ERROR 5

[macl...@gmail.com]

Hi there.

I am getting this error 5

This is unfortunate! An error occurred during the process of your job (job ID: 89281, job title: None).
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.

An I think I do have significant SNPs into my data. Here is the hrader:

CHR BP A1 A2 pval OR Beta SE N
19 2050823 T G 0.7124 0.0795 -0.0118 0.032 482730
4 116750182 T C 0.9752 0.4877 -5e-04 0.0177 482730
5 175804013 T C 0.3832 0.0687 0.0301 0.0346 482730
6 32342691 A C 0.359 0.4799 -0.0177 0.0192 480593
2 241813782 A G 0.2513 0.4753 -0.0202 0.0176 482730
7 150753769 A G 0.07719 0.9523 0.08 0.0453 27693

Could you please let me know what's going on?

Best,

Alejandro.

[Kyoko Watanabe]

Hi Alejandro,

I do not have access to your input file but I can check the top SNPs output file.

The most significant SNP had a P-value of 5.7e-5 which does not pass the threshold you set (5e-8).

If you have significant SNPs in your input file, they might have been filtered out for some reason.

Could you paste rows of significant (with P<5e-8) SNPs?

I will check why they were filtered out.

Best,

Kyoko

[macl...@gmail.com]

Hi Kyoko.

Thanks for the early reply. You guys are doing a great job.

I am doing some research through my data. I may was doing a wrong consideration.

Cheers,

Alejandro.