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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Crash on processing tims tof pro mgf (from msconvert) #121

Closed bsphinney closed 5 years ago

bsphinney commented 5 years ago

Log

System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_211, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190222 Philosopher version v1.1.2 (build 1560970349)

LCMS files: Experiment/Group: 1

35 commands to execute: Workspace [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init MsFragger [Work dir: C:\brett\ttp] java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\brett\fragpipe\Brett\MSFragger-20190222\MSFragger-20190222\MSFragger-20190222.jar C:\brett\ttp\fragger.params C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.mgf C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.mgf C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.mgf MsFragger java -cp C:\brett\fragpipe\FragPipe.exe umich.msfragger.util.FileMove C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pepXML C:\brett\ttp\1\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pepXML MsFragger java -cp C:\brett\fragpipe\FragPipe.exe umich.msfragger.util.FileMove C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.pepXML C:\brett\ttp\2\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.pepXML MsFragger java -cp C:\brett\fragpipe\FragPipe.exe umich.msfragger.util.FileMove C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.pepXML C:\brett\ttp\3\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.pepXML ReportDbAnnotate [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe database --annotate C:\brett\fragpipe\2018-11-02-td-UP000005640.fas --prefix rev ReportDbAnnotate [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe database --annotate C:\brett\fragpipe\2018-11-02-td-UP000005640.fas --prefix rev ReportDbAnnotate [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe database --annotate C:\brett\fragpipe\2018-11-02-td-UP000005640.fas --prefix rev ReportDbAnnotate [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe database --annotate C:\brett\fragpipe\2018-11-02-td-UP000005640.fas --prefix rev PeptideProphet [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\brett\fragpipe\2018-11-02-td-UP000005640.fas 190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.pepXML PeptideProphet [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\brett\fragpipe\2018-11-02-td-UP000005640.fas 190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pepXML PeptideProphet [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\brett\fragpipe\2018-11-02-td-UP000005640.fas 190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.pepXML iProphet [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe iprophet --decoy rev --nonsp --output interact --threads 14 C:\brett\ttp\2\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.pep.xml C:\brett\ttp\1\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pep.xml C:\brett\ttp\3\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.pep.xml ProteinProphet [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 C:\brett\ttp\2\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.pep.xml C:\brett\ttp\1\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pep.xml C:\brett\ttp\3\interact-190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.pep.xml ReportFilter [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\brett\ttp\2 --protxml C:\brett\ttp\interact.prot.xml ReportFilter [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\brett\ttp\3 --protxml C:\brett\ttp\interact.prot.xml ReportFilter [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\brett\ttp\1 --protxml C:\brett\ttp\interact.prot.xml ReportFreequant [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\brett\ttp ReportFreequant [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\brett\ttp ReportFreequant [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\brett\ttp ReportReport [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe report --mzid ReportReport [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe report --mzid ReportReport [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe report --mzid ReportAbacus [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windowsamd64\philosopher.exe abacus --razor --reprint --tag rev --protein C:\brett\ttp\interact.prot.xml --peptide C:\brett\ttp\interact.pep.xml 2 3 1 Workspace [Work dir: C:\brett\ttp] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\1] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\2] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\brett\ttp\3] C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean


Workspace [Work dir: C:\brett\ttp]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean
INFO[14:18:03] Executing Workspace v1.1.2                   
INFO[14:18:04] Removing workspace                           
INFO[14:18:04] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init
INFO[14:18:04] Executing Workspace v1.1.2                   
INFO[14:18:04] Creating workspace                           
INFO[14:18:04] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\1]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean
INFO[14:18:04] Executing Workspace v1.1.2                   
INFO[14:18:05] Removing workspace                           
INFO[14:18:05] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\1]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init
INFO[14:18:05] Executing Workspace v1.1.2                   
INFO[14:18:05] Creating workspace                           
INFO[14:18:05] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\2]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean
INFO[14:18:06] Executing Workspace v1.1.2                   
INFO[14:18:06] Removing workspace                           
INFO[14:18:06] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\2]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init
INFO[14:18:06] Executing Workspace v1.1.2                   
INFO[14:18:07] Creating workspace                           
INFO[14:18:07] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\3]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --clean
INFO[14:18:07] Executing Workspace v1.1.2                   
WARN[14:18:07] GitHub unreachable for the moment, can't check for versions right now. 
INFO[14:18:07] Removing workspace                           
INFO[14:18:07] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\brett\ttp\3]
C:\brett\fragpipe\philosopher_v1.1.2_windows_amd64\philosopher.exe workspace --init
INFO[14:18:07] Executing Workspace v1.1.2                   
WARN[14:18:07] GitHub unreachable for the moment, can't check for versions right now. 
INFO[14:18:07] Creating workspace                           
INFO[14:18:07] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: C:\brett\ttp]
java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\brett\fragpipe\Brett\MSFragger-20190222\MSFragger-20190222\MSFragger-20190222.jar C:\brett\ttp\fragger.params C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.mgf C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep2_90min_gradient_Slot2-19_01_3372.mgf C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep3_90min_gradient_Slot2-19_01_3373.mgf
MSFragger version MSFragger-20190222
MSFTBX version 1.8.6
(c) University of Michigan

