No mecA found (and no prediction) for MRSA strain

[juanu]

Hi!

First of all, thanks for making this amazing tool available! I'm seeing a strange result, and wondering if this could be a problem on my end. I'm running the script against this genome from NCBI, and I'm getting False for all sccmec types and mecA.

When I check the annotation and run amrfinder on the same isolate, it can detect the mecA gene. I wonder if I'm making a mistake when running the script? I'm using this command:

staphopia-sccmec.py --assembly GCF_000723965.1_MV8_genomic.fna

And this is the output

sample  I   II  III IV  V   VI  VII VIII    IX  meca    Ia  IIa IIb IIIa    IVa IVb IVc IVd IVg IVh
GCF_000723965.1_MV8_genomic False   False   False   False   False   False   False   False   False   False   False   False   False   False   False   False   False   False   False   False

and the result showing the hamming distances

sample  I   II  III IV  V   VI  VII VIII    IX  meca    Ia  IIa IIb IIIa    IVa IVb IVc IVd IVg IVh
cds_from_genomic    84  82  105 60  84  100 84  122 66  42  44  44  43  40  40  40  40  40  40  40

Any thoughts? Thank you!!!

[abourles]

Hi, I have the same problem, Any idea ? Thank you Alexandre