Hello Bernard, My best guess is that the '.' in your filename before the .mzXML is causing some parsing to break. Please change your file basename (everything before the extension) to include only alphanumeric characters and try again.
Thanks, -David On Sat, Jul 4, 2009 at 10:20 AM, Bernt<[email protected]> wrote: > > Hi, > > I would like to continue an old thread: > http://groups.google.com/group/spctools-discuss/browse_thread/thread/4fd1ce8369511c8c/5b357a153c4a1b24?lnk=gst&q=viewing+spectrum#5b357a153c4a1b24, > which has already been taken off. > > My problem is similar, but I have tried my best to verify that all the > places referring to the raw data "path" are consistent, as advised by > Jimmy in the thread. What I did was: I made a Tandem DB search at one > folder level (e.g. c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/P00158), > generating a set of .raw.tandem files. But later, for the reason of > trying to combine 529 mzXML files together from separate folders, I > moved all the mzXML and associated .raw.tandem files to another folder > level (c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/). > > I know of this spectra viewing problem if the files were relocated, so > I used a text replacing application to ensure that all .raw.tandem > and .raw.tandem.params files with the string "c:/Inetpub/wwwroot/ISB/ > data/OC/OGEmRPTD10/P00158" were replaced to "c:/Inetpub/wwwroot/ISB/ > data/OC/OGEmRPTD10/". Only then I generated the .raw.tandem.pep.xml > files from the modified .raw.tandem files and then the > interact.pep.xml file. > > But the error still persists: command "C:\Inetpub\tpp-bin\tar.exe -tzf > c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > HUO00159S00168GL05B01.raw.tandem.pep.tgz "*HUO00159S00168GL05B01.raw. > 0659.0659.3.dta" > /dev/null" failed: Operation not permitted Error - > cannot read spectrum; tried direct .dta, from mzXML/mzData and > from .tgz > > Below is an example of a spectra path that I tried to track: > > Spectra URL = > > &Dta=c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > HUO00159S00168GL05B01.raw.tandem.pep/HUO00159S00168GL05B01.raw. > 0660.0660.2.dta& > > Interact.pep.xml file = > > <interact_summary filename="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > OGEmRPTD10_Tandem_interact.pep.xml" directory="C:/Inetpub/wwwroot/ISB/ > data/OC/OGEmRPTD10"> > <inputfile name="HUO00159S00168GL05B01.raw.tandem.pep.xml"/> > <msms_run_summary base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > HUO00159S00168GL05B01.raw.tandem.pep" > <search_summary base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGEmRPTD10/ > HUO00159S00168GL05B01.raw.tandem.pep" > <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/OC/ > OGEmRPTD10/HUO00159S00168GL05B01.raw.mzXML"/> > > HUO00159S00168GL05B01.raw.tandem.pep.xml file = > > <parameter name="spectrum, path" value="c:/Inetpub/wwwroot/ISB/data/ > OC/OGEmRPTD10/HUO00159S00168GL05B01.raw.mzXML"/> > > > Sorry for this long and unreadable email, but I really don't know what > else I might have missed out, and I would hate to redo the Tandem > search for 529 mzXML files. Would really appreciate some suggestions > and advice. Thanks in advance! > > > Bernard > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
