Subject: Cell Type analysis failed with ERROR despite receiving both completion and failure emails

[qinglin zhang]

Dear FUMA team,

I am trying to run a Cell Type analysis in FUMA using a MAGMA gene analysis output file (*.genes.raw) generated locally. However, the job status on the FUMA website is shown as:

ERROR:Undefined

The job information is:

• Job ID: 738768
• Job name: ASD
• Submission time: 2026-05-28 03:12:43
• Module: Cell Type analysis
• Input file: MAGMA *.genes.raw

Interestingly, for the same job, I received two email notifications from FUMA: one email indicated that the job had completed successfully, while another email indicated that the job had failed. On the website, the final displayed status is still ERROR:Undefined.

I also tried opening the job and submitting/checking the results using a different browser, but the same issue persisted. Therefore, this does not seem to be a browser-specific display problem.

My understanding is that the Cell Type module accepts MAGMA gene-level association results, so I uploaded the *.genes.raw file rather than SNP-level GWAS summary statistics. Could you please help me confirm what usually causes this ERROR:Undefined status in the Cell Type module, especially when both completion and failure emails are sent for the same job?

Thank you very much for your help.

Best regards,
Qinglin Zhang

[Tanya Phung]

Hi Qinglin, 

I do not know why there were 2 emails sent.

I inspected this job and it finished successfully. I had therefore changed the status of this job to successful and you should be able to view the results:

Your understanding of the Celltype module that you described is correct. In addition, I also wanted to add a few things: 
- You select 1 dataset, and also step 2 and 3. 
- Step 3 is not appropriate here because step 3 is cross datasets conditional analyses. Because you selected 1 dataset, step 3 is not appropriate. 

- Step 2 is only perform when there are more than 1 significant cell type per dataset. As you can see above, there is only 1 significant cell type. Therefore, step 2 was not performed. 

I hope this helps,
Tanya

[qinglin zhang]

Dear Tanya,

Thank you very much for your help. I appreciate you inspecting the previous job and manually changing the status. The issue for that job has been partially resolved, and I am now able to understand the result better based on your explanation.

I also appreciate your clarification regarding the Cell Type module. I now understand that Step 3 is not appropriate when only one dataset is selected, since it is intended for cross-dataset conditional analyses. I also understand that Step 2 is only performed when there is more than one significant cell type within a dataset.

However, I encountered the same issue again after submitting another Cell Type analysis job. This new job also showed ERROR:Undefined on the FUMA website, and I again received both a completion email and a failure email for the same job.

The new job information is:

Job ID: 739669
Job name: social
Submission time: 2026-05-30 03:07:45
Module: Cell Type analysis
Input file: *MAGMA .genes.raw

Like the previous job, I am currently unable to enter or view the results page from the FUMA system because the job status is ERROR:Undefined.

Could you please help me check whether this job also finished successfully on the backend? If so, would it be possible to update the job status so that I can access the results page?

Thank you again for your time and help.

Best regards,
Qinglin Zhang

[flutter]

I received the same error and the same double email. The Job ID is 739793.

From qinglin: "Like the previous job, I am currently unable to enter or view the results page from the FUMA system because the job status is ERROR:Undefined."

One way to still access your results is to go to the following URL, but replace the number at the end with the job ID: https://fuma.ctglab.nl/celltype/12345

The results don't seem to show on the website, but if you click "Download files", then those files contain all the results.

[qinglin zhang]

Dear flutter,

Thank you very much for sharing this workaround. I really appreciate your help.

I tried accessing the results by replacing the job ID in the URL, and this is very helpful. I will check the downloaded files to see whether all the expected results are included.

[Tanya Phung]

Hi both, 

Thank you for reporting the issues and for providing the workaround. 

I'm not 100% sure that the issue is, but I restarted the queue and it seems that the problem is now fixed.
I confirmed by testing a job selecting a previously snp2gene job and a job by submitting my own magma.gene.raw file. Both jobs finish successfully, sent email only once, and I can view the results: 

I have updated the status of your job to OK now so you should be able to view the results. 

Thank you,
Tanya