Mercurial > repos > crs4 > prokka

annotate test-data/out.err @ 19:8a22554cdde2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
author iuc
date Tue, 16 Nov 2021 18:59:22 +0000
parents bf68eb663bc3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
iuc
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1 Discrepancy Report Results
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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2
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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3 Summary
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
iuc
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4 DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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5 FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
iuc
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6 DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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7 DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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8 DISC_FEATURE_COUNT:CDS: 5 present
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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9 DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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10 FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
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11 NO_ANNOTATION:3 bioseqs have no features
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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12 DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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13 ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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14 SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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15 MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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16 MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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17 TECHNIQUE_NOT_TSA:7 technique are not set as TSA
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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18 MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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19 MISSING_PROJECT:12 sequences do not include project.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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20 DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
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a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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23 Detailed Report
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a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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25 DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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26
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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27 FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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28 outdir/prokka:contig2_1 (length 152)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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29 outdir/prokka:contig2_2 (length 38)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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30 outdir/prokka:contig4_1 (length 287)
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31 outdir/prokka:contig5_1 (length 43)
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32 outdir/prokka:contig6_1 (length 253)
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34 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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35 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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36 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
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37 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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38 DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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39 DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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40 outdir/prokka:contig1 (length 350)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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41 outdir/prokka:contig2 (length 840)
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42 outdir/prokka:contig3 (length 210)
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43 outdir/prokka:contig4 (length 1260)
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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44 outdir/prokka:contig5 (length 490)
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45 outdir/prokka:contig6 (length 1960)
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46 outdir/prokka:contig7 (length 276)
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48 DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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49 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
14
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50 outdir/prokka:CDS hypothetical protein contig2:40-498 HMJLFLJH_00001
13
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52 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
14
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53 outdir/prokka:CDS hypothetical protein contig2:498-614 HMJLFLJH_00002
13
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55 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
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56 outdir/prokka:CDS hypothetical protein contig4:21-884 HMJLFLJH_00003
13
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58 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
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59 outdir/prokka:CDS hypothetical protein contig5:275-406 HMJLFLJH_00004
13
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61 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
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62 outdir/prokka:CDS hypothetical protein contig6:6-767 HMJLFLJH_00005
13
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64 DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
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65 outdir/prokka:contig1 (length 350)
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66 outdir/prokka:contig3 (length 210)
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67 outdir/prokka:contig7 (length 276)
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69 DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
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71 DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)
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bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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72 outdir/prokka:contig1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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73 outdir/prokka:contig2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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74 outdir/prokka:contig3:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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75 outdir/prokka:contig4:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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76 outdir/prokka:contig5:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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77 outdir/prokka:contig6:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
bf68eb663bc3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 0d2c8359cf38498b417b395d081daad47d08ee40"
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78 outdir/prokka:contig7:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
13
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80 DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
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81 outdir/prokka:contig2_2 (length 38)
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82 outdir/prokka:contig5_1 (length 43)
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84 DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
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85 outdir/prokka:contig1 (length 350)
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86 outdir/prokka:contig2 (length 840)
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87 outdir/prokka:contig3 (length 210)
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88 outdir/prokka:contig4 (length 1260)
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89 outdir/prokka:contig5 (length 490)
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90 outdir/prokka:contig6 (length 1960)
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91 outdir/prokka:contig7 (length 276)
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92
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93 DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
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94 outdir/prokka:contig1 (length 350)
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95 outdir/prokka:contig2 (length 840)
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96 outdir/prokka:contig3 (length 210)
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97 outdir/prokka:contig4 (length 1260)
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98 outdir/prokka:contig5 (length 490)
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99 outdir/prokka:contig6 (length 1960)
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100 outdir/prokka:contig7 (length 276)
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101
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102 DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
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103 outdir/prokka:contig1 (length 350)
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104 outdir/prokka:contig2 (length 840)
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105 outdir/prokka:contig3 (length 210)
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106 outdir/prokka:contig4 (length 1260)
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107 outdir/prokka:contig5 (length 490)
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108 outdir/prokka:contig6 (length 1960)
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109 outdir/prokka:contig7 (length 276)
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111 DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
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112 outdir/prokka:contig1 (length 350)
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113 outdir/prokka:contig2 (length 840)
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114 outdir/prokka:contig3 (length 210)
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115 outdir/prokka:contig4 (length 1260)
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117 outdir/prokka:contig6 (length 1960)
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118 outdir/prokka:contig7 (length 276)
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119
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120 DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
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121 outdir/prokka:contig1 (length 350)
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122 outdir/prokka:contig2 (length 840)
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123 outdir/prokka:contig2_1 (length 152)
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124 outdir/prokka:contig2_2 (length 38)
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125 outdir/prokka:contig3 (length 210)
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126 outdir/prokka:contig4 (length 1260)
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127 outdir/prokka:contig4_1 (length 287)
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129 outdir/prokka:contig5_1 (length 43)
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130 outdir/prokka:contig6 (length 1960)
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131 outdir/prokka:contig6_1 (length 253)
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132 outdir/prokka:contig7 (length 276)
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134 DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
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135 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
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136 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique
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137 outdir/prokka:contig1 (length 350)
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138 outdir/prokka:contig2 (length 840)
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139 outdir/prokka:contig3 (length 210)
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140 outdir/prokka:contig4 (length 1260)
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141 outdir/prokka:contig5 (length 490)
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142 outdir/prokka:contig6 (length 1960)
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143 outdir/prokka:contig7 (length 276)
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