How big is the pepXML file? Maybe you can share it so I can track the failure directly?
Thanks, -David On Thu, Jan 15, 2015 at 1:13 PM, Sarah Parker <[email protected]> wrote: > Thanks David, > > There weren't any errors, the search seemed to go OK - it's from an IP and > I am seeing peptides in the pep.xml from the target protein among the top > XCORR scores. > > The end of the file says this: > > </search_hit> > </search_result> > </spectrum_query> > </msms_run_summary> > </msms_pipeline_analysis> > > For the sake of completeness and maybe some insight, here is the first > portion of the pep.xml: > > <?xml version="1.0" encoding="UTF-8"?> > <msms_pipeline_analysis date="2015-01-15T12:16:05" xmlns=" > http://regis-web.systemsbiology.net/pepXML"; xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation=" > http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"; > summary_xml="c:\Inetpub\wwwroot\ISB\data\parameters\1hour_Set4_C.pep.xml"> > <msms_run_summary > base_name="c:\Inetpub\wwwroot\ISB\data\Data\SarahParker\1hour_Set4_C" > msManufacturer="" msModel="" raw_data_type="raw" raw_data=".mzXML"> > <sample_enzyme name="Trypsin"> > <specificity cut="KR" no_cut="P" sense="C"/> > </sample_enzyme> > <search_summary > base_name="c:\Inetpub\wwwroot\ISB\data\parameters\1hour_Set4_C" > search_engine="Comet" search_engine_version="2014.02 rev. 2" > precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" > search_id="1"> > <search_database > local_path="c:/Inetpub/wwwroot/ISB/data/Databases/uniprot_mouse_reviewed_canonical_Nov2014_iRT_DECOY.fasta" > type="AA"/> > <enzymatic_search_constraint enzyme="Trypsin" > max_num_internal_cleavages="2" min_number_termini="2"/> > <aminoacid_modification aminoacid="M" massdiff="15.994900" > mass="147.035385" variable="Y" symbol="*"/> > <aminoacid_modification aminoacid="S" massdiff="79.966331" > mass="166.998359" variable="Y" symbol="#"/> > <aminoacid_modification aminoacid="T" massdiff="79.966331" > mass="181.014010" variable="Y" symbol="#"/> > <aminoacid_modification aminoacid="Y" massdiff="79.966331" > mass="243.029660" variable="Y" symbol="#"/> > <aminoacid_modification aminoacid="C" massdiff="57.021464" > mass="160.030649" variable="N"/> > <parameter name="# comet_version " value="2014.02"/> > <parameter name="activation_method" value="ALL"/> > <parameter name="add_A_alanine" value="0.000000"/> > <parameter name="add_B_user_amino_acid" value="0.000000"/> > <parameter name="add_C_cysteine" value="57.021464"/> > <parameter name="add_Cterm_peptide" value="0.000000"/> > <parameter name="add_Cterm_protein" value="0.000000"/> > <parameter name="add_D_aspartic_acid" value="0.000000"/> > <parameter name="add_E_glutamic_acid" value="0.000000"/> > <parameter name="add_F_phenylalanine" value="0.000000"/> > <parameter name="add_G_glycine" value="0.000000"/> > <parameter name="add_H_histidine" value="0.000000"/> > <parameter name="add_I_isoleucine" value="0.000000"/> > <parameter name="add_J_user_amino_acid" value="0.000000"/> > <parameter name="add_K_lysine" value="0.000000"/> > <parameter name="add_L_leucine" value="0.000000"/> > <parameter name="add_M_methionine" value="0.000000"/> > <parameter name="add_N_asparagine" value="0.000000"/> > <parameter name="add_Nterm_peptide" value="0.000000"/> > <parameter name="add_Nterm_protein" value="0.000000"/> > <parameter name="add_O_ornithine" value="0.000000"/> > <parameter name="add_P_proline" value="0.000000"/> > <parameter name="add_Q_glutamine" value="0.000000"/> > <parameter name="add_R_arginine" value="0.000000"/> > <parameter name="add_S_serine" value="0.000000"/> > <parameter name="add_T_threonine" value="0.000000"/> > <parameter name="add_U_user_amino_acid" value="0.000000"/> > <parameter name="add_V_valine" value="0.000000"/> > <parameter name="add_W_tryptophan" value="0.000000"/> > <parameter name="add_X_user_amino_acid" value="0.000000"/> > <parameter name="add_Y_tyrosine" value="0.000000"/> > <parameter name="add_Z_user_amino_acid" value="0.000000"/> > <parameter name="allowed_missed_cleavage" value="2"/> > <parameter name="clear_mz_range" value="0.000000 0.000000"/> > <parameter name="clip_nterm_methionine" value="0"/> > <parameter name="database_name" > value="c:/Inetpub/wwwroot/ISB/data/Databases/uniprot_mouse_reviewed_canonical_Nov2014_iRT_DECOY.fasta"/> > <parameter name="decoy_prefix" value="DECOY_"/> > <parameter name="decoy_search" value="1"/> > <parameter name="digest_mass_range" value="600.000000 5000.000000"/> > <parameter name="fragment_bin_offset" value="0.000000"/> > <parameter