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PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

Home Page: https://philosopher.nesvilab.org

License: GNU General Public License v3.0

Dockerfile 0.06% Go 99.67% Makefile 0.27%

bioinformatics proteomics mass-spectrometry ms-data go data-analysis

philosopher's Introduction

Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. It is also a depencency-free wraper of Trans-Proteomic Pipeline (PeptideProphet, iProphet, PTMProphet, and ProteinProphet).

Database downloading and formatting.
Peptide assignment validation with PeptideProphet.
Multi-level integrative analysis with iProphet.
PTM site localization with PTMProphet.
Protein inference with ProteinProphet.
FDR filtering with custom algorithms.
- Two-dimensional filtering for simultaneous control of PSM and Protein FDR levels.
- Sequential FDR estimation for large data sets using filtered PSM and proteins lists.
Label-free quantification via spectral counting and MS1 intensities.
Label-based quantification using TMT and iTRAQ.
Multi-level detailed reports for peptides, ions, and proteins.
Support for REPRINT and MSstats.

How to Use

Philosopher is part of FragPipe which has a user-friendly GUI.

Documentation

See the documentation for more details about the available commands.

Questions, requests and bug reports

If you have any questions or remarks please use the Discussion board. If you want to report a bug, please use the Issue tracker.

How to cite

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

About the authors

Alexey Nesvizhskii's research group

philosopher's People

Contributors

Stargazers

Watchers

Forkers

jxwangxl sarah-haynes trishorts zzsnow qiangzims profoak7 pac0388 reverendcasy guoci hayoung-hiro wangjie07070910 00mjk anuragraj fabianegli chhh dpolasky wook2014

philosopher's Issues

MSFraggerGUI & Philosopher problem "Failed to open input file"

Dear developer,
unfortunately i have a problem running MSFraggerGUI with Philosopher (i have TPP installed on this Win8.1 64 Bit system). The output of the data analysis is not correct. There are a lot of DECOYS in the Top hits.
I guess the problem originates somehow from a folder parsing error or whatsoever.

Here the main error line:

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_75mM.pepXML
Process started
INFO[19:22:05] Executing PeptideProphet

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data**\test1/20180108_mE_Pea_Ko3_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/**20180108_mE_Pea_Ko3_75mM.mzXML in msms_run_summary tag... trying .mzML ...

The folder slash looks strange...

Anyway. I've running the https://github.com/prvst/philosopher/releases/tag/20180212 philosopher.
On a Win10 system with german language settings and TPP the MSFraggerGUI and Philosopher are also not running like they should.

And this is the full log:

Will execute 23 commands:
java -jar C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger.jar C:\MassSpec\DATA\20180108_Pea_data\test1\fragger.params C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_75mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_75mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_75mM.mzXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_250mM.pepXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_75mM.pepXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_250mM.pepXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_75mM.pepXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_250mM.pepXML

java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_75mM.pepXML

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_250mM.pepXML

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe proteinprophet --output interact interact-20180108_mE_Pea_Ko1_250mM.pep.xml interact-20180108_mE_Pea_Ko1_75mM.pep.xml interact-20180108_mE_Pea_Ko2_250mM.pep.xml interact-20180108_mE_Pea_Ko2_75mM.pep.xml interact-20180108_mE_Pea_Ko3_250mM.pep.xml interact-20180108_mE_Pea_Ko3_75mM.pep.xml

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe database --annotate C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe filter --sequential --mapmods --tag DECOY_ --pepxml C:\MassSpec\DATA\20180108_Pea_data\test1 --protxml C:\MassSpec\DATA\20180108_Pea_data\test1\interact.prot.xml

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe report

C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean



Executing command:
$> java -jar C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger.jar C:\MassSpec\DATA\20180108_Pea_data\test1\fragger.params C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_75mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_75mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_250mM.mzXML C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_75mM.mzXML 
Process started
MSFragger version MSFragger-20171106
(c) University of Michigan


Peptide index read in 219ms
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 4970.60MB

207776968 fragments to be searched in 1 slices (1.55GB total)
Operating on slice 1 of 1: 
3547ms
	20180108_mE_Pea_Ko1_250mM.mzXML 
2984ms

	20180108_mE_Pea_Ko1_250mM.mzXML 2984ms [progress: 13450/13450 (100.00%) - 19577.87 spectra/s] - completed 750ms

	20180108_mE_Pea_Ko1_75mM.mzXML 
766ms

	20180108_mE_Pea_Ko1_75mM.mzXML 766ms [progress: 10054/10054 (100.00%) - 10217.48 spectra/s] - completed 1000ms
	20180108_mE_Pea_Ko2_250mM.mzXML 
1141ms

	20180108_mE_Pea_Ko2_250mM.mzXML 1141ms [progress: 12431/12431 (100.00%) - 56762.56 spectra/s] - completed 234ms

	20180108_mE_Pea_Ko2_75mM.mzXML 
687ms

	20180108_mE_Pea_Ko2_75mM.mzXML 687ms [progress: 8169/8169 (100.00%) - 74944.95 spectra/s] - completed 109ms
	20180108_mE_Pea_Ko3_250mM.mzXML 
625ms

	20180108_mE_Pea_Ko3_250mM.mzXML 625ms [progress: 12345/12345 (100.00%) - 56628.44 spectra/s]
 - completed 234ms
	20180108_mE_Pea_Ko3_75mM.mzXML 
609ms

	20180108_mE_Pea_Ko3_75mM.mzXML 609ms [progress: 7890/7890 (100.00%) - 36027.40 spectra/s] - completed 235ms

Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_250mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko1_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_75mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_250mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko2_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_75mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_250mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_250mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> java -cp C:\MassSpec\XL-MS_Tools\MSFragger\MSFragger-GUI(4).exe umich.msfragger.util.FileMove C:\MassSpec\DATA\20180108_Pea_data\20180108_mE_Pea_Ko3_75mM.pepXML C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_75mM.pepXML 
Process started
Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init 
Process started
WARN[19:21:50] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:21:50] Creating workspace                           
INFO[19:21:50] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_250mM.pepXML 
Process started
INFO[19:21:51] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_250mM.mzML in msms_run_summary tag...

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_250mM.pepXML
 processed altogether 2316 results

INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko1_250mM.pep.xml


  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko1_250mM.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 "DECOY".
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 v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 1403 2+, 830 3+, 77 4+, 6 5+, 0 6+, and 0 7+ spectra.
Found 95 Decoys, and 2221 Non-Decoys

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: ..
...
....
10...
...
...20
....
WARNING: Mixture model quality test failed for charge (1+).
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+).

.
model complete after 26 iterations

INFO[19:21:54] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_75mM.pepXML 
Process started
INFO[19:21:54] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko1_75mM.mzML in msms_run_summary tag...
INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko1_75mM.pep.xml

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko1_75mM.pepXML
 processed altogether 1605 results

  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko1_75mM.pep.xml

  - Building Commentz-Walter keyword tree...

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


 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 1213 2+, 388 3+, 4 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 81 Decoys, and 1524 Non-Decoys

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "DECOY".
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 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: ..
.....
..10..
.....
..20..
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (4+).
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+).

...
model complete after 26 iterations

INFO[19:21:56] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_250mM.pepXML 
Process started
INFO[19:21:57] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_250mM.mzML in msms_run_summary tag...

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_250mM.pepXML
 processed altogether 2201 results

INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko2_250mM.pep.xml


  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko2_250mM.pep.xml

  - Building Commentz-Walter keyword tree... PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 1301 2+, 819 3+, 77 4+, 3 5+, 1 6+, and 0 7+ spectra.
Found 97 Decoys, and 2104 Non-Decoys


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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "DECOY".
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 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...

Iterations: ...
...
...10
...
....
..20.
WARNING: Mixture model quality test failed for charge (1+).

....

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+).

model complete after 26 iterations

INFO[19:22:00] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_75mM.pepXML 
Process started
INFO[19:22:00] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko2_75mM.mzML in msms_run_summary tag...

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko2_75mM.pepXML

INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko2_75mM.pep.xml

 processed altogether 1241 results

  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko2_75mM.pep.xml

  - Building Commentz-Walter keyword tree... PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 894 2+, 343 3+, 4 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 60 Decoys, and 1181 Non-Decoys


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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "DECOY".
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 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...

Iterations: ......
...10...
......20
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (4+).
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+).

.....
model complete after 26 iterations

INFO[19:22:02] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_250mM.pepXML 
Process started
INFO[19:22:02] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_250mM.mzML in msms_run_summary tag...

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_250mM.pepXML
 processed altogether 2298 results

INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko3_250mM.pep.xml


  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko3_250mM.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 "DECOY".
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 v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 1349 2+, 867 3+, 75 4+, 6 5+, 1 6+, and 0 7+ spectra.
Found 88 Decoys, and 2210 Non-Decoys

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: ..
...
....
10..
....
...20
....
WARNING: Mixture model quality test failed for charge (1+).
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+).

.
model complete after 26 iterations

INFO[19:22:05] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe peptideprophet --decoy DECOY --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_75mM.pepXML 
Process started
INFO[19:22:05] Executing PeptideProphet                     

Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzML in msms_run_summary tag...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzXML'.
WARNING: cannot open data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzML'.
WARNING: CANNOT correct data file C:\MassSpec\DATA\20180108_Pea_data\test1/20180108_mE_Pea_Ko3_75mM.mzML in msms_run_summary tag...

 file 1: C:\MassSpec\DATA\20180108_Pea_data\test1\20180108_mE_Pea_Ko3_75mM.pepXML

INFO: Results written to file: C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko3_75mM.pep.xml

 processed altogether 1266 results

  - C:\MassSpec\DATA\20180108_Pea_data\test1\interact-20180108_mE_Pea_Ko3_75mM.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 "DECOY".
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 v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 831 2+, 426 3+, 9 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 58 Decoys, and 1208 Non-Decoys

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: .....
....10.
.......
.20.....
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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).


model complete after 26 iterations
INFO[19:22:07] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean 
Process started
WARN[19:22:08] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:22:08] Removing workspace                           
INFO[19:22:08] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init 
Process started
WARN[19:22:10] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:22:10] Creating workspace                           
INFO[19:22:10] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe proteinprophet --output interact interact-20180108_mE_Pea_Ko1_250mM.pep.xml interact-20180108_mE_Pea_Ko1_75mM.pep.xml interact-20180108_mE_Pea_Ko2_250mM.pep.xml interact-20180108_mE_Pea_Ko2_75mM.pep.xml interact-20180108_mE_Pea_Ko3_250mM.pep.xml interact-20180108_mE_Pea_Ko3_75mM.pep.xml 
Process started
INFO[19:22:11] Executing ProteinProphet                     

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64))
 (no FPKM) (using degen pep info)
Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko1_250mM.pep.xml...
...read in 0 1+, 1231 2+, 681 3+, 60 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko1_75mM.pep.xml...

...read in 0 1+, 1085 2+, 264 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko2_250mM.pep.xml...
...read in 0 1+, 1170 2+, 674 3+, 62 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko2_75mM.pep.xml...

...read in 0 1+, 780 2+, 252 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko3_250mM.pep.xml...
...read in 0 1+, 1194 2+, 738 3+, 54 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in C:/MassSpec/DATA/20180108_Pea_data/test1/interact-20180108_mE_Pea_Ko3_75mM.pep.xml...
...read in 0 1+, 0 2+, 336 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05


Initializing 3189 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/MassSpec/FASTA_Files/Pisum_sativum/pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........  Total: 42792
Computing degenerate peptides for 849 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 907 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 907 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 907 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 907 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 907 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing 777 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%
...90%...100%
Calculating sensitivity...and error tables...