System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_211, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 18204MB memory

Unknown parmameters:
    calibrate_mass = 1
    decoy_prefix = rev_
    delta_mass_exclude_ranges = (-1.5,3.5)
    fragment_ion_series = b,y
    localize_delta_mass = 0
Peptide index read in 301ms
Selected fragment tolerance 0.20 Da and maximum fragment slice size of 13693.15MB
418266908 fragments to be searched in 1 slices (3.12GB total)
Operating on slice 1 of 1: 2761ms
    190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.mgf Exception in thread "main" java.lang.reflect.InvocationTargetException
    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 com.simontuffs.onejar.Boot.run(Boot.java:340)
    at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 16384
    at java.util.concurrent.FutureTask.report(Unknown Source)
    at java.util.concurrent.FutureTask.get(Unknown Source)
    at edu.umich.andykong.msfragger.l.a(Unknown Source)
    at edu.umich.andykong.msfragger.o.a(Unknown Source)
    at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source)
    at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source)
    ... 6 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: 16384
    at edu.umich.andykong.msfragger.l.a(Unknown Source)
    at edu.umich.andykong.msfragger.m.run(Unknown Source)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Process 'MsFragger' finished, exit code: 1

Process returned non-zero exit code, stopping
MsFragger
java -cp C:\brett\fragpipe\FragPipe.exe umich.msfragger.util.FileMove C:\brett\ttp\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pepXML C:\brett\ttp\1\190329_Aurora_UCDAVIS_HeLa_spike_A_R1_2_Rep1_90min_gradient_Slot2-19_01_3371.pepXML

Stopping 27/36 processes (9 already finished) Processing interrupted, stopping MsFragger

Parameters

database_name = C:\brett\fragpipe\2018-11-02-td-UP000005640.fas num_threads = 14 # 0=poll CPU to set num threads; else specify num threads directly (max 64)

precursor_mass_lower = -20 precursor_mass_upper = 20 precursor_mass_units = 1 # 0=Daltons, 1=ppm precursor_true_tolerance = 20 precursor_true_units = 1 # 0=Daltons, 1=ppm fragment_mass_tolerance = 40 fragment_mass_units = 1 # 0=Daltons, 1=ppm calibrate_mass = 1 # 0=Off, 1=On, 2=On and find optimal parameters decoyprefix = rev

isotope_error = 0/1/2 # 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) precursor_mass_mode = selected

localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y

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

maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini

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

variable_mod_06 = 0.00000 site_06

variable_mod_07 = 0.00000 site_07

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 report_alternative_proteins = 0 # 0=no, 1=yes

precursor_charge = 1 4 # 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)

open search parameters

track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin zero_bin_accept_expect = 0.00 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable zero_bin_mult_expect = 1.00 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect) add_topN_complementary = 0

spectral processing

minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10) use_topN_peaks = 150 min_fragments_modelling = 2 min_matched_fragments = 4 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

additional modifications

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

fcyu commented 5 years ago

Hi,

Thanks for your interest in MSFragger. Since MGF format has many flavor of its title, we need an example of yours so that we can add it to the parser function.

Thanks,

Fengchao

anesvi commented 5 years ago

Best to use mzML/mzXML from MSConvert, this is what we really support well

From: Fengchao [mailto:notifications@github.com] Sent: Wednesday, June 26, 2019 5:41 PM To: Nesvilab/FragPipe Cc: Subscribed Subject: Re: [Nesvilab/FragPipe] Crash on processing tims tof pro mgf (from msconvert) (#121)

External Email - Use Caution

Hi,

Thanks for your interest in MSFragger. Since MGF format has many flavor of its title, we need an example of yours so that we can add it to the parser function.

Thanks,

Fengchao

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/121?email_source=notifications&email_token=AIIMM64EI2IIXEDXGNUTDDLP4PPAHA5CNFSM4H3WFJJ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYU42NQ#issuecomment-506055990, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM67P26OOQO7RRCSE6PDP4PPAHANCNFSM4H3WFJJQ.

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