--- a/test-data/predict_scratch/Genus_species.discrepency.report.txt	Sun Jan 22 17:33:29 2023 +0000
+++ b/test-data/predict_scratch/Genus_species.discrepency.report.txt	Thu Apr 13 17:13:04 2023 +0000
@@ -3,11 +3,12 @@
 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_FEATURE_COUNT:gene: 70 present
+DISC_FEATURE_COUNT:CDS: 69 present
+DISC_FEATURE_COUNT:mRNA: 69 present
+DISC_FEATURE_COUNT:tRNA: 1 present
 DISC_COUNT_NUCLEOTIDES:4 nucleotide Bioseqs are present
-JOINED_FEATURES:26 features have joined locations.
+JOINED_FEATURES:116 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
@@ -16,7 +17,7 @@
 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.
+MISSING_PROJECT:73 sequences do not include project.
 DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
 
 
@@ -26,43 +27,134 @@
 
 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_FEATURE_COUNT::gene: 70 present
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 69 present
+DiscRep_ALL:DISC_FEATURE_COUNT::mRNA: 69 present
+DiscRep_ALL:DISC_FEATURE_COUNT::tRNA: 1 present
 DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present
-genome:sample (length 215740)
+genome:sample (length 720580)
 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:JOINED_FEATURES::116 features have joined locations.
+DiscRep_SUB:JOINED_FEATURES::116 features have joined location but no exception
+genome:CDS	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284-3490, 3727-3855)	FUN_000069
+genome:mRNA	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284-3490, 3727-3855)	FUN_000069
+genome:mRNA	hypothetical protein	(sample:2126-2199, 2258-3224, 3284-3490, 3727-3855)	FUN_000001
+genome:CDS	hypothetical protein	(sample:2126-2199, 2258-3224, 3284-3490, 3727-3855)	FUN_000001
+genome:CDS	hypothetical protein	(sample:c5671-5666, c5539-4930, c4759-4248)	FUN_000002
+genome:mRNA	hypothetical protein	(sample:c5671-5666, c5539-4930, c4759-4248)	FUN_000002
+genome:CDS	hypothetical protein	(sample4:c5671-5666, c5539-4930, c4759-4248)	FUN_000070
+genome:mRNA	hypothetical protein	(sample4:c5671-5666, c5539-4930, c4759-4248)	FUN_000070
+genome:CDS	hypothetical protein	(sample:c11104-10853, c10794-10663, c10501-8707, c8385-7691)	FUN_000003
+genome:mRNA	hypothetical protein	(sample:c11104-10853, c10794-10663, c10501-8707, c8385-7691)	FUN_000003
+genome:CDS	hypothetical protein	(sample:c21523-21517, c21454-19638, c19482-18513, c18490-18378, c18274-18215, c18099-17296, c17188-15353, c15289-15101, c14995-14794, c14659-14247)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c21523-21517, c21454-19638, c19482-18513, c18490-18378, c18274-18215, c18099-17296, c17188-15353, c15289-15101, c14995-14794, c14659-14247)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c27475-27470, c27042-26112, c25838-25828)	FUN_000005
+genome:CDS	hypothetical protein	(sample:c27475-27470, c27042-26112, c25838-25828)	FUN_000005
+genome:CDS	hypothetical protein	(sample:40223-40226, 40239-40396, 40659-41193, 41707-42107)	FUN_000007
+genome:mRNA	hypothetical protein	(sample:40223-40226, 40239-40396, 40659-41193, 41707-42107)	FUN_000007
+genome:CDS	hypothetical protein	(sample:43455-43462, 43623-44130)	FUN_000008
+genome:mRNA	hypothetical protein	(sample:43455-43462, 43623-44130)	FUN_000008
+genome:CDS	hypothetical protein	(sample:c57154-57146, c56873-56484)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:c57154-57146, c56873-56484)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:79168-79175, 79510-80518)	FUN_000010
+genome:CDS	hypothetical protein	(sample:79168-79175, 79510-80518)	FUN_000010
+genome:mRNA	hypothetical protein	(sample:94445-94448, 94563-94732, 94873-95583)	FUN_000011