INFO: mu=3.70059e-006, db_size=29494144

Computing MU for 907 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Finished

INFO[19:22:13] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean 
Process started
WARN[19:22:14] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:22:14] Removing workspace                           
INFO[19:22:14] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --init 
Process started
WARN[19:22:15] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:22:15] Creating workspace                           

INFO[19:22:15] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe database --annotate C:\MassSpec\FASTA_Files\Pisum_sativum\pisum_sativum_Mario_joined_with_X_DECOY_rev.fasta 
Process started
INFO[19:22:15] Processing database                          

INFO[19:22:20] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe filter --sequential --mapmods --tag DECOY_ --pepxml C:\MassSpec\DATA\20180108_Pea_data\test1 --protxml C:\MassSpec\DATA\20180108_Pea_data\test1\interact.prot.xml 
Process started
INFO[19:22:20] Executing filter                             
INFO[19:22:20] Processing peptide identification files      

INFO[19:22:21] 1+ Charge profile                             decoy=0 target=0
INFO[19:22:21] 2+ Charge profile                             decoy=0 target=5553
INFO[19:22:21] 3+ Charge profile                             decoy=0 target=2992
INFO[19:22:21] 4+ Charge profile                             decoy=0 target=179
INFO[19:22:21] 5+ Charge profile                             decoy=0 target=0
INFO[19:22:21] 6+ Charge profile                             decoy=0 target=0
INFO[19:22:21] Database search results                       ions=3233 peptides=2553 psms=8724
INFO[19:22:21] Converged to 0.00 % FDR with 8724 PSMs        decoy=0 threshold=0.0519 total=8724
INFO[19:22:21] Converged to 0.00 % FDR with 2553 Peptides    decoy=0 threshold=0.0519 total=2553

INFO[19:22:21] Converged to 0.00 % FDR with 3233 Ions        decoy=0 threshold=0.0519 total=3233

INFO[19:22:21] Protein inference results                     decoy=0 target=777
INFO[19:22:21] Converged to 0.00 % FDR with 567 Proteins     decoy=0 threshold=0.8568 total=567
INFO[19:22:21] Applying sequential FDR estimation            ions=3087 peptides=2407 psms=8547
INFO[19:22:21] Converged to 0.00 % FDR with 8547 PSMs        decoy=0 threshold=0.0539 total=8547
INFO[19:22:21] Converged to 0.00 % FDR with 2407 Peptides    decoy=0 threshold=0.1532 total=2407
INFO[19:22:21] Converged to 0.00 % FDR with 3087 Ions        decoy=0 threshold=0.1532 total=3087

INFO[19:22:21] Post processing identifications              

INFO[19:22:22] Mapping modifications                        

INFO[19:22:22] Processing modifications                     

INFO[19:22:23] Processing Protein Inference                 

INFO[19:22:23] Correcting PSM to Protein mappings           
INFO[19:22:23] Mapping Ion status to PSMs                   
INFO[19:22:23] Calculating Spectral Counts                  

INFO[19:22:42] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe report 
Process started
INFO[19:22:42] Executing report                             

INFO[19:22:43] Creating Protein FASTA report                
INFO[19:22:43] Creating Protein report                      
INFO[19:22:43] Creating PSM report                          

INFO[19:22:43] Creating peptide report                      
INFO[19:22:43] Creating peptide Ion report                  
INFO[19:22:43] Creating modification reports                
INFO[19:22:43] Plotting mass distribution                   

INFO[19:22:43] Done                                         

Process finished, exit value: 0

Executing command:
$> C:\MassSpec\XL-MS_Tools\MSFragger\philosopher_windows_amd64(2).exe workspace --clean 
Process started
WARN[19:22:44] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases 
INFO[19:22:44] Removing workspace                           
INFO[19:22:44] Done                                         

Process finished, exit value: 0

=========================
===
===        Done
===
=========================

Print current version and build number when Philosopher is started

Print the version when it's started without parameters or with some valid command. This makes easier debugging when something doesn't work for people and they just send you the output without running philosopher version.

msconvert erases home directory

Just tried to use philosopher/msconvert on my computing cluster, and it completely erased my entire home folder. I had parts of it backed up so it's not that bad... but posting this so others don't run into the same problem.

OS: CentOS 7, with slurm job manager

Command:

>$ srun ./philosopher_linux_amd64 msconvert /path/to/raw_file.raw
$ time="17:53:43" level=info msg="Executing Msconvert 20190319"
$ time="17:53:43" level=info msg=Done

... and then all my files are gone. I tested this twice and the same thing happened both times.

>$ ls -a
.  ..

Any idea why this is happening?

Filtering step fails

I tried running philosopher (20181128) on a sample but it fails at the filtering step.

./philosopher_linux_amd64 workspace --clean ./philosopher_linux_amd64 workspace --init ./philosopher_linux_amd64 comet --param comet.params TMT1_1.mzML ./philosopher_linux_amd64 peptideprophet --database 2019-01-08-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam TMT1_1.pep.xml ./philosopher_linux_amd64 proteinprophet interact-TMT1_1.pep.xml ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml INFO[10:18:51] Executing Filter 20181128 INFO[10:18:51] Processing peptide identification files INFO[10:18:54] 1+ Charge profile decoy=0 target=0 INFO[10:18:54] 2+ Charge profile decoy=540 target=7375 INFO[10:18:54] 3+ Charge profile decoy=710 target=8356 INFO[10:18:54] 4+ Charge profile decoy=177 target=2261 INFO[10:18:54] 5+ Charge profile decoy=0 target=0 INFO[10:18:54] 6+ Charge profile decoy=0 target=0 INFO[10:18:54] Database search results ions=8208 peptides=6996 psms=19419 INFO[10:18:54] Converged to 1.00 % FDR with 16116 PSMs decoy=162 threshold=0.7821 total=16278 INFO[10:18:54] Converged to 0.99 % FDR with 4944 Peptides decoy=49 threshold=0.9156 total=4993 INFO[10:18:54] Converged to 0.99 % FDR with 6038 Ions decoy=60 threshold=0.8988 total=6098 FATA[10:18:54] Database data not available, interrupting processing

Output explaination - Difference between Original.Delta.Mass and Adjusted.Delta.Mass

Hello,

I am using philosopher for a open-search analysis in combination with msfragger and I find it pretty useful. Thanks for the tool.

However, I have some questions.

If I apply, psmFDR, pepFDR and protFDR using filter tool, is psm.tsv the output of the whole analysis?
What is the difference between Original.Delta.Mass and Adjusted.Delta.Mass in psm.tsv?
Do you have a brief explaination of the psm.tsv file columns?

Thank you.

Kind regards
Alba

Add flag to not check for new versions with every command

checking for new version takes a long time in many cases
needed in FragPipe
FragPipe checks for philosopher updates once it starts up

Philosopher and TPP

Hi,

there is a problem with Philosopher and the trans proteomics pipeline (tpp):
I installed tpp some days ago to test it. Afterwards i wanted to compare the results with MSFragger + Philosopher. However the single, separated installation of Philosopher connected with MSFragger didn't work anymore, because it couldn't generate tmp files. The tpp also had problems with generating temporary files. I narrowed the problem down to the mkdir.exe of the tpp installation. To test this i generated folders in the cmd like this tpp/mkdir.exe -p tmp which worked. The tpp does something like this tpp/mkdir.exe -p /tmp which fails. In conclusion, i think that every Philosopher installation trys to access the mkdir.exe of tpp and generate folders not the way it is supposed to be. I hope this is interesting for you as well although your software works perfectly fine on its own.

Best,
tom

TL;DR: Philosopher installations try to access the mkdir.exe of tpp and generate folders not the way it is supposed to be.

Workspace init failed.

Hi,

I can not build the work space by philosopher. Here is the output.

panic: Post https://www.google-analytics.com/collect: dial tcp: lookup www.google-analytics.com: getaddrinfow: The requested name is valid, but no data of the requested type was found.

goroutine 1 [running]:
github.com/prvst/philosopher/cmd.init.17()
/home/felipevl/go/src/github.com/prvst/philosopher/cmd/workspace.go:54 +0x4ac

My OS is Window 10. And the version of philosopher I used is "philosopher_windows_amd64.exe(20180530)".

Extended Mass Model, MSFragger/MSFragger-GUI

Hi,

I'd like to do downstream analysis on an Msfragger generated pepxml file, and was wondering which utility out of philosopher implements the extended mass model described in Kong et al. 2017. Would it be correct to guess that it's done through the 'filter' program?

Thanks!

decoys are missing from output

mapped decoys are not being included into the outputs after running the report commands using the decoys flag.

v2.0+ `mv` problems on Windows

Looks like the mv command is not working for Windows users. From two reports on Fragger GUI repo, looks like it might be more Windows 7 specific.

How do you unpack the tools that are used? Has it been changed since 1.9?

Reports:

chhh/MSFragger-GUI#37
chhh/MSFragger-GUI#34

macOS permissions

➜ tmp ~/bin/philosopher workspace --init
INFO[16:24:39] Executing Workspace 20180518
INFO[16:24:40] Creating workspace
FATA[16:24:40] cannot create directory: Can't find temporary directory; check folder permissions

Current directory is writable, .meta directory is created, but then nothing:
➜ tmp ls -la .meta
total 0
drwxr-xr-x 2 staff 64 May 21 16:24 .
drwxr-xr-x 7 staff 224 May 21 16:24 ..

But, executing philosopher with sudo works. Which folders does it try to access?

Enhancement - Spectral counting for each files in report

This enhancement would be handy, as mentioned here:

https://github.com/chhh/MSFragger-GUI/issues/3

(in addition i was able to note that the latest release is supposed to integrate ptm-prophet, nonetheless i was not able to see it in any form of documentation)
Best ! (thanks for the piece of software)

psm.tsv column header name bug

As Tom mentions in a ticket in the gui repo:

there's a small bug with the report tables: The psm.tsv from open search has a typo in the column header. 'Oberved modifications' is created instead of 'Observed modifications'

https://github.com/chhh/MSFragger-GUI/issues/45

Filtered pep.xml in text format

To whom it may concern,
I am using philosopher in my pipeline and I think it is a very stable and useful tool. At the moment I am trying to process the filtered output of "philosopher filter" command and I need the data in a pep.xml format. However, the "filter" command stores the filtered pep.xml file in a binary format inside of the "workspace".

Could you help me convert the pepxml.bin inside the workspace (.meta folder) to a non binary format?

Thank you.

Interpretation of report tables

Dear Dev-Team,
I am currently working with the reports produced by philosopher.exe report, that I obtained from MSFragger GUI. When the reports are finished, there are four tables produced for open and closed search: report.tsv, peptide.tsv, psm.tsv, and modifications.tsv or ion.tsv.
I didn't understand how to obtain a list of identified protein groups, since the Protein ID column in report.tsv contains only unique id's, but the Indistinguishable Proteins column is empty.
Thanks,
Tom
Is there more documentation available on the reports? I only found https://prvst.github.io/philosopher/report.html?

Wrong hint when illegal command is run

Issued command:
/c/data/andy/fragger-programs/philosopher-source_windows_amd64.exe database --id UP000005640 --reviewed --contam

Got:
FATA[16:51:29] Workspace not found. Run 'philosopher init' to create a workspace

philosopher init is not a valid command anymore.

Also, I tried calling philospher workspace when I was in a different directory from the executable and it didn't work.

dmitr@chhh MINGW64 /c/data/fasta
$ ls -a
./  ../  ensembl_Homo_sapiens.GRCh38.pep.all.fa  uniprot-proteome_UP000005640_HUMAN.fasta  uniprot-proteome_UP000005640_HUMAN_concatenated_target_decoy.fasta

dmitr@chhh MINGW64 /c/data/fasta
$ ../andy/fragger-programs/philosopher_windows_amd64.exe workspace

dmitr@chhh MINGW64 /c/data/fasta
$ ls -a
./  ../  ensembl_Homo_sapiens.GRCh38.pep.all.fa  uniprot-proteome_UP000005640_HUMAN.fasta  uniprot-proteome_UP000005640_HUMAN_concatenated_target_decoy.fasta

dmitr@chhh MINGW64 /c/data/fasta
$ ../andy/fragger-programs/philosopher_windows_amd64.exe database --id UP000005640 --reviewed --contam
FATA[17:03:22] Workspace not found. Run 'philosopher init' to create a workspace

That's with version 1.1:

dmitr@chhh MINGW64 /c/data/fasta
$ ../andy/fragger-programs/philosopher_windows_amd64.exe
Philosopher: A tool for Proteomics data analysis and post-processing filtering
version: 1.1
...

Fatal Error: workspace not found.

Describe the problem

Fatal Error: workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory"
Using the MSFragger/FragPipe issue reporting template as I'm getting the error while running MSFragger-GUI, but I get the same error when I run philosopher from the command line. Tested on both an Ubuntu and Windows machine with the same error. Running philosopher workspace --init immediately followed by $> /home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml in the working directory results in the same error. Some information redacted with "xxx".

System info

You can find that printed on the Config tab.

