Error regional plot: Could not parse result of annotPlot/getGenes data SyntaxError

94 views
Skip to first unread message

Nils Horstink

unread,
Sep 12, 2022, 10:11:49 AM9/12/22
to FUMA GWAS users
Hi,

I noticed that the 'Regional plot with annotation' is not working.
Multiple jobs ran successfully (e.g. ID:204485) and everything seems fine. However, when I try to look at the 'Regional plot with annotation' I get an error:

Could not parse result of annotPlot/getGenes data
SyntaxError: Unexpected end of JSON input


I get this error for all my jobs. Now I am wondering whether this an issue from my side or a server error? 

Thanks in advance!


Best,
Nils

rajya grg

unread,
Sep 19, 2022, 11:52:59 PM9/19/22
to FUMA GWAS users
Hi, 
I am having similar issues. I see this problem with my previous jobs as well (there was no such issue in the past while plotting but i get the error for all my jobs. 
Do let me know if you solved the error.

Thank you
P
Message has been deleted

Marijn Schipper

unread,
Sep 21, 2022, 8:27:48 AM9/21/22
to FUMA GWAS users
Hi Nils and P, 

This relates to the v85 ensemble genes not being available in biomart, rerunning the analysis with the most current ensemble version selected in FUMA would resolve the issue.
Alternatively you could let me know which job ID's you would like to see fixed, so I can update the version no used for those jobs on the server side.

Cheers,

Marijn

Op dinsdag 20 september 2022 om 05:52:59 UTC+2 schreef rajya grg:

Junhao Wen

unread,
Jul 17, 2023, 12:19:37 PM7/17/23
to FUMA GWAS users
HI Marjin, 

It seems that the problem has come back again these days (the version of v85 ensemble genes); one of my job ID is: 264539

Can we solve this issue?

Thanks for this wonderful tool

Junhao Wen

unread,
Jul 17, 2023, 12:20:51 PM7/17/23
to FUMA GWAS users
Another post with the same problem: https://groups.google.com/g/fuma-gwas-users/c/zHxJ-Fz7O9w/m/qZtHbM1pBQAJ

On Wednesday, 21 September 2022 at 08:27:48 UTC-4 Marijn Schipper wrote:

Marijn Schipper

unread,
Jul 18, 2023, 5:24:40 AM7/18/23
to FUMA GWAS users
Hi Junhao, 
Yes, Ensemble/biomart has stopped support for v85.
Resubmitting your jobs with a newer version will solve this issue.
We will be working on a fix, but it might be a while before the issue is resolved entirely.
Best,

Marijn

Op maandag 17 juli 2023 om 18:20:51 UTC+2 schreef Junhao Wen:

Ming-Ju Tsai

unread,
Jul 18, 2023, 9:31:30 AM7/18/23
to FUMA GWAS users
Hi,

I received the same error message on my jobs (ID: 267861 and 267751) and I used Ensemble v92. Could you please let me know how can I fix this issue?

Thanks for the amazing platform.

Junhao Wen

unread,
Jul 18, 2023, 9:22:36 PM7/18/23
to FUMA GWAS users
Sorry for my naive question. When you mentioned a newer version, can you indicate where I can indicate the version of Ensemble/biomart? In the regional plot, I did not see an option:


Did you mean that I should resubmit the job? Even for submitting the job, I did not see an option to choose the version of Ensemble for gene mapping.

Thnanks 

Junhao Wen

unread,
Jul 18, 2023, 9:29:39 PM7/18/23
to FUMA GWAS users
Here is the version of Ensemble for the job that I had an issue with:

FUMA = v1.5.4
ensembl = v92

From the software log: https://fuma.ctglab.nl/updates

It seems that you have already fixed this issue:

27 July 2022
v1.4.0

Major update 1: Ensembl v85 genes have been removed from the job options for SNP2GENE and GENE2FUNC. v85 is no longer available in the BioMart databases."

Marijn Schipper

unread,
Jul 19, 2023, 3:54:37 AM7/19/23
to FUMA GWAS users
Hi all,

I can indeed confirm that this error is not caused by ensembl versions.
We are currently looking into the problem and hope to resolve this issue quickly.
I will keep you up to date.

Cheers,
Marijn

Op woensdag 19 juli 2023 om 03:29:39 UTC+2 schreef Junhao Wen:

Junhao Wen

unread,
Jul 21, 2023, 11:51:13 AM7/21/23
to FUMA GWAS users
Thanks. Please keep us posted if you have solved the issue. It seems that the FUMA platform does not work for new job submissions now.

Cheers

Junhao Wen

unread,
Jul 23, 2023, 10:08:59 PM7/23/23
to FUMA GWAS users
Not sure if this is relevant to the same error here, but now when I submitted a new job, it always returns me the error: 

ERROR:001
Not available

Not available


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

unread,
Jul 24, 2023, 3:34:51 AM7/24/23
to FUMA GWAS users
Hello,

Can your share the jobID for one of these jobs? I can then investigate the error.

Cheers,
Doug

Junhao Wen

unread,
Jul 24, 2023, 7:59:50 AM7/24/23
to FUMA GWAS users
Sorry, I made a stupid error on the column name for my GWAS summary stats. FUMA works. 

The regional plot functionality still has the same issues (ID:264539):
"Could not parse result of annotPlot/getGenes data
SyntaxError: Unexpected end of JSON input"

I think you are working on this now.

Thanks again for this wonderful platform!

Cheers

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

unread,
Jul 26, 2023, 9:40:37 AM7/26/23
to FUMA GWAS users
Hi all, 

I updated FUMA to fix this problem by adding new Ensembl versions (v102 and v110) and removing the old version v92. Please let me know if you run into any problems.

Cheers,
Doug

Junhao Wen

unread,
Jul 26, 2023, 1:01:11 PM7/26/23
to FUMA GWAS users
Confirmation from me: all work perfectly now, even for the old jobs for the regional plot!

Thank you very much, Doug!

Cheers

Reply all
Reply to author
Forward
0 new messages