view test-data/predict_scratch/Genus_species.discrepency.report.txt @ 11:9c15ca7e764e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d
author iuc
date Wed, 26 Jun 2024 09:41:52 +0000
parents 9feee7fc49a1
children
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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: 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: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
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:73 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: 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 720580)
genome:sample2 (length 2030)
genome:sample3 (length 2100)
genome:sample4 (length 7560)

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)
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 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 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 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 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 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 720580)
genome:sample2 (length 2030)
genome:sample3 (length 2100)
genome:sample4 (length 7560)

DiscRep_ALL:MISSING_PROJECT::73 sequences do not include project.
genome:sample (length 720580)
genome:ncbi:FUN_000001-T1 (length 458)
genome:ncbi:FUN_000002-T1 (length 375)
genome:ncbi:FUN_000003-T1 (length 957)
genome:ncbi:FUN_000004-T1 (length 2136)
genome:ncbi:FUN_000005-T1 (length 315)
genome:ncbi:FUN_000006-T1 (length 278)
genome:ncbi:FUN_000007-T1 (length 365)
genome:ncbi:FUN_000008-T1 (length 171)
genome:ncbi:FUN_000009-T1 (length 132)
genome:ncbi:FUN_000010-T1 (length 338)
genome:ncbi:FUN_000011-T1 (length 294)
genome:ncbi:FUN_000012-T1 (length 341)
genome:ncbi:FUN_000013-T1 (length 589)
genome:ncbi:FUN_000014-T1 (length 146)
genome:ncbi:FUN_000015-T1 (length 576)
genome:ncbi:FUN_000016-T1 (length 139)
genome:ncbi:FUN_000017-T1 (length 224)
genome:ncbi:FUN_000018-T1 (length 151)
genome:ncbi:FUN_000019-T1 (length 68)
genome:ncbi:FUN_000020-T1 (length 182)
genome:ncbi:FUN_000021-T1 (length 193)
genome:ncbi:FUN_000022-T1 (length 550)
genome:ncbi:FUN_000023-T1 (length 515)
genome:ncbi:FUN_000024-T1 (length 96)
genome:ncbi:FUN_000025-T1 (length 277)
genome:ncbi:FUN_000026-T1 (length 406)
genome:ncbi:FUN_000027-T1 (length 635)
genome:ncbi:FUN_000028-T1 (length 1138)
genome:ncbi:FUN_000029-T1 (length 307)
genome:ncbi:FUN_000030-T1 (length 229)
genome:ncbi:FUN_000031-T1 (length 397)
genome:ncbi:FUN_000032-T1 (length 430)
genome:ncbi:FUN_000033-T1 (length 214)
genome:ncbi:FUN_000034-T1 (length 67)
genome:ncbi:FUN_000035-T1 (length 506)
genome:ncbi:FUN_000036-T1 (length 143)
genome:ncbi:FUN_000037-T1 (length 785)
genome:ncbi:FUN_000038-T1 (length 198)
genome:ncbi:FUN_000039-T1 (length 501)
genome:ncbi:FUN_000040-T1 (length 282)
genome:ncbi:FUN_000041-T1 (length 562)
genome:ncbi:FUN_000042-T1 (length 186)
genome:ncbi:FUN_000043-T1 (length 215)
genome:ncbi:FUN_000044-T1 (length 170)
genome:ncbi:FUN_000045-T1 (length 550)
genome:ncbi:FUN_000046-T1 (length 392)
genome:ncbi:FUN_000047-T1 (length 231)
genome:ncbi:FUN_000048-T1 (length 179)
genome:ncbi:FUN_000049-T1 (length 280)
genome:ncbi:FUN_000050-T1 (length 117)
genome:ncbi:FUN_000051-T1 (length 120)
genome:ncbi:FUN_000052-T1 (length 209)
genome:ncbi:FUN_000053-T1 (length 132)
genome:ncbi:FUN_000054-T1 (length 268)
genome:ncbi:FUN_000055-T1 (length 687)
genome:ncbi:FUN_000056-T1 (length 207)
genome:ncbi:FUN_000057-T1 (length 131)
genome:ncbi:FUN_000058-T1 (length 527)
genome:ncbi:FUN_000059-T1 (length 271)
genome:ncbi:FUN_000060-T1 (length 1569)
genome:ncbi:FUN_000062-T1 (length 477)
genome:ncbi:FUN_000063-T1 (length 1091)
genome:ncbi:FUN_000064-T1 (length 157)
genome:ncbi:FUN_000065-T1 (length 394)
genome:ncbi:FUN_000066-T1 (length 293)
genome:ncbi:FUN_000067-T1 (length 370)
genome:ncbi:FUN_000068-T1 (length 438)
genome:sample2 (length 2030)
genome:sample3 (length 2100)
genome:sample4 (length 7560)
genome:ncbi:FUN_000069-T1 (length 458)
genome:ncbi:FUN_000070-T1 (length 375)

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 720580)
genome:sample2 (length 2030)
genome:sample3 (length 2100)
genome:sample4 (length 7560)