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 On Mon, Aug 12, 2019 at 4:58 AM sangramjit basu <[email protected]> wrote: > > > 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 > <https://groups.google.com/d/msgid/spctools-discuss/45d0f9f4-898b-4533-9934-50835616d8d4%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAGJJY%3D-WmViMpyzc4D-UXeNqp2ow33dCkr2OU2Z23cCCc89jNQ%40mail.gmail.com.