name="fragment_bin_tol" value="0.020000"/> > <parameter name="isotope_error" value="1"/> > <parameter name="mass_type_fragment" value="1"/> > <parameter name="mass_type_parent" value="1"/> > <parameter name="max_fragment_charge" value="3"/> > <parameter name="max_precursor_charge" value="6"/> > <parameter name="max_variable_mods_in_peptide" value="5"/> > <parameter name="minimum_intensity" value="0"/> > <parameter name="minimum_peaks" value="10"/> > <parameter name="ms_level" value="2"/> > <parameter name="nucleotide_reading_frame" value="0"/> > <parameter name="num_enzyme_termini" value="2"/> > <parameter name="num_output_lines" value="5"/> > <parameter name="num_results" value="50"/> > <parameter name="num_threads" value="0"/> > <parameter name="output_outfiles" value="0"/> > <parameter name="output_pepxmlfile" value="1"/> > <parameter name="output_percolatorfile" value="0"/> > <parameter name="output_sqtfile" value="0"/> > <parameter name="output_sqtstream" value="0"/> > <parameter name="output_suffix" value=""/> > <parameter name="output_txtfile" value="0"/> > <parameter name="override_charge" value="0"/> > <parameter name="peptide_mass_tolerance" value="20.000000"/> > <parameter name="peptide_mass_units" value="2"/> > <parameter name="precursor_charge" value="0 0"/> > <parameter name="print_expect_score" value="1"/> > <parameter name="remove_precursor_peak" value="0"/> > <parameter name="remove_precursor_tolerance" value="1.500000"/> > <parameter name="sample_enzyme_number" value="1"/> > <parameter name="scan_range" value="0 0"/> > <parameter name="search_enzyme_number" value="1"/> > <parameter name="show_fragment_ions" value="0"/> > <parameter name="skip_researching" value="1"/> > <parameter name="spectrum_batch_size" value="5000"/> > <parameter name="theoretical_fragment_ions" value="0"/> > <parameter name="use_A_ions" value="0"/> > <parameter name="use_B_ions" value="1"/> > <parameter name="use_C_ions" value="0"/> > <parameter name="use_NL_ions" value="1"/> > <parameter name="use_X_ions" value="0"/> > <parameter name="use_Y_ions" value="1"/> > <parameter name="use_Z_ions" value="0"/> > <parameter name="use_sparse_matrix" value="1"/> > <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/> > <parameter name="variable_mod02" value="79.966331 STY 0 3 -1 0"/> > <parameter name="variable_mod03" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod04" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod05" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod06" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod07" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod08" value="0.000000 X 0 3 -1 0"/> > <parameter name="variable_mod09" value="0.000000 X 0 3 -1 0"/> > </search_summary> > > > > On Thursday, January 15, 2015 at 1:30:25 PM UTC-6, David Shteynberg wrote: >> >> Hello Sarah, >> >> Is your pepXML file 1hour_Set4_C.pep.xml complete? Did you observe any >> errors during the search? Can you look at the last few lines of that file, >> they should contain something like this: >> >> ... >> </analysis_result> </search_hit> </search_result> </spectrum_query> >> </msms_run_summary> </msms_pipeline_analysis> >> >> >> -David >> >> >> >> On Thu, Jan 15, 2015 at 10:30 AM, Sarah Parker <[email protected]> wrote: >> >>> Hello, >>> >>> Trying to run xinteract on comet search results (obtained via TPP). >>> >>> >>> >>> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/parameters& >>> c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM -OARP >>> -dDECOY 1hour_Set4_C.pep.xml *Getting this error: >>> >>> 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" >>> "1hour_Set4_C.pep.xml" -L"7"" >>> file 1: 1hour_Set4_C.pep.xml >>> SUCCESS: CORRECTED data file >>> c:\Inetpub\wwwroot\ISB\data\Data\SarahParker\1hour_Set4_C.mzXML in >>> msms_run_summary tag ... >>> >>> This application has requested the Runtime to terminate it in an unusual >>> way. >>> Please contact the application's support team for more information. >>> >>> command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>> "1hour_Set4_C.pep.xml" -L"7"" failed: Unknown error >>> >>> command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>> "1hour_Set4_C.pep.xml" -L"7"" exited with non-zero exit code: 255 >>> QUIT - the job is incomplete >>> >>> I can't figure out what's wrong, can anyone help? >>> >>> >>> -- >>> 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 http://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 http://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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