+genome:CDS	hypothetical protein	(sample:94445-94448, 94563-94732, 94873-95583)	FUN_000011
+genome:mRNA	hypothetical protein	(sample:133134-133142, 133209-134216, 134234-134242)	FUN_000012
+genome:CDS	hypothetical protein	(sample:133134-133142, 133209-134216, 134234-134242)	FUN_000012
+genome:mRNA	hypothetical protein	(sample:134353-134357, 134396-134539, 134668-135510, 135569-136346)	FUN_000013
+genome:CDS	hypothetical protein	(sample:134353-134357, 134396-134539, 134668-135510, 135569-136346)	FUN_000013
+genome:mRNA	hypothetical protein	(sample:c154297-154294, c153638-153202)	FUN_000014
+genome:CDS	hypothetical protein	(sample:c154297-154294, c153638-153202)	FUN_000014
+genome:mRNA	hypothetical protein	(sample:167121-168360, 168722-169212)	FUN_000015
+genome:CDS	hypothetical protein	(sample:167121-168360, 168722-169212)	FUN_000015
+genome:CDS	hypothetical protein	(sample:c178787-178780, c177172-176887, c176824-176699)	FUN_000016
+genome:mRNA	hypothetical protein	(sample:c178787-178780, c177172-176887, c176824-176699)	FUN_000016
+genome:mRNA	hypothetical protein	(sample:c180759-180756, c180698-180028)	FUN_000017
+genome:CDS	hypothetical protein	(sample:c180759-180756, c180698-180028)	FUN_000017
+genome:CDS	hypothetical protein	(sample:c184433-184429, c184054-183921, c183856-183710, c183658-183489)	FUN_000018
+genome:mRNA	hypothetical protein	(sample:c184433-184429, c184054-183921, c183856-183710, c183658-183489)	FUN_000018
+genome:CDS	hypothetical protein	(sample:c186328-186324, c186254-186053)	FUN_000019
+genome:mRNA	hypothetical protein	(sample:c186328-186324, c186254-186053)	FUN_000019
+genome:CDS	hypothetical protein	(sample:194065-194461, 194518-194669)	FUN_000020
+genome:mRNA	hypothetical protein	(sample:194065-194461, 194518-194669)	FUN_000020
+genome:CDS	hypothetical protein	(sample:c215109-214958, c214878-214671, c213306-213085)	FUN_000021
+genome:mRNA	hypothetical protein	(sample:c215109-214958, c214878-214671, c213306-213085)	FUN_000021
+genome:CDS	hypothetical protein	(sample:386187-386191, 386272-387075, 387120-387144)	FUN_000025
+genome:mRNA	hypothetical protein	(sample:386187-386191, 386272-387075, 387120-387144)	FUN_000025
+genome:CDS	hypothetical protein	(sample:391297-391301, 391479-391489, 391758-392254, 392500-392851, 393283-393638)	FUN_000026
+genome:mRNA	hypothetical protein	(sample:391297-391301, 391479-391489, 391758-392254, 392500-392851, 393283-393638)	FUN_000026
+genome:CDS	hypothetical protein	(sample:c402790-402786, c402710-400817, c400781-400773)	FUN_000027
+genome:mRNA	hypothetical protein	(sample:c402790-402786, c402710-400817, c400781-400773)	FUN_000027
+genome:CDS	hypothetical protein	(sample:c411102-410699, c410403-410197, c409305-408840, c408474-407989, c407903-407694, c407225-406272, c406091-405530, c405518-405391)	FUN_000028
+genome:mRNA	hypothetical protein	(sample:c411102-410699, c410403-410197, c409305-408840, c408474-407989, c407903-407694, c407225-406272, c406091-405530, c405518-405391)	FUN_000028
+genome:CDS	hypothetical protein	(sample:c429748-429644, c429578-429470, c429273-429076, c428990-428479)	FUN_000029
+genome:mRNA	hypothetical protein	(sample:c429748-429644, c429578-429470, c429273-429076, c428990-428479)	FUN_000029
+genome:CDS	hypothetical protein	(sample:c445172-445169, c445114-444429)	FUN_000030
+genome:mRNA	hypothetical protein	(sample:c445172-445169, c445114-444429)	FUN_000030
+genome:CDS	hypothetical protein	(sample:446127-446275, 446336-446553, 446619-446752, 446956-447105, 447169-447711)	FUN_000031
+genome:mRNA	hypothetical protein	(sample:446127-446275, 446336-446553, 446619-446752, 446956-447105, 447169-447711)	FUN_000031
