I am analyzing metabolomics data with workflow4metabolomics pipeline . I have only normal samples no QC, Pool, and blank samples in our experiment. I want to do batch correction but getting following error when I perform batch correction tool -
one additional query if i don’t have those data still I can perform my metabolomics analysis ?
Error in check.err(table.check) :
- - - - - - - - -
Error: less than 2 pools specified in at least one batch in sample metadata.
Make sure this is not due to errors in your sampleType coding.
- - - - - - - - -
Calls: meth3L -> check.err
Execution halted
Which protocol are you following? These details will help:
tutorial link (if following one)
workflow link (if using one)
full name/version of the tool that produced this error (top of the tool form)
how this job was set up – find this information on the job information Details page (using the i-icon)
If you share links for the item 1 above then a link to the shared history that would include everything else. Or, you can explain directly, maybe with screenshots. How to. → How to get faster help with your question
Then, as a guess for why this message was reported
It seems the tool is reporting that it expected replicates for one of the batches. Meaning, at least two samples per batch. This seems important for a batch correction step, any tool, otherwise, there is nothing to compare within a “batch” using just one sample.
And for the larger question here
I’m not sure if you need to reorganize your data or if this is all you have, but if you don’t have two samples then batch correction at a minimum is likely not possible. Whether the remainder of the protocol is possible is hard to answer without seeing more details. You might need to find an example that sets up the data the way you plan to and then follow the modified protocol. This could involve parameter differences, or different tools. We can try to point you to the scientists who can answer the larger questions if you share where the protocol was sourced from originally.
HMDB MS search tool is not working, giving blank output in the workflow for metabolomics (https://workflow4metabolomics.usegalaxy.fr/). I have already the required file needed as an input. I provided the screenshot of the input file , which I processed with the given tutorial link below with lcms data.
Got the output in HMDB Tool generated file - Testing HMDB server connexion (1 time(s) )…
Status: 200 The HMDB server returns that your request (connexion test) was fulfilled
All searches should be sent successfully to HMDB…(Set verbose to “High” for more information!)
got the error - Error GETing https://www.hmdb.ca/spectra/ms/search: Gateway Timeout at /shared/ifbstor1/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/29195cb5d378/hmdb_ms_search/lib/hmdb.pm line 638.
Great! Thanks for sharing more details and let’s keep this tutorial’s questions all together since they seem to be related.
Would you like to generate a share link to the history that contains the error? This will allow us to see all of the data and tool details in context. Then we can tease out whether this is something you should adjust in the usage or inputs versus a technical issue on the server. We can reach out to the https://workflow4metabolomics.usegalaxy.fr/ administrators as well with that context.
Sir,
Greetings of the day. I hope you are doing well.
The website of workflow for metabolomics is not working currently . https://workflow4metabolomics.usegalaxy.fr/
Kindly help me
Where I was checking at the dedicated community forum the server hosts for discussions
I don’t see any topics about the batch correction step having a technical issue in their workflows (or, I missed it) but I do see people asking about other tool errors and getting direct help. This is one example. The community is waiting for more information about the error to help.
The forum hosts discussions in French by default but that can be adjusted for anyone who has an account there. I don’t speak French well enough to read/write myself, and I wanted to test using a browser level translation, so I just tried this using Google Chrome and turned on automatic translation from French to English. It works great! It allows the entire site to be navigated even without an account all in your own language. You can write back in English and the community will be able to read your messages with the Discourse translation settings, or with using the browser-level translations (how I did it or with another browser’s language options).
How to get help with your current error on the W4M server
Share your history with error here and we can try to help with the usage. Using Galaxy is about the same no matter which server you are working at. Then, if it needs more, we can help you to report this to the administrators at their forum with the context we create here from the review.
Share your error with the error directly at the W4M site. You can get usage help the same as here but also two more things: help with making scientific or logical decisions when using their workflow (since these are the authors) and help with any issues that might be at a lower level on the server (the administrators who run the server).
We hope this helps to explain! It can be difficult to diagnose tool errors without seeing all of the details. I’ll watch for your reply. If you decide to create a topic at the other forum, you are welcome to link it back here to let us know! Thanks!
Sharing an error for feedback
If you are not sure how to generate a history share link to the history that contains the workflow output with the error, please see this guide. There is a toggle in the application, then you copy the link and paste it back into your messages.
Galaxy Training Network (GTN) versions of the workflow that you can run at other UseGalaxy servers. Check the “Available at these Galaxies” pull-down menu on each to learn which.
