Calculate the cgMLST ChewBBaca

Calculate the cgMLST ChewBBaca


Hi, i’m trying to solve this exercise but I don’t understand were i’m wrong.
Starting from the assembly obtained in excercise point n. 4, calculate the cgMLST using “ChewBBaca”.
For chewBBaca use:
a) the parameter “-w /home” in order to specify the working directory for the docker
b) the parameter “–fr –cpu 2”
c) copy this folder /data/last_scheme_952019 in your home and use your local copy as schema
d) this prodigal training dataset /data/Listeria_monocytogenes.trn
Put the files “results_alleles.tsv” and “results_statistics.tsv” in the “typing” folder and delete the others files. Delete also the folder “last_scheme_952019” created.

This is my docker call:
docker run -v /data:/data -v ~:/home–py35_0 AlleleCall –cpu 2 –fr -i contigs.fasta -g ~/last_scheme_952019 -o ~/typing -v –ptf /data/Listeria_monocytogenes.trn

Thanks in advance for the support.




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