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Topic: FILE_READ_ERROR (Read 4583 times) previous topic - next topic

FILE_READ_ERROR

Hi there,

I'm having a problem with 3 files in one of my datasets.  I get an error message after submitting the job: FILE_READ_ERROR and then when I look through my datasets, 3 of the files have this message (or similar):

Error in xcmsRaw(file, profstep = 0) : Time for scan 7998 (3600) greater than scan 7999 (0.402).

I tried re-uploading the files, and then tried re-converting them from .raw to .mzXML and re-uploading again but I get the same message with the same 3 files.  All of my other files are fine, and are all from the same instrument (Perkin Elmer), same type of samples.

For my chromatograms, scans with values around 7998 are right at the end, and I'd be happy to remove these scans if there's a problem with them.  Is it possible to do this?  Or is there any other way to work around this?

This is job no. 1002815, I'm using Firefox and Windows 7.

Thanks,
Katherine.

Re: FILE_READ_ERROR

Reply #1 –
What program are you using to convert the .raw files to mzXML ?

Re: FILE_READ_ERROR

Reply #2 –
MS Convert from ProteoWizard 3.0.3768 32 bit.
Katherine.

Re: FILE_READ_ERROR

Reply #3 –
The solution for this problem is described here.
You have to use the "sortByScanTime" filter to make sure the scans are in the right order in the mzXML file.

Since the msconvertGUI does not seem to support the "sortByScanTime" filter at the moment you have to do the conversion on the command line, using something like

Code: [Select]
msconvert D:DataMyFile.RAW --filter "sortByScanTime" --mzXML -o D:DataOutput
 

Re: FILE_READ_ERROR

Reply #4 –
Hi Ralf,

Thanks for your help.  I've never used anything other than the GUI version of msconvert before .  I have the file for the non-GUI version on my computer but am having difficulties opening it, when I try to open it, a window opens, it scrolls through a load of command lines and then shuts again.  Do you have any suggestions for this one?  I'm afraid I've never really used command-line type software at all!

Katherine.