Hi, I am trying to run peptideprophet on Phosphoproteomics Data from Lumos.
I am using the following command line on comet search results (note: Tandem kscore went through successfully) *xinteract -OARPwd -dDECOY_ -N/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml *.comet.pep.xml* *This is my output log:* xinteract (TPP v5.2.0 Flammagenitus, Build 201903181054-exported (Linux-x86_64)) running: "/hpc/apps/TPP/5.2.0/bin/DatabaseParser '/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml'" command completed in 24 sec running: "/hpc/apps/TPP/5.2.0/bin/RefreshParser '/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml' '/scratch/soetkampd/iphronesis/reference_files/Databases/Uniprot_rat_8060_20190321_DECOY.fasta'" - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 264 sec running: "/hpc/apps/TPP/5.2.0/bin/PeptideProphetParser '/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml' ACCMASS RT NONPARAM INSTRWARN DECOYPROBS DECOY=DECOY_" using Accurate Mass Bins using RT Using no error on different instrument types. Using Decoy Label "DECOY_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution adding Retention Time mixture distr init with Comet trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: Orbitrap Fusion, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20.....Estimating Retention Time Model ... please wait ... model complete after 26 iterations command completed in 5180 sec running: "/hpc/apps/TPP/5.2.0/bin/ProphetModels.pl -i /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml -d "DECOY_"" Analyzing /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml ... Reading Accurate Mass Model model +1 ... Reading kernel density RTCalc RT [RT] model +1 ... Reading Accurate Mass Model model +2 ... Reading kernel density RTCalc RT [RT] model +2 ... Reading Accurate Mass Model model +3 ... Reading kernel density RTCalc RT [RT] model +3 ... Reading Accurate Mass Model model +4 ... Reading kernel density RTCalc RT [RT] model +4 ... Reading Accurate Mass Model model +5 ... Reading kernel density RTCalc RT [RT] model +5 ... Reading Accurate Mass Model model +6 ... Reading kernel density RTCalc RT [RT] model +6 ... Reading Accurate Mass Model model +7 ... Reading kernel density RTCalc RT [RT] model +7 ... Parsing search results "/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_54_Phospho_centroid (Comet)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) .... .... .... Parsing search results "/scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_01_Phospho_centroid (Comet)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) command completed in 5 sec running: "/hpc/apps/TPP/5.2.0/cgi-bin/PepXMLViewer.cgi -I /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml" *command "/hpc/apps/TPP/5.2.0/cgi-bin/PepXMLViewer.cgi -I /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.comet.interact.pep.xml" exited with non-zero exit code: 139* *QUIT - the job is incomplete* *This is my error log:* INFO: Results written to file: /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/peptideprophet/2018.kscore.interact.pep.xml - Building Commentz-Walter keyword tree... PeptideProphet (TPP v5.2.0 Flammagenitus, Build 201903181054-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 495215 2+, 990646 3+, 429079 4+, 105824 5+, 0 6+, and 0 7+ spectra. Found 971133 Decoys, and 1049631 Non-Decoys Run Index: /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_30_Phospho_centroid, slope=0.510115, intercept=665.195, r_sq=0.633259 Run Index: /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_09_Phospho_centroid, slope=0.420776, intercept=663.458, r_sq=0.679369 WARNING: Not enough correlation r_sq=0.268561 between theoretical RT values and scan numbers in run index /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_55_Phospho_centroid. RT Model has been disabled. .... .... .... WARNING: Not enough correlation r_sq=0.296415 between theoretical RT values and scan numbers in run index /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_14_Phospho_centroid. RT Model has been disabled. Run Index: /scratch/soetkampd/iphronesis/platform_workspace/jobs/SJOB2018/msconvert/DS_190126_DDA_H9C2_14_Phospho_centroid, slope=0.425669, intercept=394.448, r_sq=0.296415 WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). *I am wondering if there is something i might have missed in my command-line (specifically needed for Phospho data) or if this is a memory issue since i do have 60 DDA runs. Any advice on how to debug this will be highly appreciated.* *I am happy to make these files available via Box if needed.* Regards, Elva -- 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]. 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