Here are the links to get the gff and the related genome files: http://genomeportal.jgi-psf.org/Crypa2/download/Cparasiticav2.GeneCatalog200... http://genomeportal.jgi-psf.org/Crypa2/download/Cryphonectria_parasiticav2.n... Whatever the file type I set for the gff file (gff3, gff or gtf), I get the transcript_id error: Traceback (most recent call last): File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 91, in main() File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 30, in main for feature in read_unordered_gtf( open( in_fname, 'r' ) ): File "/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 375, in read_unordered_gtf transcript_id = line_attrs[ 'transcript_id' ] KeyError: 'transcript_id' If I fix the transcript_id problem, I get the other error: Traceback (most recent call last): File "~/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 91, in main() File "~/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 30, in main for feature in read_unordered_gtf( open( in_fname, 'r' ) ): File "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 389, in read_unordered_gtf feature = GFFFeature( None, intervals=intervals ) File "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 65, in __init__ ( interval.chrom, self.chrom ) ) ValueError: interval chrom does not match self chrom: scaffold_10 != scaffold_10 Is the gff file not correct? PS : I use the galaxy changeset : 7828:b5bda7a5c345 Yec'han ================================================ Yec'han LAIZET Ingenieur Plateforme Genome Transcriptome Tel: 05 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================ Le 23/10/2012 18:37, Jeremy Goecks a écrit :
Yes, you should be able to use a single GFF for the complete genome.
This error stems from the same issue as before, namely that Galaxy is treating your GFF file as GTF.
If you think your GFF is well formatted and there is an issue with Galaxy's handling of GFF, please send me your GFF and I'll take a look.
Best, J.
On Oct 23, 2012, at 9:24 AM, Yec'han Laizet wrote:
Hello,
Is it possible to load a unique gff file with the annotations of several chromosomes for my custom build in one step (one gff file)?
With the current version of galaxy, it seems that I can load a gff file referring only to one chromosome. That's pretty tedious to load 43 gff files separatly for my custom build...
If I try, I get this error:
Traceback (most recent call last): File "~/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 91, in main() File "~/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py", line 30, in main for feature in read_unordered_gtf( open( in_fname, 'r' ) ): File "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 389, in read_unordered_gtf feature = GFFFeature( None, intervals=intervals ) File "~/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 65, in __init__ ( interval.chrom, self.chrom ) ) ValueError: interval chrom does not match self chrom: SAGS2 != SAGS1
Thanks
Yec'han
================================================
Yec'han LAIZET Ingenieur Plateforme Genome Transcriptome Tel: 05 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================
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