Here are the links to get the gff and the related genome files:
http://genomeportal.jgi-psf.org/Crypa2/download/Cparasiticav2.GeneCatalog20091217.gff.gz
http://genomeportal.jgi-psf.org/Crypa2/download/Cryphonectria_parasiticav2.nuclearAssembly.unmasked.gz
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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