Error 006

[Chisom Soremekun]

Dear FUMA Team,

I am writing because of the error above.

I successfully ran fuma the first time (ID:624420) without any error.

Then i ran it again (ID: 624454) and only changed the ancestry from EUR to AFR (only thing that changed in both jobs)

From the previous messages in this group, i don't have NAs in my alleles nor any Pval ==0

What do you think is wrong?

I will appreciate your help.

[Tanya Phung]

Hi Chisom, 

The problematic variant in your file is 15:45744387:G:T. Can you double-check if this variant has the same number of columns as other variants? 

The reason why it worked with the EUR population is because this variant was not considered because it is not found in the EUR reference database that FUMA uses. 

Whereas for the AFR population, this variant is included in the AFR population database that FUMA uses. There is a formatting issue with this variant and that's why there is an error. 

If you can't figure out what the issue is, you can send your input file to fuma....@gmail.com.

Best,
Tanya

[Tanya Phung]

Hi Chisom, 

Thank you for sending your input gwas file. It appears that 2 variants with the same chr:pos:allele1:allele2 have 2 different rsID. This causes the error: 

zless fuma_egfr_ma_filtered_rsID.txt.gz | awk '$2==15{print}' | grep 45744387
rs534441254     15      45744387        T       G       -0.0382 0.0045  185849  2.757e-17
rs2486281       15      45744387        T       G       -0.0382 0.0045  185849  2.757e-17

I removed the line   rs534441254     15      45744387        T       G       -0.0382 0.0045  185849  2.757e-17 and ran FUMA with a file with just chromosome 15 (for testing) and it was successful. 

There might be other places where this occurs (same chr:pos:allele1:allele2) but with different rsID so you might need to double-check. 

Best,
Tanya