Closed t-goul closed 3 years ago
fcyu
commented
3 years ago Could you help to check
ext folder in MSFragger.jar's folder?BatmassIoThermoServer running when checking the spectral file. Something like the following
Thanks,
Fengchao
kabalak
commented
3 years ago We also have this same error at the same stage: I am querying only one run as a .raw file from an Exploris480 (no FAIMS attached) and performing an open search with default settings + TSV export enabled. With MaxQuant 1.6.17.0 the same file runs perfectly. Converting the .raw file into a .mzML ahead of the search with MSConvert did not help either.
I checked also 1. we have an ext folder there, 2. BatmassIoThermoServer is busy several times until the error occurs and 3. other searches on this computer with other files (but just from a QE) worked out with the same MSFragger/FragPipe version, but with the Exploris480 file it seems problematic. Does MSFragger not like ProfileMode data or are Exploris480 .raws somehow problematic and not supported?
`System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group: HeLa_50ng
19 commands to execute: WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx119G C:\MSPrograms\fragpipe\MSFragger-3.1.1\MSFragger-3.1.1.jar E:\20210303_HeLa_Open\fragger.params E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.raw MsFragger move pepxml C:\MSPrograms\fragpipe\jre\bin\java.exe -cp C:\MSPrograms\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.pepXML E:\20210303_HeLa_Open\HeLa_50ng\20210302_HeLaStd_50ng_20210302133311.pepXML MsFragger move tsv C:\MSPrograms\fragpipe\jre\bin\java.exe -cp C:\MSPrograms\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.tsv E:\20210303_HeLa_Open\HeLa_50ng\20210302_HeLaStd_50ng_20210302133311.tsv Crystal-C [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\MSPrograms\fragpipe\MSFragger-3.1.1\ext\thermo" -Xmx119G -cp "C:\MSPrograms\fragpipe\tools\original-crystalc-1.3.2.jar;C:\MSPrograms\fragpipe\tools\batmass-io-1.19.5.jar;C:\MSPrograms\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run E:\20210303_HeLa_Open\HeLa_50ng\crystalc-0-20210302_HeLaStd_50ng_20210302133311.pepXML.params E:\20210303_HeLa_Open\HeLa_50ng\20210302_HeLaStd_50ng_20210302133311.pepXML PeptideProphet [Work dir: E:\20210303_HeLa_Open\HeLa50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MSPrograms\fragpipe\PHILOSOPHER_FASTAS\2020-09-04-decoys-isoforms-contam-UP000005640.fas --combine 20210302_HeLaStd_50ng_20210302133311_c.pepXML Rewrite pepxml [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\jre\bin\java.exe -cp C:\MSPrograms\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210303_HeLa_Open\HeLa_50ng\interact.pep.xml E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.raw ProteinProphet [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210303_HeLa_Open\HeLa_50ng\interact.pep.xml PhilosopherDbAnnotate [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MSPrograms\fragpipe\PHILOSOPHERFASTAS\2020-09-04-decoys-isoforms-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MSPrograms\fragpipe\PHILOSOPHERFASTAS\2020-09-04-decoys-isoforms-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: E:\20210303_HeLa_Open\HeLa50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml E:\20210303_HeLa_Open\HeLa_50ng --protxml E:\20210303_HeLa_Open\combined.prot.xml PhilosopherReport [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe report IonQuant [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\jre\bin\java.exe -Xmx119G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe\MSFragger-3.1.1\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe\MSFragger-3.1.1\ext\thermo" -cp "C:\MSPrograms\fragpipe\tools\ionquant-1.4.6.jar;C:\MSPrograms\fragpipe\tools\batmass-io-1.19.5.