ERROR:5

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Chengguang Zou

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Sep 14, 2023, 6:18:52 AM9/14/23
to FUMA GWAS users
I was running FUMA today and got an error information described below:
This is unfortunate! An error occurred during the process of your job (job ID: 280718, job title: gingivitis).
ERROR: 5 (Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified)
This error can occur when no candidate SNPs were identified. Note that indels are included in the FUMA from v1.3.0 but both alleles need to match exactly with selected reference panel. MHC region is also excluded by default. 1. If there is no significant hit at your defined P-value cutoff for lead SNPs and GWAS tagged SNPs, you can try to use a less stringent P-value threshold or provide predefined lead SNPs. 2. If there are significant SNPs with very low minor allele frequency, try decreasing MAF threshold (default 0.01). Manhattan plots and significant top 10 SNPs in your input file are available from SNP2GENE.
The p value of all SNPs in my input data range from 5e-08 to 1e-05, and I have already set the option Maximum P-value of lead SNPs to 1e-05 in the submission page,  but I still got no significant SNPs. I wonder why that happens and how to solve it.
Following picture is the information of SNPs I inputed today.
屏幕截图 2023-09-14 181648.png

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

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Sep 14, 2023, 8:04:28 AM9/14/23
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Hi,

Are these variants present in the manhattan plot? If not, then there is likely something going wrong with the data being parsed. 
If they are, then it is likely that these variants are not in your selected reference panel. You can download a list of variants in the reference panel here https://fuma.ctglab.nl/tutorial#refpanel
Can you check whether the variants below your threshold are present in your selected reference panel? If they are present, can you check that the information in your data matches the information in the reference panel (chr, position, alleles, and rsID)?

Cheers,
Doug

Chengguang Zou

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Sep 15, 2023, 1:51:14 PM9/15/23
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Hello Doug,

I have already checked the reference panel you sent me, and compared the information of my selected SNPs between the reference panel and my dataset. I found that the values in "A1" column and "A2" column is reversed. It seems that the denifition of Effect Allele is different between your reference panel and my dataset. I believe this is the core of the problem. So what should I do next? Should I swap these two columns to make their values match those in your reference panel?

Thank you for your time and assistance.
Chengguang Zou

Chengguang Zou

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Sep 15, 2023, 2:09:34 PM9/15/23
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Hello Doug,

I have another problem just now, in addition to A1 and A2, the Positions of SNPs between my dataset and reference panel are also different. I wonder what's the cause of this difference. And do you think is it reasonable to change the Positions in my dataset to make them match those in the reference panel?

I'm grateful for your support.
Chengguang Zou

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

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Sep 19, 2023, 5:58:11 AM9/19/23
to FUMA GWAS users
Hello, 

The order of the alleles will not make a difference as long as the two alleles for each variant match. So it can be the a1 allele in your dataset but the a2 in the reference. 

It is likely that your data is on a different build, FUMA used GRCh37 as a build whereas your data is likely GRCh38. Can you check your build? If your data is GRCh38, you can select the following option on the submission page "Input is build GRCh38".

Cheers,
Doug

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