Dear All,
I am trying to run xinteract with the following command ...
/home/APCF/tpp/bin/xinteract -Njagan-J2906.pepprophet.xml -p0.05 -l7 -
x20 -O jagan-J2906.pep.xml
I cab able to view jagan-J2906.pep.xml with pepXMLViewer and
got 3209 unique peptides.
==============================================================================
trypsin digest, MASCOT search engine, quantitation: [none]
displaying 3489 of 3489 total spectra, page 1 of 70
3209 unique peptides, 3209 unique stripped peptides, 3209 unique
proteins, 3089 single hits
PepXML Viewer, 2006 SPC/ISB
==============================================================================
Here is the output the xinteract execution ....
=================================
[a...@apcf-hn3 2010-02-26]$ /home/APCF/tpp/bin/xinteract -Njagan-
J2906.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J2906.pep.xml
/home/APCF/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build
200912151720 (linux))
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan-
J2906.pepprophet.xml' 'jagan-J2906.pep.xml' -L'7'"
file 1: jagan-J2906.pep.xml
processed altogether 3489 results
results written to file /mnt/sanfs/APCF/results/tpp/2010-02-26/jagan-
J2906.pepprophet.shtml
command completed in 1 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'jagan-
J2906.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20"
(MASCOT)
results for charge 1: 1797 id tot and 0 adj scores
results for charge 2: 1399 id tot and 0 adj scores
results for charge 3: 259 id tot and 0 adj scores
results for charge 4: 34 id tot and 0 adj scores
results for charge 5: 0 id tot and 0 adj scores
results for charge 6: 0 id tot and 0 adj scores
results for charge 7: 0 id tot and 0 adj scores
init with MASCOT trypsin
MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ
Orbitrap, Ionization: NSI, Analyzer: FTMS, Detector: unknown
PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200912151720
(linux)) akel...@isb
read in 915 1+, 1372 2+, 247 3+, 34 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Iterations: .........10.........20....
WARNING: Mixture model quality test failed for charge (1+).
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+).
model complete after 25 iterations
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i jagan-
J2906.pepprophet.xml"
Analyzing jagan-J2906.pepprophet.xml ...
Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-02-26/jagan-
J2906 (MASCOT)"...
=> Total of 0 hits.
Could not find/open font when opening font "arial", using internal non-
scalable font
Warning: empty y range [0:0], adjusting to [0:1]
Could not find/open font when opening font "arial", using internal non-
scalable font
plot "jagan-J2906.pepprophet_PPPROB.tsv" using 2:1 title
"PeptideProphet" with line lc 2 , x notitle with line lt 0 lc -1
^
"jagan-J2906.pepprophet_PPPROB.gp", line 16: warning: Skipping data
file with no valid points
Could not find/open font when opening font "arial", using internal non-
scalable font
plot "jagan-J2906.pepprophet_IPPROB.tsv" using 2:1 title "iProphet"
with line lc 2 , x notitle with line lt 0 lc -1
^
"jagan-J2906.pepprophet_IPPROB.gp", line 16: warning: Skipping data
file with no valid points
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan-
J2906.pepprophet.xml'"
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan-
J2906.pepprophet.xml' '/mnt/sanfs/APCF/mascot/default/sequence/
LudwigNR/current/LudwigNR_Q409_generic_forward.fasta'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 69 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /
mnt/sanfs/APCF/results/tpp/2010-02-26/jagan-J2906.pepprophet.xml"
command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /mnt/
sanfs/APCF/results/tpp/2010-02-26/jagan-J2906.pepprophet.xml" exited
with non-zero exit code: 11
QUIT - the job is incomplete
[a...@apcf-hn3 2010-02-26]$
========================================================================
Results xml file (jagan-J2906.pepprophet.xml) has been uploaded to the
server and can be accessed with the following web pointer ...
---------------------------------------------------------------------------------------------------------------------------------------------------
http://spctools-discuss.googlegroups.com/web/jagan-J2906.pepprophet.xml?hl=en&gsc=3420SgsAAACVaNsKeeBwMvW1i4V39DLW
--------------------------------------------------------------------------------------------------------------------------------------------------
For your immediate reference sake, I am here with sending tail
contents of the result file (jagan-J2906.pepprophet.xml) ..
