--- a/test-data/out.err	Fri Jan 20 03:39:08 2017 -0500
+++ b/test-data/out.err	Tue Mar 21 10:13:06 2017 -0400
@@ -1,46 +1,144 @@
->PROKKA_00001 hypothetical protein
-ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC
-ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC
-AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT
-GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC
-GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC
-GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG
-TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
-AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
->PROKKA_00002 hypothetical protein
-ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT
-ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
->PROKKA_00003 hypothetical protein
-ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT
-TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT
-GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT
-TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC
-TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG
-TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
-CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT
-CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG
-TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT
-CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG
-CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
-CGCGATTCAATCATGACTTCGTGA
->PROKKA_00004 hypothetical protein
-TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT
-TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA
-ACAATACTGTAG
->PROKKA_00005 hypothetical protein
-ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT
-TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG
-GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT
-GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT
-AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
-ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA
-AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA
-AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA
-GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT
-AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT
-ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT
-GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC
-GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
+Discrepancy Report Results
+
+Summary
+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
+FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
+DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
+DISC_FEATURE_COUNT:CDS: 5 present
+DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
+FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
+NO_ANNOTATION:3 bioseqs have no features
+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
+ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
+SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
+MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
+MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
+TECHNIQUE_NOT_TSA:7 technique are not set as TSA
+MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
+MISSING_PROJECT:12 sequences do not include project.
+DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
+
+
+Detailed Report
+
+DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
+
+FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6_1 (length 253)
+
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
+DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations.
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig2:40-498	PROKKA_00001
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig2:498-614	PROKKA_00002
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig4:21-884	PROKKA_00003
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig5:275-406	PROKKA_00004
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig6:6-767	PROKKA_00005
+
+DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
+
+DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)
+outdir/prokka:contig1:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig2:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig3:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig4:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig5:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig6:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+outdir/prokka:contig7:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
+
+DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig5_1 (length 43)
+
+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig6_1 (length 253)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+