pepXML

[Golden-proteogenomics]

I use the command line to process the MSFragger,but the result files which genarated by MSFragger were not be understand when I want to found the identified PSM, peptides and proteins. another question is how to find the used time about this procession.

[fcyu]

Thanks for your interest in MSFragger. You may start from this tutorial.

Best,

Fengchao

[Golden-proteogenomics]

there is no result and facing the other problems as the follow when do it as the tutorial.

[Golden-proteogenomics]

![Uploading 2.jpg…]()

[Golden-proteogenomics]

[Golden-proteogenomics]

So, what can I do for my dilemma using the search Tools?

[fcyu]

Could you please share the log (the file starts with log-fragpipe-run-at) with me?

Thanks,

Fengchao

[Golden-proteogenomics]

Thank you for timely reply, the appendix file is the process log. Please cheak it.

Thanks, jinshuai Sun

At 2019-07-16 21:57:40, "Fengchao" notifications@github.com wrote:

Could you please share the log (the file starts with log-fragpipe-run-at) with me?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread. INFO[21:53:58] Executing Filter v1.4.5
INFO[21:53:58] Processing peptide identification files
INFO[21:54:00] 1+ Charge profile decoy=0 target=0 INFO[21:54:00] 2+ Charge profile decoy=0 target=10400 INFO[21:54:00] 3+ Charge profile decoy=0 target=5602 INFO[21:54:00] 4+ Charge profile decoy=0 target=1184 INFO[21:54:00] 5+ Charge profile decoy=0 target=157 INFO[21:54:00] 6+ Charge profile decoy=0 target=29 INFO[21:54:00] Database search results ions=16095 peptides=14544 psms=17375 INFO[21:54:00] Converged to 0.00 % FDR with 17375 PSMs decoy=0 threshold=0 total=17375 INFO[21:54:01] Converged to 0.00 % FDR with 14544 Peptides decoy=0 threshold=0 total=14544 INFO[21:54:01] Converged to 0.00 % FDR with 16095 Ions decoy=0 threshold=0 total=16095 panic: runtime error: invalid memory address or nil pointer dereference [signal 0xc0000005 code=0x0 addr=0x28 pc=0x5048c0]

goroutine 1 [running]: github.com/prvst/philosopher/lib/err.(Error).Error(0x0, 0x24, 0xc00009e630) /home/prvst/go/src/github.com/prvst/philosopher/lib/err/err.go:134 +0x30 github.com/prvst/philosopher/cmd.glob..func5(0x8718ee0, 0xc0000e4580, 0x0, 0xb) /home/prvst/go/src/github.com/prvst/philosopher/cmd/filter.go:53 +0xbc4 github.com/spf13/cobra.(Command).execute(0x8718ee0, 0xc0000e44d0, 0xb, 0xb, 0x8718ee0, 0xc0000e44d0) /home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2b5 github.com/spf13/cobra.(Command).ExecuteC(0x8717980, 0x405826, 0xc000078058, 0x0) /home/prvst/go/src/github.com/spf13/cobra/command.go:850 +0x303 github.com/spf13/cobra.(Command).Execute(...) /home/prvst/go/src/github.com/spf13/cobra/command.go:800 github.com/prvst/philosopher/cmd.Execute() /home/prvst/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x35 main.main() /home/prvst/go/src/github.com/prvst/philosopher/main.go:24 +0x75

[fcyu]

This is not the whole log. Could you please upload the whole log-fragpipe-run-at_2019-07-xx_xx-xx-xx.log file so that I can locate the problem?

Thanks,

Fengchao

[Golden-proteogenomics]

this files that named log-fragpipe-run-at_2019-07-xx_xx-xx-xx.log is not exit in my all result files

[fcyu]

Sorry about that. The file will be written after clicking "Stop":

Best,

Fengchao

[Golden-proteogenomics]

OK, there is the log written as the follow:

System info: System OS: Windows 7, Architecture: AMD64 Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190628 Philosopher version v1.4.5 (build 1563205050)

LCMS files: Experiment/Group:

• I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML

12 commands to execute: Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --init MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\shi\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML Crystal-C [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] java -Xmx10G -cp "C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.5.jar" Main I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\crystalc-0-LysC2.pepXML.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPPSeq.fasta --prefix rev PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\Onereveice\mzML\shi\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta LysC2_c.pepXML ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-LysC2_c.pep.xml ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\Onereveice\mzML\shi\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact.prot.xml ReportFreequant [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628 ReportReport [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe report Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean
INFO[21:51:56] Executing Workspace v1.4.5                   
INFO[21:52:00] Removing workspace                           
INFO[21:52:00] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --init
INFO[21:52:03] Executing Workspace v1.4.5                   
INFO[21:52:06] Creating workspace                           
INFO[21:52:06] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML
MSFragger version MSFragger-20190628
MSFTBX version 1.9.10
(c) University of Michigan
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 9102 MB memory

***********************************FIRST SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta
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
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 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 = 7
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 6.29 GB.
81428380 fragments to be searched in 1 slices (1.21 GB total)
Operating on slice 1 of 1: 
    001. LysC2.mzML 5.5 s
    001. LysC2.mzML 5.5 s [progress: 26779/26779 (100.00%) - 10415.79 spectra/s] - completed 2.6 s
***************************FIRST SEARCH DONE IN 0.189 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   5.64   1.53 |   0.08   1.43 |   4.56   2.95 |   0.34   3.11  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
  MS2  |    7  |   10  |   15  |   20  |   25  |   30  
-------|-------|-------|-------|-------|-------|-------
 Count |  12899|  13563|  14215|  14600|  14934|  15262
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
 Peaks |  50_1 |  75_1 | 100_1 | 125_1 | 150_1 
-------|-------|-------|-------|-------|-------
 Count |  14473|  15049|  15192|  15238|  15262
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 30 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 0.677 MIN***********************

************************************MAIN SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta
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 = 30.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1/2
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 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 = 7
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Selected fragment tolerance 0.15 Da and maximum fragment slice size of 6.28 GB.
159661936 fragments to be searched in 1 slices (2.38 GB total)
Operating on slice 1 of 1: 
    001. LysC2.mzBIN_calibrated 0.4 s
    001. LysC2.mzBIN_calibrated 0.4 s [progress: 26438/26438 (100.00%) - 6957.37 spectra/s] - completed 3.8 s
***************************MAIN SEARCH DONE IN 0.146 MIN***************************

*******************************TOTAL TIME 1.012 MIN********************************
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\shi\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML
Process 'MsFragger' finished, exit code: 0

Crystal-C [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
java -Xmx10G -cp "C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.5.jar" Main I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\crystalc-0-LysC2.pepXML.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML
LysC2.pepXML Done!!! The execution time is 0.39298 min.
Process 'Crystal-C' finished, exit code: 0

ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta --prefix rev_
INFO[21:53:37] Executing Database v1.4.5                    
INFO[21:53:38] Processing database                          
INFO[21:53:38] Done                                         
Process 'ReportDbAnnotate' finished, exit code: 0

PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta LysC2_c.pepXML
INFO[21:53:38] Executing PeptideProphet v1.4.5              
Unknown file type. No file loaded.I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated
WARNING: cannot open data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ...
WARNING: CANNOT correct data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzML in msms_run_summary tag...
Unknown file type. No file loaded.I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated
WARNING: cannot open data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ...
WARNING: CANNOT correct data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzML in msms_run_summary tag...
 file 1: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2_c.pepXML
 processed altogether 17375 results
INFO: Results written to file: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact-LysC2_c.pep.xml

  - I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact-LysC2_c.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
init with X! Tandem trypsin 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 10400 2+, 5602 3+, 1184 4+, 157 5+, 29 6+, and 3 7+ spectra.
Found 0 Decoys, and 17375 Non-Decoys
WARNING: No decoys with label rev_ were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
INFO[21:53:55] Done                                         
Process 'PeptideProphet' finished, exit code: 0

ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-LysC2_c.pep.xml
INFO[21:53:56] Executing ProteinProphet v1.4.5              
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64))
 (no FPKM) (using degen pep info)
Reading in I:/Shuai/2019-CHPP/One_reveice/mzML/shi/result/interact-LysC2_c.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

WARNING: no data - output file will be empty
INFO[21:53:58] Done                                         
Process 'ProteinProphet' finished, exit code: 0

ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact.prot.xml
INFO[21:53:58] Executing Filter v1.4.5                      
INFO[21:53:58] Processing peptide identification files      
INFO[21:54:00] 1+ Charge profile                             decoy=0 target=0
INFO[21:54:00] 2+ Charge profile                             decoy=0 target=10400
INFO[21:54:00] 3+ Charge profile                             decoy=0 target=5602
INFO[21:54:00] 4+ Charge profile                             decoy=0 target=1184
INFO[21:54:00] 5+ Charge profile                             decoy=0 target=157
INFO[21:54:00] 6+ Charge profile                             decoy=0 target=29
INFO[21:54:00] Database search results                       ions=16095 peptides=14544 psms=17375
INFO[21:54:00] Converged to 0.00 % FDR with 17375 PSMs       decoy=0 threshold=0 total=17375
INFO[21:54:01] Converged to 0.00 % FDR with 14544 Peptides   decoy=0 threshold=0 total=14544
INFO[21:54:01] Converged to 0.00 % FDR with 16095 Ions       decoy=0 threshold=0 total=16095
panic: runtime error: invalid memory address or nil pointer dereference
[signal 0xc0000005 code=0x0 addr=0x28 pc=0x5048c0]

goroutine 1 [running]:
github.com/prvst/philosopher/lib/err.(*Error).Error(0x0, 0x24, 0xc00009e630)
    /home/prvst/go/src/github.com/prvst/philosopher/lib/err/err.go:134 +0x30
github.com/prvst/philosopher/cmd.glob..func5(0x8718ee0, 0xc0000e4580, 0x0, 0xb)
    /home/prvst/go/src/github.com/prvst/philosopher/cmd/filter.go:53 +0xbc4
github.com/spf13/cobra.(*Command).execute(0x8718ee0, 0xc0000e44d0, 0xb, 0xb, 0x8718ee0, 0xc0000e44d0)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2b5
github.com/spf13/cobra.(*Command).ExecuteC(0x8717980, 0x405826, 0xc000078058, 0x0)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:850 +0x303
github.com/spf13/cobra.(*Command).Execute(...)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:800
github.com/prvst/philosopher/cmd.Execute()
    /home/prvst/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x35
main.main()
    /home/prvst/go/src/github.com/prvst/philosopher/main.go:24 +0x75
Process 'ReportFilter' finished, exit code: 2

Process returned non-zero exit code, stopping

Stopping 5/13 processes (8 already finished)

Stopping 0/0 processes (0 already finished)

[Golden-proteogenomics]

the log is found and put it in appendix.

