in silico digestion parameters

I'm submitting a:
- [x ] problem running the software
- [ ] bug report
- [ ] feature request
- [ ] question
My MSFragger use case:
- [ ] Closed search (standard small precursor mass tolerance)
- [x ] Open search (large precursor mass tolerance)
put your general problem description here The default setting with trypsin works just fine with the same MZML file. I'm trying to digest with other enzymes, this particular case, the enzyme was Lyc-C. I changed the enzyme name to "Lys-C", Cut after to "K", and left blank the But not before parameter. The remaining parameters were the same as those with default trypsin parameters. However, the run stops before completion. I want to find out how to set the enzyme parameters. Thanks for your help.

System info

You can find that printed on the Config tab.

OS and version: _Windows 10
Java version: _Java 8

Describe your experiment

Genral proteomics experiment description

enzymatic digestion of a relative pure protein

...

Input data files

one 2 Gb MZML file

Sequence database

custom database containing a single protein sequence

Attach fragger.params file

Run log output

System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_212, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 9.4 MSFragger version 20190628 Philosopher version v1.2.3 (build 1562095019)

LCMS files: Experiment/Group:

C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\Lum_19may2301.mzML

9 commands to execute: Workspace [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe workspace --init MsFragger [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] java -jar -Dfile.encoding=UTF-8 -Xmx8G C:\Users\mxm35\Documents\MSFragger\MSFragger-20190628\MSFragger-20190628.jar C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\fragger.params C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\Lum_19may2301.mzML ReportDbAnnotate [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe database --annotate C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.ErkJohn Wang special.fasta --prefix REV PeptideProphet [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy REV --database C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.Erk_John Wang special.fasta Lum_19may2301.pepXML ProteinProphet [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact-Lum_19may2301.pep.xml ReportFilter [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag REV --pepxml C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test --protxml C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact.prot.xml ReportReport [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe report Workspace [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test] C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe workspace --clean


Workspace [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe workspace --clean
INFO[16:14:12] Executing Workspace v1.2.3                   
WARN[16:14:12] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[16:14:12] Removing workspace                           
INFO[16:14:12] Done                                         
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe workspace --init
INFO[16:14:13] Executing Workspace v1.2.3                   
WARN[16:14:13] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[16:14:13] Creating workspace                           
INFO[16:14:13] Done                                         
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
java -jar -Dfile.encoding=UTF-8 -Xmx8G C:\Users\mxm35\Documents\MSFragger\MSFragger-20190628\MSFragger-20190628.jar C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\fragger.params C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\Lum_19may2301.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 10, Architecture: AMD64
Java Info: 1.8.0_212, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 7282 MB memory

***********************************FIRST SEARCH************************************
Parameters:
num_threads = 4
database_name = C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.Erk_John Wang special.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 = Lys-C
search_enzyme_cutafter = K
search_enzyme_butnotafter = 
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 = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
minIonsScoring = 3
min_matched_fragments = 5
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: 4
    of length 8: 6
    of length 9: 2
    of length 11: 4
    of length 12: 2
    of length 13: 10
    of length 14: 2
    of length 15: 2
    of length 17: 2
    of length 18: 1
    of length 19: 5
    of length 21: 2
    of length 22: 1
    of length 23: 1
    of length 24: 4
    of length 26: 2
    of length 28: 4
    of length 33: 4
    of length 34: 3
    of length 37: 2
    of length 38: 1
    of length 39: 6
    of length 40: 2
    of length 43: 2
In total 74 peptides.
Generated 154 modified peptides.
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 4.89 GB.
8064 fragments to be searched in 1 slices (0.00 GB total)
Operating on slice 1 of 1: 
    001. Lum_19may2301.mzML 10.8 s
    001. Lum_19may2301.mzML 10.8 s [progress: 57006/82931 (68.74%) - 11290.55 spectra/s]
    001. Lum_19may2301.mzML 10.8 s [progress: 82931/82931 (100.00%) - 11580.92 spectra/s] - completed 7.2 s
***************************FIRST SEARCH DONE IN 0.313 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 | Not enough data to perform mass calibration. Using the uncalibrated data.
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
  MS2  |    7  |   10  |   15  |   20  |   25  |   30  
-------|-------|-------|-------|-------|-------|-------
 Count |      0|      0|      0|      0|      0|      0
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
 Peaks |  50_1 |  75_1 | 100_1 | 125_1 | 150_1 
-------|-------|-------|-------|-------|-------
 Count |      0|      0|      0|      0|      0
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 20 PPM
New use_topN_peaks = 100
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 2.630 MIN***********************