OS and version: Ubuntu 16.04 LTS amd64
Java version: java version "10.0.1" 2018-04-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.1+10)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.1+10, mixed mode)

Describe your experiment

Genral proteomics experiment description

Rabbit polyclonal antibodies digested with trypsin

Input data files

1 mzML file ~150 Mb in size

Sequence database

Custom rabbit V region sequence database and decoys
3 Mb

Run log output

System info:
System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"

Version info:
MSFragger-GUI version 6.0
MSFragger version 20180223-RC1
Philosopher version Philosopher 20180530

Will execute 9 commands:
java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 

java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 workspace --clean 

/home/xxx/xxx/philosopher_linux_amd64 workspace --init 

/home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database /home/xxx/xxx/run1/AVH.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact --maxppmdiff 20 interact-QExxxxx-LUMOS.pep.xml 

/home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/AVH.fas --prefix rev_ 

/home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 

/home/xxx/xxx/philosopher_linux_amd64 report 

~~~~~~~~~~~~~~~~~~~~~~


Executing command:
$> java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 
Process started
MSFragger version MSFragger-20180223
(c) University of Michigan

System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"
JVM started with 4004MB memory


Peptide index read in 153ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 2382.75MB
14511148 fragments to be searched in 1 slices (0.11GB total)
Operating on slice 1 of 1: 
986ms
	QExxxxx-LUMOS.mzML 
3556ms

	QExxxxx-LUMOS.mzML 3556ms [progress: 15040/21404 (70.27%) - 2991.84 spectra/s]

	QExxxxx-LUMOS.mzML 3556ms [progress: 21404/21404 (100.00%) - 1766.31 spectra/s] - completed 8770ms

Process finished, exit value: 0
Executing command:
$> java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --clean 
Process started
time="21:17:15" level=info msg="Executing Workspace 20180530"

time="21:17:16" level=info msg="Removing workspace"
time="21:17:16" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --init 
Process started
time="21:17:16" level=info msg="Executing Workspace 20180530"

time="21:17:16" level=info msg="Creating workspace"

time="21:17:16" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database /home/xxx/xxx/run1/AVH.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
time="21:17:17" level=info msg="Executing PeptideProphet 20180530"

 file 1: /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML

 processed altogether 15148 results

INFO: Results written to file: /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml


  - /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml

  - Building Commentz-Walter keyword tree...

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

Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin 

 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
 read in 0 1+, 3754 2+, 8425 3+, 2490 4+, 439 5+, 40 6+, and 0 7+ spectra.
Found 3767 Decoys, and 11381 Non-Decoys

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...

Iterations: .
.
.
.
.
.
.
.
.
10
.
.
.
.
.
.
.
.
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20
.
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.
WARNING: Mixture model quality test failed for charge (1+).

.

WARNING: Mixture model quality test failed for charge (7+).

model complete after 26 iterations

time="21:17:51" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact --maxppmdiff 20 interact-QExxxxx-LUMOS.pep.xml 
Process started
time="21:17:51" level=info msg="Executing ProteinProphet 20180530"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64))
 (no FPKM) (using degen pep info)
Reading in /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml...

...read in 0 1+, 639 2+, 432 3+, 168 4+, 51 5+, 3 6+, 0 7+ spectra with min prob 0.05


Initializing 269 peptide weights: 0%...10%...20%...30%
...40%...50%...60%...70%...80%...90%
...100%
Calculating protein lengths and molecular weights from database /home/xxx/xxx/run1/AVH.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.......  Total: 38676

Computing degenerate peptides for 27778 proteins: 0%...10%
...20%...30%
...40%
...50%...60%...70%...80%...90%
...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%
...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%
...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%
...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing 485 protein groups: 0%...10%
...20%
...30%
...40%
...50%
...60%
...70%
...80%
...90%
...100%
Calculating sensitivity...
and error tables...


INFO: mu=1.1061e-05, db_size=3165618

Computing MU for 28138 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%


Finished

time="21:19:52" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/AVH.fas --prefix rev_ 
Process started
time="21:19:52" level=info msg="Executing Database 20180530"
time="21:19:52" level=info msg="Processing database"

time="21:19:57" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 
Process started
time="21:19:57" level=info msg="Executing Filter 20180530"
time="21:19:57" level=info msg="Processing peptide identification files"

time="21:20:09" level=info msg="1+ Charge profile" decoy=0 target=0
time="21:20:09" level=info msg="2+ Charge profile" decoy=520 target=1941
time="21:20:09" level=info msg="3+ Charge profile" decoy=1770 target=4831
time="21:20:09" level=info msg="4+ Charge profile" decoy=123 target=1741
time="21:20:09" level=info msg="5+ Charge profile" decoy=1 target=364
time="21:20:09" level=info msg="6+ Charge profile" decoy=0 target=24
time="21:20:09" level=info msg="Database search results" ions=1938 peptides=1708 psms=11315

time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0

time="21:20:21" level=info msg="Protein inference results" decoy=152 target=333
time="21:20:21" level=info msg="Converged to 9.09 % FDR with 11 Proteins" decoy=1 threshold=0.9983 total=12
time="21:20:21" level=info msg="Applying sequential FDR estimation" ions=0 peptides=0 psms=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0

time="21:20:21" level=info msg="Post processing identifications"

time="21:20:21" level=info msg="Mapping modifications"

time="21:20:22" level=info msg="Processing modifications"
time="21:20:22" level=info msg="Processing Protein Inference"

time="21:20:22" level=info msg="Correcting PSM to Protein mappings"
time="21:20:22" level=info msg="Mapping Ion status to PSMs"
time="21:20:22" level=info msg="Calculating Spectral Counts"
time="21:20:22" level=fatal msg="workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory"

Process finished, exit value: 1
Previous process returned exit code [1], cancelling further processing..
Cancelled execution of: 
/home/xxx/xxx/philosopher_linux_amd64 report 
=========================
===
===        Done
===
=========================

latest commit wont download database

tested latested commit with:
philosopher.exe database --id [anyid]

and it says its fetching but then it errors that it cannot find the file.

The version from September works.

Multi-experiment report, intensities missing

When using multi-experiment report, with label-free intensities option, combined_peptide.tsv file is missing intensity data (only spectral counts). The protein report (combined_protein.tsv) is OK, both intensities and spectral counts are there.

In the future, it would also be nice to generate reprint.tsv with intensities as well (as a separate file). E.g., when intensity data is available, there will be reprint_spc.tsv and reprint_int.tsv. Otherwise just reprint_spc.tsv

divergence in protein mapping between PSMs and Peptides

There is a divergence in the razor assignment between the PSM and other data structures

Is it possible only give the annotations to specific modifications

In the philosopher's report, it looks like it gave the user all the possible modification(PTM, amino acid substitution, isotope, etc). However, because I didn't use isotope in my experiments, I don't think the annotations of isotope are right. Is it possible to turn off these kinds of modifications? Could the philosopher give a possibility or score whether the modification annotations are "right"? Thank you so much.

label-free quant problem in latest release

It looks like there is bug in the latest release of philosopher (label-free command)
Details will be passed to Felipe directly

labelquant

Hi,
I downloaded philosopher and completed the tutorial (database, comet search, peptideprophet, proteinprophet and report, etc).
However, when I wanna go further doing the quantification, it seemed to be unknown command "labelquant".
Had the labelquant functionality been implemented on philosopher yet?

panic: runtime error: index out of range

Describe the problem

"Index out of range" error before run is completed
Using the MSFragger/FragPipe issue reporting template as I'm getting the error while running MSFragger-GUI, but I get the same error when I run philosopher from the command line. Tested on both an Ubuntu and Windows machine with the same error. Some information redacted with "xxx".

System info

You can find that printed on the Config tab.

OS and version: Ubuntu 16.04 LTS amd64
Java version: java version "10.0.1" 2018-04-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.1+10)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.1+10, mixed mode)

Describe your experiment

Genral proteomics experiment description

Mouse polyclonal antibodies digested with trypsin

Input data files

1 mzML file ~150 Mb in size

Sequence database

UP000001811 with custom V region sequences and decoys
45 Mb

Attach fragger.params file

num_threads = 0			# 0=poll CPU to set num threads; else specify num threads directly (max 64)
precursor_mass_tolerance = 500.00
precursor_mass_lower = -100			# Overrides the lower bound of the window set by precursor_mass_tolerance
precursor_mass_upper = 100			# Overrides the upper bound of the window set by precursor_mass_tolerance
precursor_mass_units = 1			# 0=Daltons, 1=ppm
precursor_true_tolerance = 20
precursor_true_units = 1			# 0=Daltons, 1=ppm
fragment_mass_tolerance = 20
fragment_mass_units = 1			# 0=Daltons, 1=ppm
isotope_error = 0/1/2			# 0=off, -1/0/1/2/3 (standard C13 error)
mass_offsets = 0			# allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue)
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2			# 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion
allowed_missed_cleavage = 1			# maximum value is 5
clip_nTerm_M = 1
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
# variable_mod_03 = 79.96633 STY
# variable_mod_04 = -17.02650 nQnC
# variable_mod_05 = -18.01060 nE
allow_multiple_variable_mods_on_residue = 1			# static mods are not considered
max_variable_mods_per_mod = 3			# maximum of 5
max_variable_mods_combinations = 5000			# maximum of 65534, limits number of modified peptides generated from sequence
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
precursor_charge = 0 0			# precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter
override_charge = 0			# 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter
digest_min_length = 7
digest_max_length = 50
digest_mass_range = 500.0 5000.0			# MH+ peptide mass range to analyze
max_fragment_charge = 2			# set maximum fragment charge state to analyze (allowed max 5)
track_zero_topN = 0			# in addition to topN results, keep track of top results in zero bin
zero_bin_accept_expect = 0			# boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable
zero_bin_mult_expect = 1			# disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect)
add_topN_complementary = 0
minimum_peaks = 15			# required minimum number of peaks in spectrum to search (default 10)
use_topN_peaks = 100
min_fragments_modelling = 3
min_matched_fragments = 4
minimum_ratio = 0.01			# filter peaks below this fraction of strongest peak
clear_mz_range = 0.0 0.0			# for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
add_Cterm_peptide = 0.000000
add_Nterm_peptide = 0.000000
add_Cterm_protein = 0.000000
add_Nterm_protein = 0.000000
add_G_glycine = 0.000000
add_A_alanine = 0.000000
add_S_serine = 0.000000
add_P_proline = 0.000000
add_V_valine = 0.000000
add_T_threonine = 0.000000
add_C_cysteine = 57.021464
add_L_leucine = 0.000000
add_I_isoleucine = 0.000000
add_N_asparagine = 0.000000
add_D_aspartic_acid = 0.000000
add_Q_glutamine = 0.000000
add_K_lysine = 0.000000
add_E_glutamic_acid = 0.000000
add_M_methionine = 0.000000
add_H_histidine = 0.000000
add_F_phenylalanine = 0.000000
add_R_arginine = 0.000000
add_Y_tyrosine = 0.000000
add_W_tryptophan = 0.000000
add_B_user_amino_acid = 0.000000
add_J_user_amino_acid = 0.000000
add_O_user_amino_acid = 0.000000
add_U_user_amino_acid = 0.000000
add_X_user_amino_acid = 0.000000
add_Z_user_amino_acid = 0.000000
database_name = /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas

Run log output

System info:
System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"

Version info:
MSFragger-GUI version 6.0
MSFragger version 20180223-RC1
Philosopher version Philosopher 20180530

Will execute 9 commands:
java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 

java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 workspace --clean 

/home/xxx/xxx/philosopher_linux_amd64 workspace --init 

/home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --decoyprobs --ppm --accmass --nonparam --expectscore --database /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact interact-QExxxxx-LUMOS.pep.xml 

/home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas --prefix rev_ 

/home/xxx/xxx/philosopher_linux_amd64 filter --sequential --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 

/home/xxx/xxx/philosopher_linux_amd64 report 

~~~~~~~~~~~~~~~~~~~~~~


Executing command:
$> java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 
Process started
MSFragger version MSFragger-20180223
(c) University of Michigan

System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"
JVM started with 4004MB memory


Peptide index read in 224ms
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 2342.79MB

344352420 fragments to be searched in 2 slices (2.57GB total)
Operating on slice 1 of 2: 
4907ms
	QExxxxx-LUMOS.mzML 
3697ms

	QExxxxx-LUMOS.mzML 3697ms [progress: 21404/21404 (100.00%) - 6302.71 spectra/s] - completed 3517ms

Operating on slice 2 of 2: 
4189ms
	QExxxxx-LUMOS.mzML 
2093ms

	QExxxxx-LUMOS.mzML 2093ms [progress: 21404/21404 (100.00%) - 14212.48 spectra/s]
 - completed 1609ms

Process finished, exit value: 0
Executing command:
$> java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --clean 
Process started
time="20:43:55" level=info msg="Executing Workspace 20180530"

time="20:43:56" level=info msg="Removing workspace"

time="20:43:56" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --init 
Process started
time="20:43:56" level=info msg="Executing Workspace 20180530"

time="20:43:57" level=info msg="Creating workspace"

time="20:43:57" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --decoyprobs --ppm --accmass --nonparam --expectscore --database /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
time="20:43:57" level=info msg="Executing PeptideProphet 20180530"

 file 1: /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML

 processed altogether 17740 results

INFO: Results written to file: /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml


  - /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.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 v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
 read in 0 1+, 5344 2+, 8881 3+, 2958 4+, 508 5+, 49 6+, and 0 7+ spectra.
Found 8023 Decoys, and 9717 Non-Decoys

MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...

Iterations: .
.
.
.
.
.
.
.
.
10
.
.
.
.
.
.
.
.
.
20
.
.
.
.
.
.
.
WARNING: Mixture model quality test failed for charge (1+).



