exit code 6400 when running xinteract on spectrast
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Andreas Quandt
Sep 22, 2009, 12:57:06 PM9/22/09
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dear list,
i tried to process several files with spectrast but get this error code which unfortunately tells me nothing :-(
hopefully one of you can help me out here ...
cheers,
andreas
p.s. the output of the xinteract run looked as follow:
/usr/local/apps/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux))
running: "/usr/local/apps/tpp/bin/InteractParser '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' '/IMSB/results/workflow/158/init/O08-10100_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10105_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10114_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10107_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10093_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10094_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10102_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10096_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10104_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10095_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10111_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10098_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10116_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10099_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10103_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10106_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10112_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10097_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10109_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10108_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10113_c.pep.xml' '/IMSB/results/workflow/158/init/O08-10115_c.pep.xml' -L'7'"
file 1: /IMSB/results/workflow/158/init/O08-10100_c.pep.xml
file 2: /IMSB/results/workflow/158/init/O08-10105_c.pep.xml
file 3: /IMSB/results/workflow/158/init/O08-10114_c.pep.xml
file 4: /IMSB/results/workflow/158/init/O08-10107_c.pep.xml
file 5: /IMSB/results/workflow/158/init/O08-10093_c.pep.xml
file 6: /IMSB/results/workflow/158/init/O08-10094_c.pep.xml
file 7: /IMSB/results/workflow/158/init/O08-10102_c.pep.xml
file 8: /IMSB/results/workflow/158/init/O08-10096_c.pep.xml
file 9: /IMSB/results/workflow/158/init/O08-10104_c.pep.xml
file 10: /IMSB/results/workflow/158/init/O08-10095_c.pep.xml
file 11: /IMSB/results/workflow/158/init/O08-10111_c.pep.xml
file 12: /IMSB/results/workflow/158/init/O08-10098_c.pep.xml
file 13: /IMSB/results/workflow/158/init/O08-10116_c.pep.xml
file 14: /IMSB/results/workflow/158/init/O08-10099_c.pep.xml
file 15: /IMSB/results/workflow/158/init/O08-10103_c.pep.xml
file 16: /IMSB/results/workflow/158/init/O08-10106_c.pep.xml
file 17: /IMSB/results/workflow/158/init/O08-10112_c.pep.xml
file 18: /IMSB/results/workflow/158/init/O08-10097_c.pep.xml
file 19: /IMSB/results/workflow/158/init/O08-10109_c.pep.xml
file 20: /IMSB/results/workflow/158/init/O08-10108_c.pep.xml
file 21: /IMSB/results/workflow/158/init/O08-10113_c.pep.xml
file 22: /IMSB/results/workflow/158/init/O08-10115_c.pep.xml
processed altogether 99822 results
results written to file /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.shtml
command completed in 23 sec
running: "/usr/local/apps/tpp/bin/PeptideProphetParser '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' DECOY=DECOY_ ACCMASS LEAVE PI INSTRWARN"
using Accurate Mass Bins
using pI
Using no error on different instrument types.
Using Decoy Label "DECOY_".
(SpectraST)
adding Accurate Mass mixture distr
adding pI mixture distr
init with SpectraST trypsin
MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ Orbitrap XL, Ionization: ESI, Analyzer: ITMS, Detector: EMT
PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux)) AKeller@ISB
read in 0 1+, 75687 2+, 21029 3+, 2960 4+, 146 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Iterations: .........10.........20.........
model complete after 30 iterations
command completed in 79 sec
running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml"
Analyzing /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml ...
Reading Accurate Mass Model model +1 ...
Reading kernel density calc pI [pI] model +1 ...
Reading Accurate Mass Model model +2 ...
Reading kernel density calc pI [pI] model +2 ...
Reading Accurate Mass Model model +3 ...
Reading kernel density calc pI [pI] model +3 ...
Reading Accurate Mass Model model +4 ...
Reading kernel density calc pI [pI] model +4 ...
Reading Accurate Mass Model model +5 ...
Reading kernel density calc pI [pI] model +5 ...
Reading Accurate Mass Model model +6 ...
Reading kernel density calc pI [pI] model +6 ...
Reading Accurate Mass Model model +7 ...
Reading kernel density calc pI [pI] model +7 ...
Parsing search results "/home/andqua/O08-10100_c (SpectraST)"...
=> Total of 2389 hits.
Parsing search results "/home/andqua/O08-10105_c (SpectraST)"...
=> Total of 2321 hits.
Parsing search results "/home/andqua/O08-10114_c (SpectraST)"...
=> Total of 1933 hits.
Parsing search results "/home/andqua/O08-10107_c (SpectraST)"...
=> Total of 1949 hits.
Parsing search results "/home/andqua/O08-10093_c (SpectraST)"...
=> Total of 2660 hits.
Parsing search results "/home/andqua/O08-10094_c (SpectraST)"...
=> Total of 2756 hits.
Parsing search results "/home/andqua/O08-10102_c (SpectraST)"...
=> Total of 2743 hits.
Parsing search results "/home/andqua/O08-10096_c (SpectraST)"...
=> Total of 2813 hits.
Parsing search results "/home/andqua/O08-10104_c (SpectraST)"...
