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: 139QUIT - 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 ?? -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/45d0f9f4-898b-4533-9934-50835616d8d4%40googlegroups.com.
