ERROR:003 - problem with P-value column

Sam Jones

unread,

Nov 13, 2020, 8:10:08 AM11/13/20

to FUMA GWAS users

Hey!

I've used FUMA GWAS many times before and have never come across this error. I have a summary stats file that fails with ERROR:003 no matter what I do. The explanation from the email notification is: "Error during SNPs filtering for Manhattan plot. This error can occur if the p-value column is mistakenly labelled wrong. Please make sure your input file have sufficient column names." The job ID is 104236.

As far as I can tell, I've entered the column names exactly as they are in the file but this hasn't fixed the issue. The first 10 lines of the file are screenshotted below.

The only things I can think of is that 1) the variant IDs that are CHR:POS_A1_A2 are causing issues or 2) there are too many decimal places in the numbers (my previous analyses have not had values to so many decimals places). Could those be causing problems?

Any help would be appreciated!

Sam

Sam Jones

unread,

Nov 13, 2020, 8:29:13 AM11/13/20

to FUMA GWAS users

The image didn't attach properly... attaching now

d.p.wi...@vu.nl

unread,

Nov 13, 2020, 8:40:35 AM11/13/20

to FUMA GWAS users

Hi Sam,

It looks like you have this value in your BP column (9e+05). Can you make sure all the BP values are integers? It will also help to remove you rsid column or change the column name to something else.