Eileen, Any chance you have a "+" in your file name? If yes, that is your problem. And based on your error message you pasted, this looks like the case. If you re-named your pep.xml and mzML files, you will also have to change all references *inside* the pep.xml file to the updated name which I mentioned in my previous reply.
To avoid all these issues with mis-naming files and not correctly updating file names & content inside the pep.xml files, consider starting from the beginning with a re-named mzML file, do the search to generate a pep.xml file and then run the TPP tools. - Jimmy On Fri, May 3, 2013 at 3:49 PM, Eileen Yue <y...@ohsu.edu> wrote: > Hi Jimmy, > thank you for your advice. I followed your advice and test the files one > by one and figured out one raw file name is different from the sequest > search file name (my colleague renamed the sequest search result file > name). After I renamed the raw file name to match the sequest results name. > then the analyze peptide went through without any problem. > > The new problem is: when I click the peptide to check the xpress ratio > infomration or ms/ms informatin, there is error information showed below. > Could you give me some advice for this error information? > > Thank you so much and have a nice weekend > Eileen > ________________________________________ > for ms/ms information erro: > > command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf > c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1 > 4-D_100ug_PierceIMAC_75um_140_20130423_VE2.tgz "*MAY1335_Yeast_1 > 4-D_100ug_PierceIMAC_75um_140_20130423_VE2.22310.22310.3.dta" > /dev/null" > failed: Operation not permitted Error - cannot read spectrum; tried direct > .dta, from mzXML/mzData and from .tgz > > > for xpress information error: > > Light scans: mass: tol: > Heavy scans: mass: Z: > > Raw file: > .out file: Norm: > > Error - cannot open file > "c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1". > > > > > ---------------------------------------------------------------------------------------------------------------------------------------- > > > From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com] > On Behalf Of Jimmy Eng [jke...@gmail.com] > Sent: Thursday, May 02, 2013 9:16 AM > To: spctools-discuss@googlegroups.com > Subject: Re: [spctools-discuss] why I got this error information? > > Eileen, > > The "+" in the file names is not a problem at this stage of processing > although it is a reserved character for a URL so you will have issues > visualizing results in the web interface. The "-" character is OK. For > future reference, it's not enough to simply change the pep.xml and mzML > file names. You will have to also make the corresponding changes to the > content within the pep.xml file, specifically the "base_name" attributes. > I always suggest that researchers stick to numbers, letters, dash "-", and > underscore "_" in naming files. > > For your specific error, does the following file exist? > > > c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML > If yes, I couldn't tell you why XPRESS is reporting that error. I would > suggest you try this analysis with just a single input file first to > confirm you can run the tools to completion. If that works, try this > processing this one > MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML file by itself. > > - Jimmy > > > On Wed, May 1, 2013 at 1:27 PM, Eileen Yue <y...@ohsu.edu<mailto: > y...@ohsu.edu>> wrote: > > Hello everyone. > I have one error information when I tried to analyze peptide for SILAC > data. I do not know whether this is possibly caused by file's name which > includes "+" and "-" . I did manually change the pep.xml and mzml files's > name (which I deleted "+" and "-" ) but I still get error information. > Could anyone give me some advice about this issue? > > Thanks > Eileen > > > > XPRESS error - cannot open file from basename > c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2, > will try to derive from scan names > > command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 > -nK,8 -nR,10 -c6 -p1" failed: Unknown error > > command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 > -nK,8 -nR,10 -c6 -p1" exited with non-zero exit code: -1073741819 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.75 -l6 -Op > -dREV -X-m1-nK,8-nR,10-c6-p1 -A-lKR-r0.5 > MAY1335_Yeast_1+4-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml > MAY1335_Yeast_1+4-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml > MAY1335_Yeast_1+4-D_100ug_PierceIMAC_75um_140_20130423_VE2.pep.xml > MAY1335_Yeast_2+3-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml > MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.pep.xml > MAY1335_Yeast_2+3-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml" failed: > Unknown error > > Command FAILED > > > -- > 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 spctools-discuss+unsubscr...@googlegroups.com<mailto: > spctools-discuss%2bunsubscr...@googlegroups.com>. > To post to this group, send email to spctools-discuss@googlegroups.com > <mailto:spctools-discuss@googlegroups.com>. > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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