At 2019-07-16 22:12:08, "Fengchao" notifications@github.com wrote:

Sorry about that. The file will be written after clicking "Stop":

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread. System info: System OS: Windows 7, Architecture: AMD64 Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190628 Philosopher version v1.4.5 (build 1563205050)

LCMS files: Experiment/Group:

• I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML

12 commands to execute: Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --init MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\shi\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML Crystal-C [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] java -Xmx10G -cp "C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.5.jar" Main I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\crystalc-0-LysC2.pepXML.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPPSeq.fasta --prefix rev PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\Onereveice\mzML\shi\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta LysC2_c.pepXML ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-LysC2_c.pep.xml ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\Onereveice\mzML\shi\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact.prot.xml ReportFreequant [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628 ReportReport [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe report Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result] I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --clean
INFO[21:51:56] Executing Workspace v1.4.5                   
INFO[21:52:00] Removing workspace                           
INFO[21:52:00] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe workspace --init
INFO[21:52:03] Executing Workspace v1.4.5                   
INFO[21:52:06] Creating workspace                           
INFO[21:52:06] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.mzML
MSFragger version MSFragger-20190628
MSFTBX version 1.9.10
(c) University of Michigan
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 9102 MB memory

***********************************FIRST SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta
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
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 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 = 7
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 6.29 GB.
81428380 fragments to be searched in 1 slices (1.21 GB total)
Operating on slice 1 of 1: 
    001. LysC2.mzML 5.5 s
    001. LysC2.mzML 5.5 s [progress: 26779/26779 (100.00%) - 10415.79 spectra/s] - completed 2.6 s
***************************FIRST SEARCH DONE IN 0.189 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   5.64   1.53 |   0.08   1.43 |   4.56   2.95 |   0.34   3.11  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
  MS2  |    7  |   10  |   15  |   20  |   25  |   30  
-------|-------|-------|-------|-------|-------|-------
 Count |  12899|  13563|  14215|  14600|  14934|  15262
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
 Peaks |  50_1 |  75_1 | 100_1 | 125_1 | 150_1 
-------|-------|-------|-------|-------|-------
 Count |  14473|  15049|  15192|  15238|  15262
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 30 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 0.677 MIN***********************

************************************MAIN SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta
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 = 30.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1/2
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 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 = 7
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Selected fragment tolerance 0.15 Da and maximum fragment slice size of 6.28 GB.
159661936 fragments to be searched in 1 slices (2.38 GB total)
Operating on slice 1 of 1: 
    001. LysC2.mzBIN_calibrated 0.4 s
    001. LysC2.mzBIN_calibrated 0.4 s [progress: 26438/26438 (100.00%) - 6957.37 spectra/s] - completed 3.8 s
***************************MAIN SEARCH DONE IN 0.146 MIN***************************

*******************************TOTAL TIME 1.012 MIN********************************
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\shi\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\LysC2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML
Process 'MsFragger' finished, exit code: 0

Crystal-C [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
java -Xmx10G -cp "C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\XU-LAB~1\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.5.jar" Main I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\crystalc-0-LysC2.pepXML.params I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2.pepXML
LysC2.pepXML Done!!! The execution time is 0.39298 min.
Process 'Crystal-C' finished, exit code: 0

ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta --prefix rev_
INFO[21:53:37] Executing Database v1.4.5                    
INFO[21:53:38] Processing database                          
INFO[21:53:38] Done                                         
Process 'ReportDbAnnotate' finished, exit code: 0

PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database I:\Shuai\2019-CHPP\One_reveice\mzML\shi\2019_CHPP_Seq.fasta LysC2_c.pepXML
INFO[21:53:38] Executing PeptideProphet v1.4.5              
Unknown file type. No file loaded.I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated
WARNING: cannot open data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ...
WARNING: CANNOT correct data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzML in msms_run_summary tag...
Unknown file type. No file loaded.I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated
WARNING: cannot open data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzBIN_calibrated in msms_run_summary tag... unrecognized extension .mzBIN_calibrated, trying .mzML ...
WARNING: CANNOT correct data file I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result/LysC2.mzML in msms_run_summary tag...
 file 1: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\LysC2_c.pepXML
 processed altogether 17375 results
INFO: Results written to file: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact-LysC2_c.pep.xml

  - I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact-LysC2_c.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
init with X! Tandem trypsin 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 10400 2+, 5602 3+, 1184 4+, 157 5+, 29 6+, and 3 7+ spectra.
Found 0 Decoys, and 17375 Non-Decoys
WARNING: No decoys with label rev_ were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
INFO[21:53:55] Done                                         
Process 'PeptideProphet' finished, exit code: 0

ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-LysC2_c.pep.xml
INFO[21:53:56] Executing ProteinProphet v1.4.5              
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64))
 (no FPKM) (using degen pep info)
Reading in I:/Shuai/2019-CHPP/One_reveice/mzML/shi/result/interact-LysC2_c.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

WARNING: no data - output file will be empty
INFO[21:53:58] Done                                         
Process 'ProteinProphet' finished, exit code: 0

ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result]
I:\Shuai\2019-CHPP\One_reveice\mzML\shi\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\shi\result\interact.prot.xml
INFO[21:53:58] Executing Filter v1.4.5                      
INFO[21:53:58] Processing peptide identification files      
INFO[21:54:00] 1+ Charge profile                             decoy=0 target=0
INFO[21:54:00] 2+ Charge profile                             decoy=0 target=10400
INFO[21:54:00] 3+ Charge profile                             decoy=0 target=5602
INFO[21:54:00] 4+ Charge profile                             decoy=0 target=1184
INFO[21:54:00] 5+ Charge profile                             decoy=0 target=157
INFO[21:54:00] 6+ Charge profile                             decoy=0 target=29
INFO[21:54:00] Database search results                       ions=16095 peptides=14544 psms=17375
INFO[21:54:00] Converged to 0.00 % FDR with 17375 PSMs       decoy=0 threshold=0 total=17375
INFO[21:54:01] Converged to 0.00 % FDR with 14544 Peptides   decoy=0 threshold=0 total=14544
INFO[21:54:01] Converged to 0.00 % FDR with 16095 Ions       decoy=0 threshold=0 total=16095
panic: runtime error: invalid memory address or nil pointer dereference
[signal 0xc0000005 code=0x0 addr=0x28 pc=0x5048c0]

goroutine 1 [running]:
github.com/prvst/philosopher/lib/err.(*Error).Error(0x0, 0x24, 0xc00009e630)
    /home/prvst/go/src/github.com/prvst/philosopher/lib/err/err.go:134 +0x30
github.com/prvst/philosopher/cmd.glob..func5(0x8718ee0, 0xc0000e4580, 0x0, 0xb)
    /home/prvst/go/src/github.com/prvst/philosopher/cmd/filter.go:53 +0xbc4
github.com/spf13/cobra.(*Command).execute(0x8718ee0, 0xc0000e44d0, 0xb, 0xb, 0x8718ee0, 0xc0000e44d0)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2b5
github.com/spf13/cobra.(*Command).ExecuteC(0x8717980, 0x405826, 0xc000078058, 0x0)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:850 +0x303
github.com/spf13/cobra.(*Command).Execute(...)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:800
github.com/prvst/philosopher/cmd.Execute()
    /home/prvst/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x35
main.main()
    /home/prvst/go/src/github.com/prvst/philosopher/main.go:24 +0x75
Process 'ReportFilter' finished, exit code: 2

Process returned non-zero exit code, stopping

Stopping 5/13 processes (8 already finished)

Stopping 0/0 processes (0 already finished)

[fcyu]

Thanks for your log.

Looks like your fasta file doesn't have decoy proteins. You may generate a file containing both target and decoy proteins. Or download a new one with the "Download" function:

Best,

Fengchao

[Golden-proteogenomics]

Thanks, there are some questions: 1) which file is recoder the used time in this complement task? 2) if I want set the Carbamidomethyl[C] as the fixed modification, but how can i do the option? 3) our tools default the precursor mass tolerance was +-50 ppm, if i want the compare different search tools , this paramer whether change to 20 or not?

[fcyu]

You are welcome. Following are my answers:

1. The log file.
2. In the "MSFragger" tab, there is a "Fixed modifications" block where you can specify fixed modifications.
3. Yes, you can change the tolerance as you want.

Best,

Fengchao

[Golden-proteogenomics]

hello, I have set the param based myself knowledge from had asked your options. However, there are still some questions as the log recoded, can you help me find which error and what can I set the tool to continue run?

Thanks， Jinshuai Sun

在 2019-07-17 21:26:05，"Fengchao" notifications@github.com 写道：

Closed #34.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread. System info: System OS: Windows 7, Architecture: AMD64 Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190628 Philosopher version v1.4.5 (build 1563205050)

LCMS files: Experiment/Group:

• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML

80 commands to execute: Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --init MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin1.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin10.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin11.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin12.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin13.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin14.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin15.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin16.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin17.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin18.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin19.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin2.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin20.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin21.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin22.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin23.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin24.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin25.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin26.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin27.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin28.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin29.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin3.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin30.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin31.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin32.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin33.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin34.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin35.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin36.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin4.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin5.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin6.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin7.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin8.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin9.pepXML ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_contd.fasta --prefix >REV PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin25.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin15.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin10.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin3.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin20.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin33.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin5.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin17.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin27.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin13.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin23.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin7.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin19.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin29.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin36.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin2.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin26.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin31.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin11.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin21.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin16.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin4.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin24.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin34.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin14.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin9.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin28.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin1.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin18.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin6.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin8.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin12.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin22.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin32.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin30.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin35.pepXML ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-Trypsin25.pep.xml interact-Trypsin15.pep.xml interact-Trypsin10.pep.xml interact-Trypsin3.pep.xml interact-Trypsin20.pep.xml interact-Trypsin33.pep.xml interact-Trypsin5.pep.xml interact-Trypsin17.pep.xml interact-Trypsin27.pep.xml interact-Trypsin13.pep.xml interact-Trypsin23.pep.xml interact-Trypsin7.pep.xml interact-Trypsin19.pep.xml interact-Trypsin29.pep.xml interact-Trypsin36.pep.xml interact-Trypsin2.pep.xml interact-Trypsin26.pep.xml interact-Trypsin31.pep.xml interact-Trypsin11.pep.xml interact-Trypsin21.pep.xml interact-Trypsin16.pep.xml interact-Trypsin4.pep.xml interact-Trypsin24.pep.xml interact-Trypsin34.pep.xml interact-Trypsin14.pep.xml interact-Trypsin9.pep.xml interact-Trypsin28.pep.xml interact-Trypsin1.pep.xml interact-Trypsin18.pep.xml interact-Trypsin6.pep.xml interact-Trypsin8.pep.xml interact-Trypsin12.pep.xml interact-Trypsin22.pep.xml interact-Trypsin32.pep.xml interact-Trypsin30.pep.xml interact-Trypsin35.pep.xml ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag >REV --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\interact.prot.xml ReportReport [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe report Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean
INFO[08:55:49] Executing Workspace v1.4.5                   
INFO[08:55:51] Removing workspace                           
INFO[08:55:51] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --init
INFO[08:55:56] Executing Workspace v1.4.5                   
INFO[08:55:58] Creating workspace                           
INFO[08:55:58] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML
MSFragger version MSFragger-20190628
MSFTBX version 1.9.10
(c) University of Michigan
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 9102 MB memory

