Hi Jimmy, David, Thanks for the advice, I tried removing the .raw and .d from the extensions and changed all occurrences of the extensions in the .tandem files accordingly. It worked. They must be interfering with the file string recognition.
Yet when I tried the same thing for Mascot .dat files converted to pep.xml (I removed the .mgf extension and even the ".d" hex string in the .dat files) but it doesn't work (the url points to the generated .tgz file, but I can't view it). I have gotten rid of all symbols in the file names including "_" and then manually traced the connections all the way to the mzXML files, and everything seems in order. The last thing i can think of is the length of the filename (Mascot search generates an index no. (e.g F065672 and attaches to the filename). Do you think there might be something else I have missed out? Bernt On Jul 7, 2:22 am, Jimmy Eng <[email protected]> wrote: > Bernt, > > The good news is that you shouldn't need to re-run Tandem searches to > address this problem. > > The easiest way that I can think of to help you is to show you the > convention of file names, base_name attributes, and paths that the tools > typically expect/generate. > > directory of data: > c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/ > > file name of one example mzXML: > c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.mzXML > > file name of Tandem search: > c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.xtan.xml > > file name of corresponding pepXML file: > c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01.pep.xml > > msms_run_summary base_name attribute in that pepXML file: > <msms_run_summary base_name="./HUOL05B01" > > msms_run_summary base_name attribute in the combined/xinteracted > interact.pep.xml file: > <msms_run_summary > base_name="c:/Inetpub/wwwroot/ISB/data/OC/OGemRPTD10/HUOL05B01" > > In your example below, you seem to carry a ".raw.tandem" extension > through everything that's a big part of the problem. After all the > tools are run and the URL is generated for the spectral viewer, some > part of this extension then is incorrectly expected to be part of the > mzXML file name. > > Digest the above and see if it helps. If I were you, in addition to > doing the text replacement (that I presumed you did correctly), I would > rename your Tandem search files (.raw.tandem) based on our convention > above and re-run analysis. If the spectral viewing still fails, report > back: > - directory data is in > - an example spectrum URL as you did > - full path name of mzXML file for that example spectrum > - msms_run_summary base_name attribute value > - full path name of the pep.xml file > > And instead of "HUOL05B01.*" in my example above, it's perfectly fine to > have "HUOL05B01.raw.*" if that's how you have things setup. Just as > long as everything is consistent. To follow-up on David's reply, I > believe periods (.) in filenames are fine. > > Good luck. > > - Jimmy > > Bernt wrote: > > Hi, > > > I would like to continue an old thread: > >http://groups.google.com/group/spctools-discuss/browse_thread/thread/..., > > 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 -~----------~----~----~----~------~----~------~--~---
