Very likely bad data (or bad analysis), since there are very few spectra: " read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra."
The modeling fails after that (see the warnings) which means that likely no data were written to an output file. Check your search results first. Cheers, --Luis On Tue, Mar 22, 2016 at 11:59 AM, Jimmy Eng <jke...@gmail.com> wrote: > Now that I look back, I could be interpreting the whole thing wrong. The > "\mydata (Comet)" might be completely normal and not meaning to reflect a > directory path but rather simply indicate that it's a Comet search. > Anyways, I don't use the Windows GUI much so I'm not the right person to > help you here beyond noting that it is complaining about a path problem. > > On Tue, Mar 22, 2016 at 11:53 AM, <bx2016...@gmail.com> wrote: > >> Hi Jimmy, >> >> I used the GUI (http://localhost/tpp-bin/tpp_gui.pl) to do what I did. >> The "\data (Comet)" part was spit out by the system. I was also puzzled by >> that myself. I clearly selected the input file (mydata.pep.xml) from a >> valid folder. I am going to try to do it from the command line using the >> "cheat" method that Brian suggested earlier. >> >> Thanks, >> >> Bob >> >> On Tuesday, March 22, 2016 at 2:40:15 PM UTC-4, Jimmy Eng wrote: >>> >>> The error is that "The system cannot find the path specified" which >>> appears to be "c:\Inetpub\wwwroot\ISB\data\mydata\mydata (Comet)\". If >>> that is the problem, get rid of the space in the directory path "\data >>> (Comet)". You should get in the habit of also not including any special >>> characters (like the parenthesis) in the path or the file names. If you >>> just stick with letters, numbers, dashes "-", and underscores "_" then you >>> won't have issues later. >>> >>> So rename the directory and try again. >>> >>> - Jimmy >>> >>> On Tue, Mar 22, 2016 at 11:18 AM, <bx20...@gmail.com> wrote: >>> >>>> Hi Jimmy, >>>> >>>> I updated comet.exe and comet.params (I grabbed comet.params.high-high >>>> because mydata was from QExactive). The database search itself seemed to >>>> have worked. But when I did Analyze Peptides, an error occurred. Please see >>>> the message below. Could you please take a look? >>>> >>>> Thanks, >>>> >>>> Bob >>>> >>>> c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 >>>> (mingw-i686)) >>>> PPM mode in Accurate Mass Model ... >>>> >>>> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>>> "mydata.pep.xml" -L"7"" >>>> file 1: mydata.pep.xml >>>> SUCCESS: CORRECTED data file >>>> c:\Inetpub\wwwroot\ISB\data\mydata\mydata.mzXML in msms_run_summary tag ... >>>> processed altogether 664 results >>>> INFO: Results written to file: >>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml >>>> command completed in 1 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" >>>> command completed in 0 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" >>>> "c:/Inetpub/wwwroot/ISB/data/dbase/speclibs/human_uniprot_sprot.fasta"" >>>> - Searching the tree... >>>> - Linking duplicate entries... - Printing results... >>>> >>>> - Building Commentz-Walter keyword tree...command completed in 3 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >>>> MINPROB=0.05 PPM" >>>> using PPM mass difference >>>> (Comet) >>>> init with Comet trypsin >>>> MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, >>>> Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >>>> >>>> PeptideProphet (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) >>>> AKeller@ISB >>>> read in 57 1+, 27 2+, 2 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >>>> Initialising statistical models ... >>>> 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+). >>>> model complete after 22 iterations >>>> command completed in 0 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml" >>>> Analyzing interact.pep.xml ... >>>> Parsing search results "c:\Inetpub\wwwroot\ISB\data\mydata\mydata >>>> (Comet)"... >>>> => Found 0 hits. (0 decoys, 0 excluded) >>>> => Total so far: 0 hits. (0 decoys, 0 excluded) >>>> The system cannot find the path specified. >>>> command completed in 0 sec >>>> >>>> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" >>>> >>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" failed: Unknown >>>> error >>>> >>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/Inetpub/wwwroot/ISB/data/parameters/interact.pep.xml" exited with >>>> non-zero exit code: 255 >>>> QUIT - the job is incomplete >>>> >>>> >>>> *Command FAILED* >>>> RETURN CODE:65280 >>>> >>>> >>>> On Tuesday, March 22, 2016 at 11:49:23 AM UTC-4, Jimmy Eng wrote: >>>>> >>>>> Besides using a very old version of Comet, there's nothing wrong with >>>>> the parameter settings that would indicate why you might see an extremely >>>>> long search. As Brian and Mike suggested, it's likely Comet's not even >>>>> running right now for whatever reason. >>>>> >>>>> You're using version 2014.02 rev. 2 that was released in September >>>>> 2014. Before doing anything else, it's in your best interest to update to >>>>> the latest 2016.01 rev. 0 release that you can download from here: >>>>> >>>>> https://sourceforge.net/projects/comet-ms/files/ >>>>> >>>>> Grab the file comet_binaries_2016010.zip. Find your current Comet >>>>> binary (should be at c:\inetpub\tpp-bin\comet.exe) and replace it with the >>>>> binary in this zip file (rename comet.2016010.win64.exe to >>>>> c:\inetpub\tpp-bin\comet.exe). Then generate a new comet.params file or >>>>> grab the comet.params.low-low >>>>> <http://comet-ms.sourceforge.net/parameters/parameters_201601/comet.params.low-low> >>>>> from link below and rename to comet.params in the appropriate directory >>>>> and >>>>> attempt a search again. >>>>> >>>>> http://comet-ms.sourceforge.net/parameters/parameters_201601/ >>>>> >>>>> This search should complete in well under 10 minutes and not hours or >>>>> days. Try the search again with the current Comet binary and report back >>>>> if you still have issues. >>>>> >>>>> - Jimmy >>>>> >>>>> On Tue, Mar 22, 2016 at 8:16 AM, <bx20...@gmail.com> wrote: >>>>> >>>>>> Hi Jimmy, Brian and Mike, >>>>>> >>>>>> Thank you all for your replies. Please see below the content of my >>>>>> comet.params file (again, this came with TPP installation, I did not >>>>>> modify >>>>>> it). >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Bob >>>>>> >>>>>> # comet_version 2014.02 rev. 2 >>>>>> # Comet MS/MS search engine parameters file. >>>>>> # Everything following the '#' symbol is treated as a comment. >>>>>> >>>>>> database_name = /some/path/db.fasta >>>>>> decoy_search = 0 # 0=no (default), >>>>>> 1=concatenated search, 2=separate search >>>>>> >>>>>> num_threads = 0 # 0=poll CPU to set num >>>>>> threads; else specify num threads directly (max 64) >>>>>> >>>>>> # >>>>>> # masses >>>>>> # >>>>>> peptide_mass_tolerance = 3.00 >>>>>> peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm >>>>>> mass_type_parent = 1 # 0=average masses, >>>>>> 1=monoisotopic masses >>>>>> mass_type_fragment = 1 # 0=average masses, >>>>>> 1=monoisotopic masses >>>>>> isotope_error = 0 # 0=off, 1=on -1/0/1/2/3 >>>>>> (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling) >>>>>> >>>>>> # >>>>>> # search enzyme >>>>>> # >>>>>> search_enzyme_number = 1 # choose from list at end of >>>>>> this params file >>>>>> num_enzyme_termini = 2 # valid values are 1 >>>>>> (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term >>>>>> allowed_missed_cleavage = 2 # maximum value is 5; for >>>>>> enzyme search >>>>>> >>>>>> # >>>>>> # Up to 9 variable modifications are supported >>>>>> # format: <mass> <residues> <0=variable/1=binary> >>>>>> <max_mods_per_peptide> <term_distance> <n/c-term> >>>>>> # e.g. 79.966331 STY 0 3 -1 0 >>>>>> # >>>>>> variable_mod01 = 15.9949 M 0 3 -1 0 >>>>>> variable_mod02 = 0.0 X 0 3 -1 0 >>>>>> variable_mod03 = 0.0 X 0 3 -1 0 >>>>>> variable_mod04 = 0.0 X 0 3 -1 0 >>>>>> variable_mod05 = 0.0 X 0 3 -1 0 >>>>>> variable_mod06 = 0.0 X 0 3 -1 0 >>>>>> variable_mod07 = 0.0 X 0 3 -1 0 >>>>>> variable_mod08 = 0.0 X 0 3 -1 0 >>>>>> variable_mod09 = 0.0 X 0 3 -1 0 >>>>>> max_variable_mods_in_peptide = 5 >>>>>> >>>>>> # >>>>>> # fragment ions >>>>>> # >>>>>> # ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), >>>>>> theoretical_fragment_ions = 1 >>>>>> # high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), >>>>>> theoretical_fragment_ions = 0 >>>>>> # >>>>>> fragment_bin_tol = 1.0005 # binning to use on fragment >>>>>> ions >>>>>> fragment_bin_offset = 0.4 # offset position to start the >>>>>> binning (0.0 to 1.0) >>>>>> theoretical_fragment_ions = 1 # 0=use flanking peaks, 1=M >>>>>> peak only >>>>>> use_A_ions = 0 >>>>>> use_B_ions = 1 >>>>>> use_C_ions = 0 >>>>>> use_X_ions = 0 >>>>>> use_Y_ions = 1 >>>>>> use_Z_ions = 0 >>>>>> use_NL_ions = 1 # 0=no, 1=yes to consider >>>>>> NH3/H2O neutral loss peaks >>>>>> use_sparse_matrix = 0 >>>>>> >>>>>> # >>>>>> # output >>>>>> # >>>>>> output_sqtstream = 0 # 0=no, 1=yes write sqt to >>>>>> standard output >>>>>> output_sqtfile = 0 # 0=no, 1=yes write sqt file >>>>>> output_txtfile = 0 # 0=no, 1=yes write >>>>>> tab-delimited txt file >>>>>> output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml >>>>>> file >>>>>> output_percolatorfile = 0 # 0=no, 1=yes write >>>>>> Percolator tab-delimited input file >>>>>> output_outfiles = 0 # 0=no, 1=yes write .out files >>>>>> print_expect_score = 1 # 0=no, 1=yes to replace Sp >>>>>> with expect in out & sqt >>>>>> num_output_lines = 5 # num peptide results to show >>>>>> show_fragment_ions = 0 # 0=no, 1=yes for out files >>>>>> only >>>>>> >>>>>> sample_enzyme_number = 1 # Sample enzyme which is >>>>>> possibly different than the one applied to the search. >>>>>> # Used to calculate NTT & NMC >>>>>> in pepXML output (default=1 for trypsin). >>>>>> >>>>>> # >>>>>> # mzXML parameters >>>>>> # >>>>>> scan_range = 0 0 # start and scan scan range to >>>>>> search; 0 as 1st entry ignores parameter >>>>>> precursor_charge = 0 0 # precursor charge range to >>>>>> analyze; does not override any existing charge; 0 as 1st entry ignores >>>>>> parameter >>>>>> override_charge = 0 # 0=no, 1=yes to override >>>>>> existing precursor charge states with precursor_charge parameter >>>>>> ms_level = 2 # MS level to analyze, valid >>>>>> are levels 2 (default) or 3 >>>>>> activation_method = ALL # activation method; used if >>>>>> activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD >>>>>> >>>>>> # >>>>>> # misc parameters >>>>>> # >>>>>> digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to >>>>>> analyze >>>>>> num_results = 50 # number of search hits to >>>>>> store internally >>>>>> skip_researching = 1 # for '.out' file output only, >>>>>> 0=search everything again (default), 1=don't search if .out exists >>>>>> max_fragment_charge = 3 # set maximum fragment charge >>>>>> state to analyze (allowed max 5) >>>>>> max_precursor_charge = 6 # set maximum precursor charge >>>>>> state to analyze (allowed max 9) >>>>>> nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward >>>>>> three, 8=reverse three, 9=all six >>>>>> clip_nterm_methionine = 0 # 0=leave sequences as-is; >>>>>> 1=also consider sequence w/o N-term methionine >>>>>> spectrum_batch_size = 0 # max. # of spectra to search >>>>>> at a time; 0 to search the entire scan range in one loop >>>>>> decoy_prefix = DECOY_ # decoy entries are denoted by >>>>>> this string which is pre-pended to each protein accession >>>>>> output_suffix = # add a suffix to output base >>>>>> names i.e. suffix "-C" generates base-C.pep.xml from base.mzXML input >>>>>> >>>>>> # >>>>>> # spectral processing >>>>>> # >>>>>> minimum_peaks = 10 # required minimum number of >>>>>> peaks in spectrum to search (default 10) >>>>>> minimum_intensity = 0 # minimum intensity value to >>>>>> read in >>>>>> remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge >>>>>> reduced precursor peaks (for ETD) >>>>>> remove_precursor_tolerance = 1.5 # +- Da tolerance for >>>>>> precursor removal >>>>>> clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; >>>>>> will clear out all peaks in the specified m/z range >>>>>> >>>>>> # >>>>>> # additional modifications >>>>>> # >>>>>> >>>>>> add_Cterm_peptide = 0.0 >>>>>> add_Nterm_peptide = 0.0 >>>>>> add_Cterm_protein = 0.0 >>>>>> add_Nterm_protein = 0.0 >>>>>> >>>>>> add_G_glycine = 0.0000 # added to G - avg. 57.0513, >>>>>> mono. 57.02146 >>>>>> add_A_alanine = 0.0000 # added to A - avg. 71.0779, >>>>>> mono. 71.03711 >>>>>> add_S_serine = 0.0000 # added to S - avg. 87.0773, >>>>>> mono. 87.03203 >>>>>> add_P_proline = 0.0000 # added to P - avg. 97.1152, >>>>>> mono. 97.05276 >>>>>> add_V_valine = 0.0000 # added to V - avg. 99.1311, >>>>>> mono. 99.06841 >>>>>> add_T_threonine = 0.0000 # added to T - avg. 101.1038, >>>>>> mono. 101.04768 >>>>>> add_C_cysteine = 57.021464 # added to C - avg. 