I am processing LC-MS based MS-MS metabolomics data but getting error in further processing steps. Link of my history is as follows.
https://workflow4metabolomics.usegalaxy.fr/u/abhisek_galaxy/h/copy-of-crf
I am following this galaxy based tutorial
Please help to rectify the error.
Hi @Abhisek_Dey
I don’t see any errors in your history. But I do see many queued datasets! Job queues are normal and expected. How to interpret job queues is discussed in topics like these → queued-gray-datasets
For unexpected delays on this particular server, or technical issues, the administrators of this server host a dedicated forum and do not track many topics here! I see recent posts about troubleshooting job errors, but no topics about excessive delays, but you could start up a new topic and ask! Maybe there is a new delay?
If a forum hosts discussions in a language other than one of yours, no problem!
Try logging into the forum. It probably has a language translation feature!
Not interested in an account? Use a browser level language translation instead.
Example: Google Chrome can apply an automatic translation from French to English. This allows an entire website to be navigated even without an account and all in your own language choice. You can write back in your language and the community will be able to read your messages. If they can’t read your message for some reason, they will help you to get set up and possibly update their site to translate your language in the future.
This forum, Galaxy itself, and the GTN training site also offer accessibility features!
Hopefully this helps! 
Dear jennaj, Thanks for your response. Maybe you couldn’t see my history correctly, or the error is not showing from your end due to any glitch. There is 4 dataset which are in red colour. I am attaching another history of the same data analysed by me for your kind reference and for the community as well.
Basically, I am analyzing an LC-MS based MS-MS dataset. Refer to the history link (Galaxy) there is some error in the process. Can anyone tell me what the max tolerated ppm m/z deviation is in consecutive scans in PPM?
Every time I process this data with PPM=3 for the subsequent steps, I get an error. Specifically, after applying this command, “xcms groupChromPeaks (group),” I have seen that if I change the PPM from 3 to 10, then the error doesn’t happen on this step, but I get a feature table with lots of zeros, and the similar error occurs in the next processing steps as well. Guide me with any tutorial for analyzing the LCMS-based MS-MS dataset.
About dataset - The ESI-MSn experiments were executed on the Thermo Q Exactive mass spectrometer, It is DDA based data. UPLC based MS system approache they used to generate the data.
Hi @Abhisek_Dey
Thanks for sharing more details!
Situation
The link you posted this time did include job errors and I noticed the server administrators now have a banner message posted! Did you see this yet? I think it explains your situation.
We currently have a technical problem leading to sporadic errors occurring on random jobs, with a typical “Unable to finish job” error. We are aware of this problem, and we do our best to find a solution to this tricky problem. If you encounter this problem, the workaround is to rerun the job with the same parameters.
Screenshot
What to do
I would suggest trying the workflow reruns, not just job reruns (although you can try that too!). How to at any Galaxy server. → Rerunning only failed jobs in a workflow: Replace and Resume functions
The problem is likely with the cluster configuration and some jobs are failing “by chance” for unclear reasons. While that is always true at some low level (these clusters process thousands, sometimes tens of thousands, of jobs a day), it is higher right now for some reason only those administrators can examine. They will likely post a notice once this is corrected, either as another server message or possibly at their forum.
This might be linked to parameter choices (since those can influence which cluster nodes jobs are sorted to) or it could be truly random! You could share your example and observations with them. Maybe it can help to sort out the underlying issue?
Frustrating I know but I still hope this helps!
