Mercurial > repos > crs4 > prokka

comparison test-data/out.err @ 13:a17498c603ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
author iuc
date Tue, 21 Mar 2017 10:13:06 -0400
parents 392255fa7ab9
children eaee459f3d69
comparison
equal deleted inserted replaced
12:da479161bbe4 13:a17498c603ec
1 >PROKKA_00001 hypothetical protein 1 Discrepancy Report Results
2 ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC 2
3 ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC 3 Summary
4 AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT 4 DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
5 GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC 5 FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
6 GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC 6 DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
7 GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG 7 DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
8 TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA 8 DISC_FEATURE_COUNT:CDS: 5 present
9 AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA 9 DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
10 >PROKKA_00002 hypothetical protein 10 FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
11 ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT 11 NO_ANNOTATION:3 bioseqs have no features
12 ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA 12 DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
13 >PROKKA_00003 hypothetical protein 13 ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
14 ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT 14 SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
15 TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT 15 MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
16 TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT 16 MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
17 GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT 17 TECHNIQUE_NOT_TSA:7 technique are not set as TSA
18 TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC 18 MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
19 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG 19 MISSING_PROJECT:12 sequences do not include project.
20 TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG 20 DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
21 CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT 21
22 CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG 22
23 TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG 23 Detailed Report
24 TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT 24
25 CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG 25 DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
26 CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG 26
27 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT 27 FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
28 CGCGATTCAATCATGACTTCGTGA 28 outdir/prokka:contig2_1 (length 152)
29 >PROKKA_00004 hypothetical protein 29 outdir/prokka:contig2_2 (length 38)
30 TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT 30 outdir/prokka:contig4_1 (length 287)
31 TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA 31 outdir/prokka:contig5_1 (length 43)
32 ACAATACTGTAG 32 outdir/prokka:contig6_1 (length 253)
33 >PROKKA_00005 hypothetical protein 33
34 ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT 34 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
35 TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG 35 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
36 GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT 36 DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
37 GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT 37 DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
38 AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG 38 DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
39 ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA 39 DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
40 AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA 40 outdir/prokka:contig1 (length 350)
41 AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA 41 outdir/prokka:contig2 (length 840)
42 GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT 42 outdir/prokka:contig3 (length 210)
43 AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT 43 outdir/prokka:contig4 (length 1260)
44 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT 44 outdir/prokka:contig5 (length 490)
45 GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC 45 outdir/prokka:contig6 (length 1960)
46 GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA 46 outdir/prokka:contig7 (length 276)
47
48 DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations.
49 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
50 outdir/prokka:CDS hypothetical protein contig2:40-498 PROKKA_00001
51
52 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
53 outdir/prokka:CDS hypothetical protein contig2:498-614 PROKKA_00002
54
55 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
56 outdir/prokka:CDS hypothetical protein contig4:21-884 PROKKA_00003
57
58 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
59 outdir/prokka:CDS hypothetical protein contig5:275-406 PROKKA_00004
60
61 DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
62 outdir/prokka:CDS hypothetical protein contig6:6-767 PROKKA_00005
63
64 DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
65 outdir/prokka:contig1 (length 350)
66 outdir/prokka:contig3 (length 210)
67 outdir/prokka:contig7 (length 276)
68
69 DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
70
71 DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)
72 outdir/prokka:contig1:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
73 outdir/prokka:contig2:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
74 outdir/prokka:contig3:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
75 outdir/prokka:contig4:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
76 outdir/prokka:contig5:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
77 outdir/prokka:contig6:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
78 outdir/prokka:contig7:Annotated using prokka 1.12 from https://github.com/tseemann/prokka
79
80 DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
81 outdir/prokka:contig2_2 (length 38)
82 outdir/prokka:contig5_1 (length 43)
83
84 DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
85 outdir/prokka:contig1 (length 350)
86 outdir/prokka:contig2 (length 840)
87 outdir/prokka:contig3 (length 210)
88 outdir/prokka:contig4 (length 1260)
89 outdir/prokka:contig5 (length 490)
90 outdir/prokka:contig6 (length 1960)
91 outdir/prokka:contig7 (length 276)
92
93 DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
94 outdir/prokka:contig1 (length 350)
95 outdir/prokka:contig2 (length 840)
96 outdir/prokka:contig3 (length 210)
97 outdir/prokka:contig4 (length 1260)
98 outdir/prokka:contig5 (length 490)
99 outdir/prokka:contig6 (length 1960)
100 outdir/prokka:contig7 (length 276)
101
102 DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
103 outdir/prokka:contig1 (length 350)
104 outdir/prokka:contig2 (length 840)
105 outdir/prokka:contig3 (length 210)
106 outdir/prokka:contig4 (length 1260)
107 outdir/prokka:contig5 (length 490)
108 outdir/prokka:contig6 (length 1960)
109 outdir/prokka:contig7 (length 276)
110
111 DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
112 outdir/prokka:contig1 (length 350)
113 outdir/prokka:contig2 (length 840)
114 outdir/prokka:contig3 (length 210)
115 outdir/prokka:contig4 (length 1260)
116 outdir/prokka:contig5 (length 490)
117 outdir/prokka:contig6 (length 1960)
118 outdir/prokka:contig7 (length 276)
119
120 DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
121 outdir/prokka:contig1 (length 350)
122 outdir/prokka:contig2 (length 840)
123 outdir/prokka:contig2_1 (length 152)
124 outdir/prokka:contig2_2 (length 38)
125 outdir/prokka:contig3 (length 210)
126 outdir/prokka:contig4 (length 1260)
127 outdir/prokka:contig4_1 (length 287)
128 outdir/prokka:contig5 (length 490)
129 outdir/prokka:contig5_1 (length 43)
130 outdir/prokka:contig6 (length 1960)
131 outdir/prokka:contig6_1 (length 253)
132 outdir/prokka:contig7 (length 276)
133
134 DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
135 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
136 DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique
137 outdir/prokka:contig1 (length 350)
138 outdir/prokka:contig2 (length 840)
139 outdir/prokka:contig3 (length 210)
140 outdir/prokka:contig4 (length 1260)
141 outdir/prokka:contig5 (length 490)
142 outdir/prokka:contig6 (length 1960)
143 outdir/prokka:contig7 (length 276)
144