--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/predict_scratch/Genus_species.discrepency.report.txt	Mon Oct 04 19:39:38 2021 +0000
@@ -0,0 +1,135 @@
+Discrepancy Report Results
+
+Summary
+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
+DISC_FEATURE_COUNT:gene: 16 present
+DISC_FEATURE_COUNT:CDS: 16 present
+DISC_FEATURE_COUNT:mRNA: 16 present
+DISC_COUNT_NUCLEOTIDES:4 nucleotide Bioseqs are present
+JOINED_FEATURES:26 features have joined locations.
+NO_ANNOTATION:2 bioseqs have no features
+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
+FATAL: DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS:1 features have partial ends that do not abut the end of the sequence or a gap, and cannot be extended by 3 or fewer nucleotides to do so
+ONCALLER_COMMENT_PRESENT:4 comment descriptors were found (all same)
+MISSING_GENOMEASSEMBLY_COMMENTS:4 bioseqs are missing GenomeAssembly structured comments
+MOLTYPE_NOT_MRNA:4 molecule types are not set as mRNA.
+TECHNIQUE_NOT_TSA:4 technique are not set as TSA
+MISSING_STRUCTURED_COMMENT:4 sequences do not include structured comments.
+MISSING_PROJECT:20 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"
+
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'Genus species' for taxname
+DiscRep_ALL:DISC_FEATURE_COUNT::gene: 16 present
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 16 present
+DiscRep_ALL:DISC_FEATURE_COUNT::mRNA: 16 present
+DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:JOINED_FEATURES::26 features have joined locations.
+DiscRep_SUB:JOINED_FEATURES::26 features have joined location but no exception
+genome:CDS	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000016
+genome:mRNA	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000016
+genome:mRNA	hypothetical protein	(sample:c3142-3138, c3004-2883, c2686-2565)	FUN_000002
+genome:CDS	hypothetical protein	(sample:c3142-3138, c3004-2883, c2686-2565)	FUN_000002
+genome:mRNA	hypothetical protein	(sample:c5802-5797, c5539-4937, c4742-4248)	FUN_000003
+genome:CDS	hypothetical protein	(sample:c5802-5797, c5539-4937, c4742-4248)	FUN_000003
+genome:CDS	hypothetical protein	(sample:c10664-10657, c10499-8707, c8385-7691)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c10664-10657, c10499-8707, c8385-7691)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c15214-15209, c14648-14247)	FUN_000005
+genome:CDS	hypothetical protein	(sample:c15214-15209, c14648-14247)	FUN_000005
+genome:CDS	hypothetical protein	(sample:15539-15543, 15646-15919, 16485-16619)	FUN_000006
+genome:mRNA	hypothetical protein	(sample:15539-15543, 15646-15919, 16485-16619)	FUN_000006
+genome:CDS	hypothetical protein	(sample:c21705-21700, c21515-19638, c19482-18358)	FUN_000007
+genome:mRNA	hypothetical protein	(sample:c21705-21700, c21515-19638, c19482-18358)	FUN_000007
+genome:CDS	hypothetical protein	(sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:87202-87207, 88054-88320)	FUN_000010
+genome:CDS	hypothetical protein	(sample:87202-87207, 88054-88320)	FUN_000010
+genome:CDS	hypothetical protein	(sample:c106221-106216, c104632-104258, c103947-103696, c103618-103229, c103151-102510)	FUN_000011
+genome:mRNA	hypothetical protein	(sample:c106221-106216, c104632-104258, c103947-103696, c103618-103229, c103151-102510)	FUN_000011
+genome:CDS	hypothetical protein	(sample:167121-168069, 168722-169212)	FUN_000012
+genome:mRNA	hypothetical protein	(sample:167121-168069, 168722-169212)	FUN_000012
+genome:CDS	hypothetical protein	(sample:180262-180267, 180400-180579)	FUN_000013
+genome:mRNA	hypothetical protein	(sample:180262-180267, 180400-180579)	FUN_000013
+genome:CDS	hypothetical protein	(sample:c210553-210548, c210474-209053, c208645-208619)	FUN_000014
+genome:mRNA	hypothetical protein	(sample:c210553-210548, c210474-209053, c208645-208619)	FUN_000014
+
+DiscRep_ALL:NO_ANNOTATION::2 bioseqs have no features
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+
+DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
+
+FATAL: DiscRep_ALL:DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS::1 featurepartial ends thands that do not abut the end of the sequence or a gap, and cannot be extended by 3 or fewer nucleotides to do so
+genome:CDS	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000016
+
+DiscRep_ALL:ONCALLER_COMMENT_PRESENT::4 comment descriptors were found (all same)
+genome:sample:"Annotated using 1.8.7"
+genome:sample2:"Annotated using 1.8.7"
+genome:sample3:"Annotated using 1.8.7"
+genome:sample4:"Annotated using 1.8.7"
+
+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MOLTYPE_NOT_MRNA::4 molecule types are not set as mRNA.
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:TECHNIQUE_NOT_TSA::4 technique are not set as TSA
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::4 sequences do not include structured comments.
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MISSING_PROJECT::20 sequences do not include project.
+genome:sample (length 215740)
+genome:ncbi:FUN_000001-T1 (length 124)
+genome:ncbi:FUN_000002-T1 (length 82)
+genome:ncbi:FUN_000003-T1 (length 367)
+genome:ncbi:FUN_000004-T1 (length 831)
+genome:ncbi:FUN_000005-T1 (length 135)
+genome:ncbi:FUN_000006-T1 (length 137)
+genome:ncbi:FUN_000007-T1 (length 1002)
+genome:ncbi:FUN_000008-T1 (length 278)
+genome:ncbi:FUN_000009-T1 (length 578)
+genome:ncbi:FUN_000010-T1 (length 90)
+genome:ncbi:FUN_000011-T1 (length 554)
+genome:ncbi:FUN_000012-T1 (length 479)
+genome:ncbi:FUN_000013-T1 (length 61)
+genome:ncbi:FUN_000014-T1 (length 484)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+genome:ncbi:FUN_000015-T1 (length 124)
+genome:ncbi:FUN_000016-T1 (length 432)
+
+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::4 Molinfos are missing field technique
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+