Is it possible to run roary without prokka output files?

[microDM]

I have 5 files for each organisms...

1. genome(.fna)
2. genome_feature(.gff)
3. proteins(.faa)
4. protein_features(.gpff)
5. genbank(.gbff)

I have tried to put all .gff files in one directory and run roary (with default param), it gives me error ----

Does the file contain the assembly as well as the annotation? BLAST Database error: No alias or index file found for protein database [/home/drdee/Desktop/roary_tutorial/strepto/gff/8WPpgYUMDG/output_contigs] in search path [/home/drdee/Desktop/roary_tutorial/strepto/gff::] Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.26/Encode.pm line 61. Use of uninitialized value in require at /usr/local/share/perl/5.26.1/File/Slurper.pm line 36.
Again, I have tried with .gpff files, it throws exception -------- does not look like GFF3 to me.

How can I run roary, without using prokka.

Note:- I had downloaded all files from NCBI.

[tseemann]

You need to combine the .gff and the .fna to make a gff3 file. Roary is failing because the GFF file has no genome sequences attached to it.

If you got your genomes from this place:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/563/515/GCA_002563515.1_ASM256351v1

You can do this:

cat genome.gff genome.fna > genome.gff3

Then just give roary all the .gff3 files. eg roary -v -p 16 *.gff3