Note: I already changed the sequence name of the genome files to correspond to the GFF3 files chromosome sequence names, which did not resolve the problem.
htsjdk.tribble.TribbleException: Attribute string ID=chromosome;Name=Pseudomonas tohonis strain Q4-3 chromosome, complete genome;Dbxref=RefSeq:NZ_CP115820.1; is invalid, for input source: Pseudomonas_tohonis_Q4-3_21793.gff
at htsjdk.tribble.gff.Gff3Codec.parseAttributes(Gff3Codec.java:196)
at htsjdk.tribble.gff.Gff3Codec.parseLine(Gff3Codec.java:219)
at htsjdk.tribble.gff.Gff3Codec.decode(Gff3Codec.java:132)
at htsjdk.tribble.gff.Gff3Codec.decode(Gff3Codec.java:90)
at htsjdk.tribble.gff.Gff3Codec.decode(Gff3Codec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:375)
at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.<init>(TribbleIndexedFeatureReader.java:342)
at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:309)
at nl.wur.bif.pantools.construction.annotations.AnnotationLayer.parseGff(AnnotationLayer.java:290)
at nl.wur.bif.pantools.construction.annotations.AnnotationLayer.getAnnotationFeatures(AnnotationLayer.java:238)
at nl.wur.bif.pantools.construction.annotations.AnnotationLayer.addAnnotations(AnnotationLayer.java:167)
at nl.wur.bif.pantools.construction.annotations.AddAnnotationsCLI.call(AddAnnotationsCLI.java:51)
at nl.wur.bif.pantools.construction.annotations.AddAnnotationsCLI.call(AddAnnotationsCLI.java:21)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
at nl.wur.bif.pantools.Pantools.executionStrategy(Pantools.java:248)
at picocli.CommandLine.execute(CommandLine.java:2078)
at nl.wur.bif.pantools.Pantools.main(Pantools.java:210)
Hi, I try to use pantools with the complete genomes from https://www.pseudomonas.com/.
Anyhow, using the official GFF3 files from Pseudomonas DB fail with pantools.
Could you please debug, why this is happening or pinpoint to the problem?
genome files: https://www.pseudomonas.com/downloads/pseudomonas/pgd_r_22_1/Pseudomonas/complete/fna-complete.tar.gz
gff3 files: https://www.pseudomonas.com/downloads/pseudomonas/pgd_r_22_1/Pseudomonas/complete/gff-complete.tar.gz
Note: I already changed the sequence name of the genome files to correspond to the GFF3 files chromosome sequence names, which did not resolve the problem.
Thank you in anticipation
Best regards
Kristian