I just followed the instructions more or less from http://frank.neatstep.com/node/11 with the directory change from C:\ to D:\.
I've uploaded my httpd.conf file in the Files section. Hope this helps, Charles On Mar 16, 9:11 am, ChargedPeptide <[email protected]> wrote: > Hi, just wanted to let you know that pepXMLCGIViewer seems to hang > when processing reuslts where > > "X:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/ > 022710_G0311_P01129 > _PQD_01 (MASCOT)"... > => Total of 0 hits. > Happens, as in your case, regardless of me not having modified the > data directory.. > You should probably try a different set of data for double checking > this, where the final hits are >0. > > On Mar 15, 3:10 am, Vishal Swaroop <[email protected]> wrote: > > > > > Hi Charles, > > > I tried everything... but it is possible that I am missing something very > > small, should I also change tpp-bin path in httpd.conf. > > > It will be of great help if you can send your httpd.conf and tppgui.pl > > > It works for other files,but hangs on PepXMLViewer.cgi while creating > > .xml.index file.. > > > Pls help. > > > Regards > > Val > > > On Sat, Mar 13, 2010 at 8:48 PM, Charles <[email protected]> wrote: > > > Hey Val, so that also happened to me when I tried to change ONLY the > > > data location as you have. the xinteract got stuck somewhere as well, > > > probably the same place you got stuck. So just change all the > > > Directory tags to point to //server/Inetpub/ .. etc. And again make > > > sure you leave a copy of the tpp-bin on the C: since it seems like > > > some of the paths are hardcoded into the executables. > > > > Charles > > > > Mar 12, 10:23 am, Vishal Swaroop <[email protected]> wrote: > > > > Thanks for replying Charles... I tried the following, but it gets stuck > > > on > > > > running "PepXMLViewer.cgi" > > > > > If any one can help on this, I will be very thankful.... > > > > > Issue : > > > > When I run XInteract even from command prompt all processes like > > > > "InteractParser, PeptideProphetParser, ProphetModels, DatabaseParser, > > > > RefreshParser" runs fine BUT it gets stuck on running "PepXMLViewer.cgi" > > > > > Brief details : > > > > a) I have exact copy of Inetpub from my c drive to mapped network drive. > > > > > b) Consider my mapped drive is X: and I can see > > > > X:\Inetpub\wwwroot and X:\Inetpub\tpp-bin > > > > > c) I can also browse using \\server\Inetpub\ <file://server/Inetpub/> > > > > d) My httpd.conf looks like this i.e. changed data drive to > > > > *Alias /ISB "//server/Inetpub/wwwroot/ISB" > > > > <Directory "//server/Inetpub/wwwroot/ISB">* > > > > --------------------------------------------------------------------------- > > > -------------- > > > > AddType text/html .shtml > > > > AddHandler server-parsed .shtml > > > > SetEnv WEBSERVER_ROOT X:/Inetpub/wwwroot > > > > SetEnv WEBSERVER_URLhttp://localhost:80<http://localhost/> > > > > *Alias /ISB "//server/Inetpub/wwwroot/ISB" > > > > <Directory "//server/Inetpub/wwwroot/ISB"> > > > > * AllowOverride None > > > > Options Includes Indexes FollowSymLinks MultiViews > > > > Order allow,deny > > > > Allow from all > > > > AddType text/html .shtml > > > > AddHandler server-parsed .shtml > > > > </Directory> > > > > Alias /tpp-bin "C:/Inetpub/tpp-bin" > > > > <Directory "C:/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 /schema "C:/Inetpub/wwwroot/schema" > > > > <Directory "C:/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> > > > > --------------------------------------------------------------------------- > > > -------------- > > > > > e) changed "www_root" in tpp_gui.pl > > > > my $base_dir = readconfig('base_dir',"c:\\Inetpub\\tpp-bin\\"); # > > > full > > > > path to this file > > > > my $www_root = readconfig('www_root',"x:/Inetpub/wwwroot/"); # full > > > path > > > > to web server root > > > > my $data_dir = readconfig('data_dir',"${www_root}ISB/data/"); > > > # > > > > full path to data directory top-level > > > > > f) When I run XInteract even from command prompt all processes like > > > > "InteractParser, PeptideProphetParser, ProphetModels, DatabaseParser, > > > > RefreshParser" runs fine BUT it gets stuck on running "PepXMLViewer.cgi" > > > > > *"running: "X:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > > > interact.xml"" > > > > * > > > > > This is the out-put on command window.... > > > > --------------------------------------------------------------------------- > > > -------------------------- > > > > X:\Inetpub\wwwroot\ISB\data\SAN\aTPPiclData\server\Test_Executer\iTRAQ_Carb > > > amidomethyl_PQD_research>run_in > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research; > > > > x:\Inetpub\tpp-bin\xinteract -NTest_interact.xml -p0.000 -l20 -Op -dREV > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/02271 > > > 0_G0311_P01129_PQD_01.pep.xml > > > > x:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build > > > 200909091257 > > > > (MinGW)) > > > > running: "C:/Inetpub/tpp-bin/InteractParser "Test_interact.xml" > > > > "x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/0227 > > > 10_G0311_P01129_PQD_01.pep.xml" > > > > -L"20"" file 1: > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/02271 > > > 0_G0311_P01129_PQD_01.pep.xml > > > > processed altogether 1445 results > > > > > results written to file > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > > > interact.xml > > > > direct your browser > > > tohttp://localhost/ISB/data/SAN/iclData/server/Test_Executer/research/T... > > > > > command completed in 33 sec > > > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "Test_interact.xml" > > > > MINPROB=0.000 DECOY=REV" > > > > Using Decoy Label "REV". > > > > (MASCOT) (minprob 0) > > > > results for charge 1: 0 id tot and 0 adj scores > > > > results for charge 2: 1152 id tot and 213 adj scores > > > > results for charge 2: 11.1517 adj_ion_mean and 18.5814 adj_ion_hom mean > > > > 39.2id mean0.937465 correlation (r) > > > > 2+ ion - id = 1.15829*(ion - hom) + -10.371 with error = 6.88606 > > > > mean ion - id: 11.1517, mean ion - hom: 18.5814 > > > > results for charge 3: 274 id tot and 63 adj scores > > > > results for charge 3: 0.766935 adj_ion_mean and 14.5513 adj_ion_hom mean > > > > 39.8226id mean0.951025 correlation (r) > > > > 3+ ion - id = 1.20602*(ion - hom) + -16.7822 with error = 4.3439 > > > > mean ion - id: 0.766935, mean ion - hom: 14.5513 > > > > results for charge 4: 17 id tot and 0 adj scores > > > > results for charge 5: 2 id tot and 0 adj scores > > > > results for charge 6: 0 id tot and 0 adj scores > > > > results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id > > > > meannan > > > > correlation (r) > > > > results for charge 7: 0 id tot and 0 adj scores > > > > init with MASCOT trypsin > > > > MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ Orbitrap > > > > XL, > > > > Ionization: ESI, Analyzer: Ion Trap, Detector: EMT > > > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) > > > > akel...@isb > > > > read in 0 1+, 4 2+, 11 3+, 2 4+, 2 5+, 0 6+, and 0 7+ spectra. > > > > Initialising statistical models ... > > > > Iterations: .........10.........20 > > > > WARNING: Mixture model quality test failed for charge (2+). > > > > WARNING: Mixture model quality test failed for charge (3+). > > > > WARNING: Mixture model quality test failed for charge (4+). > > > > WARNING: Mixture model quality test failed for charge (5+). > > > > model complete after 21 iterations > > > > command completed in 19 sec > > > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i Test_interact.xml" > > > > Analyzing Test_interact.xml ... > > > > Parsing search results > > > > "X:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/0227 > > > 10_G0311_P01129 > > > > _PQD_01 (MASCOT)"... > > > > => Total of 0 hits. > > > > command completed in 3 sec > > > > running: "C:/Inetpub/tpp-bin/DatabaseParser "Test_interact.xml"" > > > > command completed in 1 sec > > > > running: "C:/Inetpub/tpp-bin/RefreshParser "Test_interact.xml" > > > > "X:/Inetpub/wwwroot/ISB/data/dataDrive/FASTA/IPI/HUMAN/IPI_HUMAN.fasta"" > > > > - Building Commentz-Walter keyword tree... - Searching the tree... > > > > - Linking duplicate entries... - Printing results... > > > > command completed in 59 sec > > > > running: "X:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > > > > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > > > interact.xml" > > > > ....gets stuck here forever > > > > --------------------------------------------------------------------------- > > > -------------------------- > > > > > Regards > > > > Val > > > > > On Thu, Mar 11, 2010 at 8:27 PM, Charles <[email protected]> > > > wrote: > > > > > Hi Val, > > > > > > Sorry for the generic description, I just wanted to keep it short. > > > > > But yes, D is just a partition on my local drive. I had a similar > > > > > situation to you when I just tried changing the > > > > > C:/Inetpub/wwwroot/ISB/ > > > > > data to D:/data or something. So if it's not going to be a hassle, > > > > > just copy the entire directory tree from C:/Inetpub to \\network > > > > > \Inetpub and make the appropriate changes in the WWWROOT and PATH to > > > > > reflect the change. > > > > > > I also found that you have to keep /tpp-bin in the default location on > > > > > the C: because it seems like some of programs (xinteract for one) have > > > > > the C:\Inetpub\tpp-bin path hard coded into the binary. > > > > > > Hope this helps, > > > > > Charles > > > > > > Vishal Swaroop wrote: > > > > > > Hi Charles, > > > > > > > For windows, is D drive local on your machine? > > > > > > > I am trying to right data to mapped network drive, when I run > > > XInteract > > > > > from > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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