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, <[email protected] <javascript:>> 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, <[email protected]> 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, <[email protected]> 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 [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. >>>>>> >>>>> >>>>> -- >>>> 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. >>>> >>> >>> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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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