-
Notifications
You must be signed in to change notification settings - Fork 11
Description
Hi, when I try to load a gff3 file using arrow:
arrow annotations load_gff3 --test "Uncinocarpus reesii 1704 [Aug 06, 2014]" "Uncinocarpis_reesei.gff"
I get the following error message:
Traceback (most recent call last):
File "/home/pwilk/apollo_env/lib/python3.7/site-packages/arrow/decorators.py", line 16, in custom_exception
return wrapped(*args, **kwargs)
File "/home/pwilk/apollo_env/lib/python3.7/site-packages/arrow/decorators.py", line 46, in str_output
print(wrapped(*args, **kwargs))
File "/home/pwilk/apollo_env/lib/python3.7/site-packages/arrow/commands/annotations/load_gff3.py", line 51, in cli
return ctx.gi.annotations.load_gff3(organism, gff3, source=source, batch_size=batch_size, test=test, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation, timing=timing)
File "/home/pwilk/apollo_env/lib/python3.7/site-packages/apollo/annotations/init.py", line 1345, in load_gff3
raise Exception("Organism name or id not found [" + organism + "]")
Exception: Organism name or id not found [Uncinocarpus reesii 1704 [Aug 06, 2014]]
Organism name or id not found [Uncinocarpus reesii 1704 [Aug 06, 2014]]
The organism is in Apollo and the name is correct as I can use arrow's show_organism command to display information
on this organism:
arrow organisms show_organism "Uncinocarpus reesii 1704 [Aug 06, 2014]"
{
"commonName": "Uncinocarpus reesii 1704 [Aug 06, 2014]",
"blatdb": "/data/apollo_data/twoBit/uree1704.2bit",
"metadata": "{"creator":"32"}",
"annotationCount": 0,
"currentOrganism": false,
"obsolete": false,
"sequences": 44,
"directory": "/data/apollo_data/uree1704",
"publicMode": true,
"valid": true,
"genomeFastaIndex": "seq/uree1704.fa.fai",
"genus": null,
"species": null,
"id": 2498934,
"nonDefaultTranslationTable": null,
"genomeFasta": "seq/uree1704.fa"
}
I've tried this with other organisms in my local apollo instance and they also fail, does anyone have any idea why this is happening? I'm using apollo v2.6.5