Mercurial > repos > iuc > funannotate_annotate

annotate test-data/predict_bam/Genus_species.discrepency.report.txt @ 6:582fd74dc2a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2c4f8172c3f452e1119b3d528c97da382750adeb
author iuc
date Tue, 25 Apr 2023 18:29:19 +0000
parents a5baa4ff168d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 Discrepancy Report Results
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2
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3 Summary
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4 DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
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5 DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
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6 DISC_FEATURE_COUNT:gene: 18 present
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7 DISC_FEATURE_COUNT:CDS: 18 present
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8 DISC_FEATURE_COUNT:mRNA: 18 present
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9 DISC_COUNT_NUCLEOTIDES:4 nucleotide Bioseqs are present
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10 JOINED_FEATURES:30 features have joined locations.
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11 NO_ANNOTATION:2 bioseqs have no features
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12 DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
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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
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14 ONCALLER_COMMENT_PRESENT:4 comment descriptors were found (all same)
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15 MISSING_GENOMEASSEMBLY_COMMENTS:4 bioseqs are missing GenomeAssembly structured comments
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16 MOLTYPE_NOT_MRNA:4 molecule types are not set as mRNA.
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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17 TECHNIQUE_NOT_TSA:4 technique are not set as TSA
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18 MISSING_STRUCTURED_COMMENT:4 sequences do not include structured comments.
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19 MISSING_PROJECT:22 sequences do not include project.
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20 DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
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21
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22
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23 Detailed Report
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24
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25 DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
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26
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27 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
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28 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'Genus species' for taxname
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29 DiscRep_ALL:DISC_FEATURE_COUNT::gene: 18 present
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30 DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 18 present
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31 DiscRep_ALL:DISC_FEATURE_COUNT::mRNA: 18 present
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32 DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present
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33 genome:sample (length 215740)
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34 genome:sample2 (length 2030)
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35 genome:sample3 (length 2100)
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36 genome:sample4 (length 7560)
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37
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38 DiscRep_ALL:JOINED_FEATURES::30 features have joined locations.
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39 DiscRep_SUB:JOINED_FEATURES::30 features have joined location but no exception
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40 genome:mRNA hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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41 genome:CDS hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
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42 genome:mRNA hypothetical protein (sample:c5802-5797, c5539-4883) FUN_000002
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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43 genome:CDS hypothetical protein (sample:c5802-5797, c5539-4883) FUN_000002
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44 genome:mRNA hypothetical protein (sample:c10557-10549, c10462-8696) FUN_000003
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45 genome:CDS hypothetical protein (sample:c10557-10549, c10462-8696) FUN_000003
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46 genome:CDS hypothetical protein (sample:c15214-15209, c14648-14247) FUN_000004
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47 genome:mRNA hypothetical protein (sample:c15214-15209, c14648-14247) FUN_000004
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48 genome:mRNA hypothetical protein (sample:c21705-21700, c21515-19533) FUN_000005
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49 genome:CDS hypothetical protein (sample:c21705-21700, c21515-19533) FUN_000005
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50 genome:CDS hypothetical protein (sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130) FUN_000007
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iuc
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51 genome:mRNA hypothetical protein (sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130) FUN_000007
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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52 genome:CDS hypothetical protein (sample:c47195-46753, c46330-46214, c46157-45527) FUN_000008
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53 genome:mRNA hypothetical protein (sample:c47195-46753, c46330-46214, c46157-45527) FUN_000008
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54 genome:CDS hypothetical protein (sample:c79527-79519, c79068-78685) FUN_000009
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55 genome:mRNA hypothetical protein (sample:c79527-79519, c79068-78685) FUN_000009
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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56 genome:mRNA hypothetical protein (sample:87202-87207, 88054-88320) FUN_000010
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57 genome:CDS hypothetical protein (sample:87202-87207, 88054-88320) FUN_000010
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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58 genome:CDS hypothetical protein (sample:133587-134504, 134720-135510, 135569-136284, 137516-137862) FUN_000011
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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59 genome:mRNA hypothetical protein (sample:133587-134504, 134720-135510, 135569-136284, 137516-137862) FUN_000011
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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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
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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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
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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62 genome:CDS hypothetical protein (sample:167121-168360, 168722-169212) FUN_000013
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63 genome:mRNA hypothetical protein (sample:167121-168360, 168722-169212) FUN_000013
