exit code 35584 when running xinteract

[Andreas Quandt]

dear list,


when running following command (tpp 4.3.1)

/usr/local/apps/tpp/bin/xinteract -N/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml -dDECOY_ -OAlIwp /IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml


i get following error:


---------------------------------------------
/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/45/Xinteract_/Xinteract.pep.xml' '/IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml' -L'7'"
file 1: /IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml
processed altogether 1290 results


results written to file /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.shtml



command completed in 0 sec
running: "/usr/local/apps/tpp/bin/PeptideProphetParser '/IMSB/results/workflow/45/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_".
(X! Tandem)
WARNING: Found unanticipated cleavage in refinement mode.  Turning off NTT model.
adding Accurate Mass mixture distr
adding pI mixture distr
init with X! Tandem 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+, 1135 2+, 137 3+, 18 4+, 0 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+).
model complete after 28 iterations
command completed in 1 sec
running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml"
Analyzing /IMSB/results/workflow/45/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 "/IMSB/scratch/andreas/O08-10105_c (X! Tandem)"...
 => Total of 0 hits.
Warning: empty y range [0:0], adjusting to [0:1]
Warning: empty y range [0:0], adjusting to [0:1]

plot "/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_PPPROB.tsv" using 2:1 title "PeptideProphet" with line  lc 2  , x notitle with line lt 0 lc -1
                                                                                                                   ^
"/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_PPPROB.gp", line 16: warning: Skipping data file with no valid points

plot "/IMSB/results/workflow/45/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/45/Xinteract_/Xinteract.pep_IPPROB.gp", line 16: warning: Skipping data file with no valid points
command completed in 0 sec
running: "/usr/local/apps/tpp/bin/DatabaseParser '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml'"
command completed in 0 sec
running: "/usr/local/apps/tpp/bin/RefreshParser '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml' '/IMSB/data/databases/uniprot/sp_9606.fasta'"
 - Building Commentz-Walter keyword tree...  - Searching the tree...
 - Linking duplicate entries...  - Printing results...

command completed in 1 sec
running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml"
Segmentation fault

command "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml" exited with non-zero exit code: 35584
QUIT - the job is incomplete
---------------------------------------


can someone explain me what the error code means and what i am doing wrong?

p.s.

i played a little bit around with the parameter but get always the same error message.
i also checked the output of the xtandem run (contains over 1000 valid models) and also the pep.xml (which is valid).

-- 
Andreas Quandt, PhD
Institute of Molecular Systems Biology
Swiss Federal Institute of Technology Zurich (ETH)
Wolfgang-Pauli-Str. 16
ETH Hönggerberg, HPT D 76
CH-8093 Zürich

Tel:  +41 44 633 3449
Fax:  +41 44 633 1051
Mobil:+41 78 899 5206 E-mail: qua...@imsb.biol.ethz.ch

[Brian Pratt]

My guess is its nothing you're doing wrong - iProphet is still pretty new and it's probably confusing the PepXMLViewer parser.  If you can upload the file that crashed pepXMLViewer to ftp://insilicos.serveftp.net/pub I Natalie or I will be happy to have a look.

 

Brian

[Andreas Quandt]

hi brian,

many thanks for looking into it!
i also tried to process the file with different options but always the same error.
it would be awesome if you (or natalie) could test the uploaded files (andreasquandt_090918.zip) as i otherwise do not know how to solve this problem :-(.

cheers,
andreas

[David Shteynberg]

Hi Andreas,

I think you are doing everything correctly. The soruce of the problem is here:

PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux))
AKeller@ISB
read in 0 1+, 1135 2+, 137 3+, 18 4+, 0 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+).

PeptideProphet modeling seems to have failed on your most abundant
charges. You can try to force the model fitting to see if the
invalidation of the mixture model (PeptideProphet QC) was warranted,
the xinteract option for this is -OF . I would not recommend using
this option for anything other than double check invalidated mixture
models. It is more likely that there is some problem with either the
data the database or the search parameters that are causing this run
to have very few positive IDs.

-David


On Fri, Sep 18, 2009 at 11:30 AM, Andreas Quandt