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]> 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]. > 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. 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