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 0 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_50ng\psm.tsv --multidir . --specdir E:\20210303_HeLa_Open HeLa_50ng\20210302_HeLaStd_50ng_20210302133311.pepXML WorkspaceClean [Work dir: E:\20210303_HeLa_Open\HeLa_50ng] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: E:\20210303_HeLa_Open] C:\MSPrograms\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\MSPrograms\fragpipe\MSFragger-3.1.1\ext\thermo" -cp "C:\MSPrograms\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\MSPrograms\fragpipe\tools\batmass-io-1.19.5.jar;C:\MSPrograms\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "E:\20210303_HeLa_Open\shepherd.config"
Execution order:
Cmd: [START], Work dir: [E:\20210303_HeLa_Open]
Cmd: [WorkspaceCleanInit], Work dir: [E:\20210303_HeLa_Open\HeLa_50ng]
Cmd: [WorkspaceCleanInit], Work dir: [E:\20210303_HeLa_Open]
Cmd: [MsFragger], Work dir: [E:\20210303_HeLa_Open]
Cmd: [Crystal-C], Work dir: [E:\20210303_HeLa_Open]
Cmd: [PeptideProphet], Work dir: [E:\20210303_HeLa_Open]
Cmd: [ProteinProphet], Work dir: [E:\20210303_HeLa_Open]
Cmd: [PhilosopherDbAnnotate], Work dir: [E:\20210303_HeLa_Open]
Cmd: [PhilosopherFilter], Work dir: [E:\20210303_HeLa_Open]
Cmd: [PhilosopherReport], Work dir: [E:\20210303_HeLa_Open]
Cmd: [IonQuant], Work dir: [E:\20210303_HeLa_Open]
Cmd: [WorkspaceClean], Work dir: [E:\20210303_HeLa_Open\HeLa_50ng]
Cmd: [WorkspaceClean], Work dir: [E:\20210303_HeLa_Open]
Cmd: [PTMShepherd], Work dir: [E:\20210303_HeLa_Open]
# FragPipe v14.0ui state cache
crystalc.run-crystalc=true
database.db-path=C\:\\MSPrograms\\fragpipe\\PHILOSOPHER_FASTAS\\2020-09-04-decoys-isoforms-contam-UP000005640.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\MSPrograms\\fragpipe\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=C\:\\MSPrograms\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Program Files\\Python39\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=tsv_pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01 --mapmods
phi-report.pep-level-summary=true
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=E\:\\20210303_HeLa_Open
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=0
WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open\HeLa_50ng]
C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck
INFO[21:11:54] Executing Workspace v3.4.13
INFO[21:11:54] Removing workspace
INFO[21:11:54] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open\HeLa_50ng]
C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck
INFO[21:11:54] Executing Workspace v3.4.13
INFO[21:11:54] Creating workspace
INFO[21:11:54] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open]
C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck
Process 'WorkspaceCleanInit' finished, exit code: 0
INFO[21:11:55] Executing Workspace v3.4.13
INFO[21:11:55] Removing workspace
INFO[21:11:55] Done
WorkspaceCleanInit [Work dir: E:\20210303_HeLa_Open]
C:\MSPrograms\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck
Process 'WorkspaceCleanInit' finished, exit code: 0
INFO[21:11:55] Executing Workspace v3.4.13
INFO[21:11:55] Creating workspace
INFO[21:11:55] Done
MsFragger [Work dir: E:\20210303_HeLa_Open]
C:\MSPrograms\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx119G C:\MSPrograms\fragpipe\MSFragger-3.1.1\MSFragger-3.1.1.jar E:\20210303_HeLa_Open\fragger.params E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.raw
MSFragger version MSFragger-3.1.1
Batmass-IO version 1.19.5
timsdata library version timsdata-2-7-0
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM,
JVM started with 105 GB memory
Checking database...
Checking E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.raw...
Checking if the data is low resolution MS/MS...
