Can't find the last locus in sheme

[Dong-Ning]

Hi

I ran the command for A. baumanii MLST: claMLST_create_database.py Ab_oxford_MLST_database AB_MLST_scheme.txt cpn60.fas gdhB.fas gltA.fas gpi.fas gyrB.fas recA.fas rpoD.fas

But keep getting the same error: Traceback (most recent call last): File "./claMLST_create_database.py", line 48, in raise Exception("Gene " + name + " not found in sheme\n"+ " ".join(header)) Exception: Gene rpoD not found in sheme ST gltA gyrB gdhB recA cpn60 gpi rpoD

I checked my scheme file and could not find the mistakes. Can you help me? Thanks. Here is the first a few lines of the scheme file:

ST gltA gyrB gdhB recA cpn60 gpi rpoD 1 1 1 1 1 1 1 6 2 2 2 2 1 1 2 7 3 1 1 1 1 2 1 4 4 1 12 3 2 2 7 3 5 1 3 3 2 2 3 1 6 1 4 3 2 2 3 3 7 3 3 3 2 3 3 8 8 4 4 4 4 4 5 9 9 1 3 3 2 2 6 8 10 1 4 3 2 2 7 3 11 4 11 6 1 7 8 6 12 8 4 4 4 4 5 5 13 1 7 8 9 1 4 14 14 1 10 8 6 1 4 14 15 1 12 11 10 1 9 4 16 10 12 4 11 11 9 5 17 1 12 12 11 4 10 3 18 10 13 4 11 12 11 5 19 1 14 3 2 2 9 3 20 1 15 13 12 4 12 2 21 1 12 3 2 2 9 3 22 1 15 13 12 4 12 37 23 1 1 1 1 1 28 10 24 1 1 22 1 4 20 16 25 1 1 41 6 23 31 26 26 1 10 36 22 20 4 24 27 1 51 1 36 1 98 6 28 1 12 3 2 2 35 4 29 1 12 3 28 2 29 4 30 1 12 3 29 2 34 4

[bvalot]

Hi,

Can you send me the schema you use or you download it from pubMLST?

Benoit

[Dong-Ning]

I uploaded the schema file here：

https://figshare.com/s/ebd2e118d0ae3a77e95d

I also tried other MLST schema including Klebsiella, Aeromonas... The same errors occurred. Thank you for your help.

[bvalot]

I'm sorry, but I can not access to you file.

You must be careful with pubmlst schema that contained some time extra columns.

[bvalot]

You can no simply import MLST scheme with the new version of pyMLST