Not getting the roary output files

[Yossma28]

I'm working on the pan genome analysis of rhizobium bacteria. For that I've taken a dataset of 1007 genomes. The pipeline works fine only when I run it for few datasets like 3-4. But when I run it for all the 1007 genomes it's not giving me two important output files. 1- The number of core and accessory genes output. 2- The alignment file.
I'm assuming the issue is with the large number of dataset. Is there any way to fix this issue. Can I use some other pipeline which can work with such large dataset or is there any way to work with the same pipeline Maybe by splitting the dataset into 10 parts containing 100 genomes each and then running the pipeline and presenting results as a collection.
Thank you

[yutmas]

Hi !
Sorry if you have already tried this. I found this FAQ on Roary website, would it help?

Q. No core alignment is produced and theres an error about too many clusters?

A. By default if there are more than 50,000 clusters, Roary will not create the core alignment. In virtually every case, having more than 50,000 clusters is a result of mixing different unrelated species and you should go back and QC your samples. In some limited cases (e.g. E. coli) you can increase the maximum number of allowed clusters by using the –g parameter (-g 60000). More clusters will mean a longer running time, and a lot more RAM usage.