***********************************FIRST SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta
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
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 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 = 100
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 6
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Number of unique peptides
    of length 7: 218678
    of length 8: 202863
    of length 9: 194949
    of length 10: 178286
    of length 11: 164195
    of length 12: 152037
    of length 13: 143644
    of length 14: 128940
    of length 15: 120767
    of length 16: 110154
    of length 17: 100878
    of length 18: 94017
    of length 19: 88288
    of length 20: 80125
    of length 21: 75067
    of length 22: 68632
    of length 23: 63786
    of length 24: 59715
    of length 25: 55358
    of length 26: 50738
    of length 27: 48195
    of length 28: 44944
    of length 29: 41329
    of length 30: 38424
    of length 31: 35400
    of length 32: 33108
    of length 33: 30467
    of length 34: 28143
    of length 35: 25574
    of length 36: 24493
    of length 37: 21687
    of length 38: 20265
    of length 39: 18081
    of length 40: 17198
    of length 41: 16183
    of length 42: 14374
    of length 43: 12585
    of length 44: 10139
    of length 45: 7954
    of length 46: 5377
    of length 47: 3507
    of length 48: 2150
    of length 49: 1139
    of length 50: 718
    of length 51: 443
    of length 52: 242
    of length 53: 140
    of length 54: 77
    of length 55: 57
    of length 56: 35
    of length 57: 17
    of length 58: 8
    of length 59: 12
    of length 60: 4
    of length 61: 6
    of length 62: 2
    of length 63: 2
    of length 66: 2
In total 2853598 peptides.
Generated 4333259 modified peptides.
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 6.27 GB.
161188014 fragments to be searched in 1 slices (2.40 GB total)
Operating on slice 1 of 1: 
    001. Trypsin1.mzML 29.3 s
    001. Trypsin1.mzML 29.3 s [progress: 41988/54055 (77.68%) - 8275.13 spectra/s]
    001. Trypsin1.mzML 29.3 s [progress: 54055/54055 (100.00%) - 9526.79 spectra/s] - completed 5.7 s
    002. Trypsin10.mzML 35.7 s
    002. Trypsin10.mzML 35.7 s [progress: 56048/61334 (91.38%) - 11015.72 spectra/s]
    002. Trypsin10.mzML 35.7 s [progress: 61334/61334 (100.00%) - 10783.05 spectra/s] - completed 5.7 s
    003. Trypsin11.mzML 30.0 s
    003. Trypsin11.mzML 30.0 s [progress: 54377/61425 (88.53%) - 10864.54 spectra/s]
    003. Trypsin11.mzML 30.0 s [progress: 61425/61425 (100.00%) - 10402.20 spectra/s] - completed 5.9 s
    004. Trypsin12.mzML 32.2 s
    004. Trypsin12.mzML 32.2 s [progress: 45901/62124 (73.89%) - 9014.34 spectra/s]
    004. Trypsin12.mzML 32.2 s [progress: 62124/62124 (100.00%) - 7723.98 spectra/s] - completed 8.0 s
    005. Trypsin13.mzML 40.0 s
    005. Trypsin13.mzML 40.0 s [progress: 49147/61245 (80.25%) - 9668.90 spectra/s]
    005. Trypsin13.mzML 40.0 s [progress: 61245/61245 (100.00%) - 8719.39 spectra/s] - completed 7.0 s
    006. Trypsin14.mzML 42.3 s
    006. Trypsin14.mzML 42.3 s [progress: 49833/62864 (79.27%) - 9938.77 spectra/s]
    006. Trypsin14.mzML 42.3 s [progress: 62864/62864 (100.00%) - 8598.55 spectra/s] - completed 7.3 s
    007. Trypsin15.mzML 40.7 s
    007. Trypsin15.mzML 40.7 s [progress: 45931/63653 (72.16%) - 9182.53 spectra/s]
    007. Trypsin15.mzML 40.7 s [progress: 63653/63653 (100.00%) - 8616.89 spectra/s] - completed 7.4 s
    008. Trypsin16.mzML 38.6 s
    008. Trypsin16.mzML 38.6 s [progress: 36191/62572 (57.84%) - 7185.03 spectra/s]
    008. Trypsin16.mzML 38.6 s [progress: 62572/62572 (100.00%) - 7165.83 spectra/s] - completed 8.7 s
    009. Trypsin17.mzML 39.7 s
    009. Trypsin17.mzML 39.7 s [progress: 53075/62816 (84.49%) - 10534.93 spectra/s]
    009. Trypsin17.mzML 39.7 s [progress: 62816/62816 (100.00%) - 9755.55 spectra/s] - completed 6.4 s
    010. Trypsin18.mzML 37.0 s
    010. Trypsin18.mzML 37.0 s [progress: 50364/62397 (80.72%) - 10058.72 spectra/s]
    010. Trypsin18.mzML 37.0 s [progress: 62397/62397 (100.00%) - 8992.22 spectra/s] - completed 6.9 s
    011. Trypsin19.mzML 31.8 s
    011. Trypsin19.mzML 31.8 s [progress: 51774/61621 (84.02%) - 10278.74 spectra/s]
    011. Trypsin19.mzML 31.8 s [progress: 61621/61621 (100.00%) - 9423.61 spectra/s] - completed 6.5 s
    012. Trypsin2.mzML 29.0 s
    012. Trypsin2.mzML 29.0 s [progress: 54297/54297 (100.00%) - 19295.31 spectra/s] - completed 2.8 s
    013. Trypsin20.mzML 38.5 s
    013. Trypsin20.mzML 38.5 s [progress: 45102/61029 (73.90%) - 8950.59 spectra/s]
    013. Trypsin20.mzML 38.5 s [progress: 61029/61029 (100.00%) - 8424.77 spectra/s] - completed 7.2 s
    014. Trypsin21.mzML 35.3 s
    014. Trypsin21.mzML 35.3 s [progress: 55284/61295 (90.19%) - 10745.19 spectra/s]
    014. Trypsin21.mzML 35.3 s [progress: 61295/61295 (100.00%) - 10139.78 spectra/s] - completed 6.0 s
    015. Trypsin22.mzML 35.3 s
    015. Trypsin22.mzML 35.3 s [progress: 47807/60728 (78.72%) - 9361.07 spectra/s]
    015. Trypsin22.mzML 35.3 s [progress: 60728/60728 (100.00%) - 6957.84 spectra/s] - completed 8.7 s
    016. Trypsin23.mzML 33.9 s
    016. Trypsin23.mzML 33.9 s [progress: 50385/61059 (82.52%) - 9977.23 spectra/s]
    016. Trypsin23.mzML 33.9 s [progress: 61059/61059 (100.00%) - 9040.42 spectra/s] - completed 6.8 s
    017. Trypsin24.mzML 24.5 s
    017. Trypsin24.mzML 24.5 s [progress: 46675/60321 (77.38%) - 9169.94 spectra/s]
    017. Trypsin24.mzML 24.5 s [progress: 60321/60321 (100.00%) - 8266.55 spectra/s] - completed 7.3 s
    018. Trypsin25.mzML 26.2 s
    018. Trypsin25.mzML 26.2 s [progress: 51334/60548 (84.78%) - 10139.05 spectra/s]
    018. Trypsin25.mzML 26.2 s [progress: 60548/60548 (100.00%) - 9290.78 spectra/s] - completed 6.5 s
    019. Trypsin26.mzML 17.6 s
    019. Trypsin26.mzML 17.6 s [progress: 47107/59800 (78.77%) - 9376.39 spectra/s]
    019. Trypsin26.mzML 17.6 s [progress: 59800/59800 (100.00%) - 8657.88 spectra/s] - completed 6.9 s
    020. Trypsin27.mzML 22.8 s
    020. Trypsin27.mzML 22.8 s [progress: 50991/58214 (87.59%) - 10181.91 spectra/s]
    020. Trypsin27.mzML 22.8 s [progress: 58214/58214 (100.00%) - 9193.62 spectra/s] - completed 6.3 s
    021. Trypsin28.mzML 22.8 s
    021. Trypsin28.mzML 22.8 s [progress: 55395/56761 (97.59%) - 11032.66 spectra/s]
    021. Trypsin28.mzML 22.8 s [progress: 56761/56761 (100.00%) - 10245.67 spectra/s] - completed 5.5 s
    022. Trypsin29.mzML 24.8 s
    022. Trypsin29.mzML 24.8 s [progress: 55919/56883 (98.31%) - 11154.80 spectra/s]
    022. Trypsin29.mzML 24.8 s [progress: 56883/56883 (100.00%) - 10706.38 spectra/s] - completed 5.3 s
    023. Trypsin3.mzML 21.8 s
    023. Trypsin3.mzML 21.8 s [progress: 53573/53573 (100.00%) - 17780.62 spectra/s] - completed 3.0 s
    024. Trypsin30.mzML 26.5 s
    024. Trypsin30.mzML 26.5 s [progress: 55285/55285 (100.00%) - 11670.89 spectra/s] - completed 4.7 s
    025. Trypsin31.mzML 28.1 s
    025. Trypsin31.mzML 28.1 s [progress: 54297/54297 (100.00%) - 11474.43 spectra/s] - completed 4.7 s
    026. Trypsin32.mzML 29.8 s
    026. Trypsin32.mzML 29.8 s [progress: 54420/54420 (100.00%) - 11232.20 spectra/s] - completed 4.8 s
    027. Trypsin33.mzML 27.6 s
    027. Trypsin33.mzML 27.6 s [progress: 52606/52606 (100.00%) - 10853.31 spectra/s] - completed 4.8 s
    028. Trypsin34.mzML 24.9 s
    028. Trypsin34.mzML 24.9 s [progress: 51572/51572 (100.00%) - 13260.99 spectra/s] - completed 3.9 s
    029. Trypsin35.mzML 22.3 s
    029. Trypsin35.mzML 22.3 s [progress: 50785/50785 (100.00%) - 18287.72 spectra/s] - completed 2.8 s
    030. Trypsin36.mzML 27.9 s
    030. Trypsin36.mzML 27.9 s [progress: 49967/49967 (100.00%) - 20810.91 spectra/s] - completed 2.4 s
    031. Trypsin4.mzML 29.8 s
    031. Trypsin4.mzML 29.8 s [progress: 56452/56452 (100.00%) - 17348.49 spectra/s] - completed 3.3 s
    032. Trypsin5.mzML 31.0 s
    032. Trypsin5.mzML 31.0 s [progress: 56655/56655 (100.00%) - 15395.38 spectra/s] - completed 3.7 s
    033. Trypsin6.mzML 29.8 s
    033. Trypsin6.mzML 29.8 s [progress: 58294/58294 (100.00%) - 13490.86 spectra/s] - completed 4.3 s
    034. Trypsin7.mzML 27.4 s
    034. Trypsin7.mzML 27.4 s [progress: 59506/59506 (100.00%) - 12335.41 spectra/s] - completed 4.8 s
    035. Trypsin8.mzML 29.8 s
    035. Trypsin8.mzML 29.8 s [progress: 60440/60673 (99.62%) - 11914.05 spectra/s]
    035. Trypsin8.mzML 29.8 s [progress: 60673/60673 (100.00%) - 11506.35 spectra/s] - completed 5.3 s
    036. Trypsin9.mzML 32.7 s
    036. Trypsin9.mzML 32.7 s [progress: 57839/59800 (96.72%) - 11446.47 spectra/s]
    036. Trypsin9.mzML 32.7 s [progress: 59800/59800 (100.00%) - 10966.44 spectra/s] - completed 5.5 s
***************************FIRST SEARCH DONE IN 24.263 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   2.11   1.47 |  -0.03   1.66 |   1.52   2.31 |   0.01   2.43  
 002 |   3.03   1.48 |   0.06   1.74 |   2.72   1.86 |  -0.02   1.90  
 003 |   2.93   1.47 |   0.06   1.73 |   2.64   1.78 |  -0.03   1.82  
 004 |   2.95   1.52 |   0.02   1.69 |   2.72   1.79 |  -0.05   1.81  
 005 |   3.03   1.46 |  -0.01   1.69 |   2.65   1.87 |  -0.04   1.92  
 006 |   3.00   1.39 |   0.01   1.66 |   2.68   1.76 |  -0.07   1.77  
 007 |   3.36   1.44 |   0.03   1.72 |   3.06   1.78 |  -0.04   1.79  
 008 |   3.63   1.41 |   0.00   1.73 |   3.33   1.78 |  -0.06   1.79  
 009 |   3.62   1.42 |   0.01   1.66 |   3.32   1.76 |  -0.03   1.79  
 010 |   3.62   1.39 |   0.02   1.70 |   3.26   1.77 |  -0.03   1.79  
 011 |   3.58   1.51 |  -0.04   1.75 |   3.31   1.82 |  -0.01   1.84  
 012 |   1.94   1.51 |  -0.07   1.74 |   1.56   2.25 |   0.01   2.31  
 013 |   3.77   1.58 |  -0.03   1.63 |   3.41   1.84 |  -0.08   1.86  
 014 |   3.59   1.41 |   0.03   1.65 |   3.24   1.87 |   0.03   1.92  
 015 |   3.89   1.45 |   0.10   1.68 |   3.46   1.83 |   0.02   1.86  
 016 |   4.17   1.41 |  -0.00   1.63 |   3.81   1.82 |  -0.03   1.83  
 017 |   4.08   1.33 |  -0.02   1.58 |   3.63   1.93 |   0.08   1.99  
 018 |   4.00   1.44 |   0.02   1.62 |   3.55   1.88 |   0.04   1.89  
 019 |   4.01   1.34 |  -0.01   1.68 |   3.48   1.94 |   0.05   1.97  
 020 |   4.20   1.39 |   0.00   1.60 |   3.72   1.99 |   0.09   2.02  
 021 |   4.06   1.40 |   0.06   1.60 |   3.34   2.11 |   0.14   2.19  
 022 |   4.00   1.39 |  -0.00   1.61 |   3.28   2.16 |   0.11   2.22  
 023 |   2.08   1.52 |   0.13   1.76 |   1.56   2.14 |   0.07   2.25  
 024 |   4.30   1.37 |   0.02   1.56 |   3.55   2.24 |   0.22   2.34  
 025 |   4.24   1.49 |   0.04   1.49 |   3.37   2.28 |   0.17   2.38  
 026 |   4.25   1.42 |  -0.07   1.53 |   3.45   2.27 |   0.17   2.34  
 027 |   4.13   1.47 |  -0.01   1.64 |   3.09   2.62 |   0.28   2.74  
 028 |   4.79   1.61 |  -0.02   1.60 |   3.41   2.95 |   0.33   3.11  
 029 |   4.92   1.61 |  -0.01   1.64 |   3.16   3.43 |   0.28   3.56  
 030 |   4.65   1.65 |  -0.09   1.61 |   2.91   3.49 |   0.28   3.64  
 031 |   2.29   1.48 |   0.01   1.72 |   1.85   2.17 |   0.08   2.25  
 032 |   2.22   1.49 |  -0.14   1.65 |   1.82   2.02 |   0.00   2.09  
 033 |   2.63   1.54 |  -0.00   1.70 |   2.25   1.97 |  -0.02   2.04  
 034 |   2.63   1.51 |   0.07   1.72 |   2.27   1.97 |  -0.02   2.02  
 035 |   2.82   1.50 |   0.04   1.85 |   2.50   1.94 |   0.03   1.98  
 036 |   2.79   1.46 |   0.07   1.70 |   2.36   1.98 |   0.05   2.05  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
  MS2  |    7  |   10  |   15  |   20  |   25  |   30  
-------|-------|-------|-------|-------|-------|-------
 Count |1699069|1742404|1786714|1812795|1832395|1849836
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
 Peaks |  50_1 |  75_1 | 100_1 | 125_1 | 150_1 
-------|-------|-------|-------|-------|-------
 Count |1642217|1783805|1825960|1842333|1849836
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 30 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 72.751 MIN***********************