+genome:CDS	hypothetical protein	(sample:c454670-454666, c454610-454412)	FUN_000034
+genome:mRNA	hypothetical protein	(sample:c454670-454666, c454610-454412)	FUN_000034
+genome:CDS	hypothetical protein	(sample:c457592-457587, c457550-457413, c457045-456442, c456248-456040, c455256-454693)	FUN_000035
+genome:mRNA	hypothetical protein	(sample:c457592-457587, c457550-457413, c457045-456442, c456248-456040, c455256-454693)	FUN_000035
+genome:CDS	hypothetical protein	(sample:459816-460113, 460220-461690, 461752-462148, 462263-462454)	FUN_000037
+genome:mRNA	hypothetical protein	(sample:459816-460113, 460220-461690, 461752-462148, 462263-462454)	FUN_000037
+genome:CDS	hypothetical protein	(sample:c463679-463652, c463593-463293, c463086-462819)	FUN_000038
+genome:mRNA	hypothetical protein	(sample:c463679-463652, c463593-463293, c463086-462819)	FUN_000038
+genome:mRNA	hypothetical protein	(sample:c466984-466799, c466039-465912, c465617-464874, c464814-464633, c464576-464311)	FUN_000039
+genome:CDS	hypothetical protein	(sample:c466984-466799, c466039-465912, c465617-464874, c464814-464633, c464576-464311)	FUN_000039
+genome:CDS	hypothetical protein	(sample:c470961-470953, c470641-470150, c470077-469730)	FUN_000040
+genome:mRNA	hypothetical protein	(sample:c470961-470953, c470641-470150, c470077-469730)	FUN_000040
+genome:CDS	hypothetical protein	(sample:479876-480089, 480295-481339, 481394-481823)	FUN_000041
+genome:mRNA	hypothetical protein	(sample:479876-480089, 480295-481339, 481394-481823)	FUN_000041
+genome:CDS	hypothetical protein	(sample:c485565-485561, c485533-484891)	FUN_000043
+genome:mRNA	hypothetical protein	(sample:c485565-485561, c485533-484891)	FUN_000043
+genome:CDS	hypothetical protein	(sample:493013-493020, 493173-493452, 493541-493621, 493683-493826)	FUN_000044
+genome:mRNA	hypothetical protein	(sample:493013-493020, 493173-493452, 493541-493621, 493683-493826)	FUN_000044
+genome:CDS	hypothetical protein	(sample:c504016-504013, c503973-502325)	FUN_000045
+genome:mRNA	hypothetical protein	(sample:c504016-504013, c503973-502325)	FUN_000045
+genome:CDS	hypothetical protein	(sample:c521592-521588, c521275-520726, c520654-520482, c520181-520050, c519790-519639, c519580-519414)	FUN_000046
+genome:mRNA	hypothetical protein	(sample:c521592-521588, c521275-520726, c520654-520482, c520181-520050, c519790-519639, c519580-519414)	FUN_000046
+genome:CDS	hypothetical protein	(sample:c523738-523733, c523044-522567, c522383-522277, c522160-522056)	FUN_000047
+genome:mRNA	hypothetical protein	(sample:c523738-523733, c523044-522567, c522383-522277, c522160-522056)	FUN_000047
+genome:CDS	hypothetical protein	(sample:c525153-524964, c524909-524560)	FUN_000048
+genome:mRNA	hypothetical protein	(sample:c525153-524964, c524909-524560)	FUN_000048
+genome:CDS	hypothetical protein	(sample:c540618-540358, c539917-539336)	FUN_000049
+genome:mRNA	hypothetical protein	(sample:c540618-540358, c539917-539336)	FUN_000049
+genome:CDS	hypothetical protein	(sample:568959-568962, 569109-569293, 569311->569481)	FUN_000051
+genome:mRNA	hypothetical protein	(sample:568959-568962, 569109-569293, 569311->569481)	FUN_000051
+genome:CDS	hypothetical protein	(sample:582311-582319, 582423-582656, 582845-583000)	FUN_000053
+genome:mRNA	hypothetical protein	(sample:582311-582319, 582423-582656, 582845-583000)	FUN_000053
+genome:CDS	hypothetical protein	(sample:c584495-584344, c584276-583775, c583703-583551)	FUN_000054
+genome:mRNA	hypothetical protein	(sample:c584495-584344, c584276-583775, c583703-583551)	FUN_000054
+genome:CDS	hypothetical protein	(sample:c588129-586399, c585970-585768, c585707-585578)	FUN_000055
