Subject: Issue with Plotting Regional Plots for Genomic Risk Loci in GWAS SNP2GENE (Job ID: 608706)

[Logic Xie]

Dear FUMA Platform Administrators,

I am writing to report an issue I've encountered while performing a GWAS SNP2GENE analysis on the FUMA platform. My Job ID is 608706.

I am trying to generate "Regional Plots" for the identified "Genomic risk loci". However, out of multiple significant loci, only one plot can be generated successfully. When I click on any of the other loci to plot, the visualization fails to appear, and I receive the following error message:

Could not parse result of annotPlot/getData data SyntaxError: Unexpected end of JSON input

I am not sure what is causing this error, especially since one of the loci works perfectly. I have confirmed that the Ensembl version for this job is set to v102.

Could you please look into this issue? Any assistance you could provide in troubleshooting this problem would be greatly appreciated.

Thank you for your time and help.

Best regards,

Logic Xie

[Tanya Phung]

Hi Logic, 

The problem was that when annotPlot script is attempting to run, it is using a file called `all.txt.gz` which is generated from the input summary statistics (see: https://github.com/vufuma/FUMA-webapp/blob/master/scripts/annotPlot/annotPlot.py#L201). However, for your job, in this file, there is no data for chr1 position 43814864 (which is the first row in your genomic risk loci). In this file for your job, chr1 starts at position 100000012

zless all.txt.gz | head
1       100000012       0.2208
1       100000827       0.5737
1       100000843       0.2759
1       100001138       0.9604
1       100001201       0.324
1       100002490       0.3067
1       100002713       0.1094
1       100002714       0.3067
1       100002991       0.1096
1       100003204       0.3244

The same thing with the other genomic risk loci, except for #3 which has position 171505994. 

So I think that there was an issue with generating this file from your input summary statistics. I don't have access to the file you submitted, so if you want me to take a look further, please send your input to fuma....@gmail.com. 

Best,
Tanya