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. 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