Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

Appearance settings

arrow load_gff3 error #55

Copy link
Copy link
@pwilx666

Description

@pwilx666
Issue body actions

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions

      Morty Proxy This is a proxified and sanitized view of the page, visit original site.