Hi, the same exception has been reported before when running msconvert under linux with wine: http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine#AB_Sciex_wiff_files_throw_an_exception And I still see the same error on a much more recent wine version in our converter Virtual Machine at https://github.com/phnmnl/pwiz-appliance
Although you work on Windows 7, you get the same error when not running under cmd.exe, so it might be some environment setting that's missing from within your TPP ? Maybe we have the same issue, and some simple setting (language ?!) could help. Yours, Steffen Am Freitag, 5. Dezember 2014 02:06:09 UTC+1 schrieb Luis: > > Hi Brian, > I have not seen that msconvert error; can you still reproduce it? (we > once encountered a similar error that went away after running msconvert > once via the command-line.) Otherwise I can only suggest looking at the > file permissions in that directory. > > Does the previous version of TPP/msconvert work with that same file? What > about other raw file formats? > > Thanks for trying out the new release, > --Luis > > > On Thu, Dec 4, 2014 at 9:56 AM, Brian Hampton <[email protected] > <javascript:>> wrote: > >> I just started using 4.8 on a 32 bit install of Win 7. Using Petunia I >> began by converting Sciex .wiff files to mzML and got the following error >> and output from this command: >> >> NOTE: I can run the same command in a CMD window and it succeeds. >> >> *c:\Inetpub\tpp-bin\msconvert >> c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t/02Dec14-BH-RABA-Fxn1.wiff >> >> -v --mzML -o c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t -z >> --filter "peakPicking true [1,2]"* >> >> format: mzML >> m/z: Compression-Zlib, 64-bit >> intensity: Compression-Zlib, 32-bit >> rt: Compression-Zlib, 64-bit >> ByteOrder_LittleEndian >> indexed="true" >> outputPath: c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t >> extension: .mzML >> contactFilename: >> >> filters: >> peakPicking true [1,2] >> >> filenames: >> >> c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t\02Dec14-BH-RABA-Fxn1.wiff >> >> processing file: >> c:/Inetpub/wwwroot/ISB/data/projects/carotid/sds/141202-3t\02Dec14-BH-RABA-Fxn1.wiff >> [WiffFileImpl::getSampleNames] The type initializer for >> 'Clearcore2.Data.WiffReader.WiffSampleRun' threw an exception. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
