Dear All,
When I run the TPP pipeline with downloaded version of the
development prerelease of TPP dated 22-04-2010, I am getting 0 hits
whereas when I run pipeline with release version of TPP (TPP v4.3
(jetstream) rev 1) for the same data and parameters, I am getting 822
hits.
------------------------------------------------------------------------------------------------------------------------------------------------------------------
Here is the STDOUT when I run the TPP pipeline with
development version downloaded on 22-04-2010
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development
prerelease) rev 0, Build 201006041141 (linux))
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan-
J78.pepprophet.xml' 'jagan-J78.pep.xml' -L'7'"
file 1: jagan-J78.pep.xml
processed altogether 3429 results
results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-
J78.pepprophet.shtml
command completed in 1 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'jagan-
J78.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20"
(X! Tandem (k-score))
init with X! Tandem (k-score) trypsin
MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ
Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector:
inductive detector
Initialising statistical models ...
Iterations: .........10.........20........
model complete after 29 iterations
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i jagan-
J78.pepprophet.xml"
Analyzing jagan-J78.pepprophet.xml ...
Parsing search results "jagan-J77 (X! Tandem (k-score))"...
=> Total of 0 hits.
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan-
J78.pepprophet.xml'"
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan-
J78.pepprophet.xml' '/home/APCF/databases/SwissProt/
uniprot_sprot.fasta'"
- Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 3 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /
mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml"
command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /mnt/
sanfs/APCF/results/tpp/2010-06-23/jagan-J78.pepprophet.xml" exited
with non-zero exit code: 11
QUIT - the job is incomplete
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the
original Perl by A. Keller (TPP v4.4 JETSTREAM (unstable development
prerelease) rev 0, Build 201006041141 (linux))
(xml input) (report Protein Length) (using degen pep info)
. . . reading in /mnt/sanfs/APCF/results/tpp/2010-06-23/jagan-
J78.pepprophet.xml. . .
did not find any PeptideProphet results in input data! Did you forget
to run PeptideProphet?
. . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with
min prob 0.05
no data - quitting
==============================================================================
But when I run the same thing with release version of TPP (TPP v4.3
(jetstream) rev 1) everything went OK.
Here is the STDOUT message ....
---------------------------------------------------------------------------------------------------------------------------------------------------------------
[r...@compute-3-0 temp]# pwd
/mnt/sanfs/APCF/results/tpp/2010-06-23/temp
[r...@compute-3-0 temp]# ls
jagan-J77.mzXML jagan-J77.xml
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/Tandem2XML jagan-J77.xml jagan-J78.pep.xml
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/InteractParser jagan-J78.pepprophet.xml jagan-J78.pep.xml -
L7
file 1: jagan-J78.pep.xml
processed altogether 3429 results
results written to file /mnt/sanfs/APCF/results/tpp/2010-06-23/temp/
jagan-J78.pepprophet.shtml
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/PeptideProphetParser jagan-J78.pepprophet.xml MINPROB=0.05
EXTRAITRS=20
(X! Tandem (k-score))
init with X! Tandem (k-score) trypsin
MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ
Orbitrap, Ionization: nanoelectrospray, Analyzer: orbitrap, Detector:
inductive detector
PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 201003241044
(linux)) akel...@isb
read in 1127 1+, 1355 2+, 361 3+, 54 4+, 0 5+, 0 6+, and 0 7+
spectra.
Initialising statistical models ...
negmean = -0.490485
negmean = -0.0225753
negmean = -0.520051
negmean = 0.801738
negmean = -0.2
negmean = -0.2
negmean = -0.2
Iterations: .........10.........20........
WARNING: Mixture model quality test failed for charge (1+).
model complete after 29 iterations
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/ProphetModels.pl -i jagan-J78.pepprophet.xml
Analyzing jagan-J78.pepprophet.xml ...
Parsing search results "jagan-J77 (X! Tandem (k-score))"...
=> Total of 822 hits.
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/DatabaseParser jagan-J78.pepprophet.xml
/home/APCF/databases/SwissProt/uniprot_sprot.fasta
[r...@compute-3-0 temp]# /share/apps/TPP431/trans_proteomic_pipeline/
build/linux/RefreshParser jagan-J78.pepprophet.xml /home/APCF/
databases/SwissProt/uniprot_sprot.fasta
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...
[r...@compute-3-0 temp]#
==============================================================================
I wonder whether there is any quick fix to this problem. Something
broken from the release version to development version.
with regards,
Jagan Kommineni
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