test_invalid_input_names/pdb_prefix',
+									 '-o', 'preped_schema']
+
 # SchemaEvaluator
 # SchemaEvaluator empty input files
 SCHEMAEVALUATOR_TEST_EMPTY_FILES = ['chewBBACA.py', 'SchemaEvaluator',
diff --git a/CHEWBBACA/tests/test_createschema.py b/CHEWBBACA/tests/test_createschema.py
index 5424dc63..d192c193 100644
--- a/CHEWBBACA/tests/test_createschema.py
+++ b/CHEWBBACA/tests/test_createschema.py
@@ -94,7 +94,11 @@ def test_createschema_valid_input(monkeypatch, args_fixture):
      (ta.CREATESCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION),
      (ta.CREATESCHEMA_INVALID_PTF_PATH, ct.INVALID_PTF_PATH),
      (ta.CREATESCHEMA_TEST_HEADER_ONLY, ct.CANNOT_PREDICT),
-     (ta.CREATESCHEMA_TEST_INVALID_GENOME, ct.CANNOT_PREDICT)
+     (ta.CREATESCHEMA_TEST_INVALID_GENOME, ct.CANNOT_PREDICT),
+	 (ta.CREATESCHEMA_TEST_BLANK_SPACE, ct.INPUTS_INCLUDE_BLANKS[:46]),
+	 (ta.CREATESCHEMA_TEST_LONG_PREFIX, ct.INPUTS_LONG_PREFIX[:65]),
+	 (ta.CREATESCHEMA_TEST_SAME_PREFIX, ct.INPUTS_SHARE_PREFIX[:56]),
+	 (ta.CREATESCHEMA_TEST_PDB_CHAIN, ct.INPUTS_PDB_PREFIX[:70])
     ],
 	indirect=True
 )
diff --git a/CHEWBBACA/tests/test_prepexternalschema.py b/CHEWBBACA/tests/test_prepexternalschema.py
index 5f5a64e4..ffcb4db7 100644
--- a/CHEWBBACA/tests/test_prepexternalschema.py
+++ b/CHEWBBACA/tests/test_prepexternalschema.py
@@ -89,7 +89,11 @@ def test_prep_valid_input(monkeypatch, args_fixture):
 		 (ta.PREPEXTERNALSCHEMA_TEST_EMPTY_DIR, ct.MISSING_FASTAS_EXCEPTION),
 		 (ta.PREPEXTERNALSCHEMA_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION),
 		 (ta.PREPEXTERNALSCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION),
-		 (ta.PREPEXTERNALSCHEMA_TEST_INVALID_PATH, ct.INVALID_INPUT_PATH)
+		 (ta.PREPEXTERNALSCHEMA_TEST_INVALID_PATH, ct.INVALID_INPUT_PATH),
+		 (ta.PREPEXTERNALSCHEMA_TEST_BLANK_SPACE, ct.INPUTS_INCLUDE_BLANKS[:46]),
+	 	 (ta.PREPEXTERNALSCHEMA_TEST_LONG_PREFIX, ct.INPUTS_LONG_PREFIX[:65]),
+	 	 (ta.PREPEXTERNALSCHEMA_TEST_SAME_PREFIX, ct.INPUTS_SHARE_PREFIX[:56]),
+	 	 (ta.PREPEXTERNALSCHEMA_TEST_PDB_CHAIN, ct.INPUTS_PDB_PREFIX[:70])
 		],
 		indirect=True
 )
diff --git a/CHEWBBACA/utils/constants.py b/CHEWBBACA/utils/constants.py
index 9f2a2f7c..e6d31a4e 100755
--- a/CHEWBBACA/utils/constants.py
+++ b/CHEWBBACA/utils/constants.py
@@ -637,8 +637,8 @@
 					  '(e.g. BLAST does not accept sequence IDs longer than 50 '
 					  'characters when creating a database).')
 
-INPUTS_PDB_PREFIX = ('The following input files have prefixes that are '
-					 'interpreted by BLAST as chain PDB IDs:\n{0}\nBLAST modifies the '
+INPUTS_PDB_PREFIX = ('The following input files have prefixes that are interpreted by BLAST '
+					 'as chain PDB IDs:\n{0}\nBLAST modifies the '
 					 'IDs of the CDSs that include these prefixes when creating a database, '
 					 'which leads to issues when chewBBACA cannot find the original '
 					 'IDs in the results. Please ensure that the file prefixes (substring '