Hi all, I am trying to run TPP with the my command
xinteract -eN -p0 -dDECOY -OpPdAMN *files for my comet searched files as my search enzyme is Formic Acid. However TPP seems like it is unable to complete the analysis for generating the Peptide Prophet Probabilities and thus cannot go through Protein Prophet analysis. Below is the log file for the TPP's analysis. Is there any way that I can send my files through TPP and have a complete analysis? xinteract (TPP v4.8.0 PHILAE, Build 201710121955-exported (CentOS-x86_64)) running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/InteractParser 'interact.pep.xml' '1.pep.xml' -L'7' -E'nonspecific'" file 1: 1.pep.xml SUCCESS: CORRECTED data file /home/rostlab/annieha/BSA/mzML/1.mzML in msms_run_summary tag ... processed altogether 6293 results INFO: Results written to file: /home/rostlab/annieha/BSA/comet/interact.pep.xml command completed in 2 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/DatabaseParser 'interact.pep.xml'" command completed in 0 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/RefreshParser 'interact.pep.xml' '/home/rostlab/annieha/BSA/BSA_target_decoy.fasta'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 0 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/PeptideProphetParser 'interact.pep.xml' MINPROB=0 DECOY=DECOY DECOYPROBS NONPARAM ACCMASS NONMC NONTT" using Accurate Mass Bins Using Decoy Label "DECOY". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (Comet) (minprob 0) adding Accurate Mass mixture distr init with Comet nonspecific MS Instrument info: Manufacturer: unknown, Model: unknown, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.8.0 PHILAE, Build 201710121955-exported (CentOS-x86_64)) AKeller@ISB read in 0 1+, 29 2+, 20 3+, 16 4+, 65 5+, 44 6+, and 0 7+ spectra. Initialising statistical models ... Found 87 Decoys, and 87 Non-Decoys Iterations: .........10.........20. WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). 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+). model complete after 22 iterations command completed in 1 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl -i interact.pep.xml -d "DECOY"" Analyzing interact.pep.xml ... Reading Accurate Mass Model model +1 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 217. Reading Accurate Mass Model model +2 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 374. Reading Accurate Mass Model model +3 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 531. Reading Accurate Mass Model model +4 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 688. Reading Accurate Mass Model model +5 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 845. Reading Accurate Mass Model model +6 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 1002. Reading Accurate Mass Model model +7 ... Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 311, <INFILE> line 1159. Parsing search results "/home/rostlab/annieha/BSA/mzML/1 (Comet)"... => Found 174 hits. (87 decoys, 0 excluded) => Total so far: 174 hits. (87 decoys, 0 excluded) Using decoy ratio of 0.5 for PeptideProphet. Can't exec "/usr/bin/gnuplot": No such file or directory at /home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProphetModels.pl line 903. command completed in 62 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/cgi-bin/PepXMLViewer.cgi -I /home/rostlab/annieha/BSA/comet/interact.pep.xml" command completed in 1 sec running: "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProteinProphet 'interact.pep.xml' 'interact.prot.xml' XML" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.8.0 PHILAE, Build 201710121955-exported (CentOS-x86_64)) (xml input) (no FPKM) (report Protein Length) (using degen pep info) . . . reading in /home/rostlab/annieha/BSA/comet/interact.pep.xml. . . . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 WARNING: no data - output file will be empty command "/home/rostlab/hrost/bin/tpp/tpp4.8/bin/ProteinProphet 'interact.pep.xml' 'interact.prot.xml' XML" exited with non-zero exit code: 256 QUIT - the job is incomplete Thanks, Annie Ha -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
