We've been having trouble with load_gff3 - I initially posted this on the Apollo repo (GMOD/Apollo#2662), reposting it here now. Thanks for considering this, I'd appreciate any pointers!
We are trying to use the python-apollo arrow annotations load_gff3 command to load annotations to the user-created annotations track. It is changing the CDS locations of the model, both with and without the --disable_cds_recalculation option.
Here is what a load without --disable_cds_recalculation looks like; the correct frame can be seen in the track below.
The gff3 that was used to load the annotation has 6 CDS lines; the gff3 for the uploaded annotation has 12 CDS lines (even though the view shows only one CDS segment). Apollo also won't calculate a protein or CDS sequence on the uploaded annotation.
Here is what a load with --disable_cds_recalculation looks like (command: arrow annotations load_gff3 --source https://apollo2-stage-node1-cbo.nal.usda.gov/apollo Anoplophora_glabripennis ~/Downloads/NW_019416298.gff3 --disable_cds_recalculation)
Again, the gff3 for the uploaded annotation in Apollo has 12 CDS lines instead of 6. Apollo also won't calculate a protein or CDS sequence on the uploaded annotation.
I'll note that if you run the same command multiple times, the single CDS will display in a different spot each time.
If you load the annotation by dragging it up, it loads correctly:
This is happening for many (but not all) annotations in multiple assemblies/organisms.
Some other observations:
- We haven't observed the problem for models with a single CDS/exon segment
- The underlying genomic sequence has lowercase nucleotides
- I tried using load_legacy_gff3, and that calculated the CDS correctly, but I'm unable to delete features when I load them with that method (Hibernate operation: could not execute statement; SQL [n/a]; ERROR: update or delete on table "feature" violates foreign key constraint "fk_8jm56covt0m7m0m191bc5jseh" on table "feature_relationship" Detail: Key (id)=(4858111) is still referenced from table "feature_relationship".; nested exception is org.postgresql.util.PSQLException: ERROR: update or delete on table "feature" violates foreign key constraint "fk_8jm56covt0m7m0m191bc5jseh" on table "feature_relationship" Detail: Key (id)=(4858111) is still referenced from table "feature_relationship".)
I've attached "before" and "after" gff3s. (Used .txt extension because GitHub wouldn't let me upload otherswise)
before.txt
after-nocdsrecalc.txt
after.txt
-
Provide the javascript console log output generated from the action.
None.
-
Provide the server log output generated from the action (typically catalina.out).
nothing is added to Catalina.out when I add the annotations.
We've been having trouble with load_gff3 - I initially posted this on the Apollo repo (GMOD/Apollo#2662), reposting it here now. Thanks for considering this, I'd appreciate any pointers!
We are trying to use the python-apollo
arrow annotations load_gff3command to load annotations to the user-created annotations track. It is changing the CDS locations of the model, both with and without the --disable_cds_recalculation option.Here is what a load without --disable_cds_recalculation looks like; the correct frame can be seen in the track below.
The gff3 that was used to load the annotation has 6 CDS lines; the gff3 for the uploaded annotation has 12 CDS lines (even though the view shows only one CDS segment). Apollo also won't calculate a protein or CDS sequence on the uploaded annotation.
Here is what a load with --disable_cds_recalculation looks like (command:
arrow annotations load_gff3 --source https://apollo2-stage-node1-cbo.nal.usda.gov/apollo Anoplophora_glabripennis ~/Downloads/NW_019416298.gff3 --disable_cds_recalculation)Again, the gff3 for the uploaded annotation in Apollo has 12 CDS lines instead of 6. Apollo also won't calculate a protein or CDS sequence on the uploaded annotation.
I'll note that if you run the same command multiple times, the single CDS will display in a different spot each time.
If you load the annotation by dragging it up, it loads correctly:
This is happening for many (but not all) annotations in multiple assemblies/organisms.
Some other observations:
I've attached "before" and "after" gff3s. (Used .txt extension because GitHub wouldn't let me upload otherswise)
before.txt
after-nocdsrecalc.txt
after.txt
Provide the javascript console log output generated from the action.
None.
Provide the server log output generated from the action (typically
catalina.out).nothing is added to Catalina.out when I add the annotations.