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AdmiralenOla / Scoary

Pan-genome wide association studies
GNU General Public License v3.0
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Scoary not accepting my traits.csv #80

Closed bkm23644 closed 4 years ago

bkm23644 commented 4 years ago

Hello.

I am trying to use Scoary to generate a GWAS from my Roary pan genome. However, the code insists that my traits.csv is incorrectly formatted, and then crashes. At first it complained that the box in the top-left should be blank (as per your instructions). However, the box was always blank. Now it is trying to tell me that the strain names are not the same from the Roary output. However, these names were taken straight from the output and placed into a list. The local bioinformatistician and I have been trying to fix this all day, and the problem persists.

The newest error is that the program reports that a strain is missing from the genes file despite no other program having this issue, and the strain in the traits list is straight from the gene file. I can manually find it within seconds by looking at the header for both files.

I have been googling this issue and it does not seem to be a common occurrence. Any advice for this problem?

bkm23644 commented 4 years ago

Apparently it has decided to start working now.