ERROR:0005 predifined SNPs

150 views
Skip to first unread message

Marianne Tuefferd

unread,
Jun 28, 2020, 4:00:13 PM6/28/20
to FUMA GWAS users
dear,

I am sorry, I submitted several jobs with predefined SNPs and got the same error message

"This is unfortunate! An error occurred during the process of your job (job ID: 87369, 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.

You can post questions, suggestions and bug reports on Google Forum: FUMA GWAS users"


My jobs are
87368
87259
I played with MAF and lead P-value but without success)

This is the header of my input file
RSID GENE CHR BP A1 TEST NMISS OR SE L95 U95 STAT P
rs10414271 --- 19 31958905 C ADD 181 0.1823 0.4659 0.07313 0.4542 -3.654 0.000259
rs11100042 --- 4 1.57E+08 C ADD 182 5.341 0.4044 2.418 11.8 4.143 3.42E-05

Any idea what could be wrong?

Thank you very much for your help!

cheers
Marianne

Kyoko Watanabe

unread,
Jul 11, 2020, 1:40:35 PM7/11/20
to FUMA GWAS users
Hi Marianne,

I'm sorry for my slow response.

If I got it correctly, you used the same input file as the pre-defined lead SNPs, correct?
For pre-defined lead SNPs, you have to have rsID, chr, and position in the first three columns in this order.
Could you re-create pre-defined lead SNPs file and try again?
You can use the same input for sumstats.

Best,
Kyoko
Reply all
Reply to author
Forward
0 new messages