Re: [proteowizard-support] Ms convert hangs

[Matthew C. <mat...@va...>]

Hi Gavin,

Does it hang when you run it outside of R? Also note that msconvert takes wildcards. *.raw would suffice instead of the FILES array.

-Matt


On 12/15/2010 7:40 AM, Gavin Blackburn wrote:
> Hi,
>
> I’m trying to use MS convert to convert .raw files from a Thermo Exactive to .mzXML files. It gets to the point where it says it is converting the files and
> them hangs and won’t go any further. I’m running it in r with the following script;
>
> msconvert <- c("C:/pwiz/msconvert.exe")
>
> setwd("c:/Rprocessing")
>
> FILES <- list.files (recursive=TRUE, full.names=TRUE, pattern="\\.raw")
>
> for (i in 1:length(FILES))
>
> {system (paste(msconvert," --mzXML --filter \"peakPicking true 1\" -v",FILES[i]))}