uonnet
commented
3 years ago The log is here:
time="15:10:57" level=info msg="Executing Workspace v3.4.13"
time="15:10:58" level=info msg="Removing workspace"
time="15:10:58" level=info msg=Done
time="15:10:58" level=info msg="Executing Workspace v3.4.13"
time="15:10:58" level=info msg="Creating workspace"
time="15:10:58" level=info msg=Done
time="15:10:58" level=info msg="Executing Database v3.4.13"
time="15:10:58" level=info msg="Processing database"
time="15:11:11" level=info msg=Done
time="15:11:11" level=info msg="Executing Workspace v3.4.13"
time="15:11:11" level=info msg="Removing workspace"
time="15:11:11" level=info msg=Done
time="15:11:11" level=info msg="Executing Pipeline v3.4.13"
time="15:11:11" level=info msg="Creating workspace"
time="15:11:11" level=info msg="Initiating the workspace on data"
time="15:11:11" level=info msg="Creating workspace"
time="15:11:11" level=warning msg="A meta data folder was found and will not be overwritten. "
time="15:11:11" level=info msg="Processing database"
time="15:11:25" level=info msg="Running the Database Search on all data"
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: Linux, Architecture: amd64
Java Info: 1.8.0_201, OpenJDK 64-Bit Server VM, Oracle Corporation
JVM started with 56 GB memory
Checking database...
Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000
Parameter 'ion_series_definitions' was not supplied. Using default value:
Parameter 'Y_type_masses' was not supplied. Using default value:
Parameter 'diagnostic_fragments' was not supplied. Using default value:
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML...
Checking /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzML...
Checking if the data is low resolution MS/MS...
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 20
database_name = /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/database/2021-02-26-decoys-human_uniprot_contam-trembl-plus-swissprot.fasta.fas
decoy_prefix = 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 = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions =
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 2
clip_nTerm_M = false
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = 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 = -1.5,1.5
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 = 15.994915 M 3
variable_mod_02 = 42.010565 [^ 1
variable_mod_03 = 79.966331 STY 2
variable_mod_06 = 229.162932 n^ 1
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_C_cysteine = 57.021464
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 = 229.162932
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.
9074814484 fragments to be searched in 4 slices (135.23 GB total)
Operating on slice 1 of 4:
Fragment index slice generated in 20.92 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML 1.5 s | deisotoping 0.1 s
[progress: 34629/34629 (100%) - 17289 spectra/s] 2.0s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzML 2.0 s | deisotoping 0.1 s
[progress: 50098/50098 (100%) - 33376 spectra/s] 1.5s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzML 1.9 s | deisotoping 0.1 s
[progress: 51763/51763 (100%) - 34463 spectra/s] 1.5s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzML 1.6 s | deisotoping 0.3 s
[progress: 41848/41848 (100%) - 43501 spectra/s] 1.0s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzML 1.5 s | deisotoping 0.0 s
[progress: 36562/36562 (100%) - 52231 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 66801 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzML 0.7 s | deisotoping 0.1 s
[progress: 17465/17465 (100%) - 24914 spectra/s] 0.7s
Operating on slice 2 of 4:
Fragment index slice generated in 19.75 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML 1.4 s | deisotoping 0.1 s
[progress: 34629/34629 (100%) - 47963 spectra/s] 0.7s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzML 2.0 s | deisotoping 0.1 s
[progress: 50098/50098 (100%) - 99996 spectra/s] 0.5s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzML 2.0 s | deisotoping 0.1 s
[progress: 51763/51763 (100%) - 69950 spectra/s] 0.7s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzML 1.6 s | deisotoping 0.0 s
[progress: 41848/41848 (100%) - 139030 spectra/s] 0.3s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzML 1.5 s | deisotoping 0.0 s
[progress: 36562/36562 (100%) - 121873 spectra/s] 0.3s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.2 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 134270 spectra/s] 0.1s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzML 0.8 s | deisotoping 0.1 s
[progress: 17465/17465 (100%) - 58023 spectra/s] 0.3s
Operating on slice 3 of 4:
Fragment index slice generated in 16.56 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML 1.4 s | deisotoping 0.1 s
[progress: 34629/34629 (100%) - 69258 spectra/s] 0.5s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzML 1.9 s | deisotoping 0.1 s
[progress: 50098/50098 (100%) - 124933 spectra/s] 0.4s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzML 2.0 s | deisotoping 0.1 s
[progress: 51763/51763 (100%) - 129085 spectra/s] 0.4s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzML 1.6 s | deisotoping 0.2 s
[progress: 41848/41848 (100%) - 139030 spectra/s] 0.3s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzML 1.5 s | deisotoping 0.0 s
[progress: 36562/36562 (100%) - 121873 spectra/s] 0.3s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 132941 spectra/s] 0.1s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzML 0.7 s | deisotoping 0.1 s
[progress: 17465/17465 (100%) - 58217 spectra/s] 0.3s
Operating on slice 4 of 4:
Fragment index slice generated in 17.71 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML 1.4 s | deisotoping 0.1 s
[progress: 34629/34629 (100%) - 57619 spectra/s] 0.6s | postprocessing 0.4 s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzML 1.9 s | deisotoping 0.1 s
[progress: 50098/50098 (100%) - 125245 spectra/s] 0.4s | postprocessing 0.3 s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzML 1.9 s | deisotoping 0.1 s
