search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
205 stars 38 forks source link

problem parsing mzXML in MSFraggerGUI (v.6.0) #72

Closed bfriedrichgrube closed 6 years ago

bfriedrichgrube commented 6 years ago

Describe the problem

It seems like MSFraggerGUI does not parse my mzXML files.

System info

System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_172, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: MSFragger-GUI version 6.0 MSFragger version 20171106 Philosopher version 20180530 (build 201805301641)

Describe your experiment

Genral proteomics experiment description

Human ovarian cancer tissue, non-enriched

...

Input data files

DDA files mzXML format, converted with ProteoWizard, measured on TTOF 5600+

Sequence database

human fasta from uniprot: ex_sp_9606.fasta about 40MB

Attach fragger.params file

As I did a trial run, I used standard parameter for closed search.

num_threads = 4 # 0=poll CPU to set num threads; else specify num threads directly (max 64) precursor_mass_tolerance = 500.00 precursor_mass_lower = -500 # Overrides the lower bound of the window set by precursor_mass_tolerance precursor_mass_upper = 500 # Overrides the upper bound of the window set by precursor_mass_tolerance precursor_mass_units = 0 # 0=Daltons, 1=ppm precursor_true_tolerance = 20 precursor_true_units = 1 # 0=Daltons, 1=ppm fragment_mass_tolerance = 20 fragment_mass_units = 1 # 0=Daltons, 1=ppm isotope_error = 0 # 0=off, -1/0/1/2/3 (standard C13 error) mass_offsets = 0 # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue) search_enzyme_name = Trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion allowed_missed_cleavage = 1 # maximum value is 5 clip_nTerm_M = 1 variable_mod_01 = 15.99490 M variable_mod_02 = 42.01060 [^

variable_mod_03 = 79.96633 STY

variable_mod_04 = -17.02650 nQnC

variable_mod_05 = -18.01060 nE

allow_multiple_variable_mods_on_residue = 1 # static mods are not considered max_variable_mods_per_mod = 3 # maximum of 5 max_variable_mods_combinations = 5000 # maximum of 65534, limits number of modified peptides generated from sequence output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 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 digest_min_length = 7 digest_max_length = 50 digest_mass_range = 500.0 5000.0 # MH+ peptide mass range to analyze max_fragment_charge = 2 # set maximum fragment charge state to analyze (allowed max 5) track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin zero_bin_accept_expect = 0 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable zero_bin_mult_expect = 1 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect) add_topN_complementary = 0 minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10) use_topN_peaks = 100 min_fragments_modelling = 3 min_matched_fragments = 6 minimum_ratio = 0.01 # filter peaks below this fraction of strongest peak clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range add_Cterm_peptide = 0.000000 add_Nterm_peptide = 0.000000 add_Cterm_protein = 0.000000 add_Nterm_protein = 0.000000 add_G_glycine = 0.000000 add_A_alanine = 0.000000 add_S_serine = 0.000000 add_P_proline = 0.000000 add_V_valine = 0.000000 add_T_threonine = 0.000000 add_C_cysteine = 57.021464 add_L_leucine = 0.000000 add_I_isoleucine = 0.000000 add_N_asparagine = 0.000000 add_D_aspartic_acid = 0.000000 add_Q_glutamine = 0.000000 add_K_lysine = 0.000000 add_E_glutamic_acid = 0.000000 add_M_methionine = 0.000000 add_H_histidine = 0.000000 add_F_phenylalanine = 0.000000 add_R_arginine = 0.000000 add_Y_tyrosine = 0.000000 add_W_tryptophan = 0.000000 add_B_user_amino_acid = 0.000000 add_J_user_amino_acid = 0.000000 add_O_user_amino_acid = 0.000000 add_U_user_amino_acid = 0.000000 add_X_user_amino_acid = 0.000000 add_Z_user_amino_acid = 0.000000 database_name = X:\ex_sp_9606.fasta

Run log output

System info:
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_172, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info:
MSFragger-GUI version 6.0
MSFragger version 20171106
Philosopher version 20180530 (build 201805301641)

