Error when reading GFF files from GenBank

Hi,

I go this issue when trying to process a bunch of genome assemblies including some that where directly downloaded from the NCBI.

It appears that panaroo cannot digest GFF files coming from GenBank as I get this error:

Traceback (most recent call last):
  File "/usr/local/bin/panaroo", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/site-packages/panaroo/__main__.py", line 273, in main
    args.n_cpu)
  File "/usr/local/lib/python3.7/site-packages/panaroo/prokka.py", line 229, in process_prokka_input
    raise RuntimeError("Error reading prokka input!")
RuntimeError: Error reading prokka input!

(the error was actually a bit longer when including the report of the error handling by master process, but i don’t think that’s relevant here)

this was obtained using panaroo version 1.2.3 (from the module installed on the Sanger farm).

One example of GFF file that fails is to be found in this assembly: https://www.ncbi.nlm.nih.gov/assembly/GCA_009746685.1

Do you have any suggestion of how this could be addressed? Is Panaroo only expecting GFF files as produced by Prokka? I used the the GenBank version of the assembly; do you think it would work better if using the RefSeq annotation?

Thank you in advance for the help.

Florent