Label-free data analysis using MaxQuant

, ,
#1

Hey there Galaxy-Team!

I tried the tutorial step by step for label free data analysis with the MaxQuant tool. It worked perfctly fine until I tried to visualize the Boxplot of the Quantitative Assessment. Galaxy requires the confirmation of the settings. If I click the confirmation button, the process is starting but somehow never ends. after a while I got a notification either in my history as well as in the saved visualizations that the job was done but I wasn’t able to open the Boxplot…
The rest of the Tutorial worked without any problem :clap:t3:

Maybe you can help me?

Thanks in advance :relaxed:

1 Like
#2

Hi @jo_sie

You are following this tutorial, correct?

Maybe you didn’t save the visualization? Or are not looking for it in the right place? See step 4 here: Label-free data analysis using MaxQuant

If that isn’t working for some reason – where are you working? Public server URL?

1 Like
#3

Hey again :slight_smile:

thank you for your quick answer, exactly this was the tutorial and I did it step by step. The thing is, I could’t save the Boxplot, because Galaxy was still in “running confirmation” status even after hours, but when i refreshed my History the notification of “Chart on Data…” (the data that should have been visualized) appeared but I couldn’t see the Boxplot.
like this:

image

and yes I think I’m working on public server URL

1 Like
#4

Hi @jo_sie

It is possible the server was just really busy. Try running the tool again.

You will need to save, otherwise, the visualization is lost.

Confirm and save galaxy-save (file is saved under “User” –> “Visualizations”)

If the rerun also fails, double-check your inputs first as problematic inputs can lead to jobs (any) that don’t fail correctly or run for unusually long times. If the really long runtime persists and you cannot save, posting back the exact server URL (the first part of what is shown in your browser link when connected: usegalaxy.eu, usegalaxy.org, etc) will help us to route you to the right people that can help with a history review (as needed) or possibly some server-side change.

Thanks for the follow-up!

1 Like
#6

Hi @jo_sie

Thanks! I was able to import the history and check the upstream steps (all of that was fine). Then I recreated a boxplot using dataset 74 as an input, saved it successfully, and it is now listed under my User > Visualizations.

Try again, please, and maybe twice. It seems the server gets busy while setting up the environment.

I also got a message about “waiting for the environment to be set up”. The first time, I quit out after a minute (probably too soon). Next time and the one after that, the process went through all steps quickly (waiting, running, then the done message). The graph displayed and was then able to click on the << in the upper right corner and use the save icon.

Note that I ignored the messages about being able to leave the tab and still find the results under User > Visualizations – as that isn’t actually true anymore. The tutorial does state to wait and save – and that is accurate. I’ll report this to the development team – there have been some changes around this functionality recently – and it isn’t necessarily a bug, but about making the usage clearer in the interface itself, or possibly switching this back to a result that is automatically saved (maybe as an optional toggle).

Update: Now just tried again, the box plot never displayed, but it was saved automatically!! Well, maybe the server is busy, but my guess is more is going on. I’ll still ask the developers about it.

Thanks for following up with this! Confusing and could be better.

1 Like
#7

Hi @jennaj

thanks for the kind support, i’ll try it again as you mentioned.
Hopefully this time it works :slight_smile:

1 Like
#8

Hey @jennaj

i let the tool run overnight, but unfortunately nothing has changed… I get the “charts on data…” information as well as a saved boxplot in my visualizations but i’m not able to open the boxplot.

1 Like
#9

Update:

Ok, we were able to reproduce the problem better today, in multiple browsers, and are looking at it now. All the follow-up is much appreciated. More feedback soon. Apologies for the troubles!

Ticket: Visualizations / Graphing: Problems with jqplot_box · Issue #12279 · galaxyproject/galaxy · GitHub

Workaround: Function may work at usegalaxy.eu and/or usegalaxy.org.au (not tested yet)

Hi @jo_sie

The graphing tool should work very quickly when using the tutorial data. When I ran it from a copy of your history it took only a few minutes (input was dataset 74).

Just to make sure you are trying to view the data from the correct place: the plot needs to be opened from the User > Visualization view. Use the pull-down menu. If that is not where you are trying to access the graph, give that a try. These particular graphs do not display via the “eye” icon in the dataset.

If that doesn’t work – I’m now wondering if there is a problem with the browser. Which are you using when the problem comes up? Is this reproducible if you use a different browser? Firefox, Safari, and Chrome work best – try at least two and let us know what happens.

1 Like
#10

Hi @jennaj

I cannot explain why, but for me it just doesn’t work… I tried now firefox and chrome, as well as usegalaxy.org and usegalaxy.eu. ( I archived my history and worked there with the same data as before) and tried it as well with creating the data set from scratch again.
I tried opening with the user → visualization → Boxplot → open and it just shows me the “please wait-sign” for hours.

I’m sorry if my descriptions are not that helpful/informative :smiley: I’m not that much into Bioinformatics
yet

1 Like
#11

Thanks @jo_sie for the feedback about the other servers/browsers.

This was reproducible by the developers in testing instances as well. The correction needs to be done, then deployed out to the servers. The ticket I linked is for the tracking of that process. When that ticket closes out, the fix will be deployed, then I’ll come back and update this post as resolved. How long that will take is still an unknown.

In practical terms, this means you should skip the problematic graphing step when doing the hands-on for now. The good news is that a screenshot of the graph is included in the Question/Solution under that step – expand the “Solution” section to view it and the discussion around interpretation.

Apoligies for the trouble, and thank you for following up!

1 Like
#12

Hey @jennaj

Thank you for your efforts and your kind help! :hugs:

Greetings
Johanna