Attribute string - GFF parsing - Pseudomonas DB

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.

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)

Thank you in anticipation

Best regards

Kristian

Sheikhizadeh / pantools

Attribute string - GFF parsing - Pseudomonas DB #16