MetaMS.runGC instant beginner error

Workflow4Metabolomics GCMS
1

Hello,

I'm fresh user of galaxy which i would like to use for GC-MS analysis. I convert the .D to MZxml and CDF which are both ok to upload but when i tried to excecute the older version i get this
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/metams_runGC/2.1.1.

Execution resulted in the following messages:

Fatal error: Exit code 1 ()

Error in matrix(unlist(lev), nrow = length(lev), byrow = TRUE) :
'data' must be of a vector type, was 'NULL'
Calls: -> as.data.frame -> matrix
In addition: Warning message:
In unzip(listArguments[["zipfile"]]) : error 1 in extracting from zip file
Execution halted
while importation was ok...

after transformation to xset.RDATA with XCMS I also get the following error....
3.0.0+metaMS1.24.0-galaxy0 .

Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis.
Error: You need more than 1 file to be able to run metaMS
Execution halted

Could anyone give me a piece of advice ?

Thank you very much,

Pierre-Yves

2

Hi Pierre-Yves,

For me the first error is linked to the fact that the zipfile entry is deprecated (we now use dataset collection). @gildaslecorguille is that right?

The second error seems to happen because you have only one cdf file in your Rdata and metaMS is not able to process only one file. Can you try with 3 files ?

Yann

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3

Dear yann,

I have used the LCMS tools up to the Merge functionand then i have import the generated Rdata in metaMS (instead of mzML files) which works fine !

I've try to run it with three files unfortunatly it did not work because it's running three analysis separetly

image
image180×587 9.11 KB

4

Dear Pierre-Yves,

Can you share your history with me yann.guitton[at]oniris-nantes.fr ?

if you don't know how to share you can have a look https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html#share-your-work

Regards
Yann

5

Hi Pierre-Yves,

Thanks for the history, can you confirm that you tried to launch metaMS on 3 Rdata files generated by xcmsSet like the image below?
image .

If yes, then I understand the error, and our tool is not able to work with such inputs

I can try to create a new metaMS version that will read individual cdf/mzML files but I don't know when I can find that time.

I hope that the results from the xcmsSet.merged.Rdata files suits you.
Regards