When I try to use the command:
ariba pubmlstget 'Escherichia coli#2' out
I get an error indicating missing files: "Error('Cannot find file "' + infile + '" for gene ' + gene_name) ariba.pubmlst_ref_preparer.Error: Cannot find file "out/pubmlst_download/adk.tfa" for gene adk".
I think the problem might be due to the downloaded file (alleles_fasta.tmp) not being renamed individually for each gene properly, or not being split into separate .tfa files.
ARIBA version: 2.14.4