Describe the problem
-
I'm submitting a:
-
My MSFragger use case:
** 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
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.
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"
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
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.
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"
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"
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
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.
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"
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
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.
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"
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"
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
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.
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"
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
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\STrap\interact.pep.xml
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.
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"
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"
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
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.
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"
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
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.
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"
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"
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