************************************MAIN SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta
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 = 30.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1/2
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 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 = 100
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 6
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Number of unique peptides
    of length 7: 263572
    of length 8: 254610
    of length 9: 252521
    of length 10: 240191
    of length 11: 228920
    of length 12: 219088
    of length 13: 214670
    of length 14: 199875
    of length 15: 191923
    of length 16: 179666
    of length 17: 169341
    of length 18: 163589
    of length 19: 159157
    of length 20: 145049
    of length 21: 139196
    of length 22: 130706
    of length 23: 122721
    of length 24: 117501
    of length 25: 110357
    of length 26: 103221
    of length 27: 98646
    of length 28: 96801
    of length 29: 86727
    of length 30: 82147
    of length 31: 77864
    of length 32: 73885
    of length 33: 69330
    of length 34: 65064
    of length 35: 59487
    of length 36: 58283
    of length 37: 53570
    of length 38: 50099
    of length 39: 45448
    of length 40: 43486
    of length 41: 40861
    of length 42: 37247
    of length 43: 32038
    of length 44: 25613
    of length 45: 19421
    of length 46: 12687
    of length 47: 7899
    of length 48: 4619
    of length 49: 2376
    of length 50: 1390
    of length 51: 817
    of length 52: 427
    of length 53: 281
    of length 54: 200
    of length 55: 89
    of length 56: 69
    of length 57: 37
    of length 58: 20
    of length 59: 17
    of length 60: 4
    of length 61: 7
    of length 62: 3
    of length 63: 2
    of length 66: 2
In total 4752837 peptides.
Generated 7545089 modified peptides.
Selected fragment tolerance 0.15 Da and maximum fragment slice size of 6.90 GB.
314516074 fragments to be searched in 1 slices (4.69 GB total)
Operating on slice 1 of 1: 
    001. Trypsin1.mzBIN_calibrated 1.2 s
    001. Trypsin1.mzBIN_calibrated 1.2 s [progress: 52990/52990 (100.00%) - 16057.58 spectra/s] - completed 3.3 s
    002. Trypsin10.mzBIN_calibrated 1.2 s
    002. Trypsin10.mzBIN_calibrated 1.2 s [progress: 48185/60848 (79.19%) - 9633.15 spectra/s]
    002. Trypsin10.mzBIN_calibrated 1.2 s [progress: 60848/60848 (100.00%) - 8945.60 spectra/s] - completed 6.8 s
    003. Trypsin11.mzBIN_calibrated 1.2 s
    003. Trypsin11.mzBIN_calibrated 1.2 s [progress: 48578/60819 (79.87%) - 9525.10 spectra/s]
    003. Trypsin11.mzBIN_calibrated 1.2 s [progress: 60819/60819 (100.00%) - 8785.06 spectra/s] - completed 6.9 s
    004. Trypsin12.mzBIN_calibrated 1.2 s
    004. Trypsin12.mzBIN_calibrated 1.2 s [progress: 48215/61502 (78.40%) - 9453.92 spectra/s]
    004. Trypsin12.mzBIN_calibrated 1.2 s [progress: 61502/61502 (100.00%) - 8423.78 spectra/s] - completed 7.3 s
    005. Trypsin13.mzBIN_calibrated 1.3 s
    005. Trypsin13.mzBIN_calibrated 1.3 s [progress: 46923/60798 (77.18%) - 9382.72 spectra/s]
    005. Trypsin13.mzBIN_calibrated 1.3 s [progress: 60798/60798 (100.00%) - 8327.35 spectra/s] - completed 7.3 s
    006. Trypsin14.mzBIN_calibrated 1.2 s
    006. Trypsin14.mzBIN_calibrated 1.2 s [progress: 45915/62434 (73.54%) - 9173.83 spectra/s]
    006. Trypsin14.mzBIN_calibrated 1.2 s [progress: 62434/62434 (100.00%) - 7997.18 spectra/s] - completed 7.8 s
    007. Trypsin15.mzBIN_calibrated 1.3 s
    007. Trypsin15.mzBIN_calibrated 1.3 s [progress: 45836/63223 (72.50%) - 9156.21 spectra/s]
    007. Trypsin15.mzBIN_calibrated 1.3 s [progress: 63223/63223 (100.00%) - 7996.84 spectra/s] - completed 7.9 s
    008. Trypsin16.mzBIN_calibrated 1.2 s
    008. Trypsin16.mzBIN_calibrated 1.2 s [progress: 46034/62108 (74.12%) - 9026.27 spectra/s]
    008. Trypsin16.mzBIN_calibrated 1.2 s [progress: 62108/62108 (100.00%) - 7860.78 spectra/s] - completed 7.9 s
    009. Trypsin17.mzBIN_calibrated 1.3 s
    009. Trypsin17.mzBIN_calibrated 1.3 s [progress: 45387/62353 (72.79%) - 9075.58 spectra/s]
    009. Trypsin17.mzBIN_calibrated 1.3 s [progress: 62353/62353 (100.00%) - 7772.75 spectra/s] - completed 8.0 s
    010. Trypsin18.mzBIN_calibrated 1.2 s
    010. Trypsin18.mzBIN_calibrated 1.2 s [progress: 45193/61986 (72.91%) - 8861.37 spectra/s]
    010. Trypsin18.mzBIN_calibrated 1.2 s [progress: 61986/61986 (100.00%) - 7652.59 spectra/s] - completed 8.1 s
    011. Trypsin19.mzBIN_calibrated 1.2 s
    011. Trypsin19.mzBIN_calibrated 1.2 s [progress: 44598/61162 (72.92%) - 8784.32 spectra/s]
    011. Trypsin19.mzBIN_calibrated 1.2 s [progress: 61162/61162 (100.00%) - 7478.85 spectra/s] - completed 8.2 s
    012. Trypsin2.mzBIN_calibrated 1.1 s
    012. Trypsin2.mzBIN_calibrated 1.1 s [progress: 53507/53507 (100.00%) - 15283.35 spectra/s] - completed 3.5 s
    013. Trypsin20.mzBIN_calibrated 1.2 s
    013. Trypsin20.mzBIN_calibrated 1.2 s [progress: 45654/60608 (75.33%) - 8951.76 spectra/s]
    013. Trypsin20.mzBIN_calibrated 1.2 s [progress: 60608/60608 (100.00%) - 7870.15 spectra/s] - completed 7.7 s
    014. Trypsin21.mzBIN_calibrated 1.0 s
    014. Trypsin21.mzBIN_calibrated 1.0 s [progress: 46174/60767 (75.99%) - 9232.95 spectra/s]
    014. Trypsin21.mzBIN_calibrated 1.0 s [progress: 60767/60767 (100.00%) - 8058.22 spectra/s] - completed 7.5 s
    015. Trypsin22.mzBIN_calibrated 1.1 s
    015. Trypsin22.mzBIN_calibrated 1.1 s [progress: 44652/60137 (74.25%) - 8896.59 spectra/s]
    015. Trypsin22.mzBIN_calibrated 1.1 s [progress: 60137/60137 (100.00%) - 7691.14 spectra/s] - completed 7.8 s
    016. Trypsin23.mzBIN_calibrated 1.2 s
    016. Trypsin23.mzBIN_calibrated 1.2 s [progress: 44635/60590 (73.67%) - 8815.92 spectra/s]
    016. Trypsin23.mzBIN_calibrated 1.2 s [progress: 60590/60590 (100.00%) - 7572.80 spectra/s] - completed 8.0 s
    017. Trypsin24.mzBIN_calibrated 1.1 s
    017. Trypsin24.mzBIN_calibrated 1.1 s [progress: 46099/59909 (76.95%) - 9039.02 spectra/s]
    017. Trypsin24.mzBIN_calibrated 1.1 s [progress: 59909/59909 (100.00%) - 7882.76 spectra/s] - completed 7.6 s
    018. Trypsin25.mzBIN_calibrated 1.3 s
    018. Trypsin25.mzBIN_calibrated 1.3 s [progress: 45498/60030 (75.79%) - 9097.78 spectra/s]
    018. Trypsin25.mzBIN_calibrated 1.3 s [progress: 60030/60030 (100.00%) - 8001.87 spectra/s] - completed 7.5 s
    019. Trypsin26.mzBIN_calibrated 0.9 s
    019. Trypsin26.mzBIN_calibrated 0.9 s [progress: 44233/59393 (74.48%) - 8795.59 spectra/s]
    019. Trypsin26.mzBIN_calibrated 0.9 s [progress: 59393/59393 (100.00%) - 7670.54 spectra/s] - completed 7.7 s
    020. Trypsin27.mzBIN_calibrated 1.0 s
    020. Trypsin27.mzBIN_calibrated 1.0 s [progress: 44831/57836 (77.51%) - 8790.39 spectra/s]
    020. Trypsin27.mzBIN_calibrated 1.0 s [progress: 57836/57836 (100.00%) - 7815.68 spectra/s] - completed 7.4 s
    021. Trypsin28.mzBIN_calibrated 1.1 s
    021. Trypsin28.mzBIN_calibrated 1.1 s [progress: 45453/56416 (80.57%) - 8912.35 spectra/s]
    021. Trypsin28.mzBIN_calibrated 1.1 s [progress: 56416/56416 (100.00%) - 7945.92 spectra/s] - completed 7.1 s
    022. Trypsin29.mzBIN_calibrated 1.1 s
    022. Trypsin29.mzBIN_calibrated 1.1 s [progress: 45318/56507 (80.20%) - 8885.88 spectra/s]
    022. Trypsin29.mzBIN_calibrated 1.1 s [progress: 56507/56507 (100.00%) - 7955.37 spectra/s] - completed 7.1 s
    023. Trypsin3.mzBIN_calibrated 1.2 s
    023. Trypsin3.mzBIN_calibrated 1.2 s [progress: 52647/52647 (100.00%) - 15484.41 spectra/s] - completed 3.4 s
    024. Trypsin30.mzBIN_calibrated 1.1 s
    024. Trypsin30.mzBIN_calibrated 1.1 s [progress: 45099/54987 (82.02%) - 9005.39 spectra/s]
    024. Trypsin30.mzBIN_calibrated 1.1 s [progress: 54987/54987 (100.00%) - 7959.90 spectra/s] - completed 6.9 s
    025. Trypsin31.mzBIN_calibrated 1.2 s
    025. Trypsin31.mzBIN_calibrated 1.2 s [progress: 45703/53987 (84.66%) - 8961.37 spectra/s]
    025. Trypsin31.mzBIN_calibrated 1.2 s [progress: 53987/53987 (100.00%) - 8057.76 spectra/s] - completed 6.7 s
    026. Trypsin32.mzBIN_calibrated 0.9 s
    026. Trypsin32.mzBIN_calibrated 0.9 s [progress: 43694/54077 (80.80%) - 8714.40 spectra/s]
    026. Trypsin32.mzBIN_calibrated 0.9 s [progress: 54077/54077 (100.00%) - 7821.38 spectra/s] - completed 6.9 s
    027. Trypsin33.mzBIN_calibrated 1.3 s
    027. Trypsin33.mzBIN_calibrated 1.3 s [progress: 49045/52214 (93.93%) - 9616.67 spectra/s]
    027. Trypsin33.mzBIN_calibrated 1.3 s [progress: 52214/52214 (100.00%) - 8849.83 spectra/s] - completed 5.9 s
    028. Trypsin34.mzBIN_calibrated 1.0 s
    028. Trypsin34.mzBIN_calibrated 1.0 s [progress: 50826/51163 (99.34%) - 9965.88 spectra/s]
    028. Trypsin34.mzBIN_calibrated 1.0 s [progress: 51163/51163 (100.00%) - 9302.36 spectra/s] - completed 5.5 s
    029. Trypsin35.mzBIN_calibrated 0.9 s
    029. Trypsin35.mzBIN_calibrated 0.9 s [progress: 50390/50390 (100.00%) - 12290.24 spectra/s] - completed 4.1 s
    030. Trypsin36.mzBIN_calibrated 0.9 s
    030. Trypsin36.mzBIN_calibrated 0.9 s [progress: 49505/49505 (100.00%) - 13379.73 spectra/s] - completed 3.7 s
    031. Trypsin4.mzBIN_calibrated 1.0 s
    031. Trypsin4.mzBIN_calibrated 1.0 s [progress: 55505/55505 (100.00%) - 14148.61 spectra/s] - completed 3.9 s
    032. Trypsin5.mzBIN_calibrated 1.2 s
    032. Trypsin5.mzBIN_calibrated 1.2 s [progress: 55911/55911 (100.00%) - 13195.89 spectra/s] - completed 4.2 s
    033. Trypsin6.mzBIN_calibrated 0.9 s
    033. Trypsin6.mzBIN_calibrated 0.9 s [progress: 57385/57808 (99.27%) - 11451.81 spectra/s]
    033. Trypsin6.mzBIN_calibrated 0.9 s [progress: 57808/57808 (100.00%) - 11310.51 spectra/s] - completed 5.1 s
    034. Trypsin7.mzBIN_calibrated 1.2 s
    034. Trypsin7.mzBIN_calibrated 1.2 s [progress: 51996/58980 (88.16%) - 10388.81 spectra/s]
    034. Trypsin7.mzBIN_calibrated 1.2 s [progress: 58980/58980 (100.00%) - 10338.30 spectra/s] - completed 5.7 s
    035. Trypsin8.mzBIN_calibrated 1.5 s
    035. Trypsin8.mzBIN_calibrated 1.5 s [progress: 50807/60190 (84.41%) - 9968.02 spectra/s]
    035. Trypsin8.mzBIN_calibrated 1.5 s [progress: 60190/60190 (100.00%) - 9712.76 spectra/s] - completed 6.2 s
    036. Trypsin9.mzBIN_calibrated 1.0 s
    036. Trypsin9.mzBIN_calibrated 1.0 s [progress: 48676/59270 (82.13%) - 9733.25 spectra/s]
    036. Trypsin9.mzBIN_calibrated 1.0 s [progress: 59270/59270 (100.00%) - 9558.14 spectra/s] - completed 6.2 s
***************************MAIN SEARCH DONE IN 12.258 MIN***************************

