PrepExternalSchema enhancement request about chewbbaca

[rfm-targa]

Greetings,

First, I think we can make some changes to PrepExternalSchema so that it runs considerably faster. After that, we can start exploring your suggestions and add an option to continue an interrupted process (just as AlleleCall has one).

Could you please tell us the total number of loci and the total number of alleles in the schema you are trying to adapt?

[eam12]

I'm using the Enterobase Salmonella cgMLST scheme which consists of 3002 loci and 4,718,005 alleles. I'm currently running PrepExternalSchema on 14 cores/48 GB. It's been running for about 24 hours now and has completed 2387/3002 loci. Thank you!

[rfm-targa]

Hello,

We have released a new version (2.1.0) with a new implementation for the PrepExternalSchema process. It is considerably faster than the previous version and outputs new files with relevant information about the schema that was adapted and sequences that the process excluded and why they were excluded. The process has new options so that schemas can be adapted based on different BSR, minimum sequence length and genetic code parameters. It is also possible to add new genes or alleles to a gene in the schema with this new implementation. You can read more about the new implementation in the Wiki, Section 1.4.
We used the new implementation to adapt the Enterobase Salmonella cgMLST schema with 3002 loci and >4M alleles in 30m37s (with 6 CPU threads and a maximum memory usage of 132MB).
We hope that it helps and appreciate any feedback that you can give us.