Hello,
I am having an issue using Philosopher to analyze the results of MSFragger. Here is the command line output of running the program:
Will execute 12 commands:
java -jar -Xmx8G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Executing command:
$> java -jar -Xmx8G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
Process started
Peptide index read in 219ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 4981.53MB
205026136 fragments to be searched in 1 slices (1.53GB total)
Operating on slice 1 of 1:
6415ms
b1906_293T_proteinID_01A_QE3_122212.mzXML
95173ms
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 1535/41820 (3.67%) - 303.66 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 3103/41820 (7.42%) - 310.25 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 4708/41820 (11.26%) - 313.66 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 6267/41820 (14.99%) - 310.25 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 7847/41820 (18.76%) - 313.74 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 9405/41820 (22.49%) - 310.17 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 11017/41820 (26.34%) - 318.89 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 12561/41820 (30.04%) - 303.64 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 14120/41820 (33.76%) - 306.53 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 15691/41820 (37.52%) - 307.74 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 17216/41820 (41.17%) - 303.48 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 18757/41820 (44.85%) - 302.04 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 20296/41820 (48.53%) - 304.51 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 21853/41820 (52.25%) - 310.90 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 23449/41820 (56.07%) - 315.79 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 25014/41820 (59.81%) - 311.44 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 26569/41820 (63.53%) - 308.35 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 28138/41820 (67.28%) - 308.49 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 29743/41820 (71.12%) - 312.68 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 31368/41820 (75.01%) - 317.57 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 32957/41820 (78.81%) - 316.34 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 34589/41820 (82.71%) - 321.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 36193/41820 (86.54%) - 313.34 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 37875/41820 (90.57%) - 327.62 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 39645/41820 (94.80%) - 345.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 41399/41820 (98.99%) - 350.24 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 41820/41820 (100.00%) - 214.25 spectra/s]
- completed 134540ms
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:47:04] Creating workspace
WARN[08:47:04] existing workspace detected, will not overwrite
INFO[08:47:04] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
Process started
file 1: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
processed altogether 34084 results
INFO: Results written to file: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.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 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 18190 2+, 12391 3+, 3101 4+, 324 5+, 73 6+, and 3 7+ spectra.
Found 0 Decoys, and 34082 Non-Decoys
WARNING: No decoys with label rev were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:17] Removing workspace
WARN[08:48:17] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:48:17] Creating workspace
WARN[08:48:17] existing workspace detected, will not overwrite
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
Process started
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:/Users/acadigan/Desktop/AlexStuff/MSFragger/TestData/interact-b1906_293T_proteinID_01A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[08:48:19] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:20] Removing workspace
WARN[08:48:20] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:20] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:48:20] Creating workspace
WARN[08:48:20] existing workspace detected, will not overwrite
INFO[08:48:20] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
Process started
INFO[08:48:20] Processing database
INFO[08:48:34] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
Process started
INFO[08:48:34] Processing peptide identification files
INFO[08:48:37] 1+ Charge profile decoy=0 target=0
INFO[08:48:37] 2+ Charge profile decoy=0 target=18190
INFO[08:48:37] 3+ Charge profile decoy=0 target=12391
INFO[08:48:37] 4+ Charge profile decoy=0 target=3101
INFO[08:48:37] 5+ Charge profile decoy=0 target=324
INFO[08:48:37] 6+ Charge profile decoy=0 target=73
INFO[08:48:37] Database search results ions=24050 peptides=20473 psms=34084
INFO[08:48:37] Converged to 0.00 % FDR with 34084 PSMs decoy=0 threshold=0 total=34084
INFO[08:48:38] Converged to 0.00 % FDR with 20473 Peptides decoy=0 threshold=0 total=20473
INFO[08:48:38] Converged to 0.00 % FDR with 24050 Ions decoy=0 threshold=0 total=24050
FATA[08:48:38] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
Process started
INFO[08:48:38] Creating PSM report
INFO[08:48:38] Creating peptide Ion report
INFO[08:48:38] Creating peptide report
INFO[08:48:38] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:38] Removing workspace
WARN[08:48:38] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:38] Done
Process finished, exit value: 0
=========================
===
=== Done
===
=========================
Here is another run using a different mzXML file:
Will execute 12 commands:
java -jar -Xmx14G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.mzXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Executing command:
$> java -jar -Xmx14G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.mzXML
Process started
Peptide index read in 203ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 9350.73MB
205026136 fragments to be searched in 1 slices (1.53GB total)