WARNING: Mixture model quality test failed for charge (7+).

model complete after 28 iterations

time="20:44:40" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact interact-QExxxxx-LUMOS.pep.xml 
Process started
time="20:44:40" level=info msg="Executing ProteinProphet 20180530"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64))
 (no FPKM) (using degen pep info)
Reading in /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml...

...read in 0 1+, 1318 2+, 897 3+, 324 4+, 90 5+, 5 6+, 0 7+ spectra with min prob 0.05


Initializing 867 peptide weights: 0%...10%
...20%...30%...40%...50%
...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........88000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........89000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........90000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........91000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........92000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........93000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........94000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........95000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........96000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........97000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........98000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........99000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........100000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........101000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........102000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........103000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........104000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........105000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........106000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........107000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........108000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........109000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........110000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........111000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........112000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........113000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........114000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........115000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........116000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........117000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........118000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........119000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........120000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........121000

.........:.........:.........:.........:.........:.........:.........:.........:.........:.........122000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........123000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........124000
.........:.........:.........:.........:.........  Total: 124495

Computing degenerate peptides for 22908 proteins: 0%...10%
...20%
...30%
...40%
...50%
...60%
...70%...80%...90%
...100%

Computing probabilities for 23550 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing probabilities for 23550 proteins.  Loop 1: 0%...20%...40%
...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 23550 proteins.  Loop 1: 0%...20%
...40%...60%
...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing probabilities for 23550 proteins.  Loop 1: 0%...20%...40%...60%
...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing probabilities for 23550 proteins.  Loop 1: 0%...20%...40%
...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 23550 proteins.  Loop 1: 0%...20%
...40%...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing 1099 protein groups: 0%...10%
...20%
...30%
...40%
...50%
...60%
...70%
...80%
...90%
...100%
Calculating sensitivity...
and error tables...


INFO: mu=3.73252e-06, db_size=72619408

Computing MU for 23550 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%


Finished

time="20:48:44" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/2018-06-22-td-2018-06-22-td-UP000001811.fas --prefix rev_ 
Process started
time="20:48:44" level=info msg="Executing Database 20180530"
time="20:48:44" level=info msg="Processing database"

time="20:49:12" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 filter --sequential --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 
Process started
time="20:49:12" level=info msg="Executing Filter 20180530"
time="20:49:12" level=info msg="Processing peptide identification files"

time="20:49:20" level=info msg="1+ Charge profile" decoy=0 target=0
time="20:49:20" level=info msg="2+ Charge profile" decoy=448 target=967
time="20:49:20" level=info msg="3+ Charge profile" decoy=347 target=616
time="20:49:20" level=info msg="4+ Charge profile" decoy=143 target=187
time="20:49:20" level=info msg="5+ Charge profile" decoy=39 target=51
time="20:49:20" level=info msg="6+ Charge profile" decoy=2 target=3
time="20:49:20" level=info msg="Database search results" ions=941 peptides=826 psms=2803
time="20:49:20" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="20:49:20" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="20:49:20" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0

time="20:50:21" level=info msg="Protein inference results" decoy=526 target=573
panic: runtime error: index out of range

goroutine 1 [running]:
github.com/prvst/philosopher/lib/fil.ProtXMLFilter(0x0, 0x0, 0x7ffdbb78d0e9, 0x4, 0xc43e3aca00, 0x130, 0x220, 0x0, 0x0, 0x3f847ae147ae147b, ...)
	/home/felipevl/go/src/github.com/prvst/philosopher/lib/fil/fil.go:1763 +0x1d46
github.com/prvst/philosopher/lib/fil.processProteinIdentifications(0x0, 0x0, 0x7ffdbb78d0e9, 0x4, 0xc43e3aca00, 0x130, 0x220, 0x0, 0x0, 0x3f847ae147ae147b, ...)
	/home/felipevl/go/src/github.com/prvst/philosopher/lib/fil/fil.go:572 +0x319
github.com/prvst/philosopher/lib/fil.Run(0xc420028750, 0x24, 0xc420024980, 0x1b, 0xc420028780, 0x29, 0xc4200287b0, 0x2a, 0xc4200287e0, 0x21, ...)
	/home/felipevl/go/src/github.com/prvst/philosopher/lib/fil/fil.go:53 +0xd44
github.com/prvst/philosopher/cmd.glob..func5(0x3c90900, 0xc420186460, 0x0, 0x7)
	/home/felipevl/go/src/github.com/prvst/philosopher/cmd/filter.go:53 +0x200
github.com/spf13/cobra.(*Command).execute(0x3c90900, 0xc4201863f0, 0x7, 0x7, 0x3c90900, 0xc4201863f0)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:766 +0x2c1
github.com/spf13/cobra.(*Command).ExecuteC(0x3c92580, 0x3c926d0, 0xc420175f78, 0x405a4c)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:852 +0x30a
github.com/spf13/cobra.(*Command).Execute(0x3c92580, 0x1, 0x0)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:800 +0x2b
github.com/prvst/philosopher/cmd.Execute()
	/home/felipevl/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x2d
main.main()
	/home/felipevl/go/src/github.com/prvst/philosopher/main.go:19 +0x70

Process finished, exit value: 2
Previous process returned exit code [2], cancelling further processing..
Cancelled execution of: 
/home/xxx/xxx/philosopher_linux_amd64 report 
=========================
===
===        Done
===
=========================

Index out of range when there is no PSM from the first pass.

Hi Felipe,

I think I just triggered a bug caused by no PSM case after the first pass. Following is the log

+ philosophe filter --sequential --razor --mapmods --models --tag rev_ --pepxml ./interact.pep.xml --protxml ./interact.prot.xml
time="16:22:21" level=info msg="Executing Filter 20190301"
time="16:22:21" level=info msg="Processing peptide identification files"
time="16:22:28" level=info msg="Printing models"
time="16:22:31" level=info msg="1+ Charge profile" decoy=0 target=0
time="16:22:31" level=info msg="2+ Charge profile" decoy=13316 target=46197
time="16:22:31" level=info msg="3+ Charge profile" decoy=3784 target=11451
time="16:22:31" level=info msg="4+ Charge profile" decoy=408 target=1543
time="16:22:31" level=info msg="5+ Charge profile" decoy=148 target=359
time="16:22:31" level=info msg="6+ Charge profile" decoy=0 target=0
time="16:22:32" level=info msg="Database search results" ions=52891 peptides=49548 psms=77206
time="16:22:32" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="16:22:32" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="16:22:32" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0
time="16:22:35" level=info msg="Protein inference results" decoy=8801 target=11444
panic: runtime error: index out of range

goroutine 1 [running]:
github.com/prvst/philosopher/lib/fil.ProtXMLFilter(0x0, 0x0, 0x7ffd1ebc15d1, 0x4, 0xc002d60000, 0x47af, 0x5733, 0xc00401ade0, 0xc, 0x3f847ae147ae147b, ...)
	/home/prvst/go/src/github.com/prvst/philosopher/lib/fil/fil.go:1069 +0x1d55
github.com/prvst/philosopher/lib/fil.processProteinIdentifications(0x0, 0x0, 0x7ffd1ebc15d1, 0x4, 0xc002d60000, 0x47af, 0x5733, 0xc00401ade0, 0xc, 0x3f847ae147ae147b, ...)
	/home/prvst/go/src/github.com/prvst/philosopher/lib/fil/fil.go:593 +0x337
github.com/prvst/philosopher/lib/fil.Run(0xc000024630, 0x24, 0xc00002e480, 0x51, 0xc000024660, 0x29, 0xc00002e4e0, 0x60, 0xc00002e540, 0x57, ...)
	/home/prvst/go/src/github.com/prvst/philosopher/lib/fil/fil.go:55 +0xee6
github.com/prvst/philosopher/cmd.glob..func5(0x3e9d5e0, 0xc0001dcb40, 0x0, 0xa)
	/home/prvst/go/src/github.com/prvst/philosopher/cmd/filter.go:55 +0x1f8
github.com/spf13/cobra.(*Command).execute(0x3e9d5e0, 0xc0001dca00, 0xa, 0xa, 0x3e9d5e0, 0xc0001dca00)
	/home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2cc
github.com/spf13/cobra.(*Command).ExecuteC(0x3e9f260, 0x3e9f720, 0xc0001b9f68, 0xc0001b9f88)
	/home/prvst/go/src/github.com/spf13/cobra/command.go:852 +0x2fd
github.com/spf13/cobra.(*Command).Execute(0x3e9f260, 0x1, 0x3e9f720)
	/home/prvst/go/src/github.com/spf13/cobra/command.go:800 +0x2b
github.com/prvst/philosopher/cmd.Execute()
	/home/prvst/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x2d
main.main()
	/home/prvst/go/src/github.com/prvst/philosopher/main.go:19 +0x6e

Thanks,

Fengchao

Pipeline example?

Hi Felipe, is there an example file for running a pipeline?
Ideally, it would write the results into the same directory.
Best, Robert

philosopher linux report error message

Hi, I searched a large number of files using comet. And further processed with peptideprophet, iprophet, proteinprophet. When I run "./philosopher_linux_amd64 report", I got this error.

cannot restore serialized data structures: gob: rep.PSMEvidence slice too big: 1600758 elements of 1000 bytes

Do you know is it due to program or my OS?

Thanks,
Liang

cannot serialize data structures

Hello,
I'm using FragPipe with the splicing database option. The splicing works to some extend but soon after I get an error saying that it cannot serialize data structures.

ReportDbAnnotate [Work dir: E:\LAO\D17Test resulst\msfraggersplice]
C:\Software\MSFragger\philosopher_windows_amd64.exe database --annotate E:\LAO\Db_Fra_Clust99_A0_Decoy.fasta --prefix rev_
INFO[10:05:38] Executing Database 20190226                  
INFO[10:05:38] Processing database                          
FATA[10:10:47] cannot serialize data structures: short write 
Process 'ReportDbAnnotate' finished, exit code: 1

