arrow load_gff3 error

[pwilx666]

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

[hexylena]

Wow! Someone else is using this, very cool :) Have you tried using the internal number of the organism? You can find this from one of the other arrow commands.

[pwilx666]

Yes, I already tried using the internal id and get the same error unfortunately:

arrow annotations load_gff3 --test "2498934" "Uncinocarpis_reesei.gff"
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 [2498934]

Organism name or id not found [2498934]

It's weird as arrow works using the same commonName and internal id for other webservices.

[hexylena]

Very odd! You said this was a local Apollo, do the logs from Apollo give any useful indication? (You may need to set the logging configuration in apolloy-config.groovy)

[pwilx666]

Hexylena, which version of arrow are you using? I've been trying and failing to upload the gff3 using arrow version 4.2.13
I found an old virtual environment on my machine that had arrow version 4.2.7 installed and when I tried the upload it works!

[hexylena]

Hey @pwilx666 I tried all versions between 4.2.7 and 4.2.13 and can't reproduce locally.

(.venv) 11:47:33|[hxr@cosima:/tmp/tmp.wPYnfmZJn1]130$ pip install apollo==4.2.13
Collecting apollo==4.2.13
...
Installing collected packages: apollo
  Attempting uninstall: apollo
    Found existing installation: apollo 4.2.12
    Uninstalling apollo-4.2.12:
      Successfully uninstalled apollo-4.2.12
Successfully installed apollo-4.2.13
(.venv) 11:47:35|[hxr@cosima:/tmp/tmp.wPYnfmZJn1]$ arrow annotations load_gff3 --test 'E. coli K12 (gx580)' ~/Downloads/augustus.gff3-NC_000913.3-1..100000.gff3
test success 79 features would have been loaded
test success 79 features would have been loaded
{}

I'm not sure what's going on there for you. You could either try the different versions in between 4.2.7 and 13 to figure out where it breaks, (pip install apollo=4.2.X) or check the apollo logs, maybe there would be an indication of the difference, because I'm looking through the code and there's absolutely nothing clear :(

[hexylena]

I wondered if it is due to the [Aug,,,] but no

$ arrow annotations load_gff3 --test 'E. coli Uncinocarpus reesii 1704 [Aug 06, 2014] (gx580)' ~/Downloads/augustus.gff3-NC_000913.3-1..100000.gff3
test success 79 features would have been loaded
test success 79 features would have been loaded
{}

[abretaud]

Odd, you're sure you're running arrow on the good server?