Operating on slice 1 of 1:
6426ms
b1922_293T_proteinID_02A_QE3_122212.mzXML
147102ms
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 1221/46856 (2.61%) - 240.07 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 2682/46856 (5.72%) - 291.79 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 4167/46856 (8.89%) - 293.77 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 5615/46856 (11.98%) - 283.87 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 7069/46856 (15.09%) - 285.04 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 8494/46856 (18.13%) - 279.36 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 9875/46856 (21.08%) - 274.06 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 11288/46856 (24.09%) - 280.30 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 12729/46856 (27.17%) - 285.97 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 14184/46856 (30.27%) - 283.35 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 15607/46856 (33.31%) - 282.40 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 17022/46856 (36.33%) - 277.40 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 18461/46856 (39.40%) - 285.57 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 19909/46856 (42.49%) - 285.49 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 21353/46856 (45.57%) - 287.36 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 22801/46856 (48.66%) - 288.16 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 24272/46856 (51.80%) - 292.68 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 25758/46856 (54.97%) - 291.32 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 27261/46856 (58.18%) - 292.87 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 28720/46856 (61.29%) - 291.22 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 30186/46856 (64.42%) - 291.74 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 31671/46856 (67.59%) - 294.70 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 33136/46856 (70.72%) - 292.59 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 34644/46856 (73.94%) - 295.51 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 36177/46856 (77.21%) - 306.11 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 37713/46856 (80.49%) - 299.18 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 39250/46856 (83.77%) - 300.25 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 40773/46856 (87.02%) - 304.11 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 42394/46856 (90.48%) - 319.60 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 44034/46856 (93.98%) - 326.37 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 45652/46856 (97.43%) - 323.08 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 46856/46856 (100.00%) - 248.09 spectra/s]
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:17:45] Creating workspace
WARN[09:17:45] existing workspace detected, will not overwrite
INFO[09:17:45] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
Process started
file 1: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
processed altogether 38597 results
INFO: Results written to file: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
-
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1922_293T_proteinID_02A_QE3_122212.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 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 21822 2+, 13646 3+, 2786 4+, 259 5+, 80 6+, and 1 7+ spectra.
Found 0 Decoys, and 38594 Non-Decoys
WARNING: No decoys with label rev were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
INFO[09:19:15] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:15] Removing workspace
WARN[09:19:15] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:15] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:19:16] Creating workspace
WARN[09:19:16] existing workspace detected, will not overwrite
INFO[09:19:16] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
Process started
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:/Users/acadigan/Desktop/AlexStuff/MSFragger/TestData/interact-b1922_293T_proteinID_02A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:18] Removing workspace
WARN[09:19:18] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:19:18] Creating workspace
WARN[09:19:18] existing workspace detected, will not overwrite
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
Process started
INFO[09:19:18] Processing database
INFO[09:19:32] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
Process started
INFO[09:19:32] Processing peptide identification files
INFO[09:19:43] 1+ Charge profile decoy=0 target=0
INFO[09:19:43] 2+ Charge profile decoy=0 target=40012
INFO[09:19:43] 3+ Charge profile decoy=0 target=26037
INFO[09:19:43] 4+ Charge profile decoy=0 target=5887
INFO[09:19:43] 5+ Charge profile decoy=0 target=583
INFO[09:19:43] 6+ Charge profile decoy=0 target=153
INFO[09:19:43] Database search results ions=49651 peptides=41576 psms=72681
INFO[09:19:43] Converged to 0.00 % FDR with 72681 PSMs decoy=0 threshold=0 total=72681
INFO[09:19:44] Converged to 0.00 % FDR with 41576 Peptides decoy=0 threshold=0 total=41576
INFO[09:19:44] Converged to 0.00 % FDR with 49651 Ions decoy=0 threshold=0 total=49651
FATA[09:19:44] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
Process started
INFO[09:19:44] Creating PSM report
INFO[09:19:44] Creating peptide Ion report
INFO[09:19:44] Creating peptide report
INFO[09:19:44] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:44] Removing workspace
WARN[09:19:44] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:44] Done
Process finished, exit value: 0
=========================
=== Done
=========================
I believe that MSFragger is running properly, but Philosopher is just producing output files with no results in them. I am using two different mzXML files I downloaded from this link: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/06/PXD001468. I have also attached a zip file of the protein data set I was using: CompleteHumanProteome.zip. Any advice on what I'm doing wrong and how to fix the issue would be greatly appreciated!
Thanks so much!
-Alex