*******************************TOTAL TIME 109.272 MIN********************************
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin1.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin10.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin11.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin12.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin13.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin14.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin15.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin16.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin17.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin18.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin19.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin2.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin20.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin21.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin22.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin23.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin24.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin25.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin26.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin27.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin28.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin29.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin3.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin30.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin31.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin32.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin33.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin34.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin35.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin36.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin4.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin5.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Tr

[fcyu]

@Golden-proteogenomics I think the log you pasted is not completed.

[Golden-proteogenomics]

Hello, when the GUI of FragPipe have been printing as the follow picture, I thinks it error to search. So, The log file was generated by the software when I stoped the software.

Then the two questions to confuse me : 1) what the reasons lead to the software error; 2) what can i do to give you a feedback to simply discription the question.

3) whether besides the log files anyfiles can track the reason or other files?

thanks, JInshuai Sun

At 2019-07-18 00:28:58, "Fengchao" notifications@github.com wrote:

@Golden-proteogenomics I think the log you pasted is not completed.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[fcyu]

I think you can attach the whole log file to the email, which can send the whole file to me.

According to your incomplete log in your last email, there is no error.

I think log is the first step and the most straightforward way to locate the error.

Best,

Fengchao

[Golden-proteogenomics]

I am very sorry to give you incomplete log fies, because I don't know what the complete log file is named for. So, the result files before the I have stop the software are in the enclosure, Please check it.

Best, Jinshuai Sun.

At 2019-07-18 00:55:03, "Fengchao" notifications@github.com wrote:

I think you can attach the whole log file to the email, which can send the whole file to me.

According to your incomplete log in your last email, there is no error.

I think log is the first step and the most straightforward way to locate the error.

Best,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread. System info: System OS: Windows 7, Architecture: AMD64 Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190628 Philosopher version v1.4.5 (build 1563205050)

LCMS files: Experiment/Group:

• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML
• I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML

80 commands to execute: Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --init MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin1.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin10.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin11.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin12.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin13.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin14.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin15.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin16.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin17.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin18.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin19.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin2.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin20.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin21.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin22.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin23.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin24.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin25.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin26.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin27.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin28.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin29.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin3.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin30.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin31.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin32.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin33.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin34.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin35.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin36.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin4.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin5.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin6.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin7.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin8.pepXML MsFragger java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin9.pepXML ReportDbAnnotate [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe database --annotate I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_contd.fasta --prefix >REV PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin25.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin15.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin10.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin3.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin20.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin33.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin5.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin17.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin27.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin13.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin23.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin7.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin19.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin29.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin36.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin2.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin26.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin31.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin11.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin21.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin16.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin4.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin24.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin34.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin14.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin9.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin28.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin1.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin18.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin6.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin8.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin12.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin22.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin32.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin30.pepXML PeptideProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy >REV --database I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta Trypsin35.pepXML ProteinProphet [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe proteinprophet --maxppmdiff 2000000 interact-Trypsin25.pep.xml interact-Trypsin15.pep.xml interact-Trypsin10.pep.xml interact-Trypsin3.pep.xml interact-Trypsin20.pep.xml interact-Trypsin33.pep.xml interact-Trypsin5.pep.xml interact-Trypsin17.pep.xml interact-Trypsin27.pep.xml interact-Trypsin13.pep.xml interact-Trypsin23.pep.xml interact-Trypsin7.pep.xml interact-Trypsin19.pep.xml interact-Trypsin29.pep.xml interact-Trypsin36.pep.xml interact-Trypsin2.pep.xml interact-Trypsin26.pep.xml interact-Trypsin31.pep.xml interact-Trypsin11.pep.xml interact-Trypsin21.pep.xml interact-Trypsin16.pep.xml interact-Trypsin4.pep.xml interact-Trypsin24.pep.xml interact-Trypsin34.pep.xml interact-Trypsin14.pep.xml interact-Trypsin9.pep.xml interact-Trypsin28.pep.xml interact-Trypsin1.pep.xml interact-Trypsin18.pep.xml interact-Trypsin6.pep.xml interact-Trypsin8.pep.xml interact-Trypsin12.pep.xml interact-Trypsin22.pep.xml interact-Trypsin32.pep.xml interact-Trypsin30.pep.xml interact-Trypsin35.pep.xml ReportFilter [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\Onereveice\mzML\MSFragger-20190628\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag >REV --pepxml I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin --protxml I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\interact.prot.xml ReportReport [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe report Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin] I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --clean
INFO[08:55:49] Executing Workspace v1.4.5                   
INFO[08:55:51] Removing workspace                           
INFO[08:55:51] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\philosopher.exe workspace --init
INFO[08:55:56] Executing Workspace v1.4.5                   
INFO[08:55:58] Creating workspace                           
INFO[08:55:58] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin]
java -jar -Dfile.encoding=UTF-8 -Xmx10G I:\Shuai\2019-CHPP\One_reveice\mzML\MSFragger-20190628\MSFragger-20190628.jar I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\fragger.params I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin6.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin7.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin8.mzML I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin9.mzML
MSFragger version MSFragger-20190628
MSFTBX version 1.9.10
(c) University of Michigan
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_202, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 9102 MB memory