=> Total of 2457 hits.
Parsing search results "/home/andqua/O08-10095_c (SpectraST)"...
=> Total of 2889 hits.
Parsing search results "/home/andqua/O08-10111_c (SpectraST)"...
=> Total of 298 hits.
Parsing search results "/home/andqua/O08-10098_c (SpectraST)"...
=> Total of 454 hits.
Parsing search results "/home/andqua/O08-10116_c (SpectraST)"...
=> Total of 2116 hits.
Parsing search results "/home/andqua/O08-10099_c (SpectraST)"...
=> Total of 1861 hits.
Parsing search results "/home/andqua/O08-10103_c (SpectraST)"...
=> Total of 2690 hits.
Parsing search results "/home/andqua/O08-10106_c (SpectraST)"...
=> Total of 1997 hits.
Parsing search results "/home/andqua/O08-10112_c (SpectraST)"...
=> Total of 492 hits.
Parsing search results "/home/andqua/O08-10097_c (SpectraST)"...
=> Total of 2191 hits.
Parsing search results "/home/andqua/O08-10109_c (SpectraST)"...
=> Total of 743 hits.
Parsing search results "/home/andqua/O08-10108_c (SpectraST)"...
=> Total of 1959 hits.
Parsing search results "/home/andqua/O08-10113_c (SpectraST)"...
=> Total of 921 hits.
Parsing search results "/home/andqua/O08-10115_c (SpectraST)"...
=> Total of 2376 hits.
Warning: empty y range [0:0], adjusting to [0:1]
plot "/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lc 2 , x notitle with line lt 0 lc -1
^
"/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep_IPPROB.gp", line 16: warning: Skipping data file with no valid points
command completed in 6 sec
running: "/usr/local/apps/tpp/bin/DatabaseParser '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml'"
command completed in 1 sec
running: "/usr/local/apps/tpp/bin/RefreshParser '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' '/IMSB/data/databases/swissprot_57.7/sp_9606.fasta'"
- Building Commentz-Walter keyword tree... - Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 14 sec
running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml"
command completed in 6 sec
running: "/usr/local/apps/tpp/bin/ProteinProphet '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml' XML"
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux))
(xml input) (report Protein Length) (using degen pep info)
. . . reading in /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml. . .
. . . read in 0 1+, 33817 2+, 8212 3+, 926 4+, 53 5+, 0 6+, 0 7+ spectra with min prob 0.05
INFO: mu=4.69978e-06, db_size=90930969
protein probabilities written to file /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml
direct your browser to http://cal//IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.shtml
command completed in 71 sec
running: "/usr/local/apps/tpp/bin/ProtProphModels.pl -i /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml"
Illegal division by zero at /usr/local/apps/tpp/bin/ProtProphModels.pl line 231.
Analyzing /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml ...
command "/usr/local/apps/tpp/bin/ProtProphModels.pl -i /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml" exited with non-zero exit code: 6400
QUIT - the job is incomplete
Luis Mendoza
Sep 22, 2009, 1:14:45 PM9/22/09
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The error seems to be coming from ProtProphModels.pl:
But it seems that ProteinProphet finished; do those results look ok?
--Luis
Illegal division by zero at /usr/local/apps/tpp/bin/ProtProphModels.pl line 231.
--Luis
Andreas Quandt
Sep 22, 2009, 1:27:08 PM9/22/09
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hey luis,
i am not really sure if the results are okay or not (as there are far too many proteins in these results ;-) )
the file is successfully rendered by petunia but if the file has been fully created, i cannot judge :-( .
cheers,
andreas
i am not really sure if the results are okay or not (as there are far too many proteins in these results ;-) )
the file is successfully rendered by petunia but if the file has been fully created, i cannot judge :-( .
cheers,
andreas
David Shteynberg
Sep 22, 2009, 1:44:50 PM9/22/09
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This error can be safely ignored. It comes up because there is not
decoy tag specified when ProtProphModel.pl runs. You are correct that
this is no way to fail, this will be corrected in the future. Luis
already pointed to the problem so this would be a quick fix.
-David
On Tue, Sep 22, 2009 at 10:27 AM, Andreas Quandt
decoy tag specified when ProtProphModel.pl runs. You are correct that
this is no way to fail, this will be corrected in the future. Luis
already pointed to the problem so this would be a quick fix.
-David
On Tue, Sep 22, 2009 at 10:27 AM, Andreas Quandt
Luis Mendoza
Sep 22, 2009, 1:45:49 PM9/22/09
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Hi Andreas,
Try to re-run only ProteinProphet directly (not via xinteract) on the existing PeptideProphet results, and see if they match the ones you already have, or if you get any errors.
Cheers,
--Luis
Andreas Quandt
Sep 22, 2009, 2:17:59 PM9/22/09
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Hey David
Many thanks for the explanation :-)
Cheers
Andreas
On Sep 22, 2009, at 7:44 PM, David Shteynberg <dshte...@systemsbiology.org
Many thanks for the explanation :-)
Cheers
Andreas
On Sep 22, 2009, at 7:44 PM, David Shteynberg <dshte...@systemsbiology.org
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