***FIRST SEARCH****
Parameters:
num_threads = 48
database_name = C:\MSPrograms\fragpipe\PHILOSOPHER_FASTAS\2020-09-04-decoys-isoforms-contam-UP000005640.fas
decoyprefix = rev
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
write_calibrated_mgf = false
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = CORRECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions =
search_enzyme_name = stricttrypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter =
num_enzyme_termini = 2
allowed_missed_cleavage = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = tsv_pepXML
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file =
mass_diff_to_variable_mod = 0
variable_mod_01 = 15.994900 M 3
variable_mod_02 = 42.010600 [^ 1
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_C_cysteine = 57.021460
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.000000
add_E_glutamic_acid = 0.000000
add_F_phenylalanine = 0.000000
add_G_glycine = 0.000000
add_H_histidine = 0.000000
add_I_isoleucine = 0.000000
add_J_user_amino_acid = 0.000000
add_K_lysine = 0.000000
add_L_leucine = 0.000000
add_M_methionine = 0.000000
add_N_asparagine = 0.000000
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da)
add_P_proline = 0.000000
add_Q_glutamine = 0.000000
add_R_arginine = 0.000000
add_S_serine = 0.000000
add_T_threonine = 0.000000
add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da)
add_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_X_user_amino_acid = 0.000000
add_Y_tyrosine = 0.000000
add_Z_user_amino_acid = 0.000000
Selected fragment index width 0.10 Da.
397096370 fragments to be searched in 1 slices (5.92 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 1.77 s
| **MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- | --------------- | --------------- | --------------- | --------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) |
|---|---|---|---|---|---|---|---|---|
| Run | Median MAD | Median MAD | Median MAD | Median MAD |
Process 'MsFragger' finished, exit code: 1 Process returned non-zero exit code, stoppingThere was an error in mass calibration. null There was an error in mass calibration. null MsFragger move pepxml C:\MSPrograms\fragpipe\jre\bin\java.exe -cp C:\MSPrograms\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove E:\20210303_HeLa_Open\20210302_HeLaStd_50ng_20210302133311.pepXML E:\20210303_HeLa_Open\HeLa_50ng\20210302_HeLaStd_50ng_20210302133311.pepXML
Cancelling 14 remaining tasks
Processing interrupted, stopping MsFragger move pepxml`H @kabalak ,
Could you send 20210302_HeLaStd_50ng_20210302133311.raw to us? Here (https://umich.app.box.com/f/3e27f91c77054be09822fceab1915a8f) is the link to upload the data.
Thanks,
Fengchao
kabalak
commented
3 years ago I have just uploaded the raw file - it is run with totally std. settings and recorded in Profile Mode; it is a tryptic shotgun of HeLa, 50 ng injected.
fcyu
commented
3 years ago Thanks @kabalak ,
I will take a look and get back to you ASAP.
Best,
Fengchao
fcyu
commented
3 years ago Hi @kabalak ,
Thanks for your file.
The error is caused by the scans with precursor mass < 200 Da in your data. We have fixed it by filtering out those scans in the pre-release version. Could you please try the version from https://umich.box.com/s/2kinfhsmnv5dvwmry40026hfn25jotlc?
Thanks,
Fengchao
anesvi
commented
3 years ago Is there a reason for generating MS/MS scans on such low m/z precursors?
Sent from my iPhone
On Mar 5, 2021, at 4:27 PM, Fengchao notifications@github.com wrote:
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Hi @kabalakhttps://github.com/kabalak ,
Thanks for your file.
The error is caused by the scans with precursor mass < 200 Da in your data. We have fixed it by filtering out those scans in the pre-release version. Could you please try the version from https://umich.box.com/s/2kinfhsmnv5dvwmry40026hfn25jotlc?
Thanks,
Fengchao
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kabalak
commented
3 years ago Hi @kabalak ,
Thanks for your file.
The error is caused by the scans with precursor mass < 200 Da in your data. We have fixed it by filtering out those scans in the pre-release version. Could you please try the version from https://umich.box.com/s/2kinfhsmnv5dvwmry40026hfn25jotlc?
Thanks,
Fengchao
Thanks for the "teaser" MSFragger Fengchao - it works nicely with that release. In this exact case, there was no real rationale why the low m/z precursor range.
t-goul
commented
3 years ago Could you help to check
1. Do you have the `ext` folder in MSFragger.jar's folder? 2. Is there a `BatmassIoThermoServer` running when checking the spectral file. Something like the following  3. Does your computer have a firewall preventing the ports from opening?Thanks,
Fengchao
Dear Fengchao,
I think the problem is the 3rd one. However, I don't know which programs you mean by the 'ports'.. Which programs should I be looking for when i am checking if they have firewall access?
