Error with panaroo-generate-gffs

[sarapita]

I'm trying to update my bakta gffs after panaroo 1.3.0 proccessing with the following command:

panaroo-generate-gffs -o panaroo_out -i *gff3 -t 1 -f 'gff3'

However, I keep getting the following error:

Traceback (most recent call last):
File "/services/tools/panaroo/1.3.0/bin/panaroo-generate-gffs", line 10, in
sys.exit(main())
File "/services/tools/panaroo/1.3.0/lib/python3.10/site-packages/panaroo/post_run_gff_output.py", line 277, in main
parsed_gffs = parse_all_gffs(isolate_names, args.input_files, args.verbose)
File "/services/tools/panaroo/1.3.0/lib/python3.10/site-packages/panaroo/post_run_gff_output.py", line 84, in parse_all_gffs
input_file = next((s[1] for s in zip(base_input, input_list) if isolate_id == s[0]))
StopIteration

Any idea on how I should address it or what might be causing it?

Thanks in advance!

Best,
Sara

[gtonkinhill]

Hi,

I am afraid I have only tested the updating of GFFs on Prokka output. I hope to extend this to Bakta GFFs soon so I will leave this issue open as a feature request and update it when the functionality is added.

[sarapita]

Ah, I see thanks.

[vonMentzer-Group]

Can you run panaroo on bakta annotated genomes?

[gtonkinhill]

Yes, it should be possible using the --remove-invalid-genes option. We are hoping to enable panaroo to take advantage of some of the extra features of Bakta soon.

[limrp]

Yes, it should be possible using the --remove-invalid-genes option. We are hoping to enable panaroo to take advantage of some of the extra features of Bakta soon.

Hi!

I'm new to this field and I was using bakta to annotate my genomes. I wanted to use their gff3 files to run panaroo. I keep getting an error, but after using the --remove-invalid-genes parameter recommended here, it all worked!.

I wanted to ask if prokka gff3 files don't need the use of the --remove-invalid-genes parameter.

If so, why? What is the difference with the gff3 from Bakta.

Thank you so much for your amazing tool and for all your work!