[progress: 51763/51763 (100%) - 76686 spectra/s] 0.7s | postprocessing 0.2 s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzML 1.8 s | deisotoping 0.0 s
[progress: 41848/41848 (100%) - 104359 spectra/s] 0.4s | postprocessing 0.2 s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzML 1.7 s | deisotoping 0.0 s
[progress: 36562/36562 (100%) - 121468 spectra/s] 0.3s | postprocessing 0.2 s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.1 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 53282 spectra/s] 0.3s | postprocessing 0.1 s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzML 0.7 s | deisotoping 0.1 s
[progress: 17465/17465 (100%) - 58217 spectra/s] 0.3s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 5.198 MIN**************************
*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | -1.24 0.72 | -0.02 0.42 | -0.28 1.05 | 0.00 0.95
002 | -0.11 0.70 | 0.04 0.41 | 0.53 1.11 | -0.02 1.02
003 | -0.31 0.66 | 0.04 0.41 | 0.35 1.14 | -0.02 1.02
004 | -0.47 0.60 | 0.04 0.40 | 0.07 1.12 | -0.02 1.03
005 | -0.20 0.60 | -0.03 0.36 | 0.37 1.09 | -0.03 1.00
006 | Not enough data to perform mass calibration. Using the uncalibrated data.
007 | -0.89 0.71 | -0.03 0.42 | 0.15 1.04 | -0.06 0.96
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
MS2 | 7 | 10 | 15 | 20 | 25 | 30
-------|-------|-------|-------|-------|-------|-------
Count | 17454| 17447| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------
Peaks | 300_0 | 200_0 | 150_1 | 100_1
-------|-------|-------|-------|-------
Count | 17410| 17410| 17454| 17532
-------|-------|-------|-------|-------
-------|-------
Int. | 1
-------|-------
Count | 17451
-------|-------
-------|-------
Rm P. | 1
-------|-------
Count | 17537
-------|-------
New fragment_mass_tolerance = 7 PPM
New use_topN_peaks = 100
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 12.770 MIN*********
************************************MAIN SEARCH************************************
Checking database...
Parameter 'labile_search_mode' was not supplied. Using default value: OFF
Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000
Parameter 'ion_series_definitions' was not supplied. Using default value:
Parameter 'Y_type_masses' was not supplied. Using default value:
Parameter 'diagnostic_fragments' was not supplied. Using default value:
Parameters:
num_threads = 20
database_name = /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/database/2021-02-26-decoys-human_uniprot_contam-trembl-plus-swissprot.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -50.0
precursor_mass_upper = 50.0
precursor_mass_units = 1
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 7.0
fragment_mass_units = 1
calibrate_mass = 2
write_calibrated_mgf = false
isotope_error = 0/1/2
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions =
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 2
clip_nTerm_M = false
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 5
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = 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 = 100
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
remove_precursor_peak = 1
remove_precursor_range = -1.5,1.5
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 = 15.994915 M 3
variable_mod_02 = 42.010565 [^ 1
variable_mod_03 = 79.966331 STY 3
variable_mod_06 = 229.162932 n^ 1
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_C_cysteine = 57.021464
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 = 229.162932
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 0.03 Da.
26552904236 fragments to be searched in 10 slices (395.67 GB total)
Operating on slice 1 of 10:
Fragment index slice generated in 27.49 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 8538 spectra/s] 4.1s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 14288 spectra/s] 3.5s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 12650 spectra/s] 4.1s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 21998 spectra/s] 1.9s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 26067 spectra/s] 1.4s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.1 s
[progress: 13427/13427 (100%) - 44608 spectra/s] 0.3s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 9689 spectra/s] 1.8s
Operating on slice 2 of 10:
Fragment index slice generated in 22.86 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 26610 spectra/s] 1.3s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 38355 spectra/s] 1.3s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 36912 spectra/s] 1.4s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 50108 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 24907 spectra/s] 0.7s
Operating on slice 3 of 10:
Fragment index slice generated in 20.82 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 38424 spectra/s] 0.9s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 44408 spectra/s] 1.1s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 39747 spectra/s] 1.3s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 43493 spectra/s] 1.0s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 29100 spectra/s] 0.6s
Operating on slice 4 of 10:
Fragment index slice generated in 21.66 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 38424 spectra/s] 0.9s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 50042 spectra/s] 1.0s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 47004 spectra/s] 1.1s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 52235 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52060 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 52245 spectra/s] 0.3s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.0 s
[progress: 17460/17460 (100%) - 24943 spectra/s] 0.7s
Operating on slice 5 of 10:
Fragment index slice generated in 19.98 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 41964 spectra/s] 0.8s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 50042 spectra/s] 1.0s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 47004 spectra/s] 1.1s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 52235 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 34920 spectra/s] 0.5s