103.1429, >>>>>> mono. 103.00918 >>>>>> add_L_leucine = 0.0000 # added to L - avg. 113.1576, >>>>>> mono. 113.08406 >>>>>> add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, >>>>>> mono. 113.08406 >>>>>> add_N_asparagine = 0.0000 # added to N - avg. 114.1026, >>>>>> mono. 114.04293 >>>>>> add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, >>>>>> mono. 115.02694 >>>>>> add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, >>>>>> mono. 128.05858 >>>>>> add_K_lysine = 0.0000 # added to K - avg. 128.1723, >>>>>> mono. 128.09496 >>>>>> add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, >>>>>> mono. 129.04259 >>>>>> add_M_methionine = 0.0000 # added to M - avg. 131.1961, >>>>>> mono. 131.04048 >>>>>> add_O_ornithine = 0.0000 # added to O - avg. 132.1610, >>>>>> mono 132.08988 >>>>>> add_H_histidine = 0.0000 # added to H - avg. 137.1393, >>>>>> mono. 137.05891 >>>>>> add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, >>>>>> mono. 147.06841 >>>>>> add_R_arginine = 0.0000 # added to R - avg. 156.1857, >>>>>> mono. 156.10111 >>>>>> add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, >>>>>> mono. 163.06333 >>>>>> add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, >>>>>> mono. 186.07931 >>>>>> add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, >>>>>> mono. 0.00000 >>>>>> add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, >>>>>> mono. 0.00000 >>>>>> add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, >>>>>> mono. 0.00000 >>>>>> add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, >>>>>> mono. 0.00000 >>>>>> add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, >>>>>> mono. 0.00000 >>>>>> >>>>>> # >>>>>> # COMET_ENZYME_INFO _must_ be at the end of this parameters file >>>>>> # >>>>>> [COMET_ENZYME_INFO] >>>>>> 0. No_enzyme 0 - - >>>>>> 1. Trypsin 1 KR P >>>>>> 2. Trypsin/P 1 KR - >>>>>> 3. Lys_C 1 K P >>>>>> 4. Lys_N 0 K - >>>>>> 5. Arg_C 1 R P >>>>>> 6. Asp_N 0 D - >>>>>> 7. CNBr 1 M - >>>>>> 8. Glu_C 1 DE P >>>>>> 9. PepsinA 1 FL P >>>>>> 10. Chymotrypsin 1 FWYL P >>>>>> >>>>>> >>>>>> On Monday, March 21, 2016 at 5:39:46 PM UTC-4, Jimmy Eng wrote: >>>>>>> >>>>>>> It would be helpful if you post (or send me) the search parameters >>>>>>> which is the contents of the comet.params file. >>>>>>> >>>>>>> On Mon, Mar 21, 2016 at 2:11 PM, <bx20...@gmail.com> wrote: >>>>>>> >>>>>>>> Hi everyone, >>>>>>>> >>>>>>>> I started a Comet search in TPP three days ago and it is still >>>>>>>> going three days later. I must have messed up something without knowing >>>>>>>> because TPP did not generate any error message. Did anyone else have >>>>>>>> similar experience? Please see my system and TPP info below. >>>>>>>> >>>>>>>> HP Z600 Workstation >>>>>>>> Windows 7 Professional >>>>>>>> Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz >>>>>>>> Installed memory (RAM): 24.0 GB >>>>>>>> System type: 64-bit Operating System >>>>>>>> >>>>>>>> TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686) >>>>>>>> >>>>>>>> Comet search >>>>>>>> >>>>>>>> mzXML input file: mydata.mzXML (110 MB) >>>>>>>> generated using command line msconvert >>>>>>>> C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML >>>>>>>> --filter "mslevel 2" --filter "threshold count 100 most-intense" >>>>>>>> >>>>>>>> Comet Parameters file: comet.params (default, came with TPP >>>>>>>> installation) >>>>>>>> Sequence database: human_uniprot_sprot.fasta >>>>>>>> >>>>>>>> Any advice/pointer is greatly appreciated. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Bob Xiong >>>>>>>> >>>>>>>> -- >>>>>>>> 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 spctools-discu...@googlegroups.com. >>>>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>>>> Visit this group at >>>>>>>> https://groups.google.com/group/spctools-discuss. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> >>>>>>> -- >>>>>> 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 spctools-discu...@googlegroups.com. >>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>> 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 spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> 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 spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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