ERROR:magma

[Chiemela Steve]

Hello FUMA team, 

I have tried to run a few jobs with the IDs below. And I am getting an "ERROR:magma"

478314

478313

478310

476760

[fuma.ctglab]

Dear Chiemela, 

Thank you for your patience. 

I only checked job 478314 but I suspect that the problem is the same for the other jobs. 

The problem is that in your input GWAS summary statistics, for some variants (rows), there are missing rsID. 
For example, in the attached image, the row circled in red has an rsID while the row circled in blue did not have an rsID. 

This is important because with missing data like this, FUMA would incorrectly determine the columns for the p value. 

What you can try is: 

1. Remove the SNP column: you can name SNP to something else other than SNP, snpid, markername, rsID so that FUMA won't automatically detect that rsID column is present. In this case, FUMA will use dbSNP to match chr and pos to rsID

or

2. Find the rows with the missing rsID and fill them yourself by looking up the rsid based on chr and pos

Before submitting, please re-read the tutorial (https://fuma.ctglab.nl/tutorial#snp2gene) to make sure that for all the required columns, there is no missing data. 

Please remember to follow the instructions so that it works. 
Thank you,
FUMA