ERROR 005

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TMU Rizki Amalia

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Apr 8, 2024, 3:55:40 AMApr 8
to FUMA GWAS users
Dear FUMA team,
Herewith, I would like to report the ERROR that I encountered while trying to submit my jobs for SNP2GENE. I already had several attempts such as change my gwas summary stat into txt file with columns were set according to tutorial but I did not work. My gwas build in GRCh 38 however when I tried to tick the GRCh 38 option it was also could not be done. What should I do? any assistance regarding this issue is appreciated.
Note : job ID 469097 469100 469103 469110 470645
Thank you. 
Rizki Amalia

fuma.ctglab

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Apr 8, 2024, 5:37:10 AMApr 8
to FUMA GWAS users
Dear Rizki, 

You can use UCSC Liftover in order to convert between different genome assemblies: https://genome.ucsc.edu/cgi-bin/hgLiftOver
FUMA utilized hg19 coordinates. Therefore, even though there are significant SNPs in your file, you encountered ERROR 005 because the chromosome position do not match with our reference database. This issue should be fixed after converting your coordinates to hg19/GRCh37. 

Thank you,
FUMA

Alejandro Martinez Carrasco

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Apr 17, 2024, 7:06:43 AMApr 17
to FUMA GWAS users
Hi,

I am encountering the same error.
In FUMA there is the option of specifying your GWAS sum stats are in hg38 build.
Is this already supported in FUMA? I try to select this option, but I do not seem to be able to click it even though I provide all the necessary input fields.

Thank you

fuma.ctglab

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Apr 17, 2024, 8:33:02 AMApr 17
to FUMA GWAS users
The GRCh38 feature was in beta testing and it resulted in a lot of issues. Due to staff shortage, we decided to pause this feature for now. 

For now, please submit your summary statistics in hg19 format, and please follow the tutorial if there's additional issues. 

Thank you for understanding,
FUMA
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