Hello,
I’m trying to upload a raw mass spectrometry file to Myrimatch for analysis, but it keeps saying “No compatible datasets available” even though my dataset is there.
Please advise. Thanks
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Welcome, @jordlang
The tool form is filtering for datasets that have an assigned datatype format that is one of the supported accepted formats for that input area on the tool form.
Screenshot
Maybe have a closer look at the data you loaded up to Galaxy? If you click on the dataset to expand it, you should see a datatype format assigned.
If you didn’t let Galaxy guess the datatype, try loading the data again using all defaults. If Galaxy guessed the wrong datatype, you can change that assignment. In some cases, you might need to create a new dataset from what you have now.
Guides and FAQs
If you are completely new to Galaxy, maybe also try a quick tutorial to learn how to navigate the workspace?
Hope this helps but please let us know if you have more questions! 
Hi @jennaj ,
Thank you so much for your feedback. I realized that the data I’m analyzing is in a “.raw” format and not in one of the acceptable formats. I’m new to the MS-proteomics field, so I am still learning how to wrangle, analyze and interpret MS data. Is there a simple and straightforward way to convert the data to an acceptable format?
Thanks.
Hi @jordlang
See the tutorials, I think they will add some context to your good questions! It is also good to be learning how this works! Give the tutorials a try, I think it will help, and you can ask more questions as you move through the processing.
The slides in that introduction show the flow of data from raw, staring here → Introduction to proteomics, protein identification, quantification and statistical modelling
You can move back through the slides or see the next few slides.
Then, if the full tutorial listing seems too much, then you can instead follow the recommended order we used for a recent training event. The Slack channel for the event is now closed, but you can use the GTN chat and this forum instead.
- Proteomics (recommended order)
- Hands-on: MaxQuant and MSstats for the analysis of label-free data / MaxQuant and MSstats for the analysis of label-free data / Proteomics (first hands-on, starting from “raw” files) ← you can start here to just jump right in!
If you are new to Galaxy, you can first try the tutorial I listed above, or follow the full introduction we recommended during the training. You can also just go back here if you run into something you want to learn more about.
Hope this helps, and don’t be afraid to share your work if you get stuck. How to do that is in the banner at this forum, also here → How to get faster help with your question 
Hi @jennaj,
Thank you for the resources; I’ll check these out. I was able to convert the MS files into an appropriate format for the software to process. The job is currently running, but when I click on the viewer tab of the queue, this error comes up (attached).
Hi @jordlang
It looks like the job is still running, so there is nothing to view?
The jobs on the public Galaxy servers are dispatched to remove cluster nodes. That means that the intermediate files are not available to inspect. So, I think you are just getting a weird message based on the datatype: there is “no root” because there isn’t a file with data in it yet.
It has been a full day since you posted. Do you have output now? A green dataset? Are things working as expected now?
More about how jobs process (just as a reference!)
Hi @jennaj,
Thank you for the explanation and references. I actually started a new job today just to see if it will go through. I still see the same error; it is still running.
Hi @jordlang
The job has to fully complete – turn green or red – before any logs are generated.
I ran a simple test in this history. The job did error if you want to see what that looks like in my shared history. I’ve reported this to the EU administrators since it is either a problem with my test data or something else (not sure, but they will). I will say that even with a small test, I didn’t use default parameters, and I think those are unlikely to work. You will need to adjust the settings to fit your data.
My current advice is for you to do the same – let your job run to completion. Then if you get an error, send that to the administrators, plus you can come back here and let us know what happened. You can even set up and run the tool multiple times with different parameter sets to see what happens if you are not sure of some setting. Each job runs independently.
As a reference, this is the publication → https://pubs.acs.org/doi/10.1021/pr0604054
Hope this helps and the EU admins may come back here, I shared the topic with them. Thanks!
@jordlang how did you convert your data? Did you use msconvert on Galaxy or proteowizard offline on your computer?
I used proteowizard on my own computer.
Did you convert to mzML or mzXML? If you could share a link to your history we can see what the exact problem is and can try other things to see if we can solve the issue Thanks a lot!
Hi @hechth
I’m not too sure what you mean by share a link; can you please clarify?
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Hi @jordlang How to share your work is in the banner at this forum or please see here directly → How to get faster help with your question
You can generate the share link for your history, copy the link, then paste it back here with your comments. This allows people to review how your work is set up – with all the technical details – to provide meaningful feedback. Sometimes we can guess from other small snippets but then the advice can be pretty general, and might not be enough to actually solve the issue.
Sometimes people worry about sharing … but it really is not that public since very few people would be able to review someone else’s experiment and then do anything with it that matters. Sharing, getting feedback, then unsharing is very common.
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Hi @jennaj
I want to share my history, but it seems like I can’t as shown in the screenshot.
Is it because the job is still running? Its been a long time now.
Hi @jordlang
Try creating an account then logging in. You are missing out on a bunch of functionality by not having an account – plus all the extra quota space.
If you are not sure how to do that, start here → Galaxy FAQs
@jordlang in general I would recommend using mzML as file format over mzXML.
Hi @jennaj ,
Yes, I did create an account and am running the job using my profile. I’m unsure if that will help it run to completion.
@hechth I’ll try running with mzML again