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
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