Process returned non-zero exit code, stopping
PeptideProphet [Work dir: E:\LAO\D17Test resulst\msfraggersplice]
C:\Software\MSFragger\philosopher_windows_amd64.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database E:\LAO\Db_Fra_Clust99_A0_Decoy.fasta 052313-SludgeD17_25-30.pepXML
~~~~~~~~~~~~~~~~~~~~
Stopping 10/20 processes (10 already finished)
Processing interrupted, stopping PeptideProphet

Here are some information on my system
System info:
OS and version: Windows 10 enterprise
java version "1.8.0_202"
Java(TM) SE Runtime Environment (build 1.8.0_202-b08)
Java HotSpot(TM) 64-Bit Server VM (build 25.202-b08, mixed mode)
Input data files
6 mzML file of 2Gb each. Converted from raw files using msconvert.
Sequence database
Metagenomic database of 2.5Gb size (counting decoy)
The entries in the database look all like this:

D01_contig_gene2_1
rev_1 (decoy)
I just realized that the decoy software sometimes produce a * at the beginning of the sequence.

Any idea? I've also attached the complete log from FragPipe.
Thanks a lot for your help,

Ben
log_2019-03-05_12-32-57.txt

Decoy proteins in result file, while the corresponding nondecoy should be present

Hello I think I found a bug. Else I cant make sense out of it.
After running the analysis in the same way as described in the wiki. I can find in the proteins.fas and protein.tsv a few proteins that are labeled with "DECOY_"
As an example I will take the following:
"DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573"
I can find the protein in the protein.tsv

Group	SubGroup	Protein	Protein ID	Entry Name	Gene	Length	Percent Coverage	Organism	Protein Description	Protein Existence	Protein Probability	Top Peptide Probability	Stripped Peptides	Total Peptide Ions	Unique Peptide Ions	Razor Peptide Ions	Total Spectral Count	Unique Spectral Count	Razor Spectral Count	Total Intensity	Unique Intensity	Razor Intensity	Razor Assigned Modifications	Razor Observed Modifications	Indistinguishable Proteins
328	a	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573			0	65.20				1.0000	0.9990	79	102102	0	111	111	0	     0	     0	     0	10C(57.0215), 12C(57.0215), 15C(57.0215), 16M(15.9949), 21M(15.9949), 3M(15.9949), 4C(57.0215), 5C(57.0215), 8C(57.0215), 9C(57.0215)

In proteins.fas like so:

>DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573
YKGCLCEYDKVPGFIRACFLGDREPKFTRYNITEPKKVEGFSWSRIMDPSALAIKIADFEETKTQAKLFKLLDKMKRTESNTENLEERLQECEQELDMSKLLAQIAEAGMKADFEDGFEELADLYQEETLIQQRELNTMGGEIVVYSEFYLVREIDRLPMDLLLGIRSPLSKLFWIHATPSALEIHGMRERRVKTQTVEVGCKECIVGRHKKRTLKKRLRNNRNIVRRYLDNLDSTAFRGGDLPVLPRLDPPLVPLVTLIMWEPKNGSQVFAELLKKRENRVIIDPAALDLKRGLLNQRFRGQKGKIMDALSKLPRKNSGTIARGRRGNDLLADVAEQLKRGKTEKGFSVIGSIEALIAPEKPRRAEFLDAVRPLGGTIDKTGGSEQPIRALTDGSSIQVGDELQVIAKGPLFYQAPMDTGPILVDNGQADVIKLAPRLDKGGATREASDLVVLSSLGTLEDTQRTITQGDIMDTFRVFGSVETIVPMTHPDWNAVTEGGAVQEGDGKALVAGYPVKYSEKTRGFEDILKLETNRSTIVLKGSSNVVSKVNSLKISGKNKVQISSEAAARSAAGGIHFTRMTLQTGPEGISQAAIVGIAEGKNIIHGRALDRGYCHACVGFDTDCSVVSRVKVADVSNEELLDCWQEHLLTNRPVLIDATGPKLVDEATVRGLVRDRLPEKVDGGEIVPTMMIGEHTGCDDETVVLDQAVDVLRRTLYGSNATKLATDALGKRAGHTSIFYQLVNLGERFNATIPTEIISGDPKAMLGRMGALQRIQAASGRAGSDAMMYISNFSVQKEEQGDRNIVTETQLNDMMAKSVRDNAAAWIDIVKNYREGATVLGSQFQEQIEAVEAEAESIIEHKKEPIVMDDIGVSAGSRAAYAFGTYMIQDAFIVTPKLGLIRYCTNLMKSIAKKGLAQNVISYPLGKPVIMWLIARGVTTDKLSTKAVLEGNADKEYETIRVKVRAHLSALGSRYLREAEKPGTLVMGEGKANVCDRTMYYLGLVVDQSPVIIPEGNAPSLINNTSMMLARAELQAELTLPVHVAMQDGDFDANYAACVLPHLQIAKGEILVPEFAQIGLRHLTPARNLLVPHERIVEDLIDWVVAEEREVMKKAAKITTALGRLELKGYIFPKFLELAMKKPLGCQHLRLYPGVTIVSRGSYDKRGAVAAETLVRTTEQFSAASIFSETALSAKTIGLLDRSYTAGVKGNAELERNAIKVRSYEVQEGELFDSSGANVITAKRLMQRVIVEIHKDNIKVGQLRYVDQVENVIYRTVAHVGRLRLIDHPAEPGDSIVDGREVREGEFVNLQRWKPIMEEYPDSGDVPTIVLKRENDSGGLGANLLEALSASADEATVQPAAPAEGAARRRMRDQHYAYGTGAPILRGVIVNEKLGRLE

In the orignal DB the corresponding protein looks like this:

>UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

In the psm.tsv I find allot lines like those:

Spectrum			Peptide	Modified Peptide	Charge	Retention	Calculated M/Z	Spectrum	Peptide	Modified Peptide	Charge	Retention	Calculated M/Z	Observed M/Z	Original Delta Mass	Adjusted Delta Mass	Experimental Mass	Peptide Mass	XCorr	DeltaCN	DeltaCNStar	SPScore	SPRank	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Intensity	Assigned Modifications	Observed Modifications	Number of Phospho Sites	Phospho Site Localization	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Proteins
experiment_P-13.05066.05066.2	IANRELEANGK		2	1330.9000	607.8281	607.8285	0.0009	0.0000	1213.6424	1213.6415	2.6440	0.5120	0.0000	0.0000	1.0000	8.210000e-06	0.0000	0.0000	0.9997	0.0000			0		true	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573
experiment_P-13.05594.05594.2	LHQCGLPK	LHQCGLPK	2	1409.5000	476.7553	476.7553	0.0000	-0.0008	951.4961	951.4960	1.4350	0.4010	0.0000	0.0000	1.0000	2.080000e-02	0.0000	0.0000	0.9830	0.0000	4C(57.0215)		0		true	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573
experiment_P-13.05785.05785.2	KPETINYR		2	1438.4000	510.7773	510.7778	0.0010	0.0001	1019.5410	1019.5400	1.7240	0.5280	0.0000	0.0000	1.0000	8.890000e-04	0.0000	0.0000	0.9995	0.0000			0		true	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573
experiment_P-13.06074.06074.3	TSLKDTTVGR		3	1480.3000	359.8682	359.8680	-0.0007	-0.0015	1076.5819	1076.5826	2.6260	0.5930	0.0000	0.0000	1.0000	8.920000e-05	0.0000	0.0000	1.0000	0.0000			0		true	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573

All have in the column "mapped proteins" just the entry of the decoy protein. And in the column "protein" and "protein id" always the original protein. When I try to match the peptides to the proteins, I can only find them in the non-decoy protein, but never in the decoy protein.
Same I get when I look into the peptide.tsv. Example lines:

Peptide	Charges	Probability	Spectral Count	Intensity	Assigned Modifications	Observed Modifications	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Proteins
AAAESSIQVK	2	1.0000	1	0.000000			DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				
AAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE	3	1.0000	1	0.000000			DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573		
AILWMIVPK	2	0.9991	1	0.000000			DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573				
AIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEAR	4	0.9744	1	0.000000	21M(15.9949), 9C(57.0215)		DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573	DECOY_UniProtKB/Swiss-Prot:P0A8T7|4185349|4189573

As you can see no peptide maps to the decoy protein, but to the non-decoy protein.
To me it seems that like i could simply take the decoy hits as normal hits.
I used the newest version.

Processing interrupted, stopping ReportFilter

Describe the problem

I'm submitting a:
- problem running the software
My MSFragger use case:
- Open search (large precursor mass tolerance)

** put your general problem description here **
The fragpipe ends with :

Stopping 9/40 processes (31 already finished)
Processing interrupted, stopping ReportFilter. 
I have attached the log file for your review. In the log file I see warnings such as "The syntax of the command is incorrect" or "Failed to open input file"


## System info

You can find that printed on the _Config_ tab.
- OS and version: ** _your response here_ I am running the FragPipe on Windows 7. 
- Java version: ** _your response here_ java version "1.8.0_191"

----

## Describe your experiment
trying to find the workflow dependent modifications for different sample preparation methods.

### Genral proteomics experiment description
e.g. Urine proteomics

...

### Input data files
** single shot. not fragmenetd. 4 mzML files


### Sequence database
human sequence database downloaded through philosopher. 


----

## Attach fragger.params file

** _You can find it in the output directory you specified for analysis._ **


## Run log output

```
** copy text from the text console in the gui here **
System info:
System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_191, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info:
FragPipe version 9.1
MSFragger version 20190222
Philosopher version 20190226 (build 201902261041)


LCMS files:
  Experiment/Group: In-Solution
  - C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_IS_03.mzML
  Experiment/Group: MStern
  - C:\MSFragger-20190222\data\urine_workflow\q181125_SS1332_HS_02.mzML
  Experiment/Group: PreOmics
  - C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_PO_01.mzML
  Experiment/Group: STrap
  - C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_ST_02.mzML

39 commands to execute:
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
MsFragger [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
java -jar -Dfile.encoding=UTF-8 C:\MSFragger-20190222\MSFragger-20190222\MSFragger-20190222.jar C:\MSFragger-20190222\result\Urine_workflow\fragger.params C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_IS_03.mzML C:\MSFragger-20190222\data\urine_workflow\q181125_SS1332_HS_02.mzML C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_PO_01.mzML C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_ST_02.mzML
MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_IS_03.pepXML C:\MSFragger-20190222\result\Urine_workflow\In-Solution\q181127_SS1332_IS_03.pepXML
MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181125_SS1332_HS_02.pepXML C:\MSFragger-20190222\result\Urine_workflow\MStern\q181125_SS1332_HS_02.pepXML
MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_PO_01.pepXML C:\MSFragger-20190222\result\Urine_workflow\PreOmics\q181127_SS1332_PO_01.pepXML
MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_ST_02.pepXML C:\MSFragger-20190222\result\Urine_workflow\STrap\q181127_SS1332_ST_02.pepXML
Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\MStern\crystalc-0-q181125_SS1332_HS_02.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\MStern\q181125_SS1332_HS_02.pepXML
Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\In-Solution\crystalc-1-q181127_SS1332_IS_03.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\In-Solution\q181127_SS1332_IS_03.pepXML
Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\STrap\crystalc-2-q181127_SS1332_ST_02.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\STrap\q181127_SS1332_ST_02.pepXML
Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\PreOmics\crystalc-3-q181127_SS1332_PO_01.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\PreOmics\q181127_SS1332_PO_01.pepXML
ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_PO_01_c.pepXML
PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_IS_03_c.pepXML
PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_ST_02_c.pepXML
PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181125_SS1332_HS_02_c.pepXML
iProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe iprophet --decoy rev_ --nonsp --output interact --threads 0 C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml
ProteinProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe proteinprophet --maxppmdiff 2000000 C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml
ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\MStern --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml
ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\PreOmics --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml
ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\STrap --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml
ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\In-Solution --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml
ReportReport [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe report
ReportReport [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe report
ReportReport [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe report
ReportReport [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe report
ReportAbacus [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe abacus --razor --reprint --tag rev_ --protein C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml --peptide C:\MSFragger-20190222\result\Urine_workflow\interact.pep.xml MStern PreOmics STrap In-Solution

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
INFO[12:04:40] Executing Workspace 20190226
INFO[12:04:40] Removing workspace
INFO[12:04:40] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
INFO[12:04:41] Executing Workspace 20190226
INFO[12:04:41] Creating workspace
INFO[12:04:41] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
INFO[12:04:42] Executing Workspace 20190226
INFO[12:04:43] Removing workspace
INFO[12:04:43] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
INFO[12:04:43] Executing Workspace 20190226
INFO[12:04:44] Creating workspace
INFO[12:04:44] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
INFO[12:04:44] Executing Workspace 20190226
INFO[12:04:45] Removing workspace
INFO[12:04:45] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
INFO[12:04:45] Executing Workspace 20190226
INFO[12:04:46] Creating workspace
INFO[12:04:46] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
INFO[12:04:46] Executing Workspace 20190226
INFO[12:04:47] Removing workspace
INFO[12:04:47] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
INFO[12:04:47] Executing Workspace 20190226
INFO[12:04:48] Creating workspace
INFO[12:04:48] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --clean
INFO[12:04:48] Executing Workspace 20190226
INFO[12:04:48] Removing workspace
INFO[12:04:48] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe workspace --init
INFO[12:04:49] Executing Workspace 20190226
INFO[12:04:49] Creating workspace
INFO[12:04:49] Done
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
java -jar -Dfile.encoding=UTF-8 C:\MSFragger-20190222\MSFragger-20190222\MSFragger-20190222.jar C:\MSFragger-20190222\result\Urine_workflow\fragger.params C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_IS_03.mzML C:\MSFragger-20190222\data\urine_workflow\q181125_SS1332_HS_02.mzML C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_PO_01.mzML C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_ST_02.mzML
MSFragger version MSFragger-20190222
MSFTBX version 1.8.6
(c) University of Michigan

System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_191, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 14548MB memory

