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view test-data/out.err @ 14:eaee459f3d69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
author iuc
date Wed, 28 Mar 2018 12:38:42 -0400
parents a17498c603ec
children bf68eb663bc3
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Discrepancy Report Results

Summary
DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
DISC_FEATURE_COUNT:CDS: 5 present
DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
NO_ANNOTATION:3 bioseqs have no features
DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
TECHNIQUE_NOT_TSA:7 technique are not set as TSA
MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
MISSING_PROJECT:12 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"

FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
outdir/prokka:contig2_1 (length 152)
outdir/prokka:contig2_2 (length 38)
outdir/prokka:contig4_1 (length 287)
outdir/prokka:contig5_1 (length 43)
outdir/prokka:contig6_1 (length 253)

DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations.
DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
outdir/prokka:CDS	hypothetical protein	contig2:40-498	HMJLFLJH_00001

DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
outdir/prokka:CDS	hypothetical protein	contig2:498-614	HMJLFLJH_00002

DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
outdir/prokka:CDS	hypothetical protein	contig4:21-884	HMJLFLJH_00003

DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
outdir/prokka:CDS	hypothetical protein	contig5:275-406	HMJLFLJH_00004

DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
outdir/prokka:CDS	hypothetical protein	contig6:6-767	HMJLFLJH_00005

DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
outdir/prokka:contig1 (length 350)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.

DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)
outdir/prokka:contig1:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig2:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig3:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig4:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig5:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig6:Annotated using prokka 1.13 from https://github.com/tseemann/prokka
outdir/prokka:contig7:Annotated using prokka 1.13 from https://github.com/tseemann/prokka

DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
outdir/prokka:contig2_2 (length 38)
outdir/prokka:contig5_1 (length 43)

DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)

DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig2_1 (length 152)
outdir/prokka:contig2_2 (length 38)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig4_1 (length 287)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig5_1 (length 43)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig6_1 (length 253)
outdir/prokka:contig7 (length 276)

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::7 Molinfos are missing field technique
outdir/prokka:contig1 (length 350)
outdir/prokka:contig2 (length 840)
outdir/prokka:contig3 (length 210)
outdir/prokka:contig4 (length 1260)
outdir/prokka:contig5 (length 490)
outdir/prokka:contig6 (length 1960)
outdir/prokka:contig7 (length 276)