************************************MAIN SEARCH************************************
Parameters:
num_threads = 4
database_name = C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.Erk_John Wang special.fasta
decoy_prefix = REV_
precursor_mass_lower = -150.0
precursor_mass_upper = 500.0
precursor_mass_units = 0
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
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = true
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
search_enzyme_name = Lys-C
search_enzyme_cutafter = K
search_enzyme_butnotafter = 
num_enzyme_termini = 2
allowed_missed_cleavage = 1
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 = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
minIonsScoring = 3
min_matched_fragments = 5
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: 4
    of length 8: 6
    of length 9: 2
    of length 11: 4
    of length 12: 2
    of length 13: 10
    of length 14: 2
    of length 15: 2
    of length 17: 2
    of length 18: 1
    of length 19: 5
    of length 21: 2
    of length 22: 1
    of length 23: 1
    of length 24: 4
    of length 26: 2
    of length 28: 4
    of length 33: 4
    of length 34: 3
    of length 37: 2
    of length 38: 1
    of length 39: 6
    of length 40: 2
    of length 43: 2
In total 74 peptides.
Generated 162 modified peptides.
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 4.89 GB.
17248 fragments to be searched in 1 slices (0.00 GB total)
Operating on slice 1 of 1: 
    001. Lum_19may2301.mzML 9.7 s
    001. Lum_19may2301.mzML 9.7 s [progress: 24328/82931 (29.34%) - 4863.65 spectra/s]
    001. Lum_19may2301.mzML 9.7 s [progress: 43586/82931 (52.56%) - 4314.59 spectra/s]
    001. Lum_19may2301.mzML 9.7 s [progress: 70035/82931 (84.45%) - 4634.40 spectra/s]
    001. Lum_19may2301.mzML 9.7 s [progress: 82931/82931 (100.00%) - 4804.81 spectra/s] - completed 17.3 s
***************************MAIN SEARCH DONE IN 0.468 MIN***************************

*******************************TOTAL TIME 3.411 MIN********************************
Process 'MsFragger' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe database --annotate C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.Erk_John Wang special.fasta --prefix REV_
INFO[16:17:41] Executing Database v1.2.3                    
INFO[16:17:41] Processing database                          
INFO[16:17:41] Done                                         
Process 'ReportDbAnnotate' finished, exit code: 0

PeptideProphet [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy REV_ --database C:\Users\mxm35\Desktop\Protein sequence database\target.decoy.Erk_John Wang special.fasta Lum_19may2301.pepXML
INFO[16:17:41] Executing PeptideProphet v1.2.3              
 file 1: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\Lum_19may2301.pepXML
INFO: Results written to file: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact-Lum_19may2301.pep.xml
 processed altogether 34 results
  - Building Commentz-Walter keyword tree...
  - C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact-Lum_19may2301.pep.xml

  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 0 2+, 26 3+, 7 4+, 1 5+, 0 6+, and 0 7+ spectra.
Found 13 Decoys, and 21 Non-Decoys
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "REV_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem lysc 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: .........10.........20
model complete after 21 iterations
INFO[16:17:53] Done                                         
Process 'PeptideProphet' finished, exit code: 0

ProteinProphet [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact-Lum_19may2301.pep.xml
INFO[16:17:54] Executing ProteinProphet v1.2.3              
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 C:/Users/mxm35/Desktop/D2 and D2CA_uninterpreted data/D2 test/interact-Lum_19may2301.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[16:17:55] Done                                         
Process 'ProteinProphet' finished, exit code: 0

ReportFilter [Work dir: C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test]
C:\Users\mxm35\Documents\MSFragger\philosopher_v1.2.3_windows_amd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag REV_ --pepxml C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test --protxml C:\Users\mxm35\Desktop\D2 and D2CA_uninterpreted data\D2 test\interact.prot.xml
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, 0xc000084340)
    /home/prvst/go/src/github.com/prvst/philosopher/lib/err/err.go:134 +0x30
github.com/prvst/philosopher/cmd.glob..func5(0x8702240, 0xc0000c8630, 0x0, 0xb)
    /home/prvst/go/src/github.com/prvst/philosopher/cmd/filter.go:53 +0xb87
github.com/spf13/cobra.(*Command).execute(0x8702240, 0xc0000c8580, 0xb, 0xb, 0x8702240, 0xc0000c8580)
    /home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2b5
github.com/spf13/cobra.(*Command).ExecuteC(0x8703c60, 0x405826, 0xc00005a058, 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
INFO[16:17:55] Executing Filter v1.2.3                      
INFO[16:17:55] Processing peptide identification files      
Process 'ReportFilter' finished, exit code: 2

Process returned non-zero exit code, stopping

Stopping 4/10 processes (6 already finished)

Nesvilab / FragPipe