ERROR: 5 (Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified)

137 views
Skip to first unread message

Wisdom A Akurugu

unread,
Jun 7, 2023, 6:14:17 PM6/7/23
to FUMA GWAS users
Hi FUMA Managers

I submitted a file for analysis. I have read all the comments on this forum related to it and made all the corrections but it has not resolved my problem.
Job ID:258715
My rsIDs and positions match that of dbSNP.

I will be grateful for your assistance

Regards
Wisdom

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

unread,
Jun 8, 2023, 6:00:51 AM6/8/23
to FUMA GWAS users
Hi Widsom, 

Based on the logs, it looks like there were only two variants correctly processed by FUMA and neither of those variants were input lead SNPs. I am guessing your file is not formatted correctly causing lots of variants to be lost. Below is the information for the log file. 

1 SNPs in chromosome 4
Input lead SNP rs113631626 does not exists in input gwas file
Start chromosome 11 ...
1 SNPs in chromosome 11
Input lead SNP rs373351583 does not exists in input gwas file

Can you share the first few lines of your input file?

Cheers,
Doug

Wisdom A Akurugu

unread,
Jun 8, 2023, 6:10:51 AM6/8/23
to FUMA GWAS users
Hi Doug,

Thanks for the reply.
I had intentionally made the input file to contain only 2 variants and the leads file to contain the same 2 varints as below:
Input:

CHR
BP P A1 A2 BETA SE

4 106156140 5.49E-08 A G 0.1146 0.01894
11
117782607 1.50E-07 T C 0.0871 0.01501

Leads:

rsID
CHR BP P A1 A2 BETA SE

rs113631626 4 106156140 5.49E-08 A G 0.1146 0.01894
rs373351583
11 117782607 1.50E-07 T C 0.0871 0.01501

There are many of them that do not get annotated and I had to pick just these 2 variants to try and see what the problem is.
I will be happy for your timely reply

Regards
Wisdom

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

unread,
Jun 8, 2023, 6:18:42 AM6/8/23
to FUMA GWAS users
Hi Wisdom, 
rs113631626 is not in the reference panel, likely because it is very rare https://www.ncbi.nlm.nih.gov/snp/rs113631626 

rs373351583 in our data does not match the position you gave (11:117782606:C:T rs369575036) but your position does match the dbSNP data https://www.ncbi.nlm.nih.gov/snp/?term=rs373351583. I am not sure why our reference data has the wrong position for this SNP. I will look into this but it may be due to an update in the new version of dbSNP that is not reflected in our data.

Cheers,
Doug

Wisdom A Akurugu

unread,
Jun 8, 2023, 6:26:36 AM6/8/23
to FUMA GWAS users
Hi Doug,
Thanks for the quick response. I have really be stuck with this issue for some weeks.
I assume that most of my variants that were dropped is probably the rarity/missing variants in your panel relative to mine or the position shift.
Will it be fine with you that I compile them from by side and send to you as an email to crosscheck for the compatibility? That could be affecting a number of other users.
Please let me know.

Regards
Wisdom

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

unread,
Jun 8, 2023, 6:31:00 AM6/8/23
to FUMA GWAS users
Hi Wisdom, 

You can download the reference panel SNP list here https://fuma.ctglab.nl/tutorial#refpanel and compare your input data to our reference panel.

Cheers,
Doug

Wisdom A Akurugu

unread,
Jun 8, 2023, 6:50:39 AM6/8/23
to FUMA GWAS users
Thank Doug. I will compare my variants and let you know

Wisdom A Akurugu

unread,
Jun 9, 2023, 6:50:34 AM6/9/23
to FUMA GWAS users
Hi Doug,
I have gone through your reference and found that were a number of variants in my data with the correct dbSNP IDs and chrom positions but not in your reference. Are they considered rare variants from your side?


rsID
                     CHR              BP                   dbSNP

rs367763945
     11             48285879       11:48285879 (GRCh37)

rs769016513
     11             48286074       11:48286074 (GRCh37)

rs1257441095
   11             48510981       11:48510981 (GRCh37)

rs369084263
     13             103268814     13:103268814 (GRCh37)

rs565127215
     5                102509631     5:102509631 (GRCh37)

rs113631626
     4               106156140      4:106156140 (GRCh37)

rs149086811***
    8                3889521          8:3889521 (GRCh37)

rs373351583
    11              117782607      11:117782607 (GRCh37)


Is possible to include them in your reference?
The variant asterisked does not have an rsID in your reference but it is a variant.

