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Nesvilab / FragPipe-Analyst

An easy-to-use and interactive web application for FragPipe
https://fragpipe-analyst-doc.nesvilab.org/
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Fragpipe-Analyst 500 internal server error #49

Open Amelia811 opened 2 months ago

Amelia811 commented 2 months ago

- Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question: I can't open this site http://fragpipe-analyst.nesvilab.org/ since yesterday. My internet seems no problem, I can open google and other websites. Can you please fix it? Thank you.

fcyu commented 2 months ago

Thank you for the notification. Leo @hsiaoyi0504, could you take a look?

Thanks,

Fengchao

hsiaoyi0504 commented 2 months ago

I restarted the sever. The underlying reason needs to be further looked into.

Amelia811 commented 2 months ago

http://fragpipe-analyst.nesvilab.org/ was temporarily working yesterday and morning today. But now I can't open it again. And when it was working yesterday and today morning, analysis using MLE imputation seemed not working, the in process page was going forever. Can you please fix it? Thank you.

hsiaoyi0504 commented 2 months ago

@Amelia811 I restarted the server again, but what I can see in the log, some people seem to upload a very long list of different conditions causing infinite combinations of differential expression analysis. We will block this kind of requests in the future, but it might still take 1~2 weeks before we deploy such changes. Sorry for the inconvenience.

Amelia811 commented 2 months ago

I see. So what is the limitation of condition numbers? How many beyond would cause troubles? Actually I have 8 conditions. But perseus type imputation seems no problems, I can get analyzed results quickly. But when changed it to MLE, it would be running forever. Then if I tried to refresh the page, I couldn't open the http://fragpipe-analyst.nesvilab.org/ anymore.
Thank you.

hsiaoyi0504 commented 2 months ago

@Amelia811 we haven't decided yet, but I didn't see the server offline now, so I guess you are not the one make the sever crash.

Amelia811 commented 1 month ago

http://fragpipe-analyst.nesvilab.org/ can not working again. Today I used Perseus imputation, and everything went smoothly. However, when I switched to MLE, the process got stuck, just like it did the last time I posted here two weeks ago. It seems that when too many conditions are loaded and MLE imputation is used, the process can run indefinitely and eventually crash.

hsiaoyi0504 commented 1 month ago

@Amelia811 Before I tried to restart the sever, I noticed the whole website is still working. Maybe if you can share the data with me then I can take a look further. yihsiao@umich.edu.

hsiaoyi0504 commented 1 month ago

@Amelia811 So I dig a little more. I think the issue of MLE is generally expensive. The issue was discussed in https://github.com/rformassspectrometry/MsCoreUtils/issues/109. We will later move this method to the lower priority.