Please help job ID: 770831

[Wei Guo]

Hello Tanya,

I have tried submitting my job to FUMA five times, but unfortunately, I have not been able to get it to run successfully.

The input is PLINK output. I lowered the significance threshold to 1e-5, and the most significant P-value in my data is approximately 3e-6. However, I still received the following error message:

“This is unfortunate! An error occurred during the process of your SNP2GENE job (job ID: 770831, job title: EBV-mgs6).
ERROR:005”

Could you please help me figure out what might be causing this error and how I can get the job to run successfully?

Thank you very much for your help.

Best,
Wei

[Tanya Phung]

Hi Wei, 

The issue is that you specify a column for chromosome, a column for position, and a column for rsID but the combination of chr, pos, rsID you provided does not match with the database that FUMA uses or it matches with the external database like gnomad. 

For example, your top SNP is: 

chr     bp      non_effect_allele       effect_allele   rsID    p       beta
10      130485223       T       C       rs7082333       0.0007716       -0.09532

In the FUMA database, the snp rs7082333 has the following chromosome and position: 
10      130595233       10:130595233:G:T        rs7082333

This matches with the information on gnomad for example: https://gnomad.broadinstitute.org/variant/10-130595233-T-G?dataset=gnomad_r2_1

You should double-check your file to see why there is such discrepancies in the chr, pos, and rsID. If you believe that the rsID is correct, you can remove the chromosome and position columns prior to submitting, and FUMA will look up that information. Similarly, if your chr and pos are correct, you can remove the rsID column and let FUMA look up the rsID. 

Regardless, it is important to understand why your chr, pos, and rsID information do not match with standard database. 

Best,
Tanya