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comparison test-data/predict_bam/Genus_species.discrepency.report.txt @ 0:857f7ac611e1 draft

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"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
author iuc
date Mon, 04 Oct 2021 19:38:37 +0000
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1 Discrepancy Report Results
2
3 Summary
4 DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
5 DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
6 DISC_FEATURE_COUNT:gene: 18 present
7 DISC_FEATURE_COUNT:CDS: 18 present
8 DISC_FEATURE_COUNT:mRNA: 18 present
9 DISC_COUNT_NUCLEOTIDES:4 nucleotide Bioseqs are present
10 JOINED_FEATURES:30 features have joined locations.
11 NO_ANNOTATION:2 bioseqs have no features
12 DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
13 FATAL: DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS:2 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
14 ONCALLER_COMMENT_PRESENT:4 comment descriptors were found (all same)
15 MISSING_GENOMEASSEMBLY_COMMENTS:4 bioseqs are missing GenomeAssembly structured comments
16 MOLTYPE_NOT_MRNA:4 molecule types are not set as mRNA.
17 TECHNIQUE_NOT_TSA:4 technique are not set as TSA
18 MISSING_STRUCTURED_COMMENT:4 sequences do not include structured comments.
19 MISSING_PROJECT:22 sequences do not include project.
20 DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
21
22
23 Detailed Report
24
25 DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
26
27 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
28 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'Genus species' for taxname
29 DiscRep_ALL:DISC_FEATURE_COUNT::gene: 18 present
30 DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 18 present
31 DiscRep_ALL:DISC_FEATURE_COUNT::mRNA: 18 present
32 DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present
33 genome:sample (length 215740)
34 genome:sample2 (length 2030)
35 genome:sample3 (length 2100)
36 genome:sample4 (length 7560)
37
38 DiscRep_ALL:JOINED_FEATURES::30 features have joined locations.
39 DiscRep_SUB:JOINED_FEATURES::30 features have joined location but no exception
40 genome:mRNA hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
41 genome:CDS hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
42 genome:mRNA hypothetical protein (sample:c5802-5797, c5539-4883) FUN_000002
43 genome:CDS hypothetical protein (sample:c5802-5797, c5539-4883) FUN_000002
44 genome:mRNA hypothetical protein (sample:c10557-10549, c10462-8696) FUN_000003
45 genome:CDS hypothetical protein (sample:c10557-10549, c10462-8696) FUN_000003
46 genome:CDS hypothetical protein (sample:c15214-15209, c14648-14247) FUN_000004
47 genome:mRNA hypothetical protein (sample:c15214-15209, c14648-14247) FUN_000004
48 genome:mRNA hypothetical protein (sample:c21705-21700, c21515-19533) FUN_000005
49 genome:CDS hypothetical protein (sample:c21705-21700, c21515-19533) FUN_000005
50 genome:CDS hypothetical protein (sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130) FUN_000007
51 genome:mRNA hypothetical protein (sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130) FUN_000007
52 genome:CDS hypothetical protein (sample:c47195-46753, c46330-46214, c46157-45527) FUN_000008
53 genome:mRNA hypothetical protein (sample:c47195-46753, c46330-46214, c46157-45527) FUN_000008
54 genome:CDS hypothetical protein (sample:c79527-79519, c79068-78685) FUN_000009
55 genome:mRNA hypothetical protein (sample:c79527-79519, c79068-78685) FUN_000009
56 genome:mRNA hypothetical protein (sample:87202-87207, 88054-88320) FUN_000010
57 genome:CDS hypothetical protein (sample:87202-87207, 88054-88320) FUN_000010
58 genome:CDS hypothetical protein (sample:133587-134504, 134720-135510, 135569-136284, 137516-137862) FUN_000011
59 genome:mRNA hypothetical protein (sample:133587-134504, 134720-135510, 135569-136284, 137516-137862) FUN_000011
