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Error in generating PubMLST database with ariba pubmlstget: Missing gene-specific .tfa files #344

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jimmlucas opened this issue Nov 8, 2024 · 0 comments

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@jimmlucas
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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

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