Peptide index read in 265ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 10771.94MB
386652560 fragments to be searched in 1 slices (2.88GB total)
Operating on slice 1 of 1: 3090ms
q181127_SS1332_IS_03.mzML 17223ms
q181127_SS1332_IS_03.mzML 17223ms [progress: 2327/74218 (3.14%) - 462.90 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 6548/74218 (8.82%) - 835.51 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 10706/74218 (14.43%) - 820.12 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 15028/74218 (20.25%) - 843.98 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 19202/74218 (25.87%) - 813.96 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 22796/74218 (30.71%) - 705.54 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 26422/74218 (35.60%) - 709.03 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 29932/74218 (40.33%) - 690.94 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 33322/74218 (44.90%) - 664.45 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 36792/74218 (49.57%) - 678.79 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 40074/74218 (53.99%) - 643.66 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 43183/74218 (58.18%) - 619.45 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 46421/74218 (62.55%) - 633.16 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 49828/74218 (67.14%) - 672.66 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 53276/74218 (71.78%) - 685.35 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 56689/74218 (76.38%) - 681.92 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 60313/74218 (81.26%) - 711.70 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 64152/74218 (86.44%) - 751.71 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 68066/74218 (91.71%) - 765.05 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 71923/74218 (96.91%) - 764.22 spectra/s]
q181127_SS1332_IS_03.mzML 17223ms [progress: 74218/74218 (100.00%) - 597.03 spectra/s] - completed 105595ms
q181125_SS1332_HS_02.mzML 19677ms
q181125_SS1332_HS_02.mzML 19677ms [progress: 4549/32675 (13.92%) - 892.84 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 9145/32675 (27.99%) - 898.01 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 14432/32675 (44.17%) - 1046.31 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 19539/32675 (59.80%) - 1013.29 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 23923/32675 (73.21%) - 868.81 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 27963/32675 (85.58%) - 806.71 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 32664/32675 (99.97%) - 928.32 spectra/s]
q181125_SS1332_HS_02.mzML 19677ms [progress: 32675/32675 (100.00%) - 49.77 spectra/s] - completed 35693ms
q181127_SS1332_PO_01.mzML 6789ms
q181127_SS1332_PO_01.mzML 6789ms [progress: 4085/47728 (8.56%) - 814.88 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 8320/47728 (17.43%) - 833.83 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 12243/47728 (25.65%) - 768.16 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 15563/47728 (32.61%) - 663.34 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 18913/47728 (39.63%) - 653.53 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 22197/47728 (46.51%) - 651.07 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 25497/47728 (53.42%) - 653.72 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 28813/47728 (60.37%) - 658.20 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 32153/47728 (67.37%) - 654.39 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 35594/47728 (74.58%) - 683.01 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 39962/47728 (83.73%) - 867.87 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 45039/47728 (94.37%) - 998.03 spectra/s]
q181127_SS1332_PO_01.mzML 6789ms [progress: 47728/47728 (100.00%) - 603.05 spectra/s] - completed 65245ms
q181127_SS1332_ST_02.mzML 10805ms
q181127_SS1332_ST_02.mzML 10805ms [progress: 3505/70295 (4.99%) - 697.93 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 7139/70295 (10.16%) - 708.93 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 10675/70295 (15.19%) - 697.44 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 14210/70295 (20.21%) - 693.00 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 17607/70295 (25.05%) - 662.57 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 20788/70295 (29.57%) - 623.85 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 23948/70295 (34.07%) - 619.24 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 27070/70295 (38.51%) - 623.28 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 30119/70295 (42.85%) - 601.97 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 33157/70295 (47.17%) - 606.39 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 36328/70295 (51.68%) - 632.18 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 39365/70295 (56.00%) - 605.70 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 42558/70295 (60.54%) - 626.57 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 45763/70295 (65.10%) - 625.00 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 48818/70295 (69.45%) - 609.29 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 51913/70295 (73.85%) - 611.66 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 55114/70295 (78.40%) - 633.11 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 58741/70295 (83.56%) - 708.81 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 62202/70295 (88.49%) - 689.99 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 65685/70295 (93.44%) - 682.01 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 69262/70295 (98.53%) - 704.69 spectra/s]
q181127_SS1332_ST_02.mzML 10805ms [progress: 70295/70295 (100.00%) - 251.40 spectra/s] - completed 110635ms
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_IS_03.pepXML C:\MSFragger-20190222\result\Urine_workflow\In-Solution\q181127_SS1332_IS_03.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181125_SS1332_HS_02.pepXML C:\MSFragger-20190222\result\Urine_workflow\MStern\q181125_SS1332_HS_02.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_PO_01.pepXML C:\MSFragger-20190222\result\Urine_workflow\PreOmics\q181127_SS1332_PO_01.pepXML
Process 'MsFragger' finished, exit code: 0

MsFragger
java -cp C:\Users\Owner\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\MSFragger-20190222\data\urine_workflow\q181127_SS1332_ST_02.pepXML C:\MSFragger-20190222\result\Urine_workflow\STrap\q181127_SS1332_ST_02.pepXML
Process 'MsFragger' finished, exit code: 0

Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\MStern\crystalc-0-q181125_SS1332_HS_02.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\MStern\q181125_SS1332_HS_02.pepXML
q181125_SS1332_HS_02.pepXML Done!!! The execution time is 2.14700 min.
Process 'Crystal-C' finished, exit code: 0

Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\In-Solution\crystalc-1-q181127_SS1332_IS_03.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\In-Solution\q181127_SS1332_IS_03.pepXML
q181127_SS1332_IS_03.pepXML Done!!! The execution time is 2.54985 min.
Process 'Crystal-C' finished, exit code: 0

Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\STrap\crystalc-2-q181127_SS1332_ST_02.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\STrap\q181127_SS1332_ST_02.pepXML
q181127_SS1332_ST_02.pepXML Done!!! The execution time is 2.59322 min.
Process 'Crystal-C' finished, exit code: 0

Crystal-C [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
java -cp "C:\Users\Owner\AppData\Local\Temp\fragpipe\common-deps-1.0.3.jar;C:\Users\Owner\AppData\Local\Temp\fragpipe\original-CrystalC-1.0.4.jar" Main C:\MSFragger-20190222\result\Urine_workflow\PreOmics\crystalc-3-q181127_SS1332_PO_01.pepXML.params C:\MSFragger-20190222\result\Urine_workflow\PreOmics\q181127_SS1332_PO_01.pepXML
q181127_SS1332_PO_01.pepXML Done!!! The execution time is 2.16865 min.
Process 'Crystal-C' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
INFO[12:20:50] Executing Database 20190226
INFO[12:20:50] Processing database
INFO[12:21:13] Done
Process 'ReportDbAnnotate' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
INFO[12:21:13] Executing Database 20190226
INFO[12:21:13] Processing database
INFO[12:21:35] Done
Process 'ReportDbAnnotate' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
INFO[12:21:35] Executing Database 20190226
INFO[12:21:35] Processing database
INFO[12:21:57] Done
Process 'ReportDbAnnotate' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
INFO[12:21:57] Executing Database 20190226
INFO[12:21:57] Processing database
INFO[12:22:19] Done
Process 'ReportDbAnnotate' finished, exit code: 0

ReportDbAnnotate [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe database --annotate C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --prefix rev_
INFO[12:22:19] Executing Database 20190226
INFO[12:22:19] Processing database
INFO[12:22:41] Done
Process 'ReportDbAnnotate' finished, exit code: 0

PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_PO_01_c.pepXML
INFO[12:22:41] Executing PeptideProphet 20190226
The syntax of the command is incorrect.
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzXML in msms_run_summary tag...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\PreOmics/q181127_SS1332_PO_01.mzXML in msms_run_summary tag...

command "mkdir -p C:/tmp" failed: Operation not permitted
warning: the webserver temporary directory C:/tmp specified by WEBSERVER_TMP does not exist and could not be created. Tempfiles will created in data directories instead. file 1: C:\MSFragger-20190222\result\Urine_workflow\PreOmics\q181127_SS1332_PO_01_c.pepXML
processed altogether 25825 results
INFO: Results written to file: C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml
Building Commentz-Walter keyword tree...The syntax of the command is incorrect.
Searching the tree...
Linking duplicate entries...
Printing results...'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no RefreshParser data written to file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\PreOmics>Code:

C:\MSFragger-20190222\result\Urine_workflow\PreOmics>move -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844" "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\PreOmics>Code:

C:\MSFragger-20190222\result\Urine_workflow\PreOmics>move -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844" "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a13844, error 2 "No such file or directory"Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 10280 2+, 11184 3+, 3584 4+, 601 5+, 159 6+, and 0 7+ spectra.
Found 7218 Decoys, and 18590 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.......WARNING: Mixture model quality test failed for charge (1+).
.
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+).
The syntax of the command is incorrect.
model complete after 29 iterations
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no peptideprophet data written to file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\PreOmics>move -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072" "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\PreOmics>Code:

C:\MSFragger-20190222\result\Urine_workflow\PreOmics>move -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072" "C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml.tmp.a15072, error 2 "No such file or directory"INFO[12:23:07] Done
Process 'PeptideProphet' finished, exit code: 0

PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\In-Solution]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_IS_03_c.pepXML
INFO[12:23:07] Executing PeptideProphet 20190226
The syntax of the command is incorrect.
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzXML in msms_run_summary tag...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\In-Solution/q181127_SS1332_IS_03.mzXML in msms_run_summary tag...

command "mkdir -p C:/tmp" failed: Operation not permitted
warning: the webserver temporary directory C:/tmp specified by WEBSERVER_TMP does not exist and could not be created. Tempfiles will created in data directories instead. file 1: C:\MSFragger-20190222\result\Urine_workflow\In-Solution\q181127_SS1332_IS_03_c.pepXML
processed altogether 49222 results
INFO: Results written to file: C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml
Building Commentz-Walter keyword tree...The syntax of the command is incorrect.
Searching the tree...
Linking duplicate entries...
Printing results...'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no RefreshParser data written to file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\In-Solution>Code:

C:\MSFragger-20190222\result\Urine_workflow\In-Solution>move -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240" "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\In-Solution>Code:

C:\MSFragger-20190222\result\Urine_workflow\In-Solution>move -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240" "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a12240, error 2 "No such file or directory"Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 16135 2+, 23946 3+, 7933 4+, 1020 5+, 164 6+, and 0 7+ spectra.
Found 12442 Decoys, and 36756 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....WARNING: Mixture model quality test failed for charge (1+).
.
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
The syntax of the command is incorrect.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no peptideprophet data written to file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\In-Solution>move -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092" "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\In-Solution>Code:

C:\MSFragger-20190222\result\Urine_workflow\In-Solution>move -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092" "C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml.tmp.a17092, error 2 "No such file or directory"INFO[12:23:52] Done
Process 'PeptideProphet' finished, exit code: 0

PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\STrap]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181127_SS1332_ST_02_c.pepXML
INFO[12:23:52] Executing PeptideProphet 20190226
The syntax of the command is incorrect.
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzXML in msms_run_summary tag...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\STrap/q181127_SS1332_ST_02.mzXML in msms_run_summary tag...

command "mkdir -p C:/tmp" failed: Operation not permitted
warning: the webserver temporary directory C:/tmp specified by WEBSERVER_TMP does not exist and could not be created. Tempfiles will created in data directories instead. file 1: C:\MSFragger-20190222\result\Urine_workflow\STrap\q181127_SS1332_ST_02_c.pepXML
processed altogether 48329 results
INFO: Results written to file: C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml
Building Commentz-Walter keyword tree...The syntax of the command is incorrect.
Searching the tree...
Linking duplicate entries...
Printing results...'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no RefreshParser data written to file C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\STrap>Code:

C:\MSFragger-20190222\result\Urine_workflow\STrap>move -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564" "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\STrap>Code:

C:\MSFragger-20190222\result\Urine_workflow\STrap>move -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564" "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a14564, error 2 "No such file or directory"Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 15077 2+, 21874 3+, 9426 4+, 1662 5+, 265 6+, and 0 7+ spectra.
Found 11692 Decoys, and 36612 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

C:\MSFragger-20190222\result\Urine_workflow\STrap>move -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516" "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\STrap>Code:

C:\MSFragger-20190222\result\Urine_workflow\STrap>move -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516" "C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml.tmp.a12516, error 2 "No such file or directory"INFO[12:24:37] Done
Process 'PeptideProphet' finished, exit code: 0

PeptideProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\MSFragger-20190222\fasta\2017-08-16-td-UP000005640.fas --combine q181125_SS1332_HS_02_c.pepXML
INFO[12:24:38] Executing PeptideProphet 20190226
The syntax of the command is incorrect.
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzXML in msms_run_summary tag...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzML'.
WARNING: cannot open data file C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzML in msms_run_summary tag... trying .mzXML ...
Failed to open input file 'C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzXML'.
WARNING: CANNOT correct data file C:\MSFragger-20190222\result\Urine_workflow\MStern/q181125_SS1332_HS_02.mzXML in msms_run_summary tag...

command "mkdir -p C:/tmp" failed: Operation not permitted
warning: the webserver temporary directory C:/tmp specified by WEBSERVER_TMP does not exist and could not be created. Tempfiles will created in data directories instead. file 1: C:\MSFragger-20190222\result\Urine_workflow\MStern\q181125_SS1332_HS_02_c.pepXML
processed altogether 15073 results
INFO: Results written to file: C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml
Building Commentz-Walter keyword tree...The syntax of the command is incorrect.
Searching the tree...
Linking duplicate entries...
Printing results...'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no RefreshParser data written to file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\MStern>Code:

C:\MSFragger-20190222\result\Urine_workflow\MStern>move -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084" "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\MStern>Code:

C:\MSFragger-20190222\result\Urine_workflow\MStern>move -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084" "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10084, error 2 "No such file or directory"Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 3578 2+, 5845 3+, 3590 4+, 1468 5+, 589 6+, and 0 7+ spectra.
Found 4812 Decoys, and 10258 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20....WARNING: Mixture model quality test failed for charge (1+).
.....
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+).
The syntax of the command is incorrect.
model complete after 30 iterations
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
'Code:' is not recognized as an internal or external command,
operable program or batch file.
The system cannot find the file specified.
error: no peptideprophet data written to file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml

C:\MSFragger-20190222\result\Urine_workflow\MStern>move -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336" "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336, error 2 "No such file or directory"
C:\MSFragger-20190222\result\Urine_workflow\MStern>Code:

