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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
GNU General Public License v2.0
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ST not given even though for all loci an exact allele match is found #134

Closed NimroddeWit closed 12 months ago

NimroddeWit commented 1 year ago

Hi, thank you for developing this useful tool. However, when I use it, the tool does not output a sequence type (ST) even though for every locus it identifies an exact match. An example output is as follows:

[08:45:00] Found exact allele match IncI1.trbA-4 [08:45:00] Found exact allele match IncI1.ardA-1 [08:45:00] Found exact allele match IncI1.pilL-2 [08:45:00] Found exact allele match IncI1.sogS-1 [08:45:00] Found exact allele match IncI1.repI1-2 53C07-1-plasmid.fasta IncI1 - repI1(2) ardA(1) trbA(4) sogS(1) pilL(2) clonal_complex

It gives a hyphen instead of the correct ST, which in this case should be 3 since the combination of these alleles is present in the scheme.txt file. Do you know what causes this and how to fix it? If you need anything else, like files or command please let me know. Thanks in advance!

NimroddeWit commented 12 months ago

This issue is solved. For some reason the tool thought clonal_complex was a locus, even though in the GitHub page it says the tool ignores columns named clonal_complex. Anyways, it works, so I am glad!