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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Invalid --schemes #101

Open nwalas opened 3 years ago

nwalas commented 3 years ago

Hi!

I am looking for help with the --legacy --schemes? MLST seems to only recognize certain schemes from the --list.

For example when I do:

% mlst --scheme neisseria *.fasta > output_mlst.txt

I get a results but when I try:

mlst --legacy --scheme camplobacter *.fasta

I get this error in return: Invalid --scheme 'camplobacter'. Check using --list

However, I checked using --list and both these schemes are listed. I feel like I'm missing something... any help would be appreciated since I hope to run these on PhylOViz and I think they need to be in the specific format.

Thanks a bunch! Niko

(also operating on Mac IOS catalina, terminal)

sbaines commented 3 years ago

Hi Niko

Noticed that there is a typo in the scheme name - "camplobacter" should be "campylobacter". Would explain the invalid --scheme error. Hope this fixes your issue.

Sarah