Adding functional annotation to reduced gff3 file

[alexvasilikop]

Are you using the latest release? I am using v. 1.8.11

Hello,

I have an updated annotation (funannotate update) which I subsequently modified as follows:

modified scaffold names
Removed some cds models with strong hits to a TE library

I used the extracted proteins (extracted with agat from the reduced gff file) to produce interproscan and eggnog-mapper annotations out of funannotate. Now I would like to add this annotation to the reduced gff and not the one produced by funannotate. I get the following error:

[Jul 14 02:09 PM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.8.12
[Jul 14 02:09 PM]: Running 1.8.11
[Jul 14 02:09 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt'
[Jul 14 02:09 PM]: Unable to detect funannotate folder as input, please provide -o,--out directory

Is there away to run "funannotate annotate" on a custom gff and protein set after some gene models have been removed?

Thanks Alex

[nextgenusfs]

$ funannotate annotate

Usage:       funannotate annotate <arguments>
version:     1.8.14

Description: Script functionally annotates the results from funannotate predict.  It pulls
             annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.

Required:
  -i, --input          Folder from funannotate predict
    or
  --genbank            Genome in GenBank format
  -o, --out            Output folder for results
    or
  --gff                Genome GFF3 annotation file
  --fasta              Genome in multi-fasta format
  -s, --species        Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
  -o, --out            Output folder for results

You can pass --gff, --fasta, -s, and -o. See the help menu.

[alexvasilikop]

Hello,

thanks for your reply. The problem is that I only have a modified gff and corresponding assembly fasta. however, the "funannotate predict" script requires the whole output dir of funannotate predict.

Is this correct?

best