missing results in the roary outputs

sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis

http://sanger-pathogens.github.io/Roary

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missing results in the roary outputs #534

Open shafi-OZ opened 3 years ago

shafi-OZ commented 3 years ago

Hi I have about 740 gff files that I produce through prokka. I copied them all into a new folder and run the following roary command, but it only give me 630 isolates results and the other files were not included in the final roary output. Wondering if there is any max limit for running roary. Thank you in advance!

roary -f roary_output2 -e -n -r *.gff

Regards Shafi

aweri commented 2 years ago

I have the same issue. did you find a solution, or can anyone else help?

erinyoung commented 2 years ago

I have also encountered roary dropping samples. The first time that I noticed, I was only running roary with six samples.

I reran my command.

roary \
        -p 20 \
        -f roary \
        -e -n \
        *.gff