60 genome:CDS hypothetical protein (sample:144294-144551, 149012-149244, 149367-149588, 149654-149897, 149952-150112, 150174-150248, 151966-152072, 152314-152429, 152496-152751, 153296-153630, 153689-155122, 155789-158975, 159190-164495) FUN_000012
61 genome:mRNA hypothetical protein (sample:144294-144551, 149012-149244, 149367-149588, 149654-149897, 149952-150112, 150174-150248, 151966-152072, 152314-152429, 152496-152751, 153296-153630, 153689-155122, 155789-158975, 159190-164495) FUN_000012
62 genome:CDS hypothetical protein (sample:167121-168360, 168722-169212) FUN_000013
63 genome:mRNA hypothetical protein (sample:167121-168360, 168722-169212) FUN_000013
64 genome:CDS hypothetical protein (sample:c178916-178873, c177172-176887, c176824-176699) FUN_000014
65 genome:mRNA hypothetical protein (sample:c178916-178873, c177172-176887, c176824-176699) FUN_000014
66 genome:CDS hypothetical protein (sample:192004-192067, 193549-193658, 194041-194455, 194518-194669) FUN_000015
67 genome:mRNA hypothetical protein (sample:192004-192067, 193549-193658, 194041-194455, 194518-194669) FUN_000015
68 genome:CDS hypothetical protein (sample:c210553-210548, c210474-209044) FUN_000016
69 genome:mRNA hypothetical protein (sample:c210553-210548, c210474-209044) FUN_000016
70
71 DiscRep_ALL:NO_ANNOTATION::2 bioseqs have no features
72 genome:sample2 (length 2030)
73 genome:sample3 (length 2100)
74
75 DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
76
77 FATAL: DiscRep_ALL:DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS::2 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
78 genome:CDS hypothetical protein sample:<2331-3254 FUN_000001
79 genome:CDS hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
80
81 DiscRep_ALL:ONCALLER_COMMENT_PRESENT::4 comment descriptors were found (all same)
82 genome:sample:"Annotated using 1.8.7"
83 genome:sample2:"Annotated using 1.8.7"
84 genome:sample3:"Annotated using 1.8.7"
85 genome:sample4:"Annotated using 1.8.7"
86
87 DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments
88 genome:sample (length 215740)
89 genome:sample2 (length 2030)
90 genome:sample3 (length 2100)
91 genome:sample4 (length 7560)
92
93 DiscRep_ALL:MOLTYPE_NOT_MRNA::4 molecule types are not set as mRNA.
94 genome:sample (length 215740)
95 genome:sample2 (length 2030)
96 genome:sample3 (length 2100)
97 genome:sample4 (length 7560)
98
99 DiscRep_ALL:TECHNIQUE_NOT_TSA::4 technique are not set as TSA
100 genome:sample (length 215740)
101 genome:sample2 (length 2030)
102 genome:sample3 (length 2100)
103 genome:sample4 (length 7560)
104
105 DiscRep_ALL:MISSING_STRUCTURED_COMMENT::4 sequences do not include structured comments.
106 genome:sample (length 215740)
107 genome:sample2 (length 2030)
108 genome:sample3 (length 2100)
109 genome:sample4 (length 7560)
110
111 DiscRep_ALL:MISSING_PROJECT::22 sequences do not include project.
112 genome:sample (length 215740)
113 genome:ncbi:FUN_000001-T1 (length 307)
114 genome:ncbi:FUN_000002-T1 (length 220)
115 genome:ncbi:FUN_000003-T1 (length 591)
116 genome:ncbi:FUN_000004-T1 (length 135)
117 genome:ncbi:FUN_000005-T1 (length 662)
118 genome:ncbi:FUN_000006-T1 (length 278)
119 genome:ncbi:FUN_000007-T1 (length 578)
120 genome:ncbi:FUN_000008-T1 (length 396)
121 genome:ncbi:FUN_000009-T1 (length 130)
122 genome:ncbi:FUN_000010-T1 (length 90)
123 genome:ncbi:FUN_000011-T1 (length 923)
124 genome:ncbi:FUN_000012-T1 (length 3977)
125 genome:ncbi:FUN_000013-T1 (length 576)
126 genome:ncbi:FUN_000014-T1 (length 151)
127 genome:ncbi:FUN_000015-T1 (length 246)
128 genome:ncbi:FUN_000016-T1 (length 478)
129 genome:sample2 (length 2030)
130 genome:sample3 (length 2100)
131 genome:sample4 (length 7560)
132 genome:ncbi:FUN_000017-T1 (length 124)
133 genome:ncbi:FUN_000018-T1 (length 432)
134
135 DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
136 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
137 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::4 Molinfos are missing field technique
138 genome:sample (length 215740)
139 genome:sample2 (length 2030)
140 genome:sample3 (length 2100)
141 genome:sample4 (length 7560)
142