Sorry for my slow reply, it has been a busy two weeks.
Regards, Thomas.
t-goul
commented
3 years ago @fcyu I have tagged you, in case you don't see my reply since the case is closed now.
fcyu
commented
3 years ago Hi Thomas,
Batmass-io in MSFragger needs to open a port to communicate with the module reading the raw file. If your computer has restrictions on the ports, you need to check with your IT department to troubleshoot. Or, you can convert the raw files to mzML according to the tutorial (https://msfragger.nesvilab.org/tutorial_convert.html), and re-do the search.
Best,
Fengchao
guoci
commented
2 years ago @t-goul to confirm that something is preventing the ports from opening, you can run the following on the command line
<PATH TO YOUR ext DIRECTORY>/thermo/BatmassIoThermoServer.exe.
If you see a line that says
BatmassIo Thermo server server running on port:
then that is not the case.
Dear Nesvi-lab, any thoughts on what might be going on here?
System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group: 2_1
64 commands to execute: WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\fragger.params C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.raw MsFragger move pepxml C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\20210116_JS_ECIG_DDA_406.pepXML MsFragger move tsv C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.tsv Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\20210116_JS_ECIG_DDA_406.tsv MsFragger move pepxml C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\20210116_JS_ECIG_DDA_407.pepXML MsFragger move tsv C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.tsv Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\20210116_JS_ECIG_DDA_407.tsv MsFragger move pepxml C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\20210116_JS_ECIG_DDA_408.pepXML MsFragger move tsv C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.tsv Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\20210116_JS_ECIG_DDA_408.tsv MsFragger move pepxml C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\20210116_JS_ECIG_DDA_409.pepXML MsFragger move tsv C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.tsv Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\20210116_JS_ECIG_DDA_409.tsv MsFragger move pepxml C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\20210116_JS_ECIG_DDA_410.pepXML MsFragger move tsv C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.tsv Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\20210116_JS_ECIG_DDA_410.tsv Crystal-C [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\crystalc-0-20210116_JS_ECIG_DDA_406.pepXML.params Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\20210116_JS_ECIG_DDA_406.pepXML Crystal-C [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\crystalc-1-20210116_JS_ECIG_DDA_410.pepXML.params Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\20210116_JS_ECIG_DDA_410.pepXML Crystal-C [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\crystalc-2-20210116_JS_ECIG_DDA_408.pepXML.params Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\20210116_JS_ECIG_DDA_408.pepXML Crystal-C [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\crystalc-3-20210116_JS_ECIG_DDA_407.pepXML.params Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\20210116_JS_ECIG_DDA_407.pepXML Crystal-C [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\crystalc-4-20210116_JS_ECIG_DDA_409.pepXML.params Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\20210116_JS_ECIG_DDA_409.pepXML PeptideProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\21] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\Users\970082_Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --combine 20210116_JS_ECIG_DDA_406_c.pepXML PeptideProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\22] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\Users\970082_Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --combine 20210116_JS_ECIG_DDA_407_c.pepXML PeptideProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\23] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\Users\970082_Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --combine 20210116_JS_ECIG_DDA_408_c.pepXML PeptideProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\24] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\Users\970082_Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --combine 20210116_JS_ECIG_DDA_409_c.pepXML PeptideProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\25] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\Users\970082_Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --combine 20210116_JS_ECIG_DDA_410_c.pepXML Rewrite pepxml [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\interact.pep.xml C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.raw Rewrite pepxml [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\interact.pep.xml C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.raw Rewrite pepxml [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\interact.pep.xml C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.raw Rewrite pepxml [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\interact.pep.xml C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.raw Rewrite pepxml [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\interact.pep.xml C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.raw ProteinProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\interact.pep.xml PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\970082Admin\Downloads\2021-01-28-decoys-contam-uniprot-proteome UP000000589.fasta.fas --prefix rev PhilosopherFilter [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\21] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1 --protxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\combined.prot.xml PhilosopherFilter [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\25] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5 --protxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\combined.prot.xml PhilosopherFilter [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\22] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2 --protxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\combined.prot.xml PhilosopherFilter [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\24] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4 --protxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\combined.prot.xml PhilosopherFilter [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\23] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev --pepxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3 --protxml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\combined.prot.xml PhilosopherReport [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report iProphet [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 3 Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2\interact.pep.xml Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4\interact.pep.xml PhilosopherAbacus [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein --peptide 2_1 2_5 2_2 2_4 2_3 WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -Xmx6G -Dbatmass.io.libs.thermo.dir="C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx6G -cp "C:\Users\labuser\Desktop\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\labuser\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\labuser\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\shepherd.config"
WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:15:48] Executing Workspace v3.4.13(Unknown Source)
at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source)
at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source)
... 6 more
Process 'MsFragger' finished, exit code: 1
Process returned non-zero exit code, stoppingMsFragger move pepxml
C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\labuser\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.pepXML Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1\20210116_JS_ECIG_DDA_406.pepXML
INFO[08:15:48] Removing workspace
WARN[08:15:48] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:48] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_3] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:49] Executing Workspace v3.4.13
INFO[08:15:49] Creating workspace
INFO[08:15:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:15:49] Executing Workspace v3.4.13
INFO[08:15:49] Removing workspace
WARN[08:15:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_2] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:50] Executing Workspace v3.4.13
INFO[08:15:50] Creating workspace
INFO[08:15:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:15:50] Executing Workspace v3.4.13
INFO[08:15:50] Removing workspace
WARN[08:15:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_1] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:50] Executing Workspace v3.4.13
INFO[08:15:50] Creating workspace
INFO[08:15:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:15:51] Executing Workspace v3.4.13
INFO[08:15:51] Removing workspace
WARN[08:15:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_5] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:51] Executing Workspace v3.4.13
INFO[08:15:51] Creating workspace
INFO[08:15:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[08:15:52] Executing Workspace v3.4.13
INFO[08:15:52] Removing workspace
WARN[08:15:52] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:52] Done
WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\2_4] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:52] Executing Workspace v3.4.13
INFO[08:15:52] Creating workspace
INFO[08:15:52] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[08:15:52] Executing Workspace v3.4.13
INFO[08:15:52] Removing workspace
WARN[08:15:52] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[08:15:52] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[08:15:53] Executing Workspace v3.4.13
INFO[08:15:53] Creating workspace
INFO[08:15:53] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410] C:\Users\labuser\Desktop\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Users\labuser\Desktop\fragpipe\tools\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar Z:\Projects\Williams_Lab\Thomas\JS_TG_ECIG_406_410\fragger.params C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.raw C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.raw MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, JVM started with 5 GB memory Checking database... Checking C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_406.raw... Checking C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_407.raw... Checking C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_408.raw... Checking C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_409.raw... Checking C:\Users\970082_Admin\Desktop\JS_TG_ECIG\20210116_JS_ECIG_DDA_410.raw... Checking if the data is low resolution MS/MS... [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. [pool-13-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:300) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:241) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. [pool-14-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:300) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:241) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. [pool-15-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:300) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:241) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. [pool-16-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:300) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:241) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: umich.ms.fileio.exceptions.FileParsingException: Could not get ThermoIndex at umich.ms.fileio.filetypes.thermo.ThermoRawFile.parseIndex(ThermoRawFile.java:331) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.fetchIndex(ThermoRawFile.java:307) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.parse(ThermoRawFile.java:554) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:807) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:791) at edu.umich.andykong.msfragger.b.a(Unknown Source) at edu.umich.andykong.msfragger.b.a(Unknown Source) at edu.umich.andykong.msfragger.E.a(Unknown Source) at edu.umich.andykong.msfragger.B.