Dear Luis: Thank you for your notice! I figured this out in the last Friday and I can go ahead to select the pepxml files. The new problem is that the protein prophet failed for unknow reason. the peptide xpress and asap ratio can not be proceeded either. the message showed:
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 -p0.85 -l6 -Op -X-m1-nK,8-nR,10-c6-p1 -A-lKR-r0.5 c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_10_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_11_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_1_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_2_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_3_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_4_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_5_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_6_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_7_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_8_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_9_20110719_VE.pep.xml c:/Inetpub/wwwroot/ISB/data/isl1000/ISL1000_PM_SCX_FT_20110719_VE.pep.xml" failed: Unknown error Command FAILED Could you give me some advice for this? Thank you Eileen ________________________________________ From: [email protected] [[email protected]] On Behalf Of Luis Mendoza [[email protected]] Sent: Friday, September 23, 2011 4:46 PM To: [email protected] Subject: Re: [spctools-discuss] Announcing TPP release: 4.5.0 "Rapture" Make sure you select "Sequest" as the pipeline type so that you are able to view those types of files in the pepXML conversion page, as it seems that Petunia is looking for "tandem" files. --Luis On Fri, Sep 23, 2011 at 4:41 PM, Joseph Slagel <[email protected]> wrote: > Hi Eileen, > > We're looking into it... > > -Joe > > > On Thu, Sep 22, 2011 at 3:20 PM, Eileen Yue <[email protected]> wrote: >> >> Dear all: >> I just download the newer version. When I tried to convert my sequest >> search results into pepxml, I can not select the files. they showed "there >> are no files of requested type (tandam) in this directory" though I can see >> my files listed in the right folder side. >> >> Also when I tried analyzed my previous PEPXML files, they will show >> errors. >> >> Does anyone know how to fix this problem? >> >> Thank you >> Eileen >> ________________________________________ >> From: [email protected] >> [[email protected]] On Behalf Of Joseph Slagel >> [[email protected]] >> Sent: Wednesday, September 21, 2011 4:50 PM >> To: [email protected]; [email protected] >> Subject: [spctools-discuss] Announcing TPP release: 4.5.0 "Rapture" >> >> Announcing the availability of Trans-Proteomic Pipeline (TPP) "Rapture" >> 4.5.0 >> >> We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) >> software, release 4.5.0 (4.5 revision). The software is available for >> Windows as well as Linux (and unofficially) through OSX source from all the >> usual locations (please see the section below, "Getting the software"). >> Most users are recommended to use the Windows installer, which installs and >> configures the TPP and other required software (such as a web server). For >> advanced users who need to customize the TPP, or for those who run >> high-throughput experiments, you can download the source code. >> >> == Release Nodes == >> >> * Release notes on the most important new features, changes, and known >> issues are available at: >> >> >> "http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.0_Release_Notes"; >> >> >> == Getting the TPP Software == >> >> * Download the TPP version 4.5.0 native windows installer >> (TPP_Setup_v4_5_RAPTURE_rev_0.exe) from the Sashimi SourceForge project file >> release page: >> >> >> >> "http://sourceforge.net/<http://goog_2056063534>http://sourceforge.net/projects/sashimi/files/Trans-Proteomic >> Pipeline >> (TPP)<http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29>" >> >> * Everyone is encouraged to read and contribute to our wiki, at >> "http://tools.proteomecenter.org/wiki/"; >> >> * For guides to installing and using our software, please see our wiki: >> "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"; >> >> * For downloading the source code, please go to the following link: >> "http://sourceforge.net/projects/sashimi/files/"; and find the 4.5.0 >> source code .zip package; >> or, check out the code directly from svn: >> "svn co >> http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-5-0<http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-0>" >> >> For building from source, please refer to the readme file in TPP/src as >> well as the wiki. >> >> >> The TPP Team: Luis, David, Mike, Joe, Brian, and Natalie, plus all other >> developers who contributed to this release from the ISB. Thanks to >> developers and users from the TPP's user community who provided feedback and >> code contributions. >> >> -- >> 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. >> >> -- >> 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. >> > > -- > 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. > -- 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. -- 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.