+genome:mRNA	hypothetical protein	(sample:c588129-586399, c585970-585768, c585707-585578)	FUN_000055
+genome:CDS	hypothetical protein	(sample:595803-595807, 596052-596670)	FUN_000056
+genome:mRNA	hypothetical protein	(sample:595803-595807, 596052-596670)	FUN_000056
+genome:CDS	hypothetical protein	(sample:598307-598335, 598398-598764)	FUN_000057
+genome:mRNA	hypothetical protein	(sample:598307-598335, 598398-598764)	FUN_000057
+genome:CDS	hypothetical protein	(sample:c600874-600870, c600730-600653, c600595-599095)	FUN_000058
+genome:mRNA	hypothetical protein	(sample:c600874-600870, c600730-600653, c600595-599095)	FUN_000058
+genome:CDS	hypothetical protein	(sample:603352-603370, 603434-604230)	FUN_000059
+genome:mRNA	hypothetical protein	(sample:603352-603370, 603434-604230)	FUN_000059
+genome:CDS	hypothetical protein	(sample:c611871-611867, c611601-611358, c611278-610049, c609998-609728, c609672-607742, c607241-607065, c606108-605908, c605852-605487, c605417-605316, c605240-605058)	FUN_000060
+genome:mRNA	hypothetical protein	(sample:c611871-611867, c611601-611358, c611278-610049, c609998-609728, c609672-607742, c607241-607065, c606108-605908, c605852-605487, c605417-605316, c605240-605058)	FUN_000060
+genome:CDS	hypothetical protein	(sample:c689310-689306, c689229-688494, c688430-687270, c687185-685812)	FUN_000063
+genome:mRNA	hypothetical protein	(sample:c689310-689306, c689229-688494, c688430-687270, c687185-685812)	FUN_000063
+genome:CDS	hypothetical protein	(sample:c692794-692573, c692447-692220, c692151-692128)	FUN_000064
+genome:mRNA	hypothetical protein	(sample:c692794-692573, c692447-692220, c692151-692128)	FUN_000064
+genome:CDS	hypothetical protein	(sample:694460-694467, 694516-694569, 694623-695049, 695109-695450, 695506-695859)	FUN_000065
+genome:mRNA	hypothetical protein	(sample:694460-694467, 694516-694569, 694623-695049, 695109-695450, 695506-695859)	FUN_000065
+genome:CDS	hypothetical protein	(sample:c696909-696904, c696856-695981)	FUN_000066
+genome:mRNA	hypothetical protein	(sample:c696909-696904, c696856-695981)	FUN_000066
+genome:CDS	hypothetical protein	(sample:697479-697750, 698245-699085)	FUN_000067
+genome:mRNA	hypothetical protein	(sample:697479-697750, 698245-699085)	FUN_000067
+genome:CDS	hypothetical protein	(sample:c700743-700586, c700523-700435, c700365-699296)	FUN_000068
+genome:mRNA	hypothetical protein	(sample:c700743-700586, c700523-700435, c700365-699296)	FUN_000068
 
 DiscRep_ALL:NO_ANNOTATION::2 bioseqs have no features
 genome:sample2 (length 2030)
@@ -70,65 +162,118 @@
 
 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
+FATAL: DiscRep_ALL: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
+genome:CDS	hypothetical protein	(sample:568959-568962, 569109-569293, 569311->569481)	FUN_000051
 
 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"
+genome:sample:"Annotated using Funannotate 1.8.15"
+genome:sample2:"Annotated using Funannotate 1.8.15"
+genome:sample3:"Annotated using Funannotate 1.8.15"
+genome:sample4:"Annotated using Funannotate 1.8.15"
 
 DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments
-genome:sample (length 215740)
+genome:sample (length 720580)
 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:sample (length 720580)
 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:sample (length 720580)
 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:sample (length 720580)
 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)
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 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
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