duplicate 'row.names' are not allowed

[PierreSnell]

Hello,

First, thanks a lot to have create this nice processing pipeline and brought made those ideas public.
I was trying to run the docker image with Waters (.raw) data that I converted to .mzML.

However, I encountered a problem, here is the traceback.

The script is the one for Ionic mobility

docker run -it --rm -v "$PWD":/data -u $(id -u ${USER}):$(id -g ${USER}) zhulab/met4dx-r Rscript run.R

========== WELCOME to Met4DX v2.0.3 ===========
Developed by zhulab for MS Data Processing
Imported packages:
  SpectraTools v0.4.0
  OpenTIMSR v1.0.13
=============================================

Warning messages:
1: multiple methods tables found for ‘ppm<-’ 
2: replacing previous import ‘mzR::peaks’ by ‘splus2R::peaks’ when loading ‘Met4DX’ 
Querying ims data...
processing files:  1 - 2 
  |======================================================================| 100%

Matching features between runs...
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  duplicate 'row.names' are not allowed
Calls: MatchBetweenRuns_DTIM_IOI ... MatchBetweenRuns_DTIM_IOI -> read.csv -> read.table
Execution halted

My supposition is that the file could be badly converted from msconvert. However, I can load it with other tools (pyteomics/pyopenms).

I can send the files if needed but would need an email (as it's ~1Gb per file)

Thanks in advance for any help.
Have a great day.

[nguyenjn1906]

Hi @PierreSnell,

Did you manage to run Met4DX? I am trying to run this with some data obtained from Bruker's timsTOF Pro, and could not get the command line to work on Windows PowerShell.

Specifically, it looks like PS couldn't read the "id" term in the command line, and it returns the following error. Let me know if you ran into similar issues, or if you were able to run it successfully. Thanks!

PS H:\data> docker run -it --rm -v "$PWD":/data -u $(id -u ${USER}):$(id -g ${USER}) zhulab/met4dx-r Rscript run.R
id : The term 'id' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the
spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:42
+ docker run -it --rm -v "$PWD":/data -u $(id -u ${USER}):$(id -g ${USE ...
+                                          ~~
    + CategoryInfo          : ObjectNotFound: (id:String) [], CommandNotFoundException
    + FullyQualifiedErrorId : CommandNotFoundException

id : The term 'id' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the
spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:59
+ docker run -it --rm -v "$PWD":/data -u $(id -u ${USER}):$(id -g ${USE ...
+                                                           ~~
    + CategoryInfo          : ObjectNotFound: (id:String) [], CommandNotFoundException
    + FullyQualifiedErrorId : CommandNotFoundException

docker: invalid reference format.
See 'docker run --help'.

Thanks for any help :)