Job ID: 468616. ERROR:005

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Nolan Wang

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Apr 1, 2024, 9:34:33 PMApr 1
to FUMA GWAS users
Dear FUMA Support,

I am reaching out regarding an issue I have encountered with job ID 468616, which is displaying ERROR:005. Upon review, I have confirmed the presence of SNP P-values<1e-5 in my data. Could you please guide me to help troubleshoot?

Thank you.

Best regards
Nolan

fuma.ctglab

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Apr 2, 2024, 5:50:14 AMApr 2
to FUMA GWAS users
Dear Nolan, 

According to the tutorial, the threshold is 5e-8: 
Capture.PNG

This is the list of your topSNPs:

From FUMA output topSNPs, I can see that this is the list of the p values from your top SNPs:
 3.63377e-06 4.08535e-06 4.27768e-06 6.73649e-06 7.12295e-06 7.86370e-06 7.97938e-06 7.97939e-06 8.49545e-06 8.62220e-06
As you can see,  10^-6 is greater than 10^-8. Thus, these snps are not considered passing the threshold. 

Thank you,
FUMA

刘昭君

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May 19, 2024, 9:12:10 AM (3 days ago) May 19
to FUMA GWAS users
Dear FUMA Support,

May I ask if error: 005 occurs because no leadsnp smaller than 1e-8 is found?

Thank you.

Best regards
June

Tanya Phung

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May 20, 2024, 3:53:51 PM (2 days ago) May 20
to FUMA GWAS users
Dear June, 

Please check the post here: https://groups.google.com/g/fuma-gwas-users/c/JdxuqR4ihS4

I also copied it here:
ERROR 005:

Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified.

This error can occur when no candidate SNPs are identified. Note that indels are included in the FUMA from v1.3.0 but both alleles need to match exactly with the selected reference panel.

MHC region is also excluded by default.

  • 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.

  • 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.

Recently, there have been cases where there are candidate SNPs where pvalue <5e-8. However, the variant id indicated that it was in GRCh38 and didn't match with our database. An example of this can be seen here: https://groups.google.com/g/fuma-gwas-users/c/coB3sLR6wUM/m/SvP84zpMAAAJ

Best,
Tanya



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