Bug with saving Regional Plots

[samuel....@exeter.ac.uk]

Hi there! I really appreciate the effort put in to make such a useful piece of software.

I'm having an issue producing the "regional plots" for a specific genomic locus. In the "results" tab of the "SNP2GENE" analysis, you can click on a specific locus and it will produce a manhattan plot of the region and includes LD information of the GWAS variants. Below the plot, you can choose up to four plots for FUMA to produce for your specific locus. For several of my loci, I have selected only the "GWAS association statistics" plot and have had them saved in pdf format in the window that subsequently opens. At one locus (in the region of the HCRTR2 gene [chr 6, pos 55MB]), FUMA succeeds in showing the plot in the web browser but when I click pdf (or other formats), it fails to plot and instead stops responding. This is completely reproducible so it's not a transient error and it only happens with this locus. If I choose any other plot ("CADD Score", "RegulomeDB score" or "Chromatine 15 state"), plotting to pdf (or png) succeeds but if I select "GWAS association statistics", I am unable to download the plot in any format. This leads me to believe that there's either a problem with this genomic locus, or an issue with my summary statistics at this locus.

Have you come across this before?

Thank you!

Sam

[Kyoko Watanabe]

Hi Sam,

Thank you for reporting the bug, I need to look into the details if the problem is due to your summary statistics or a specific genomic region.

Could you share with me the job ID that you are having this problem?

Best,

Kyoko

[samuel....@exeter.ac.uk]

Many thanks for the quick reply!

Job ID is (I think) 4478

Thank you!

Sam

[Kyoko Watanabe]

Hi Sam,

I was not able to reproduce your situation, unfortunately.

So only the thing I can think of is time out due to very heavy plot, since the region you are failing to plot seems to have a lot of SNPs.

Does it take more than 30 sec to download PDF file for other regions?

If so, this might because your internet is not fast enough to get the heavy plot. I will try to extent timeout of php.

Best,

Kyoko

[samuel....@exeter.ac.uk]

Interesting!

We have a fast connection here and the "save file" prompt comes up instantly for other loci. If I select PDF (or any other format) for this locus and wait, it does seem like the page times out. I get the error message with firefox: "The connection was reset. The connection to the server was reset while the page was loading." Firefox seems to get stuck on the "sending request to fuma.ctglab.nl..." (as seen in the little box at the bottom left of the window) before displaying the connection reset error.

I get a bit more information with chrome, in that if you're uploading data, it tells you the upload progress. On clicking the PDF box (to save a pdf plot), a new window opens, then the little box in the bottom left gets stuck on "Uploading (88%)" before displaying the error message "This site can’t be reached. The connection was reset."

Rather than having issues downloading the plot, this seems like an error server-side, with the server not letting my browser upload all the data for that locus?

Thanks and apologies for the trouble!

Sam

[Kyoko Watanabe]

Ok, then it sounds like the php execution time out.

I will extend timeout for input and execution, and restart server.

But FUMA is currently busy and I do not want to interrupt a lot of users, so I will do that tonight.

I will let you know so could you please come back later and try this again?

I am sorry for the inconvenience, hope this will solve the problem.

Best,

Kyoko

[samuel....@exeter.ac.uk]

Thank you for looking into this! I'll wait for your response before trying again.

Thanks!

Sam

[Kyoko Watanabe]

Hi Sam,

I have extended the timeout. Could you try again to see if this works now?

Best,

Kyoko

[samuel....@exeter.ac.uk]

Hi Kyoko,

I'm afraid it hasn't fixed the problem for me. It still only reaches 88% when using chrome. What data is my browser trying to upload? Is it passing the summary stats for that region to the plotting routine? Is there any way I can inspect the content of this data?

Apologies for the trouble!

Thank you!

Sam

[Kyoko Watanabe]

Hi Sam,

The clicking PDF button should not upload anything but just passing svg data to server side to create PDF file.

Does it only happen to the region (chr6 55Mb) or does this also happen  to the region with more SNPs?

Best,

Kyoko

[samuel....@exeter.ac.uk]

I've just tested for other regions and it does seem to be the number of SNPs that is causing the issue. It manages to plot a locus with nSNPs = 803 but fails for nSNPs = 838 and higher.

Thanks!

Sam

[Kyoko Watanabe]

Ok, then it should be because of memory or time out.

I will investigate more and will let you know as soon as we fix the problem.

Best,

Kyoko

[samuel....@exeter.ac.uk]

Thanks for looking into this! I just thought I should add that it affects other plots too. I'm also unable to download large gene enrichment plotsm as well as manhattan and QQ plots.

Sam

[Kyoko Watanabe]

Hi Sam,

I could not find any server side error and I have been trying to reproduce the same error with different compute and slower internet.

But I was not able to reproduce them and that make it's very difficult to debug.

It must be some client side setting but I do not have clear idea what it's causing.

It will take a some time to fix this but as a temporal solution, I added additional filtering for regional plot with annotations.

So this should allow you to download at least regional plots.

For manhattan and QQ plots, SNPs/genes are already filtered and I'm no in favour of filtering anymore. For these, I need to find out the actual problem causing this.

To further investigate this problem, could you please share the following information?

Your computer, OS, browser and it's version, internet speed (something like http://beta.speedtest.net/).

Best,

Kyoko

[Wei Guo]

Hi

does this issue fixed? I have the same problem in my job  613961. The regional plot is black and hard to read when I was trying to open the download file (in any format).

thanks.

Best,

Wei

[Tanya Phung]

Hi Wei, 

I do not know what the issue was from this thread from 2017, but I do know that some issues with downloading images can be solved with downloading in SVG. Please check the more recent thread here: https://groups.google.com/g/fuma-gwas-users/c/xEsfWTh5C-4/m/0PAwU2alAgAJ

Best,
Tanya