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64 genome:CDS hypothetical protein (sample:c178916-178873, c177172-176887, c176824-176699) FUN_000014
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65 genome:mRNA hypothetical protein (sample:c178916-178873, c177172-176887, c176824-176699) FUN_000014
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66 genome:CDS hypothetical protein (sample:192004-192067, 193549-193658, 194041-194455, 194518-194669) FUN_000015
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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67 genome:mRNA hypothetical protein (sample:192004-192067, 193549-193658, 194041-194455, 194518-194669) FUN_000015
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68 genome:CDS hypothetical protein (sample:c210553-210548, c210474-209044) FUN_000016
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69 genome:mRNA hypothetical protein (sample:c210553-210548, c210474-209044) FUN_000016
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70
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71 DiscRep_ALL:NO_ANNOTATION::2 bioseqs have no features
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72 genome:sample2 (length 2030)
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73 genome:sample3 (length 2100)
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74
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75 DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
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76
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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
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78 genome:CDS hypothetical protein sample:<2331-3254 FUN_000001
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iuc
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79 genome:CDS hypothetical protein (sample4:2126-2199, 2258-3224, 3284->3537) FUN_000018
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80
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81 DiscRep_ALL:ONCALLER_COMMENT_PRESENT::4 comment descriptors were found (all same)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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82 genome:sample:"Annotated using 1.8.7"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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83 genome:sample2:"Annotated using 1.8.7"
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84 genome:sample3:"Annotated using 1.8.7"
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85 genome:sample4:"Annotated using 1.8.7"
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86
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87 DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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88 genome:sample (length 215740)
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iuc
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89 genome:sample2 (length 2030)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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90 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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91 genome:sample4 (length 7560)
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iuc
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92
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93 DiscRep_ALL:MOLTYPE_NOT_MRNA::4 molecule types are not set as mRNA.
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
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94 genome:sample (length 215740)
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95 genome:sample2 (length 2030)
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iuc
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96 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
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97 genome:sample4 (length 7560)
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iuc
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98
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parents:
diff changeset
99 DiscRep_ALL:TECHNIQUE_NOT_TSA::4 technique are not set as TSA
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
100 genome:sample (length 215740)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
101 genome:sample2 (length 2030)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
102 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
103 genome:sample4 (length 7560)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
104
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
105 DiscRep_ALL:MISSING_STRUCTURED_COMMENT::4 sequences do not include structured comments.
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
106 genome:sample (length 215740)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
107 genome:sample2 (length 2030)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
108 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
109 genome:sample4 (length 7560)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
110
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
111 DiscRep_ALL:MISSING_PROJECT::22 sequences do not include project.
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
112 genome:sample (length 215740)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
113 genome:ncbi:FUN_000001-T1 (length 307)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
114 genome:ncbi:FUN_000002-T1 (length 220)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
115 genome:ncbi:FUN_000003-T1 (length 591)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
116 genome:ncbi:FUN_000004-T1 (length 135)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
117 genome:ncbi:FUN_000005-T1 (length 662)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
118 genome:ncbi:FUN_000006-T1 (length 278)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
119 genome:ncbi:FUN_000007-T1 (length 578)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
120 genome:ncbi:FUN_000008-T1 (length 396)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
121 genome:ncbi:FUN_000009-T1 (length 130)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
122 genome:ncbi:FUN_000010-T1 (length 90)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
123 genome:ncbi:FUN_000011-T1 (length 923)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
124 genome:ncbi:FUN_000012-T1 (length 3977)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
125 genome:ncbi:FUN_000013-T1 (length 576)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
126 genome:ncbi:FUN_000014-T1 (length 151)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
127 genome:ncbi:FUN_000015-T1 (length 246)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
128 genome:ncbi:FUN_000016-T1 (length 478)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
129 genome:sample2 (length 2030)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
130 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
131 genome:sample4 (length 7560)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
132 genome:ncbi:FUN_000017-T1 (length 124)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
133 genome:ncbi:FUN_000018-T1 (length 432)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
134
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
135 DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
136 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
137 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::4 Molinfos are missing field technique
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
138 genome:sample (length 215740)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
139 genome:sample2 (length 2030)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
140 genome:sample3 (length 2100)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
141 genome:sample4 (length 7560)
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
142