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/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
>
> >
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