***********************************FIRST SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta
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
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 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 = 100
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 6
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Number of unique peptides
    of length 7: 218678
    of length 8: 202863
    of length 9: 194949
    of length 10: 178286
    of length 11: 164195
    of length 12: 152037
    of length 13: 143644
    of length 14: 128940
    of length 15: 120767
    of length 16: 110154
    of length 17: 100878
    of length 18: 94017
    of length 19: 88288
    of length 20: 80125
    of length 21: 75067
    of length 22: 68632
    of length 23: 63786
    of length 24: 59715
    of length 25: 55358
    of length 26: 50738
    of length 27: 48195
    of length 28: 44944
    of length 29: 41329
    of length 30: 38424
    of length 31: 35400
    of length 32: 33108
    of length 33: 30467
    of length 34: 28143
    of length 35: 25574
    of length 36: 24493
    of length 37: 21687
    of length 38: 20265
    of length 39: 18081
    of length 40: 17198
    of length 41: 16183
    of length 42: 14374
    of length 43: 12585
    of length 44: 10139
    of length 45: 7954
    of length 46: 5377
    of length 47: 3507
    of length 48: 2150
    of length 49: 1139
    of length 50: 718
    of length 51: 443
    of length 52: 242
    of length 53: 140
    of length 54: 77
    of length 55: 57
    of length 56: 35
    of length 57: 17
    of length 58: 8
    of length 59: 12
    of length 60: 4
    of length 61: 6
    of length 62: 2
    of length 63: 2
    of length 66: 2
In total 2853598 peptides.
Generated 4333259 modified peptides.
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 6.27 GB.
161188014 fragments to be searched in 1 slices (2.40 GB total)
Operating on slice 1 of 1: 
    001. Trypsin1.mzML 29.3 s
    001. Trypsin1.mzML 29.3 s [progress: 41988/54055 (77.68%) - 8275.13 spectra/s]
    001. Trypsin1.mzML 29.3 s [progress: 54055/54055 (100.00%) - 9526.79 spectra/s] - completed 5.7 s
    002. Trypsin10.mzML 35.7 s
    002. Trypsin10.mzML 35.7 s [progress: 56048/61334 (91.38%) - 11015.72 spectra/s]
    002. Trypsin10.mzML 35.7 s [progress: 61334/61334 (100.00%) - 10783.05 spectra/s] - completed 5.7 s
    003. Trypsin11.mzML 30.0 s
    003. Trypsin11.mzML 30.0 s [progress: 54377/61425 (88.53%) - 10864.54 spectra/s]
    003. Trypsin11.mzML 30.0 s [progress: 61425/61425 (100.00%) - 10402.20 spectra/s] - completed 5.9 s
    004. Trypsin12.mzML 32.2 s
    004. Trypsin12.mzML 32.2 s [progress: 45901/62124 (73.89%) - 9014.34 spectra/s]
    004. Trypsin12.mzML 32.2 s [progress: 62124/62124 (100.00%) - 7723.98 spectra/s] - completed 8.0 s
    005. Trypsin13.mzML 40.0 s
    005. Trypsin13.mzML 40.0 s [progress: 49147/61245 (80.25%) - 9668.90 spectra/s]
    005. Trypsin13.mzML 40.0 s [progress: 61245/61245 (100.00%) - 8719.39 spectra/s] - completed 7.0 s
    006. Trypsin14.mzML 42.3 s
    006. Trypsin14.mzML 42.3 s [progress: 49833/62864 (79.27%) - 9938.77 spectra/s]
    006. Trypsin14.mzML 42.3 s [progress: 62864/62864 (100.00%) - 8598.55 spectra/s] - completed 7.3 s
    007. Trypsin15.mzML 40.7 s
    007. Trypsin15.mzML 40.7 s [progress: 45931/63653 (72.16%) - 9182.53 spectra/s]
    007. Trypsin15.mzML 40.7 s [progress: 63653/63653 (100.00%) - 8616.89 spectra/s] - completed 7.4 s
    008. Trypsin16.mzML 38.6 s
    008. Trypsin16.mzML 38.6 s [progress: 36191/62572 (57.84%) - 7185.03 spectra/s]
    008. Trypsin16.mzML 38.6 s [progress: 62572/62572 (100.00%) - 7165.83 spectra/s] - completed 8.7 s
    009. Trypsin17.mzML 39.7 s
    009. Trypsin17.mzML 39.7 s [progress: 53075/62816 (84.49%) - 10534.93 spectra/s]
    009. Trypsin17.mzML 39.7 s [progress: 62816/62816 (100.00%) - 9755.55 spectra/s] - completed 6.4 s
    010. Trypsin18.mzML 37.0 s
    010. Trypsin18.mzML 37.0 s [progress: 50364/62397 (80.72%) - 10058.72 spectra/s]
    010. Trypsin18.mzML 37.0 s [progress: 62397/62397 (100.00%) - 8992.22 spectra/s] - completed 6.9 s
    011. Trypsin19.mzML 31.8 s
    011. Trypsin19.mzML 31.8 s [progress: 51774/61621 (84.02%) - 10278.74 spectra/s]
    011. Trypsin19.mzML 31.8 s [progress: 61621/61621 (100.00%) - 9423.61 spectra/s] - completed 6.5 s
    012. Trypsin2.mzML 29.0 s
    012. Trypsin2.mzML 29.0 s [progress: 54297/54297 (100.00%) - 19295.31 spectra/s] - completed 2.8 s
    013. Trypsin20.mzML 38.5 s
    013. Trypsin20.mzML 38.5 s [progress: 45102/61029 (73.90%) - 8950.59 spectra/s]
    013. Trypsin20.mzML 38.5 s [progress: 61029/61029 (100.00%) - 8424.77 spectra/s] - completed 7.2 s
    014. Trypsin21.mzML 35.3 s
    014. Trypsin21.mzML 35.3 s [progress: 55284/61295 (90.19%) - 10745.19 spectra/s]
    014. Trypsin21.mzML 35.3 s [progress: 61295/61295 (100.00%) - 10139.78 spectra/s] - completed 6.0 s
    015. Trypsin22.mzML 35.3 s
    015. Trypsin22.mzML 35.3 s [progress: 47807/60728 (78.72%) - 9361.07 spectra/s]
    015. Trypsin22.mzML 35.3 s [progress: 60728/60728 (100.00%) - 6957.84 spectra/s] - completed 8.7 s
    016. Trypsin23.mzML 33.9 s
    016. Trypsin23.mzML 33.9 s [progress: 50385/61059 (82.52%) - 9977.23 spectra/s]
    016. Trypsin23.mzML 33.9 s [progress: 61059/61059 (100.00%) - 9040.42 spectra/s] - completed 6.8 s
    017. Trypsin24.mzML 24.5 s
    017. Trypsin24.mzML 24.5 s [progress: 46675/60321 (77.38%) - 9169.94 spectra/s]
    017. Trypsin24.mzML 24.5 s [progress: 60321/60321 (100.00%) - 8266.55 spectra/s] - completed 7.3 s
    018. Trypsin25.mzML 26.2 s
    018. Trypsin25.mzML 26.2 s [progress: 51334/60548 (84.78%) - 10139.05 spectra/s]
    018. Trypsin25.mzML 26.2 s [progress: 60548/60548 (100.00%) - 9290.78 spectra/s] - completed 6.5 s
    019. Trypsin26.mzML 17.6 s
    019. Trypsin26.mzML 17.6 s [progress: 47107/59800 (78.77%) - 9376.39 spectra/s]
    019. Trypsin26.mzML 17.6 s [progress: 59800/59800 (100.00%) - 8657.88 spectra/s] - completed 6.9 s
    020. Trypsin27.mzML 22.8 s
    020. Trypsin27.mzML 22.8 s [progress: 50991/58214 (87.59%) - 10181.91 spectra/s]
    020. Trypsin27.mzML 22.8 s [progress: 58214/58214 (100.00%) - 9193.62 spectra/s] - completed 6.3 s
    021. Trypsin28.mzML 22.8 s
    021. Trypsin28.mzML 22.8 s [progress: 55395/56761 (97.59%) - 11032.66 spectra/s]
    021. Trypsin28.mzML 22.8 s [progress: 56761/56761 (100.00%) - 10245.67 spectra/s] - completed 5.5 s
    022. Trypsin29.mzML 24.8 s
    022. Trypsin29.mzML 24.8 s [progress: 55919/56883 (98.31%) - 11154.80 spectra/s]
    022. Trypsin29.mzML 24.8 s [progress: 56883/56883 (100.00%) - 10706.38 spectra/s] - completed 5.3 s
    023. Trypsin3.mzML 21.8 s
    023. Trypsin3.mzML 21.8 s [progress: 53573/53573 (100.00%) - 17780.62 spectra/s] - completed 3.0 s
    024. Trypsin30.mzML 26.5 s
    024. Trypsin30.mzML 26.5 s [progress: 55285/55285 (100.00%) - 11670.89 spectra/s] - completed 4.7 s
    025. Trypsin31.mzML 28.1 s
    025. Trypsin31.mzML 28.1 s [progress: 54297/54297 (100.00%) - 11474.43 spectra/s] - completed 4.7 s
    026. Trypsin32.mzML 29.8 s
    026. Trypsin32.mzML 29.8 s [progress: 54420/54420 (100.00%) - 11232.20 spectra/s] - completed 4.8 s
    027. Trypsin33.mzML 27.6 s
    027. Trypsin33.mzML 27.6 s [progress: 52606/52606 (100.00%) - 10853.31 spectra/s] - completed 4.8 s
    028. Trypsin34.mzML 24.9 s
    028. Trypsin34.mzML 24.9 s [progress: 51572/51572 (100.00%) - 13260.99 spectra/s] - completed 3.9 s
    029. Trypsin35.mzML 22.3 s
    029. Trypsin35.mzML 22.3 s [progress: 50785/50785 (100.00%) - 18287.72 spectra/s] - completed 2.8 s
    030. Trypsin36.mzML 27.9 s
    030. Trypsin36.mzML 27.9 s [progress: 49967/49967 (100.00%) - 20810.91 spectra/s] - completed 2.4 s
    031. Trypsin4.mzML 29.8 s
    031. Trypsin4.mzML 29.8 s [progress: 56452/56452 (100.00%) - 17348.49 spectra/s] - completed 3.3 s
    032. Trypsin5.mzML 31.0 s
    032. Trypsin5.mzML 31.0 s [progress: 56655/56655 (100.00%) - 15395.38 spectra/s] - completed 3.7 s
    033. Trypsin6.mzML 29.8 s
    033. Trypsin6.mzML 29.8 s [progress: 58294/58294 (100.00%) - 13490.86 spectra/s] - completed 4.3 s
    034. Trypsin7.mzML 27.4 s
    034. Trypsin7.mzML 27.4 s [progress: 59506/59506 (100.00%) - 12335.41 spectra/s] - completed 4.8 s
    035. Trypsin8.mzML 29.8 s
    035. Trypsin8.mzML 29.8 s [progress: 60440/60673 (99.62%) - 11914.05 spectra/s]
    035. Trypsin8.mzML 29.8 s [progress: 60673/60673 (100.00%) - 11506.35 spectra/s] - completed 5.3 s
    036. Trypsin9.mzML 32.7 s
    036. Trypsin9.mzML 32.7 s [progress: 57839/59800 (96.72%) - 11446.47 spectra/s]
    036. Trypsin9.mzML 32.7 s [progress: 59800/59800 (100.00%) - 10966.44 spectra/s] - completed 5.5 s
***************************FIRST SEARCH DONE IN 24.263 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   2.11   1.47 |  -0.03   1.66 |   1.52   2.31 |   0.01   2.43  
 002 |   3.03   1.48 |   0.06   1.74 |   2.72   1.86 |  -0.02   1.90  
 003 |   2.93   1.47 |   0.06   1.73 |   2.64   1.78 |  -0.03   1.82  
 004 |   2.95   1.52 |   0.02   1.69 |   2.72   1.79 |  -0.05   1.81  
 005 |   3.03   1.46 |  -0.01   1.69 |   2.65   1.87 |  -0.04   1.92  
 006 |   3.00   1.39 |   0.01   1.66 |   2.68   1.76 |  -0.07   1.77  
 007 |   3.36   1.44 |   0.03   1.72 |   3.06   1.78 |  -0.04   1.79  
 008 |   3.63   1.41 |   0.00   1.73 |   3.33   1.78 |  -0.06   1.79  
 009 |   3.62   1.42 |   0.01   1.66 |   3.32   1.76 |  -0.03   1.79  
 010 |   3.62   1.39 |   0.02   1.70 |   3.26   1.77 |  -0.03   1.79  
 011 |   3.58   1.51 |  -0.04   1.75 |   3.31   1.82 |  -0.01   1.84  
 012 |   1.94   1.51 |  -0.07   1.74 |   1.56   2.25 |   0.01   2.31  
 013 |   3.77   1.58 |  -0.03   1.63 |   3.41   1.84 |  -0.08   1.86  
 014 |   3.59   1.41 |   0.03   1.65 |   3.24   1.87 |   0.03   1.92  
 015 |   3.89   1.45 |   0.10   1.68 |   3.46   1.83 |   0.02   1.86  
 016 |   4.17   1.41 |  -0.00   1.63 |   3.81   1.82 |  -0.03   1.83  
 017 |   4.08   1.33 |  -0.02   1.58 |   3.63   1.93 |   0.08   1.99  
 018 |   4.00   1.44 |   0.02   1.62 |   3.55   1.88 |   0.04   1.89  
 019 |   4.01   1.34 |  -0.01   1.68 |   3.48   1.94 |   0.05   1.97  
 020 |   4.20   1.39 |   0.00   1.60 |   3.72   1.99 |   0.09   2.02  
 021 |   4.06   1.40 |   0.06   1.60 |   3.34   2.11 |   0.14   2.19  
 022 |   4.00   1.39 |  -0.00   1.61 |   3.28   2.16 |   0.11   2.22  
 023 |   2.08   1.52 |   0.13   1.76 |   1.56   2.14 |   0.07   2.25  
 024 |   4.30   1.37 |   0.02   1.56 |   3.55   2.24 |   0.22   2.34  
 025 |   4.24   1.49 |   0.04   1.49 |   3.37   2.28 |   0.17   2.38  
 026 |   4.25   1.42 |  -0.07   1.53 |   3.45   2.27 |   0.17   2.34  
 027 |   4.13   1.47 |  -0.01   1.64 |   3.09   2.62 |   0.28   2.74  
 028 |   4.79   1.61 |  -0.02   1.60 |   3.41   2.95 |   0.33   3.11  
 029 |   4.92   1.61 |  -0.01   1.64 |   3.16   3.43 |   0.28   3.56  
 030 |   4.65   1.65 |  -0.09   1.61 |   2.91   3.49 |   0.28   3.64  
 031 |   2.29   1.48 |   0.01   1.72 |   1.85   2.17 |   0.08   2.25  
 032 |   2.22   1.49 |  -0.14   1.65 |   1.82   2.02 |   0.00   2.09  
 033 |   2.63   1.54 |  -0.00   1.70 |   2.25   1.97 |  -0.02   2.04  
 034 |   2.63   1.51 |   0.07   1.72 |   2.27   1.97 |  -0.02   2.02  
 035 |   2.82   1.50 |   0.04   1.85 |   2.50   1.94 |   0.03   1.98  
 036 |   2.79   1.46 |   0.07   1.70 |   2.36   1.98 |   0.05   2.05  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
  MS2  |    7  |   10  |   15  |   20  |   25  |   30  
-------|-------|-------|-------|-------|-------|-------
 Count |1699069|1742404|1786714|1812795|1832395|1849836
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
 Peaks |  50_1 |  75_1 | 100_1 | 125_1 | 150_1 
-------|-------|-------|-------|-------|-------
 Count |1642217|1783805|1825960|1842333|1849836
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 30 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 72.751 MIN***********************