=============================================================================
<search_summary base_name="/mnt/sanfs/APCF/results/tpp/2010-02-26/
jagan-J2906" search_engine="MASCOT" precursor_mass_type="monoisotopic"
fragment_mass_type="monoisotopic" out_data_type="out" out_data=".tgz"
search_id="1">
<search_database local_path="/mnt/sanfs/APCF/mascot/default/sequence/
LudwigNR/current/LudwigNR_Q409_generic_forward.fasta" type="AA"/>
<enzymatic_search_constraint enzyme="trypsin"
max_num_internal_cleavages="1" min_number_termini="2"/>
<aminoacid_modification aminoacid="B" mass="114.534940"
massdiff="114.534940" variable="N"/>
<aminoacid_modification aminoacid="J" mass="0.000000"
massdiff="0.000000" variable="N"/>
<aminoacid_modification aminoacid="O" mass="0.000000"
massdiff="0.000000" variable="N"/>
<aminoacid_modification aminoacid="U" mass="150.953630"
massdiff="150.953630" variable="N"/>
<aminoacid_modification aminoacid="X" mass="111.000000"
massdiff="111.000000" variable="N"/>
<aminoacid_modification aminoacid="Z" mass="128.550590"
massdiff="128.550590" variable="N"/>
<parameter name="LICENSE" value="Licensed to: Australian Proteomics
Computational Facility, (64 processors)."/>
<parameter name="MP" value=""/>
<parameter name="NM" value=""/>
<parameter name="COM" value="Conversion of C:\Documents and Settings
\Jagan Kommineni\My Documents\APCF\temp\O080119-01.mzXML to mascot
generic"/>
<parameter name="IATOL" value=""/>
<parameter name="IA2TOL" value=""/>
<parameter name="IASTOL" value=""/>
<parameter name="IBTOL" value=""/>
<parameter name="IB2TOL" value=""/>
<parameter name="IBSTOL" value=""/>
<parameter name="IYTOL" value=""/>
<parameter name="IY2TOL" value=""/>
<parameter name="IYSTOL" value=""/>
<parameter name="SEG" value=""/>
<parameter name="SEGT" value=""/>
<parameter name="SEGTU" value=""/>
<parameter name="LTOL" value=""/>
<parameter name="TOL" value="1.2"/>
<parameter name="TOLU" value="Da"/>
<parameter name="ITH" value=""/>
<parameter name="ITOL" value="0.6"/>
<parameter name="ITOLU" value="Da"/>
<parameter name="PFA" value="1"/>
<parameter name="DB" value="LudwigNR"/>
<parameter name="MODS" value=""/>
<parameter name="MASS" value="Monoisotopic"/>
<parameter name="CLE" value="Trypsin"/>
<parameter name="FILE" value="jagan-J2907.mgf"/>
<parameter name="PEAK" value="AUTO"/>
<parameter name="QUE" value=""/>
<parameter name="TWO" value=""/>
<parameter name="SEARCH" value="MIS"/>
<parameter name="USERNAME" value=""/>
<parameter name="USEREMAIL" value=""/>
<parameter name="CHARGE" value="2+ and 3+"/>
<parameter name="INTERMEDIATE" value=""/>
<parameter name="REPORT" value="20"/>
<parameter name="OVERVIEW" value=""/>
<parameter name="FORMAT" value="Mascot generic"/>
<parameter name="FORMVER" value="1.01"/>
<parameter name="FRAG" value=""/>
<parameter name="IT_MODS" value=""/>
<parameter name="USER00" value=""/>
<parameter name="USER01" value=""/>
<parameter name="USER02" value=""/>
<parameter name="USER03" value=""/>
<parameter name="USER04" value=""/>
<parameter name="USER05" value=""/>
<parameter name="USER06" value=""/>
<parameter name="USER07" value=""/>
<parameter name="USER08" value=""/>
<parameter name="USER09" value=""/>
<parameter name="USER10" value=""/>
<parameter name="USER11" value=""/>
<parameter name="USER12" value=""/>
<parameter name="PRECURSOR" value=""/>
<parameter name="TAXONOMY" value="All entries"/>
<parameter name="ACCESSION" value=""/>
<parameter name="REPTYPE" value="peptide"/>
<parameter name="SUBCLUSTER" value="0"/>
<parameter name="ICAT" value=""/>
<parameter name="INSTRUMENT" value="Default"/>
<parameter name="ERRORTOLERANT" value=""/>
<parameter name="FRAMES" value=""/>
<parameter name="CUTOUT" value=""/>
<parameter name="USERID" value="1012"/>
<parameter name="QUANTITATION" value="None"/>
<parameter name="DECOY" value=""/>
<parameter name="PEP_ISOTOPE_ERROR" value="0"/>
<parameter name="RULES" value="1,2,5,6,8,9,13,14"/>
<parameter name="INTERNALS" value="0.0,700.0"/>
</search_summary>
<analysis_timestamp analysis="database_refresh"
time="2010-03-01T10:22:25" id="1">
<database_refresh_timestamp database="/mnt/sanfs/APCF/mascot/default/
sequence/LudwigNR/current/LudwigNR_Q409_generic_forward.fasta"/>
</analysis_timestamp>
<analysis_timestamp analysis="peptideprophet"
time="2010-03-01T10:22:25" id="1"/>
</msms_run_summary>
</msms_pipeline_analysis>
------------------------------------------------------------------------------------------------------------------------------------------------------------
It looks like the data relating spectrum_query, search_hit etc .. are
missing from the result file.
==============================================================================
When run PepXMLViewer.cgi on commandline then the result is
Segmentation fault
---------------------------------------------------------------------------------------------------------------------------
[a...@apcf-hn3 2010-02-26]$ /mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/
PepXMLViewer.cgi -I /mnt/sanfs/APCF/results/tpp/2010-02-26/jagan-
J2906.pepprophet.xml
Segmentation fault
=============================================================
However when I run /home/APCF/tpp/bin/xinteract -Njagan-
J2906.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J2906.pep.xml
I am able to produce and view the result file with PepXMLViewer ....
==========================================================================
Can anybody has any experience with this type of error message?
I wonder whether there is any check to see pepXML file is suitable to
run Prophets such as PeptideProphet and proteinProphet.
--------------------------------------------------------------------------------------------------------------------------------------------
with regards,
Jagan Kommineni
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