Will execute 31 commands:
java -jar -Xmx11G C:\Users\fbetty\Downloads\MSFragger-20171106\MSFragger-20171106\MSFragger-20171106.jar X:\MSfragger_20180713\fragger.params X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-1664-01A-01_D_W_JHU_140820.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-2056-01B-01_D_W_JHU_140612.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1404-01A-01_D_W_JHU_140808.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1409-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1410-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1482-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1483-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1485-01A-02_D_W_JHU_140822.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1487-01A-01_D_W_JHU_140820.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1488-01A-01_D_W_JHU_140808.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1489-01A-01_D_W_JHU_140612.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1492-01A-01_D_W_JHU_140817.mzXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML X:\MSfragger_20180713\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML X:\MSfragger_20180713\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML X:\MSfragger_20180713\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML X:\MSfragger_20180713\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML X:\MSfragger_20180713\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML X:\MSfragger_20180713\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML X:\MSfragger_20180713\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML 

java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML X:\MSfragger_20180713\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe workspace --clean 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe workspace --init 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20 interact-TCGA-09-1664-01A-01_D_W_JHU_140820.pep.xml interact-TCGA-09-2056-01B-01_D_W_JHU_140612.pep.xml interact-TCGA-13-1404-01A-01_D_W_JHU_140808.pep.xml interact-TCGA-13-1409-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1410-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1482-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1483-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1485-01A-02_D_W_JHU_140822.pep.xml interact-TCGA-13-1487-01A-01_D_W_JHU_140820.pep.xml interact-TCGA-13-1488-01A-01_D_W_JHU_140808.pep.xml interact-TCGA-13-1489-01A-01_D_W_JHU_140612.pep.xml interact-TCGA-13-1492-01A-01_D_W_JHU_140817.pep.xml 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe database --annotate X:\ex_sp_9606.fasta --prefix DECOY_ 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe filter --sequential --tag DECOY_ --pepxml X:\MSfragger_20180713 --protxml X:\MSfragger_20180713\interact.prot.xml 

