Hi Magnus, This is one job I want to tackle at some point but haven't the time yet. Mostly because Tandem runs so much faster on Ubuntu than Win7. But I have difficulties getting a fully functioning Pipeline on linux. So I use Win7 for all the post search analysis. I use a series of SED commands to remap the embedded directory paths for use on the Wiin7 box. Thanks for posting your config file. It will help me when the time comes.
Have a look at (assuming you are using Tandem) the contents of the .tandem search result file and the input file specific tandem.params files in a browser window or text editor and note the directory paths in there. Does it say: G:.... or C:.... The path written in the result file comes from the location of the input files e.g. .mzXML file and locations of the params and database used for the search. My guess is the problem is the embedded directory paths in the search result are not G:... but are C:... and the Pipeline can't find the files because they are looking in G:... as per your config files. This would indicate your setup is the problem. Just a guess but is a place to start. Good luck, Brian Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 800 West Baltimore Street Rm 307 Baltimore MD 21201 V: 410-706-8207 F: 410-706-8234 On Fri, Nov 2, 2012 at 11:35 AM, [email protected] < [email protected]> wrote: > Dear All, > > This is a "favorite" problem among TPP users, and we thought we had solved > it once and for all. But with the new TPP version (4.6.0 and 4.6.1) there > are issues with some of the tools when working with data on another drive > (G: in our case). I have changed the WEBSERVER_ROOT environment variable, > the tpp_gui.pl and of course the httpd.conf to point at G:, and keeping > the C:\Inetpub\tpp-bin\ directory. X!Tandem works, but not PeptideProphet > or the viewers. > > Below is our httpd.conf settings and the output from PeptideProphet. > > Changing everything back to C: makes everything work again, so the TPP > installation itself is OK I think. > > Any ideas? > > > Magnus > > > httpd.conf: > > # > # Begin settings for the Trans Proteomic Pipeline > # > > # Add 24-hour timeout > Timeout 86400 > > Alias /tpp-bin "G:/Inetpub/tpp-bin" > <Directory "G:/Inetpub/tpp-bin"> > Options Indexes MultiViews ExecCGI > AllowOverride None > Order allow,deny > Allow from all > > AddHandler cgi-script .cgi .pl > ScriptInterpreterSource Registry > > PassEnv WEBSERVER_ROOT > PassEnv WEBSERVER_TMP > </Directory> > > Alias /ISB "G:/Inetpub/wwwroot/ISB" > > Alias /schema "G:/Inetpub/wwwroot/schema" > > <Directory "G:/Inetpub/wwwroot"> > Options Indexes MultiViews Includes > AllowOverride None > Order allow,deny > Allow from all > > AddType text/html .shtml > AddHandler server-parsed .shtml > > PassEnv WEBSERVER_ROOT > PassEnv WEBSERVER_TMP > </Directory> > # > # End settings for the Trans Proteomic Pipeline > # > > > output from PeptideProphet: > > g:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 1, Build 201209261035 > (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > "121009.LC1.IT1.EC.S0XXXX.Ecoli_1-B,1_01_3621.tandem.pep.xml" -L"7"" file > 1: 121009.LC1.IT1.EC.S0XXXX.Ecoli_1-B,1_01_3621.tandem.pep.xml processed > altogether 8922 results results written to file > g:/Inetpub/wwwroot/ISB/data/interact.pep.xml direct your browser to > http://localhost/ISB/data/interact.pep.shtml command completed in 2 sec > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" command > completed in 0 sec running: "C:/Inetpub/tpp-bin/RefreshParser > "interact.pep.xml" "g:/Inetpub/wwwroot/ISB/data/dbase/18.E_coli_K12.fasta"" > - Searching the tree... - Linking duplicate entries... - Printing > results... - Building Commentz-Walter keyword tree...command completed in 1 > sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > MINPROB=0.05" (X! Tandem (k-score)) init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: Bruker Daltonics, Model: esquire, > Ionization: ESI, Analyzer: Quadrupole Ion Trap, Detector: MS:1000253 > PeptideProphet (TPP v4.6 OCCUPY rev 1, Build 201209261035 (MinGW)) > AKeller@ISB read in 31 1+, 4238 2+, 4472 3+, 0 4+, 0 5+, 0 6+, and 0 7+ > spectra. Initialising statistical models ... negmean = -1.1254 negmean = > -1.74678 negmean = -1.51536 negmean = -0.2 negmean = -0.2 negmean = -0.2 > negmean = -0.2 Iterations: .........10.........20......... model complete > after 30 iterations command completed in 1 sec running: > "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" Analyzing > interact.pep.xml ... Parsing search results > "g:/Inetpub/wwwroot/ISB/data/121009.LC1.IT1.EC.S0XXXX.Ecoli_1-B,1_01_3621 > (X! Tandem (k-score))"... => Total of 1623 hits. => Total of 0 decoy hits. > => Total of 0 excluded hits. command completed in 1 sec running: > "G:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > g:/Inetpub/wwwroot/ISB/data/interact.pep.xml" This application has > requested the Runtime to terminate it in an unusual way. Please contact the > application's support team for more information. command > "G:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > g:/Inetpub/wwwroot/ISB/data/interact.pep.xml" failed: Unknown error command > "G:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > g:/Inetpub/wwwroot/ISB/data/interact.pep.xml" exited with non-zero exit > code: 255 QUIT - the job is incomplete command > "g:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > 121009.LC1.IT1.EC.S0XXXX.Ecoli_1-B,1_01_3621.tandem.pep.xml" failed: > Unknown error > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/dZT8y3fYhfYJ. > 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. 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