************************************MAIN SEARCH************************************
Parameters:
num_threads = 10
database_name = I:\Shuai\2019-CHPP\One_reveice\mzML\GluC\2019_CHPP_Seq_con_td.fasta
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 = 30.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1/2
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
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
allowed_missed_cleavage = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 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 = 100
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 6
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
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Number of unique peptides
    of length 7: 263572
    of length 8: 254610
    of length 9: 252521
    of length 10: 240191
    of length 11: 228920
    of length 12: 219088
    of length 13: 214670
    of length 14: 199875
    of length 15: 191923
    of length 16: 179666
    of length 17: 169341
    of length 18: 163589
    of length 19: 159157
    of length 20: 145049
    of length 21: 139196
    of length 22: 130706
    of length 23: 122721
    of length 24: 117501
    of length 25: 110357
    of length 26: 103221
    of length 27: 98646
    of length 28: 96801
    of length 29: 86727
    of length 30: 82147
    of length 31: 77864
    of length 32: 73885
    of length 33: 69330
    of length 34: 65064
    of length 35: 59487
    of length 36: 58283
    of length 37: 53570
    of length 38: 50099
    of length 39: 45448
    of length 40: 43486
    of length 41: 40861
    of length 42: 37247
    of length 43: 32038
    of length 44: 25613
    of length 45: 19421
    of length 46: 12687
    of length 47: 7899
    of length 48: 4619
    of length 49: 2376
    of length 50: 1390
    of length 51: 817
    of length 52: 427
    of length 53: 281
    of length 54: 200
    of length 55: 89
    of length 56: 69
    of length 57: 37
    of length 58: 20
    of length 59: 17
    of length 60: 4
    of length 61: 7
    of length 62: 3
    of length 63: 2
    of length 66: 2
In total 4752837 peptides.
Generated 7545089 modified peptides.
Selected fragment tolerance 0.15 Da and maximum fragment slice size of 6.90 GB.
314516074 fragments to be searched in 1 slices (4.69 GB total)
Operating on slice 1 of 1: 
    001. Trypsin1.mzBIN_calibrated 1.2 s
    001. Trypsin1.mzBIN_calibrated 1.2 s [progress: 52990/52990 (100.00%) - 16057.58 spectra/s] - completed 3.3 s
    002. Trypsin10.mzBIN_calibrated 1.2 s
    002. Trypsin10.mzBIN_calibrated 1.2 s [progress: 48185/60848 (79.19%) - 9633.15 spectra/s]
    002. Trypsin10.mzBIN_calibrated 1.2 s [progress: 60848/60848 (100.00%) - 8945.60 spectra/s] - completed 6.8 s
    003. Trypsin11.mzBIN_calibrated 1.2 s
    003. Trypsin11.mzBIN_calibrated 1.2 s [progress: 48578/60819 (79.87%) - 9525.10 spectra/s]
    003. Trypsin11.mzBIN_calibrated 1.2 s [progress: 60819/60819 (100.00%) - 8785.06 spectra/s] - completed 6.9 s
    004. Trypsin12.mzBIN_calibrated 1.2 s
    004. Trypsin12.mzBIN_calibrated 1.2 s [progress: 48215/61502 (78.40%) - 9453.92 spectra/s]
    004. Trypsin12.mzBIN_calibrated 1.2 s [progress: 61502/61502 (100.00%) - 8423.78 spectra/s] - completed 7.3 s
    005. Trypsin13.mzBIN_calibrated 1.3 s
    005. Trypsin13.mzBIN_calibrated 1.3 s [progress: 46923/60798 (77.18%) - 9382.72 spectra/s]
    005. Trypsin13.mzBIN_calibrated 1.3 s [progress: 60798/60798 (100.00%) - 8327.35 spectra/s] - completed 7.3 s
    006. Trypsin14.mzBIN_calibrated 1.2 s
    006. Trypsin14.mzBIN_calibrated 1.2 s [progress: 45915/62434 (73.54%) - 9173.83 spectra/s]
    006. Trypsin14.mzBIN_calibrated 1.2 s [progress: 62434/62434 (100.00%) - 7997.18 spectra/s] - completed 7.8 s
    007. Trypsin15.mzBIN_calibrated 1.3 s
    007. Trypsin15.mzBIN_calibrated 1.3 s [progress: 45836/63223 (72.50%) - 9156.21 spectra/s]
    007. Trypsin15.mzBIN_calibrated 1.3 s [progress: 63223/63223 (100.00%) - 7996.84 spectra/s] - completed 7.9 s
    008. Trypsin16.mzBIN_calibrated 1.2 s
    008. Trypsin16.mzBIN_calibrated 1.2 s [progress: 46034/62108 (74.12%) - 9026.27 spectra/s]
    008. Trypsin16.mzBIN_calibrated 1.2 s [progress: 62108/62108 (100.00%) - 7860.78 spectra/s] - completed 7.9 s
    009. Trypsin17.mzBIN_calibrated 1.3 s
    009. Trypsin17.mzBIN_calibrated 1.3 s [progress: 45387/62353 (72.79%) - 9075.58 spectra/s]
    009. Trypsin17.mzBIN_calibrated 1.3 s [progress: 62353/62353 (100.00%) - 7772.75 spectra/s] - completed 8.0 s
    010. Trypsin18.mzBIN_calibrated 1.2 s
    010. Trypsin18.mzBIN_calibrated 1.2 s [progress: 45193/61986 (72.91%) - 8861.37 spectra/s]
    010. Trypsin18.mzBIN_calibrated 1.2 s [progress: 61986/61986 (100.00%) - 7652.59 spectra/s] - completed 8.1 s
    011. Trypsin19.mzBIN_calibrated 1.2 s
    011. Trypsin19.mzBIN_calibrated 1.2 s [progress: 44598/61162 (72.92%) - 8784.32 spectra/s]
    011. Trypsin19.mzBIN_calibrated 1.2 s [progress: 61162/61162 (100.00%) - 7478.85 spectra/s] - completed 8.2 s
    012. Trypsin2.mzBIN_calibrated 1.1 s
    012. Trypsin2.mzBIN_calibrated 1.1 s [progress: 53507/53507 (100.00%) - 15283.35 spectra/s] - completed 3.5 s
    013. Trypsin20.mzBIN_calibrated 1.2 s
    013. Trypsin20.mzBIN_calibrated 1.2 s [progress: 45654/60608 (75.33%) - 8951.76 spectra/s]
    013. Trypsin20.mzBIN_calibrated 1.2 s [progress: 60608/60608 (100.00%) - 7870.15 spectra/s] - completed 7.7 s
    014. Trypsin21.mzBIN_calibrated 1.0 s
    014. Trypsin21.mzBIN_calibrated 1.0 s [progress: 46174/60767 (75.99%) - 9232.95 spectra/s]
    014. Trypsin21.mzBIN_calibrated 1.0 s [progress: 60767/60767 (100.00%) - 8058.22 spectra/s] - completed 7.5 s
    015. Trypsin22.mzBIN_calibrated 1.1 s
    015. Trypsin22.mzBIN_calibrated 1.1 s [progress: 44652/60137 (74.25%) - 8896.59 spectra/s]
    015. Trypsin22.mzBIN_calibrated 1.1 s [progress: 60137/60137 (100.00%) - 7691.14 spectra/s] - completed 7.8 s
    016. Trypsin23.mzBIN_calibrated 1.2 s
    016. Trypsin23.mzBIN_calibrated 1.2 s [progress: 44635/60590 (73.67%) - 8815.92 spectra/s]
    016. Trypsin23.mzBIN_calibrated 1.2 s [progress: 60590/60590 (100.00%) - 7572.80 spectra/s] - completed 8.0 s
    017. Trypsin24.mzBIN_calibrated 1.1 s
    017. Trypsin24.mzBIN_calibrated 1.1 s [progress: 46099/59909 (76.95%) - 9039.02 spectra/s]
    017. Trypsin24.mzBIN_calibrated 1.1 s [progress: 59909/59909 (100.00%) - 7882.76 spectra/s] - completed 7.6 s
    018. Trypsin25.mzBIN_calibrated 1.3 s
    018. Trypsin25.mzBIN_calibrated 1.3 s [progress: 45498/60030 (75.79%) - 9097.78 spectra/s]
    018. Trypsin25.mzBIN_calibrated 1.3 s [progress: 60030/60030 (100.00%) - 8001.87 spectra/s] - completed 7.5 s
    019. Trypsin26.mzBIN_calibrated 0.9 s
    019. Trypsin26.mzBIN_calibrated 0.9 s [progress: 44233/59393 (74.48%) - 8795.59 spectra/s]
    019. Trypsin26.mzBIN_calibrated 0.9 s [progress: 59393/59393 (100.00%) - 7670.54 spectra/s] - completed 7.7 s
    020. Trypsin27.mzBIN_calibrated 1.0 s
    020. Trypsin27.mzBIN_calibrated 1.0 s [progress: 44831/57836 (77.51%) - 8790.39 spectra/s]
    020. Trypsin27.mzBIN_calibrated 1.0 s [progress: 57836/57836 (100.00%) - 7815.68 spectra/s] - completed 7.4 s
    021. Trypsin28.mzBIN_calibrated 1.1 s
    021. Trypsin28.mzBIN_calibrated 1.1 s [progress: 45453/56416 (80.57%) - 8912.35 spectra/s]
    021. Trypsin28.mzBIN_calibrated 1.1 s [progress: 56416/56416 (100.00%) - 7945.92 spectra/s] - completed 7.1 s
    022. Trypsin29.mzBIN_calibrated 1.1 s
    022. Trypsin29.mzBIN_calibrated 1.1 s [progress: 45318/56507 (80.20%) - 8885.88 spectra/s]
    022. Trypsin29.mzBIN_calibrated 1.1 s [progress: 56507/56507 (100.00%) - 7955.37 spectra/s] - completed 7.1 s
    023. Trypsin3.mzBIN_calibrated 1.2 s
    023. Trypsin3.mzBIN_calibrated 1.2 s [progress: 52647/52647 (100.00%) - 15484.41 spectra/s] - completed 3.4 s
    024. Trypsin30.mzBIN_calibrated 1.1 s
    024. Trypsin30.mzBIN_calibrated 1.1 s [progress: 45099/54987 (82.02%) - 9005.39 spectra/s]
    024. Trypsin30.mzBIN_calibrated 1.1 s [progress: 54987/54987 (100.00%) - 7959.90 spectra/s] - completed 6.9 s
    025. Trypsin31.mzBIN_calibrated 1.2 s
    025. Trypsin31.mzBIN_calibrated 1.2 s [progress: 45703/53987 (84.66%) - 8961.37 spectra/s]
    025. Trypsin31.mzBIN_calibrated 1.2 s [progress: 53987/53987 (100.00%) - 8057.76 spectra/s] - completed 6.7 s
    026. Trypsin32.mzBIN_calibrated 0.9 s
    026. Trypsin32.mzBIN_calibrated 0.9 s [progress: 43694/54077 (80.80%) - 8714.40 spectra/s]
    026. Trypsin32.mzBIN_calibrated 0.9 s [progress: 54077/54077 (100.00%) - 7821.38 spectra/s] - completed 6.9 s
    027. Trypsin33.mzBIN_calibrated 1.3 s
    027. Trypsin33.mzBIN_calibrated 1.3 s [progress: 49045/52214 (93.93%) - 9616.67 spectra/s]
    027. Trypsin33.mzBIN_calibrated 1.3 s [progress: 52214/52214 (100.00%) - 8849.83 spectra/s] - completed 5.9 s
    028. Trypsin34.mzBIN_calibrated 1.0 s
    028. Trypsin34.mzBIN_calibrated 1.0 s [progress: 50826/51163 (99.34%) - 9965.88 spectra/s]
    028. Trypsin34.mzBIN_calibrated 1.0 s [progress: 51163/51163 (100.00%) - 9302.36 spectra/s] - completed 5.5 s
    029. Trypsin35.mzBIN_calibrated 0.9 s
    029. Trypsin35.mzBIN_calibrated 0.9 s [progress: 50390/50390 (100.00%) - 12290.24 spectra/s] - completed 4.1 s
    030. Trypsin36.mzBIN_calibrated 0.9 s
    030. Trypsin36.mzBIN_calibrated 0.9 s [progress: 49505/49505 (100.00%) - 13379.73 spectra/s] - completed 3.7 s
    031. Trypsin4.mzBIN_calibrated 1.0 s
    031. Trypsin4.mzBIN_calibrated 1.0 s [progress: 55505/55505 (100.00%) - 14148.61 spectra/s] - completed 3.9 s
    032. Trypsin5.mzBIN_calibrated 1.2 s
    032. Trypsin5.mzBIN_calibrated 1.2 s [progress: 55911/55911 (100.00%) - 13195.89 spectra/s] - completed 4.2 s
    033. Trypsin6.mzBIN_calibrated 0.9 s
    033. Trypsin6.mzBIN_calibrated 0.9 s [progress: 57385/57808 (99.27%) - 11451.81 spectra/s]
    033. Trypsin6.mzBIN_calibrated 0.9 s [progress: 57808/57808 (100.00%) - 11310.51 spectra/s] - completed 5.1 s
    034. Trypsin7.mzBIN_calibrated 1.2 s
    034. Trypsin7.mzBIN_calibrated 1.2 s [progress: 51996/58980 (88.16%) - 10388.81 spectra/s]
    034. Trypsin7.mzBIN_calibrated 1.2 s [progress: 58980/58980 (100.00%) - 10338.30 spectra/s] - completed 5.7 s
    035. Trypsin8.mzBIN_calibrated 1.5 s
    035. Trypsin8.mzBIN_calibrated 1.5 s [progress: 50807/60190 (84.41%) - 9968.02 spectra/s]
    035. Trypsin8.mzBIN_calibrated 1.5 s [progress: 60190/60190 (100.00%) - 9712.76 spectra/s] - completed 6.2 s
    036. Trypsin9.mzBIN_calibrated 1.0 s
    036. Trypsin9.mzBIN_calibrated 1.0 s [progress: 48676/59270 (82.13%) - 9733.25 spectra/s]
    036. Trypsin9.mzBIN_calibrated 1.0 s [progress: 59270/59270 (100.00%) - 9558.14 spectra/s] - completed 6.2 s
***************************MAIN SEARCH DONE IN 12.258 MIN***************************