Operating on slice 6 of 10:
Fragment index slice generated in 21.10 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 34551 spectra/s] 1.0s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 45456 spectra/s] 1.1s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 51648 spectra/s] 1.0s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 50715 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 34850 spectra/s] 0.5s
Operating on slice 7 of 10:
Fragment index slice generated in 19.35 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 43221 spectra/s] 0.8s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.2 s
[progress: 50092/50092 (100%) - 45497 spectra/s] 1.1s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 46961 spectra/s] 1.1s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 52235 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.1 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 29052 spectra/s] 0.6s
Operating on slice 8 of 10:
Fragment index slice generated in 20.57 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 49387 spectra/s] 0.7s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 45497 spectra/s] 1.1s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.2 s
[progress: 51751/51751 (100%) - 51699 spectra/s] 1.0s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 50715 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52134 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.1 s
[progress: 17460/17460 (100%) - 24907 spectra/s] 0.7s
Operating on slice 9 of 10:
Fragment index slice generated in 19.58 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.1 s
[progress: 34620/34620 (100%) - 43221 spectra/s] 0.8s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.2 s
[progress: 50092/50092 (100%) - 45497 spectra/s] 1.1s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 46961 spectra/s] 1.1s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 52235 spectra/s] 0.8s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 52209 spectra/s] 0.7s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.1 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.0 s
[progress: 17460/17460 (100%) - 29052 spectra/s] 0.6s
Operating on slice 10 of 10:
Fragment index slice generated in 21.41 s
001. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzBIN_calibrated 0.2 s
[progress: 34620/34620 (100%) - 34551 spectra/s] 1.0s | postprocessing 4.0 s
002. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.mzBIN_calibrated 0.1 s
[progress: 50092/50092 (100%) - 38503 spectra/s] 1.3s | postprocessing 3.4 s
003. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.mzBIN_calibrated 0.1 s
[progress: 51751/51751 (100%) - 31157 spectra/s] 1.7s | postprocessing 4.3 s
004. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.mzBIN_calibrated 0.1 s
[progress: 41840/41840 (100%) - 34838 spectra/s] 1.2s | postprocessing 3.8 s
005. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.mzBIN_calibrated 0.1 s
[progress: 36546/36546 (100%) - 36509 spectra/s] 1.0s | postprocessing 1.9 s
006. SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.mzML 1.0 s | deisotoping 0.0 s
[progress: 13427/13427 (100%) - 67135 spectra/s] 0.2s | postprocessing 1.2 s
007. SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.mzBIN_calibrated 0.0 s
[progress: 17460/17460 (100%) - 34920 spectra/s] 0.5s | postprocessing 1.6 s
***************************MAIN SEARCH DONE IN 6.083 MIN***************************
*******************************TOTAL TIME 24.051 MIN********************************
time="15:35:39" level=info msg="Running the validation and inference on data"
time="15:35:39" level=info msg="Executing PeptideProphet on data"
file 1: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.pepXML
file 2: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F2_Fr7.pepXML
file 3: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F3_Fr6.pepXML
file 4: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_F4_Fr5.pepXML
file 5: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_Fr8.pepXML
file 6: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phospho_pooledFrac_Tio2_FT_extra.pepXML
file 7: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_7Apr_Phospho_Tio2_FT_Fr1_extra.pepXML
processed altogether 102170 results
INFO: Results written to file: /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/interact.pep.xml
- /home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/interact.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906251008-exported (Linux-x86_64)) AKeller@ISB
read in 0 1+, 41674 2+, 49940 3+, 8763 4+, 1358 5+, 410 6+, and 25 7+ spectra.
Initialising statistical models ...
Found 23063 Decoys, and 79107 Non-Decoys
Iterations: .........10.........20......
WARNING: Mixture model quality test failed for charge (1+).
model complete after 27 iterations
time="15:39:29" level=info msg="Running the validation and inference on data"
time="15:39:29" level=info msg="Executing PTMProphet on data"
INFO: Applying PSM specific mass offset and tolerance ...
time="15:39:29" level=info msg="Executing PTMProphet on data"
INFO: Writing file interact.pep.xml.tmp.9izEAE ...
Creating 20 threads
Wait for threads to finish ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
Unknown file type. No file loaded./home/Projects/LeungSY_LBQ_CPOS-200716-DMS-3509.Pilot/MSFragger.results/Phospho/data/SY_Batch1_4P_GC_TMT11plex_MS2_18Apr_Phoshpo_Tio2_Fr3_extra.mzML
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
INFO: Reading file interact.pep.xml ...
time="15:39:33" level=fatal msg="Cannot execute program. There was an error with PTMProphet, please check your parameters and input files"
prvst
I am getting this error message when running the Philosopher pipeline on phosphoproteomics data
time="15:39:33" level=fatal msg="Cannot execute program. There was an error with PTMProphet, please check your parameters and input files"I checked the parameters and mzML files but everything looks fine. What might be causing this error? Any help will be appreciated. Thanks!