C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe report 

~~~~~~~~~~~~~~~~~~~~~~

Executing command:
$> java -jar -Xmx11G C:\Users\fbetty\Downloads\MSFragger-20171106\MSFragger-20171106\MSFragger-20171106.jar X:\MSfragger_20180713\fragger.params X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-1664-01A-01_D_W_JHU_140820.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-2056-01B-01_D_W_JHU_140612.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1404-01A-01_D_W_JHU_140808.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1409-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1410-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1482-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1483-01A-01_D_W_JHU_140613.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1485-01A-02_D_W_JHU_140822.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1487-01A-01_D_W_JHU_140820.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1488-01A-01_D_W_JHU_140808.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1489-01A-01_D_W_JHU_140612.mzXML X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1492-01A-01_D_W_JHU_140817.mzXML 
Process started
MSFragger version MSFragger-20171106
(c) University of Michigan

Unknown parmameters:
    mass_offsets = 0

Sequence database filtered and tagged in 47ms

Digestion completed in 172ms
Merged digestion results in 63ms
Sorting digested sequences...

    of length 7: 238618
    of length 8: 216171

    of length 9: 212550

    of length 10: 188453

    of length 11: 173241

    of length 12: 158904
    of length 13: 149552

    of length 14: 133955
    of length 15: 126099

    of length 16: 113417
    of length 17: 104275

    of length 18: 96924
    of length 19: 90607

    of length 20: 81926
    of length 21: 76752
    of length 22: 70102
    of length 23: 65411

    of length 24: 60831
    of length 25: 56417
    of length 26: 51686
    of length 27: 48861
    of length 28: 45631

    of length 29: 42051
    of length 30: 39093
    of length 31: 35891
    of length 32: 33688
    of length 33: 30840
    of length 34: 28569
    of length 35: 25859
    of length 36: 24740
    of length 37: 22017
    of length 38: 20494

    of length 39: 18204
    of length 40: 17586
    of length 41: 16418
    of length 42: 14492
    of length 43: 12651
    of length 44: 10211
    of length 45: 8048
    of length 46: 5373
    of length 47: 3500
    of length 48: 2163
    of length 49: 1146
    of length 50: 701
    DONE
Removing duplicates and compacting...
Reduced to 2820919  peptides in 2469ms
Generating modified peptides...
DONE in 1047ms
Generated 4320910 modified peptides
Merging peptide pools from threads... DONE in 156ms
Sorting modified peptides by mass...
DONE in 328ms

Peptide index written in 828ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 7151.24MB
321303888 fragments to be searched in 1 slices (2.39GB total)
Operating on slice 1 of 1: 
12876ms
    TCGA-09-1664-01A-01_D_W_JHU_140820.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-09-1664-01A-01_D_W_JHU_140820.mzXML1389ms
    TCGA-09-2056-01B-01_D_W_JHU_140612.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-09-2056-01B-01_D_W_JHU_140612.mzXML610ms
    TCGA-13-1404-01A-01_D_W_JHU_140808.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1404-01A-01_D_W_JHU_140808.mzXML594ms
    TCGA-13-1409-01A-01_D_W_JHU_140613.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1409-01A-01_D_W_JHU_140613.mzXML718ms
    TCGA-13-1410-01A-01_D_W_JHU_140613.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1410-01A-01_D_W_JHU_140613.mzXML391ms
    TCGA-13-1482-01A-01_D_W_JHU_140613.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1482-01A-01_D_W_JHU_140613.mzXML312ms
    TCGA-13-1483-01A-01_D_W_JHU_140613.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1483-01A-01_D_W_JHU_140613.mzXML344ms
    TCGA-13-1485-01A-02_D_W_JHU_140822.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1485-01A-02_D_W_JHU_140822.mzXML313ms
    TCGA-13-1487-01A-01_D_W_JHU_140820.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1487-01A-01_D_W_JHU_140820.mzXML297ms
    TCGA-13-1488-01A-01_D_W_JHU_140808.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1488-01A-01_D_W_JHU_140808.mzXML296ms
    TCGA-13-1489-01A-01_D_W_JHU_140612.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1489-01A-01_D_W_JHU_140612.mzXML547ms
    TCGA-13-1492-01A-01_D_W_JHU_140817.mzXML 
java.lang.NullPointerException
    at umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser.parse(MZXMLRunHeaderParser.java:127)
    at umich.ms.fileio.filetypes.mzxml.MZXMLFile.parseRunInfo(MZXMLFile.java:88)
    at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
    at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:119)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763)
    at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747)
    at o.a(Unknown Source)
    at n.c(Unknown Source)
    at n.a(Unknown Source)
    at MSFragger.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

Error parsing: TCGA-13-1492-01A-01_D_W_JHU_140817.mzXML313ms

Process finished, exit value: 0
Executing command:
$> java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML X:\MSfragger_20180713\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML 
Process started
File does not exist: X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML
Process finished, exit value: 1
Previous process returned exit code [1], cancelling further processing..
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML X:\MSfragger_20180713\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML X:\MSfragger_20180713\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML X:\MSfragger_20180713\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML X:\MSfragger_20180713\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML X:\MSfragger_20180713\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML X:\MSfragger_20180713\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML X:\MSfragger_20180713\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML 
Cancelled execution of: 
java -cp C:\Users\fbetty\Downloads\MSFragger-GUI_v6.0\MSFragger-GUI.exe umich.msfragger.util.FileMove X:\CPTAC_IPF_161121\OpenMod_IPF_CPTAC_103\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML X:\MSfragger_20180713\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe workspace --clean 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe workspace --init 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-09-1664-01A-01_D_W_JHU_140820.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-09-2056-01B-01_D_W_JHU_140612.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1404-01A-01_D_W_JHU_140808.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1409-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1410-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1482-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1483-01A-01_D_W_JHU_140613.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1485-01A-02_D_W_JHU_140822.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1487-01A-01_D_W_JHU_140820.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1488-01A-01_D_W_JHU_140808.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1489-01A-01_D_W_JHU_140612.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe peptideprophet --decoy DECOY_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database X:\ex_sp_9606.fasta X:\MSfragger_20180713\TCGA-13-1492-01A-01_D_W_JHU_140817.pepXML 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20 interact-TCGA-09-1664-01A-01_D_W_JHU_140820.pep.xml interact-TCGA-09-2056-01B-01_D_W_JHU_140612.pep.xml interact-TCGA-13-1404-01A-01_D_W_JHU_140808.pep.xml interact-TCGA-13-1409-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1410-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1482-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1483-01A-01_D_W_JHU_140613.pep.xml interact-TCGA-13-1485-01A-02_D_W_JHU_140822.pep.xml interact-TCGA-13-1487-01A-01_D_W_JHU_140820.pep.xml interact-TCGA-13-1488-01A-01_D_W_JHU_140808.pep.xml interact-TCGA-13-1489-01A-01_D_W_JHU_140612.pep.xml interact-TCGA-13-1492-01A-01_D_W_JHU_140817.pep.xml 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe database --annotate X:\ex_sp_9606.fasta --prefix DECOY_ 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe filter --sequential --tag DECOY_ --pepxml X:\MSfragger_20180713 --protxml X:\MSfragger_20180713\interact.prot.xml 
Cancelled execution of: 
C:\Users\fbetty\Downloads\philosopher_windows_amd64.exe report 
=========================
===
===        Done
===
=========================
chhh commented 6 years ago

Something is wrong with the headers in the mzxml. Could you please:

  1. Share a sample mzxml file (dmitriya at umich edu).
  2. Try converting the files to mzML, mzML support is much better.
bfriedrichgrube commented 6 years ago

Hey thanks, I was also talking to some more people and got the same hint to convert the files again. I will try this. If it is not working then. I will send you an example file.