*******************************TOTAL TIME 109.272 MIN********************************
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin1.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin1.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin10.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin10.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin11.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin11.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin12.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin12.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin13.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin13.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin14.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin14.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin15.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin15.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin16.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin16.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin17.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin17.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin18.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin18.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin19.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin19.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin2.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin2.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin20.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin20.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin21.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin21.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin22.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin22.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin23.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin23.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin24.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin24.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin25.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin25.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin26.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin26.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin27.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin27.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin28.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin28.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin29.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin29.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin3.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin3.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin30.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin30.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin31.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin31.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin32.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin32.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin33.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin33.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin34.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin34.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin35.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin35.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin36.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin36.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin4.pepXML I:\Shuai\2019-CHPP\One_reveice\mzML\Reuslt\Trypsin\Trypsin4.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp I:\Shuai\2019-CHPP\One_reveice\mzML\FragPipe.exe umich.msfragger.util.FileMove I:\Shuai\2019-CHPP\One_reveice\mzML\Trypsin\Trypsin5.pepXML I:\Shu

[fcyu]

Since the log is still not complete, I can only guess one possible issue: You put ">REV_" as your decoy prefix. Could you please check that? Normally, there is no ">" at the beginning.

Best,

Fengchao

[Golden-proteogenomics]

I have been finished the check, the search database all begining at ">REV", ">Protein name", and ">CON". Those fasta files can be used for searching?

At 2019-07-18 01:45:03, "Fengchao" notifications@github.com wrote:

Since the log is still not complete, I can only guess one possible issue: You put ">REV_" as your decoy prefix. Could you please check that? Normally, there is no ">" at the beginning.

Best,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[fcyu]

You may try with "REV_".

[Golden-proteogenomics]

OK，can you give me a fasta file which contains the targe proteins, decoy proteins and contaminate proteins so that I can build the search database？

At 2019-07-18 02:05:27, "Fengchao" notifications@github.com wrote:

You may try with "REV_".

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[fcyu]

Sure. What species are you using?

[anesvi]

There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com> wrote:

External Email - Use Caution

Sure. What species are you using?

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[Golden-proteogenomics]

The database which contains the proteins filted by our Lab research. if you can give me a files example of database, i will re-rebuild a database for my project.

At 2019-07-18 02:13:48, "Alexey Nesvizhskii" notifications@github.com wrote: There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com> wrote:

External Email - Use Caution

Sure. What species are you using?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/MSFragger/issues/34?email_source=notifications&email_token=AIIMM65DPYSYNYDG5CFUDM3P75OHTA5CNFSM4ID54NU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GD7OY#issuecomment-512507835, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM6ZB3JULCMSN77XIAJLP75OHTANCNFSM4ID54NUQ.

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[anesvi]

Please take a look here

https://github.com/Nesvilab/philosopher/wiki/How-to-Prepare-a-Protein-Database

To get a sample database, use FragPipe and download the database from UniProt by clicking on Download button in Database tab

Best Alexey

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Wednesday, July 17, 2019 2:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] pepXML (#34)

External Email - Use Caution

The database which contains the proteins filted by our Lab research. if you can give me a files example of database, i will re-rebuild a database for my project.

At 2019-07-18 02:13:48, "Alexey Nesvizhskii" notifications@github.com<mailto:notifications@github.com> wrote: There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

External Email - Use Caution

Sure. What species are you using?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/MSFragger/issues/34?email_source=notifications&email_token=AIIMM65DPYSYNYDG5CFUDM3P75OHTA5CNFSM4ID54NU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GD7OY#issuecomment-512507835, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM6ZB3JULCMSN77XIAJLP75OHTANCNFSM4ID54NUQ.

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[Golden-proteogenomics]

OK, Thanks, I change it and try! Thanks Jinshuai Sun

At 2019-07-18 02:25:01, "Alexey Nesvizhskii" notifications@github.com wrote: Please take a look here

https://github.com/Nesvilab/philosopher/wiki/How-to-Prepare-a-Protein-Database

To get a sample database, use FragPipe and download the database from UniProt by clicking on Download button in Database tab

Best Alexey

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Wednesday, July 17, 2019 2:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] pepXML (#34)

External Email - Use Caution

The database which contains the proteins filted by our Lab research. if you can give me a files example of database, i will re-rebuild a database for my project.

At 2019-07-18 02:13:48, "Alexey Nesvizhskii" notifications@github.com<mailto:notifications@github.com> wrote: There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

External Email - Use Caution

Sure. What species are you using?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/MSFragger/issues/34?email_source=notifications&email_token=AIIMM65DPYSYNYDG5CFUDM3P75OHTA5CNFSM4ID54NU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GD7OY#issuecomment-512507835, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM6ZB3JULCMSN77XIAJLP75OHTANCNFSM4ID54NUQ.

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[Golden-proteogenomics]

Hello, I am sorry to distrube you again about my task to search used the FragPipe.exe. The specific dataset and log files of my searching task are placed in attachments to mail. please give me a hand in your leisure time to help me to use it. thanks again! jinshuai Sun National Center for Protein Sciences Beijing

At 2019-07-18 02:25:01, "Alexey Nesvizhskii" notifications@github.com wrote: Please take a look here

https://github.com/Nesvilab/philosopher/wiki/How-to-Prepare-a-Protein-Database

To get a sample database, use FragPipe and download the database from UniProt by clicking on Download button in Database tab

Best Alexey

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Wednesday, July 17, 2019 2:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] pepXML (#34)

External Email - Use Caution

The database which contains the proteins filted by our Lab research. if you can give me a files example of database, i will re-rebuild a database for my project.

At 2019-07-18 02:13:48, "Alexey Nesvizhskii" notifications@github.com<mailto:notifications@github.com> wrote: There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

External Email - Use Caution

Sure. What species are you using?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/MSFragger/issues/34?email_source=notifications&email_token=AIIMM65DPYSYNYDG5CFUDM3P75OHTA5CNFSM4ID54NU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GD7OY#issuecomment-512507835, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIIMM6ZB3JULCMSN77XIAJLP75OHTANCNFSM4ID54NUQ.

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从网易126邮箱发来的云附件 log-fragpipe-run-at_2019-07-30_17-30-46.log (47.79K, 2019年8月14日 21:11 到期) 下载 CHPP_Seq.fasta (25.79M, 2019年8月14日 21:11 到期) 下载

[fcyu]

I am sorry but it looks like you put your files to 网易云附件, which is not supported by GitHub. Could you please send your file as a normal email attachment? If the file is too large, you may give me your email account so that I can share a Box folder with you.

Best,

Fengchao

[Golden-proteogenomics]

OK, I have submit the questions which title is "Processing interrupted, stopping MsFragge", please cheack it.

At 2019-07-30 21:20:46, "金史留青" sjsshuai@126.com wrote:

Hello, I am sorry to distrube you again about my task to search used the FragPipe.exe. The specific dataset and log files of my searching task are placed in attachments to mail. please give me a hand in your leisure time to help me to use it. thanks again! jinshuai Sun National Center for Protein Sciences Beijing

At 2019-07-18 02:25:01, "Alexey Nesvizhskii" notifications@github.com wrote: Please take a look here

https://github.com/Nesvilab/philosopher/wiki/How-to-Prepare-a-Protein-Database

To get a sample database, use FragPipe and download the database from UniProt by clicking on Download button in Database tab

Best Alexey

From: Golden-proteogenomics [mailto:notifications@github.com] Sent: Wednesday, July 17, 2019 2:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] pepXML (#34)

External Email - Use Caution

The database which contains the proteins filted by our Lab research. if you can give me a files example of database, i will re-rebuild a database for my project.

At 2019-07-18 02:13:48, "Alexey Nesvizhskii" notifications@github.com<mailto:notifications@github.com> wrote: There is Download option in FragPipe in Database tab

Is that not working for you for some reason?

Sent from my iPhone

On Jul 17, 2019, at 2:12 PM, Fengchao notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

External Email - Use Caution

Sure. What species are you using?

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从网易126邮箱发来的云附件 log-fragpipe-run-at_2019-07-30_17-30-46.log (47.79K, 2019年8月14日 21:11 到期) 下载 CHPP_Seq.fasta (25.79M, 2019年8月14日 21:11 到期) 下载

[Golden-proteogenomics]

OK, I have submit the questions which title is "Processing interrupted, stopping MsFragge", please cheack it.

At 2019-07-30 22:02:50, "Fengchao" notifications@github.com wrote:

I am sorry but it looks like you put your files to 网易云附件, which is not supported by GitHub. Could you please send your file as a normal email attachment? If the file is too large, you may give me your email account so that I can share a Box folder with you.

Best,

Fengchao

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