C:\MSFragger-20190222\result\Urine_workflow\MStern>move -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336"

command "mv -f "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336" "C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml"" failed: Operation not permitted
failed to update C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml from temp file C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml.tmp.a10336, error 2 "No such file or directory"INFO[12:24:54] Done
Process 'PeptideProphet' finished, exit code: 0

iProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe iprophet --decoy rev_ --nonsp --output interact --threads 0 C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml
INFO[12:24:54] Executing InterProphet 20190226
Running NSS NRS NSE NSI NSM FPKM Model EM:
Computing NSS values ...
done
Computing NRS values ...
done
Computing NSE values ...
done
Computing NSI values ...
done
Computing NSM values ...
done
FPKM values are unavailable ...
Iterations: .done
INFO[12:24:58] Done
Process 'iProphet' finished, exit code: 0

ProteinProphet [Work dir: C:\MSFragger-20190222\result\Urine_workflow]
C:\MSFragger-20190222\philosopher_windows_amd64.exe proteinprophet --maxppmdiff 2000000 C:\MSFragger-20190222\result\Urine_workflow\MStern\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\In-Solution\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\STrap\interact.pep.xml C:\MSFragger-20190222\result\Urine_workflow\PreOmics\interact.pep.xml
INFO[12:24:58] Executing ProteinProphet 20190226
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64))
(no FPKM) (using degen pep info)
Reading in C:/MSFragger-20190222/result/Urine_workflow/MStern/interact.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

Reading in C:/MSFragger-20190222/result/Urine_workflow/In-Solution/interact.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

Reading in C:/MSFragger-20190222/result/Urine_workflow/STrap/interact.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

Reading in C:/MSFragger-20190222/result/Urine_workflow/PreOmics/interact.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[12:25:02] Done
Process 'ProteinProphet' finished, exit code: 0

ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\MStern]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\MStern --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml
INFO[12:25:02] Executing Filter 20190226
INFO[12:25:02] Processing peptide identification files
INFO[12:25:03] 1+ Charge profile decoy=0 target=0
INFO[12:25:03] 2+ Charge profile decoy=906 target=2675
INFO[12:25:03] 3+ Charge profile decoy=1790 target=4055
INFO[12:25:03] 4+ Charge profile decoy=1262 target=2328
INFO[12:25:03] 5+ Charge profile decoy=604 target=864
INFO[12:25:03] 6+ Charge profile decoy=250 target=339
INFO[12:25:03] Database search results ions=11976 peptides=11008 psms=15073
INFO[12:25:03] Converged to 0.00 % FDR with 0 PSMs decoy=0 threshold=10 total=0
INFO[12:25:03] Converged to 0.00 % FDR with 0 Peptides decoy=0 threshold=10 total=0
INFO[12:25:03] Converged to 0.00 % FDR with 0 Ions decoy=0 threshold=10 total=0
FATA[12:25:03] No Protein groups detected, check your file and try again
Process 'ReportFilter' finished, exit code: 1

Process returned non-zero exit code, stopping
ReportFilter [Work dir: C:\MSFragger-20190222\result\Urine_workflow\PreOmics]
C:\MSFragger-20190222\philosopher_windows_amd64.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml C:\MSFragger-20190222\result\Urine_workflow\PreOmics --protxml C:\MSFragger-20190222\result\Urine_workflow\interact.prot.xml

Stopping 10/40 processes (30 already finished)
Processing interrupted, stopping ReportFilter

sort modifications list in PSM table

sort all modifications in the list for better reading. Requested by @fcyu

No_enzyme search issues

Hello. I have tried this before and couldn't get it to work. Some of the problem was on my end for sure. I think some of the issues have been resolved on both my end and in the new implementations of the software. However, I'm still failing getting things through this search pipeline. I'm trying to search a peptide pool enriched with molecular weight cutoffs and that does not have an enzymatic digestion at all. I previously went through the help board when it was located not on Github and we clarified a params file (pasted below) for the MSFragger search. I have peptides that could be any length with any termini, which is a bit less refined than the MHC experiment. I have now gotten the search to work as I have access to a machine with a lot of RAM, but it's failling in peptideprophet through philosopher now saying that it does not recognize the enzyme. Please let me know if you see any egregious errors or have any ideas how I can fix the issues.

I tried the following peptideprophet :

./philosopher_linux_amd64 peptideprophet --combine --accmass --clevel -2 --ppm --decoyprobs --enzyme No_enzyme --nonparam --decoy rev_ --database 2019-03-13-td-uniprot_all_Mus_musculus_20160219_reviewed.fasta *.pepXML

ERROR:
INFO[09:38:25] Executing PeptideProphet 20180317
file 1: /processing/cpba/MSFragger_working_directory/working_directory/20190124_LUM1_CPBA_EASY04_053_30_SA_15209-02_bRP1_01.pepXML
ERROR: Unrecognized enzyme No_enzyme - please specify enzyme with -E option

/processing/cpba/MSFragger_working_directory/working_directory/interact.pep.xml
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure >'
what(): failed opening file: No such file or directory
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure >'
what(): failed opening file: No such file or directory
INFO[09:38:26] Done

Here is my search command in MSFragger:

java -Xmx1000G -jar MSFragger-20190222.jar ./fragger_no_enzyme-3.params *.mzXML

No_enzyme params file:
database_name = 2019-03-13-td-uniprot_all_Mus_musculus_20160219_reviewed.fasta
num_threads = 40 # 0=poll CPU to set num threads; else specify num threads directly (max 64)

precursor_mass_tolerance = 500.00
precursor_mass_units = 0 # 0=Daltons, 1=ppm
precursor_true_tolerance = 20.00
precursor_true_units = 1 # 0=Daltons, 1=ppm
fragment_mass_tolerance = 20.00
fragment_mass_units = 1 # 0=Daltons, 1=ppm

isotope_error = 0 # 0=off, 0/1/2 (standard C13 error)

search_enzyme_name = No_enzyme
search_enzyme_cutafter = ARNDCQEGHILKMFPSTWYV
search_enzyme_butnotafter =

num_enzyme_termini = 0 # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion
allowed_missed_cleavage = 1 # maximum value is 5

clip_nTerm_M = 1

#maximum of 7 mods - amino acid codes, * for any amino acid, ^ for termini, [ and ] specifies protein termini, n and c specifies peptide termini
variable_mod_01 = 15.9949 M
variable_mod_02 = 42.0106 [^]^
variable_mod_03 = -17.0265 nQnC
variable_mod_04 = -18.0106 nE

allow_multiple_variable_mods_on_residue = 1 # static mods are not considered
max_variable_mods_per_mod = 3 # maximum of 5
max_variable_mods_combinations = 1000 # maximum of 65534, limits number of modified peptides generated from sequence

output_file_extension = pepXML #pepXML
output_format = pepXML #pepXML or tsv
output_report_topN = 1
output_max_expect = 50

precursor_charge = 0 0 # precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter
override_charge = 0 # 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter

digest_min_length = 7
digest_max_length = 50
digest_mass_range = 500.0 5000.0 # MH+ peptide mass range to analyze
max_fragment_charge = 2 # set maximum fragment charge state to analyze (allowed max 5)

#open search parameters
track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin
zero_bin_accept_expect = 0 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable
zero_bin_mult_expect = 1 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect)
add_topN_complementary = 0

spectral processing

minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10)
use_topN_peaks = 100
min_fragments_modelling = 3
min_matched_fragments = 6
minimum_ratio = 0.01 # filter peaks below this fraction of strongest peak
clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range

additional modifications

add_Cterm_peptide = 0.0
add_Nterm_peptide = 0.0
add_Cterm_protein = 0.0
add_Nterm_protein = 0.0

add_G_glycine = 0.0000 add_A_alanine = 0.0000 add_S_serine = 0.0000 add_P_proline = 0.0000 add_V_valine = 0.0000 add_T_threonine = 0.0000 add_C_cysteine = 57.021464 add_L_leucine = 0.0000 add_I_isoleucine = 0.0000 add_N_asparagine = 0.0000 add_D_aspartic_acid = 0.0000 add_Q_glutamine = 0.0000 add_K_lysine = 0.0000 add_E_glutamic_acid = 0.0000 add_M_methionine = 0.0000 add_H_histidine = 0.0000 add_F_phenylalanine = 0.0000 add_R_arginine = 0.0000 add_Y_tyrosine = 0.0000 add_W_tryptophan = 0.0000 add_B_user_amino_acid = 0.0000 add_J_user_amino_acid = 0.0000 add_O_user_amino_acid = 0.0000 add_U_user_amino_acid = 0.0000 add_X_user_amino_acid = 0.0000 add_Z_user_amino_acid = 0.0000 # added to G - avg. 57.0513, mono. 57.02146
# added to A - avg. 71.0779, mono. 71.03711
# added to S - avg. 87.0773, mono. 87.03203
# added to P - avg. 97.1152, mono. 97.05276
# added to V - avg. 99.1311, mono. 99.06841
# added to T - avg. 101.1038, mono. 101.04768
# added to C - avg. 103.1429, mono. 103.00918
# added to L - avg. 113.1576, mono. 113.08406
# added to I - avg. 113.1576, mono. 113.08406
# added to N - avg. 114.1026, mono. 114.04293
# added to D - avg. 115.0874, mono. 115.02694
# added to Q - avg. 128.1292, mono. 128.05858
# added to K - avg. 128.1723, mono. 128.09496
# added to E - avg. 129.1140, mono. 129.04259
# added to M - avg. 131.1961, mono. 131.04048
# added to H - avg. 137.1393, mono. 137.05891
# added to F - avg. 147.1739, mono. 147.06841
# added to R - avg. 156.1857, mono. 156.10111
# added to Y - avg. 163.0633, mono. 163.06333
# added to W - avg. 186.0793, mono. 186.07931
# added to B - avg. 0.0000, mono. 0.00000
# added to J - avg. 0.0000, mono. 0.00000
# added to O - avg. 0.0000, mono 0.00000
# added to U - avg. 0.0000, mono. 0.00000
# added to X - avg. 0.0000, mono. 0.00000
# added to Z - avg. 0.0000, mono. 0.00000

labeled MS1-based quantification

Hi there,
Is it possible to analysed SILAC or Dimethylation-labelled samples with Philosopher?
Thanks

output tables are missing protein ID

all tsv tables with the exception of the PSM are missing the protein id and mapping when the razor flag is not used.

Filter and Report Throwing Errors

Hi,

I'm trying to do an analysis of an ITRAQ labeled human proteome sample via MSFragger/Philosopher. The MSFragger search hits were able to successfully go through proteinprophet and peptideprophet, but I can't seem to get past the 'Filter' stage. I'm wondering what I might be doing wrong.

Here's my set of commands in my bash script:

./philosopher peptideprophet --database uniprot-reviewed_yes+taxonomy_9606_W_DECOYS_v3.fasta --nonparam --expectscore --decoy DECOY_ --decoyprobs --masswidth 500 --clevel 2 --forcedistr 053113_Wang_ITRAQ_1_search_3.pepXML
./philosopher proteinprophet interact-053113_Wang_ITRAQ_1_search_3.pep.xml --output interact-053113_Wang_ITRAQ_1_search_3.prot.xml
./philosopher filter --pepxml interact-053113_Wang_ITRAQ_1_search_3.pep.xml --protxml interact-053113_Wang_ITRAQ_1_search_3.prot.xml.prot.xml
./philosopher report

Here's where the FATAL messages start (upon starting filter):

INFO[16:45:24] Processing peptide identification files
INFO[16:45:27] 1+ Charge profile decoy=0 target=0
INFO[16:45:27] 2+ Charge profile decoy=0 target=2937
INFO[16:45:27] 3+ Charge profile decoy=0 target=1183
INFO[16:45:27] 4+ Charge profile decoy=0 target=644
INFO[16:45:27] 5+ Charge profile decoy=0 target=147
INFO[16:45:27] 6+ Charge profile decoy=0 target=27
INFO[16:45:27] Database search results ions=3682 peptides=3195 psms=4940
INFO[16:45:27] Converged to 0.00 % FDR with 4940 PSMs decoy=0 threshold=-7 total=4940
INFO[16:45:27] Converged to 0.00 % FDR with 3195 Peptides decoy=0 threshold=0.0503 total=3195
INFO[16:45:28] Converged to 0.00 % FDR with 3682 Ions decoy=0 threshold=-7 total=3682
INFO[16:45:28] Protein inference results decoy=0 target=565
INFO[16:45:28] Converged to 0.00 % FDR with 549 Proteins decoy=0 threshold=0.7228 total=549
INFO[16:45:28] 2D FDR estimation: Protein mirror image decoy=549 target=549
INFO[16:45:28] Second filtering results ions=1444 peptides=1144 psms=2155
INFO[16:45:28] Converged to 0.00 % FDR with 2155 PSMs decoy=0 threshold=-7 total=2155
INFO[16:45:29] Converged to 0.00 % FDR with 1144 Peptides decoy=0 threshold=0.0558 total=1144
INFO[16:45:29] Converged to 0.00 % FDR with 1444 Ions decoy=0 threshold=-7 total=1444
FATA[16:45:29] Database data not available, interrupting processing
FATA[16:45:29] cannot restore serialized data structures: invalid argument

idconvert erases all files in the working dir if no workspace exists

Philosopher report command fails at "Creating Protein FASTA report"

Tried running with two small mzml files, just 1000 spectra in each. Philosopher report failed, see log below.

