Error:005, 3 jobs

[Miquel Gallardo Penas]

Good morning, I have uploaded some jobs to FUMA and it has returned error 005 stating that it has not found any significant SNPs (threshold e-8), however there are significant SNPs in the job data and I don't know what is really happening. I'm leaving the IDs here in case you can take a look.
ID: 468798, ID: 468802, ID: 468803. 

Thank you very much.

[fuma.ctglab]

Dear Miquel, 

ID: 468798

In this job, 1 SNP has p value < 5e-8: 
chr     bp      non_effect_allele       effect_allele   rsID    p       beta    se      N
5       141841444       G       T       rs2974701       2.38926e-08     -28.2941        5.06957 234

However, the position of this SNP seems to be incorrect. 
In our database,  rs2974701 is associated with chr5 position 141221009.

Please double check. 

ID: 468802

In this job, 1 SNP has p value < 5e-8: 
chr     bp      non_effect_allele       effect_allele   rsID    p       beta    se      N
7       3943268 C       T       rs73038416      3.55169e-08     -0.663862       0.120444        251

However, the position of this SNP seems to be incorrect. 
In our database,  rs73038416 is associated with chr7 position 3982900. 

Please double check. 

ID: 468803

In this job, 1 SNP has p value < 5e-8: 
chr     bp      non_effect_allele       effect_allele   rsID    p       beta    se      N
7       155923947       C       G       rs7789601       3.53774e-08     0.703946        0.1277  234

However, the position of this SNP seems to be incorrect. 
In our database,  rs7789601is associated with chr7 position 155716641. 

Please double check. 

Please double-check to make sure that your coordinates are in hg19. 

Thank you,
FUMA

[wenhui liu]

Good afternoon. I have uploaded some work to fua, and it returned error 005, indicating that it did not find any important SNPS (threshold e-8), but there were important SNPS in the work data. I tried to relax the threshold and lower the MAF, but it was still the same. I left my ID  here. You can have a look.


Id: 690424, Id: 690422, Id: 468803.

Thank you very much.

[Tanya Phung]

Hello, 

All of these jobs (Id: 690424, Id: 690422, Id: 468803) have been deleted by the user from our database so I can't check what were wrong with them. 

Best,
Tanya

[Cephas Akpabio]

Hello,

I keep getting Error:005, but once I switch to 5e-6 or 5e-7, the job runs. I also got an email that there's no significant SNP, whereas there's one at 4.94e-08.

I did liftOver from v38 to v37.

Job IDs: 698349 and 699589

Thank you,

Best regards,

Cephas

[Tanya Phung]

Hi Cephas, 

In the job 698349 you selected the 1000 genome AFR population. The snp with the p value 4.94288e-08 has the variant ID 20:36208013:A:G. This variant does not exist in the 1000 genome AFR population that is on FUMA.

This variant does not seem to exist in gnomad either (https://gnomad.broadinstitute.org/variant/20-36208013-A-G?dataset=gnomad_r2_1). 

Similar issue in the other job 699589, which is that the variants with the top p values do not exist in the database. 

Best,
Tanya