Kind regards
Wisdom

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

unread,
Jun 9, 2023, 9:13:07 AM6/9/23
to FUMA GWAS users
Hi Wisdom, 

Unfortunately not, the data we have is from the 1000 genomes project and we cannot add variants that are not present in this data. We need these variants to be present in the people included in the 1000 genomes data so we can get linkage disequilibrium estimates for them. Unfortunately, the variants not present in the reference panel will be ignored when creating genomic risk loci in FUMA.

I am not sure why these variants are not present in the people included in the 1000 genomes data, them being rare is one possibility. 

Cheers,
Doug

Rui Marçalo

unread,
Aug 29, 2023, 6:57:58 AM8/29/23
to FUMA GWAS users
Hi Doug,

I am also getting error 5 (jobID: 276931) on FUMA.
I have a significant SNP in the imput file (p=4.778e-8) however it is not being recognized by FUMA.
I have checked the that the variant is present in the 1000G (EUR) project and that it has the same position (5167688) and effect allele (GTT) as in my input file.
I have set the MAF threshold parameter to 0, so that should not be the reason.
I have also tried providing the rsID (both the current and the one in the 1000G project (which has been deprecated)) but the error persisted.
Could you please give me some guidance on how to solve this? 

7 118504249:A:C 118504249 C ADD 598 3.271 4.536 6.934e-06
7 118510105:GA:G 118510105 G ADD 598 3.271 4.536 6.934e-06
7 118512118:A:C 118512118 C ADD 598 3.209 4.486 8.726e-06
8 5165998:C:T 5165998 C ADD 598 3.195 4.661 3.894e-06
8 5166336:T:C 5166336 T ADD 598 3.195 4.661 3.894e-06
8 5166353:T:C 5166353 T ADD 598 3.195 4.661 3.894e-06
8 5166615:A:G 5166615 A ADD 598 3.215 4.69 3.391e-06
8 5166623:T:C 5166623 T ADD 598 3.144 4.585 5.551e-06
8 5167168:A:T 5167168 A ADD 598 3.195 4.661 3.894e-06
8 5167333:G:A 5167333 G ADD 598 3.195 4.661 3.894e-06
8 5167688:GT:G 5167688 GT ADD 598 3.195 4.661 3.894e-06
8 5167688:GT:GTT 5167688 GTT ADD 598 4.174 5.531 4.778e-08
8 5168044:T:A 5168044 T ADD 598 3.195 4.661 3.894e-06
8 5168886:G:A 5168886 G ADD 598 3.101 4.517 7.563e-06

Thank you
Rui

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

unread,
Sep 11, 2023, 5:12:52 AM9/11/23
to FUMA GWAS users
Hi Rui,

Can you try adding a column to your input data that specifies the non-effect allele? Here it would be GT.

Cheers,
Doug

Rui Marçalo

unread,
Sep 15, 2023, 12:58:08 PM9/15/23
to FUMA GWAS users
Hi Doug,

I am having trouble finding a way to test your suggestion.
I can't figure out how to run the GWAS using PLINK and have the non-effect allele in the output file.

Do you have any suggestion on how to do this?
Maybe it is very simple and I am just not finding it.

Thanks
Rui

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

unread,
Sep 19, 2023, 5:53:37 AM9/19/23
to FUMA GWAS users
Hi Rui,

You can merge your summary statistics file with the plink .bim file and select the allele that is not the tested allele from the .bim file. I would do this using R but there are many ways to do this.

Cheers,
Doug
Reply all
Reply to author
Forward
0 new messages