Full log: log_2018-02-28_15-05-03.txt

All the input files (mzml, fastsa, fragger.params) and the whole output directory are on the server in my data folder "for_felipe".

Short log:

System info:
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info:
MSFragger-GUI version 4.9
MSFragger version 20171106
Philosopher version 20180227 (build 201802271552)

Will execute 11 commands:
java -jar C:\data\andy\fragger-programs\MSFragger-20171106\MSFragger-20171106.jar C:\data\andy\fragger-gui-test-output-04\fragger.params C:\data\mzml\1000-scans-anonymous\file-001.mzML C:\data\mzml\1000-scans-anonymous\file-002.mzML 

java -cp C:\projects\msfragger-gui\MSFragger-GUI\build\classes umich.msfragger.util.FileMove C:\data\mzml\1000-scans-anonymous\file-001.pepXML C:\data\andy\fragger-gui-test-output-04\file-001.pepXML 

java -cp C:\projects\msfragger-gui\MSFragger-GUI\build\classes umich.msfragger.util.FileMove C:\data\mzml\1000-scans-anonymous\file-002.pepXML C:\data\andy\fragger-gui-test-output-04\file-002.pepXML 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe workspace --clean 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe workspace --init 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\data\andy\fasta\Uniprot.20151009.Hs.revDecoys.fa C:\data\andy\fragger-gui-test-output-04\file-001.pepXML 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --database C:\data\andy\fasta\Uniprot.20151009.Hs.revDecoys.fa C:\data\andy\fragger-gui-test-output-04\file-002.pepXML 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe proteinprophet --output interact interact-file-001.pep.xml interact-file-002.pep.xml 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe database --annotate C:\data\andy\fasta\Uniprot.20151009.Hs.revDecoys.fa 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe filter --sequential --pepxml C:\data\andy\fragger-gui-test-output-04 --protxml C:\data\andy\fragger-gui-test-output-04\interact.prot.xml 

C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe report 

~~~~~~~~~~~~~~~~~~~~~~

.....
.....
.....

INFO[15:02:39] Calculating Spectral Counts                  

INFO[15:02:39] Done                                         

Process finished, exit value: 0
Executing command:
$> C:\data\andy\fragger-programs\philosopher_windows_amd64_20180227.exe report 
Process started
panic: runtime error: index out of range

goroutine 1 [running]:
github.com/prvst/philosopher/lib/rep.Run(0xc0420866f0, 0x24, 0xc042086720, 0x27, 0xc042098500, 0x46, 0xc04209a380, 0x36, 0xc042086750, 0x2d, ...)
	/home/felipevl/go/src/github.com/prvst/philosopher/lib/rep/rep.go:276 +0x703
github.com/prvst/philosopher/cmd.glob..func14(0x2c1c0a0, 0x2c3f208, 0x0, 0x0)
	/home/felipevl/go/src/github.com/prvst/philosopher/cmd/report.go:26 +0xea
github.com/spf13/cobra.(*Command).execute(0x2c1c0a0, 0x2c3f208, 0x0, 0x0, 0x2c1c0a0, 0x2c3f208)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:757 +0x2c8
github.com/spf13/cobra.(*Command).ExecuteC(0x2c1c300, 0xaf5b05, 0xc042091f78, 0x404083)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:843 +0x311
github.com/spf13/cobra.(*Command).Execute(0x2c1c300, 0x1, 0x0)
	/home/felipevl/go/src/github.com/spf13/cobra/command.go:791 +0x32
github.com/prvst/philosopher/cmd.Execute()
	/home/felipevl/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x34
main.main()
	/home/felipevl/go/src/github.com/prvst/philosopher/main.go:19 +0x77

INFO[15:02:39] Executing report                             
INFO[15:02:39] Creating Protein FASTA report                

Process finished, exit value: 2

fatal error: out of memory

Hi,
I am having an issue processing a huge data set (~1600 files). For convenience I have all the files in the same folder.
I was able to successfully process the data with MSfragger and protein/peptide-Prophet (via the MSfragger GUI), but I hit the out of memory at the execution of

philosopher_windows_amd64.exe filter --sequential --mapmods --tag rev_ --pepxml X:\ --protxml X:\interact.prot.xml

I am going to try to run the command on a machine with ~300GB of RAM soon, to see if this would be enough, but just in case it won't work, what would be the best option to get the processing complete?

I was thinking of splitting the data in multiple batch, by creating multiple folder and moving ~ 10 pep.xml files in them, and then run multiple times the philosopher command, something like

philosopher_windows_amd64.exe filter --sequential --mapmods --tag rev_ --pepxml X:\batch1 --protxml X:\interact.prot.xml

philosopher_windows_amd64.exe filter --sequential --mapmods --tag rev_ --pepxml X:\batch2 --protxml X:\interact.prot.xml

Would this work? My concern is that the interact.prot.xml is just one for all the data, is this a problem?
I guess, I would then need to run

philosopher_windows_amd64.exe report

for each batch, which will probably return multiple .tsv files. Is there a way to get everything in a single output?

Thanks

Any documents for filter/Freequant?

Hi, I wonder if there is any detailed documents for the tools in the philosopher, especially for filter and freequant. What's the name of the tool you used in the filter and how it works? Besides, after I run the freequant and report, it generate several graphs without any explain/description, which makes me difficult to understand. Thank you so much.

non uniprot fasta support

Could we have support for custom fasta files which don't meet the uniprot header format? Support for simple header structures such as that below would be appreciated as uniprot is often quite out of date.

customidentifier1
AMINOACIDSEQUENCE1
customidentifier2
AMINOACIDSEQUENCE2

Regards,

Owen

EDIT: simple naming structures do seem to be supported, fasta files just appear to need to be named *.fas rather than *.fa or *.fasta

tutorial on os x

Got the latest version of mac darwin binary. Can't fetch the database:
ph ./philosopher_darwin_amd64-2.dms database --id UP000001013 --contam --reviewed
INFO[17:19:07] Fetching database
INFO[17:19:07] Processing decoys
INFO[17:19:07] Creating file
INFO[17:19:07] Done

But nothing is being downloaded.

Mapped Proteins, how to interpret result when decoy protein is mapped

Hi again,

I have a question regarding the interpretation of the psm.tsv result.
For some psms in the file, in the Mapped Proteins column, one or multiple decoy proteins are reported e.g.

Peptide	Hyperscore	Nextscore	PeptideProphet Probability	Protein	Mapped Proteins
KIQEESLR	19.67	14.267	0.9997	sp\|Q8R1B4\|EIF3C_MOUSE	rev_sp\|Q8R197\|SAST_MOUSE

How should one interpret this psm? I would think it should e filtered out because it is a decoy hit, but I am not sure as I would expect philosopher to remove it 'for me'.

Thanks

How to distinguish doubly modified from singly modified peptides in open search

Hi,

To my understanding, mass shifts are matched to unimod with a delta of 0.002 Da (as in the paper?) and, when a match is not found philosopher tries to combine up to 3 mods (from previously assigned mods) to assign the mass shift. Is there a way to find out when this happened?

Applying evaluation to all search hits in PSM

Thanks for providing with this nice wrapper for the whole Prophetsuite. It is easy to use.
I would like to know if I can use PeptideProphet to evaluate all peptide spectrum matches. Not just only the first/best one. If not I would like to make this as a feature request.

Mixture Model Quality Test Failure: Searched Entire Proteome + Decoys against 4 protein sample

Hello,

I'm currently testing out MSFragger with a 4 protein dataset (4 glycoproteins known to be in the sample, and nothing else should be in there), and tried using a human proteome fasta file (from uniprot) with reversed decoys appended. I was able to generate search results via MSFragger, but when I try and use philosopher's implementation of peptideprophet, I get messages saying that the mixture model fails quality test for charges +1 to +7.

Here's the command:

philosopher peptideprophet --database uniprot-reviewed_yes+taxonomy_9606_W_DECOYS_v3.fasta --nonparam --decoy DECOY_ --masswidth 2000 --decoyprobs 4ProteinMix_01_pickpeak_v3.pepXML

Here's the output:

file 1: C:\Users\newot\ms_fragger\MSFragger_20170103\4ProteinMix_01_pickpeak_v3.pepXML
processed altogether 6119 results
INFO: Results written to file: C:\Users\newot\ms_fragger\MSFragger_20170103\interact-4ProteinMix_01_pickpeak_v3.pep.xml

C:\Users\newot\ms_fragger\MSFragger_20170103\interact-4ProteinMix_01_pickpeak_v3.pep.xml
Building Commentz-Walter keyword tree...
Searching the tree...
Linking duplicate entries...
Printing results...

Using Decoy Label "DECOY_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem)
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 18 2+, 4707 3+, 1010 4+, 319 5+, 65 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 2932 Decoys, and 3187 Non-Decoys
Iterations: .........10.........20.....
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 (4+).
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+).
model complete after 26 iterations

I'm going to guess that most 'non-decoy' peptide sequences are going to have matches with spectra due to chance or overlap in fragment masses with peptides from the 4 'correct' proteins (that are actually in the sample). Thus, the probability of getting a high score from MSFragger given that you have a 'non-decoy' peptide should be roughly equivalent to that for peptides from decoy proteins.

Should philosopher's peptideprophet be able to identify the peptides tiny subset of non-decoy proteins (4) that should have very high scores?

Thanks,
Owen

reprint output (abacus) - mislabeled columns

Reprint formatted file generated by Abacus has the second annotation line incorrect
See below
Bait and controls flipped. The second line should correspond to the first line, just stripping '_SPC' from the columns name

PROTID | CONTROL_1_SPC | CONTROL_2_SPC | HDAC5_1_SPC | HDAC5_2_SPC
na | CONTROL | HDAC5 | HDAC5 | CONTROL
P19474 | 164 | 20 | 200 | 153
Q9UQL6 | 0 | 0 | 179 | 201
P62258 | 4 | 7 | 175 | 87
P63104 | 2 | 8 | 88 | 33
P60709 | 21 | 55 | 86 | 15
P61981 | 1 | 2 | 81 | 25
P07437 | 19 | 53 | 80 | 60
P04264 | 370 | 186 | 77 | 116

Following are the commands:

philosopher_windows_amd64.exe workspace --clean
philosopher_windows_amd64.exe workspace --init
philosopher_windows_amd64.exe database --annotate some.fasta --prefix DECOY_
philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --decoy DECOY_ --combine --database some.fasta *_c.pepXML
philosopher_windows_amd64.exe proteinprophet --maxppmdiff 1000000 interact.pep.xml
philosopher_windows_amd64.exe filter --sequential --razor --mapmods --tag DECOY_ --pepxml interact.pep.xml
philosopher_windows_amd64.exe labelquant --plex 10 --purity 0 --dir C:\some\
philosopher_windows_amd64.exe report

Following are the console output of `philosopher_windows_amd64.exe report':

INFO[15:12:07] Executing Report 20190206
INFO[15:12:30] Creating TMT PSM report
panic: runtime error: index out of range

goroutine 1 [running]:
github.com/prvst/philosopher/lib/rep.Run(0xc0000806f0, 0x24, 0xc0001321c0, 0x6d, 0xc00009e500, 0x49, 0xc00009c580, 0x7c, 0xc00009c600, 0x73, ...)
        /home/prvst/go/src/github.com/prvst/philosopher/lib/rep/rep.go:340 +0xa8d
github.com/prvst/philosopher/cmd.glob..func14(0x2de3760, 0x2e06688, 0x0, 0x0)
        /home/prvst/go/src/github.com/prvst/philosopher/cmd/report.go:28 +0x104
github.com/spf13/cobra.(*Command).execute(0x2de3760, 0x2e06688, 0x0, 0x0, 0x2de3760, 0x2e06688)
        /home/prvst/go/src/github.com/spf13/cobra/command.go:766 +0x2d3
github.com/spf13/cobra.(*Command).ExecuteC(0x2de39c0, 0x2de3e80, 0xc000093f68, 0xc000093f88)
        /home/prvst/go/src/github.com/spf13/cobra/command.go:852 +0x304
github.com/spf13/cobra.(*Command).Execute(0x2de39c0, 0x1, 0x2de3e80)
        /home/prvst/go/src/github.com/spf13/cobra/command.go:800 +0x32
github.com/prvst/philosopher/cmd.Execute()
        /home/prvst/go/src/github.com/prvst/philosopher/cmd/root.go:32 +0x34
main.main()
        /home/prvst/go/src/github.com/prvst/philosopher/main.go:19 +0x75

Thanks,

Fengchao

nesvilab / philosopher Goto Github PK

philosopher's Introduction

Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. It is also a depencency-free wraper of Trans-Proteomic Pipeline (PeptideProphet, iProphet, PTMProphet, and ProteinProphet).

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