xinteract exited with non-zero exit code: 139 [stuck on PeptideProphetParser command]

[sangramjit basu]

Hello,

I have successfully setup TPP tools in Red Hat Enterprise Server 7 and trying to analyze NALM6 [leukemia cell line] cell lysate protein extract and data is acquired from Sciex TripleTOF 6600 in DDA mode.

Now I execute this command:

xinteract -Ninteract.pep.xml -OARPd -dDECOY -I1 -I4 -I5 -THREADS=45 -i tandem_search_output.2019_07_19_00_16_40.t.xml NALM6_WO-ACETONE-1_CometS.pep.xml

[....I have executed comet and xtandem searches independently and not through TPP modules.]

Then the following messages are shown:

xinteract (TPP v5.2.0 Flammagenitus, Build 201908081732-exported (Linux-x86_64))
 using THREADS=45 for iProphet...

running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' 'tandem_search_output.2019_07_19_00_16_40.t.xml' 'NALM6_WO-ACETONE-1_CometS.pep.xml' -L'7'"
 file 1: tandem_search_output.2019_07_19_00_16_40.t.xml
 file 2: NALM6_WO-ACETONE-1_CometS.pep.xml
 processed altogether 121381 results
INFO: Results written to file: /data/proteomics_analysis/interact.pep.xml
command completed in 60 sec

running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
command completed in 1 sec

running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' '/data/proteomics_analysis/ipi.HUMAN.v3.87.fasta'"
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

command completed in 31 sec

running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY IGNORECHG=1 IGNORECHG=4 IGNORECHG=5"
using Accurate Mass Bins
using RT
Using Decoy Label "DECOY".
Decoy Probabilities will be reported.
Ignoring charge 1+ spectra.
Ignoring charge 4+ spectra.
Ignoring charge 5+ spectra.
Using non-parametric distributions
 (Comet)
adding ACCMASS mixture distribution
adding Retention Time mixture distr
init with Comet trypsin
MS Instrument info: Manufacturer: SCIEX, Model: TripleTOF 6600, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
 PeptideProphet  (TPP v5.2.0 Flammagenitus, Build 201908081732-exported (Linux-x86_64)) AKeller@ISB
 read in 13 1+, 43135 2+, 47498 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 0 Decoys, and 90646 Non-Decoys
WARNING: No decoys with label DECOY were found in this dataset. reverting to fully unsupervised method.
Iterations: .........10.........20Estimating Retention Time Model ... please wait ...
WARNING: Not enough IDs in run index /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1 to generate RT Gradient Correction.
WARNING: Not enough high probability IDs in run index /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1 to generate RT model. RT Model has been disabled.
Run Index: /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1, slope=-nan, intercept=-nan, r_sq=-nan
WARNING: Not enough high probability IDs in run index /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1 to generate RT model. RT Model has been disabled.
Run Index: /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1, slope=-nan, intercept=-nan, r_sq=-nan

command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY IGNORECHG=1 IGNORECHG=4 IGNORECHG=5" exited with non-zero exit code: 139
QUIT - the job is incomplete

Now error 139 is often associated to memory falling short but I have 200gb RAM....so what exactly am i doing wrong ?? or is it a bug ??

[David Shteynberg]

It appears there are several WARNINGS associated with running this command on this data. The first warning reads:   "WARNING: No decoys with label DECOY were found in this dataset. reverting to fully unsupervised method."  Are you sure you have decoy sequences labeled with "DECOY" prefix in your database?  The next two warnings read: "WARNING: Not enough IDs in run index /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1 to generate RT Gradient Correction.
WARNING: Not enough high probability IDs in run index /data/proteomics_analysis/NALM6-WO_ACETONE-1_MS1-NALM6-WO_ACETONE-1_MS1 to generate RT model. RT Model has been disabled."  So, it appears that this search generated not enough high probability results.  The most common reasons are: bad data, wrong parameters or wrong database.  In any case, the problem is likely upstream of the TPP.  Please check your data and parameters and run the search again.

-David

-David

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