search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
205 stars 38 forks source link

Process returned non-zero exit code, stoppingTmtIntegrator #250

Closed DanielConole closed 4 years ago

DanielConole commented 4 years ago

Hi there Alexey and team,

I tried to run a site-ID and TMT quant analysis on some files, which went well up until the TMT integrator part. Not sure what went wrong here - can you help?

Log is as below:

System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.3.11 (build 1601497354)

LCMS files: Experiment/Group:

45 commands to execute: WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-10-DC-DUB-Site-ID-2-E2-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-11-DC-DUB-Site-ID-2-E1-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-12-DC-DUB-Site-ID-2-E1-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-13-DC-DUB-Site-ID-2-E2-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-14-DC-DUB-Site-ID-2-E1-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-15-DC-DUB-Site-ID-2-E2-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML PeptideProphet [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas --combine DC-DUB-Site-ID-2-E1-f1_c.pepXML DC-DUB-Site-ID-2-E1-f7_c.pepXML DC-DUB-Site-ID-2-E2-f4_c.pepXML DC-DUB-Site-ID-2-E1-f5_c.pepXML DC-DUB-Site-ID-2-E1-f8_c.pepXML DC-DUB-Site-ID-2-E2-f3_c.pepXML DC-DUB-Site-ID-2-E2-f7_c.pepXML DC-DUB-Site-ID-2-E1-f4_c.pepXML DC-DUB-Site-ID-2-E2-f1_c.pepXML DC-DUB-Site-ID-2-E2-f8_c.pepXML DC-DUB-Site-ID-2-E2-f2_c.pepXML DC-DUB-Site-ID-2-E1-f3_c.pepXML DC-DUB-Site-ID-2-E1-f2_c.pepXML DC-DUB-Site-ID-2-E2-f6_c.pepXML DC-DUB-Site-ID-2-E1-f6_c.pepXML DC-DUB-Site-ID-2-E2-f5_c.pepXML Rewrite pepxml [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp C:\Users\dconole\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML PhilosopherDbAnnotate [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\DanC\2020-10-19-decoys-Human proteome_2003219606.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev_ --pepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis FreeQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected LabelQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 6 --annot D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\annotation.txt --brand tmt --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected PhilosopherReport [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp "C:\Users\dconole\Desktop\fragpipe\tools\tmt-integrator-2.1.5.jar" TMTIntegrator D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\tmt-integrator-conf.yml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\psm.tsv WorkspaceClean [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -cp "C:\Users\dconole\Desktop\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\shepherd.config"


Execution order:

    Cmd: [START], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [MsFragger], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [Crystal-C], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [PeptideProphet], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [PhilosopherFilter], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [FreeQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [LabelQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [PhilosopherReport], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [TmtIntegrator], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [WorkspaceClean], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]
    Cmd: [PTMShepherd], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

# FragPipe v14.0ui state cache

crystalc.run-crystalc=true
database.db-path=D\:\\DanC\\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\dconole\\Desktop\\MSFragger-3.1.1\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\dconole\\Desktop\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\dconole\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=true
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 254.105500,C,true,1; 304.088100,C,true,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=false
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=P13_Probe\:254.1055, P14_Probe\:304.0881
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.04
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=true
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\DanC\\DUB10-Site-ID-2\\MSFragger-analysis
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=true
workflow.ram=0
workflow.threads=11

WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:50:53] Executing Workspace v3.3.11
INFO[10:50:53] Removing workspace
INFO[10:50:53] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:50:53] Executing Workspace v3.3.11
INFO[10:50:53] Creating workspace
INFO[10:50:53] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML... Checking if the data is low resolution MS/MS... The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance. ***FIRST SEARCH**** Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 300.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 1.50 Da. 318866252 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.62 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 8.6 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s | postprocessing 0.0 s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 7.4 s [progress: 19683/19683 (100%) - 41790 spectra/s] 0.5s | postprocessing 0.1 s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 56268 spectra/s] 0.4s | postprocessing 0.0 s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 6.8 s [progress: 26296/26296 (100%) - 59092 spectra/s] 0.4s | postprocessing 0.0 s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 2.1 s [progress: 32846/32846 (100%) - 47329 spectra/s] 0.7s | postprocessing 0.0 s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.9 s [progress: 30776/30776 (100%) - 46986 spectra/s] 0.7s | postprocessing 0.0 s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.2 s [progress: 27057/27057 (100%) - 49555 spectra/s] 0.5s | postprocessing 0.0 s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.8 s [progress: 9932/9932 (100%) - 29126 spectra/s] 0.3s | postprocessing 0.0 s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.6 s [progress: 16370/16370 (100%) - 49757 spectra/s] 0.3s | postprocessing 0.0 s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32661 spectra/s] 0.1s | postprocessing 0.0 s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.2 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.0 s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.5 s [progress: 14725/14725 (100%) - 67237 spectra/s] 0.2s | postprocessing 0.0 s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.6 s [progress: 21089/21089 (100%) - 59406 spectra/s] 0.4s | postprocessing 0.0 s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.7 s [progress: 23608/23608 (100%) - 42614 spectra/s] 0.6s | postprocessing 0.0 s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.3 s [progress: 24250/24250 (100%) - 45158 spectra/s] 0.5s | postprocessing 0.0 s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.8 s [progress: 24907/24907 (100%) - 44319 spectra/s] 0.6s | postprocessing 0.0 s ***FIRST SEARCH DONE IN 5.929 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 Not enough data to perform mass calibration. Using the uncalibrated data.
002 Not enough data to perform mass calibration. Using the uncalibrated data.
003 Not enough data to perform mass calibration. Using the uncalibrated data.
004 Not enough data to perform mass calibration. Using the uncalibrated data.
005 Not enough data to perform mass calibration. Using the uncalibrated data.
006 Not enough data to perform mass calibration. Using the uncalibrated data.
007 Not enough data to perform mass calibration. Using the uncalibrated data.
008 Not enough data to perform mass calibration. Using the uncalibrated data.
009 Not enough data to perform mass calibration. Using the uncalibrated data.
010 Not enough data to perform mass calibration. Using the uncalibrated data.
011 Not enough data to perform mass calibration. Using the uncalibrated data.
012 Not enough data to perform mass calibration. Using the uncalibrated data.
013 Not enough data to perform mass calibration. Using the uncalibrated data.
014 Not enough data to perform mass calibration. Using the uncalibrated data.
015 Not enough data to perform mass calibration. Using the uncalibrated data.
016 Not enough data to perform mass calibration. Using the uncalibrated data.
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 150 200 250 300 350 400
Count 179 121 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- ------- -------
Peaks 500_0 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- ------- -------
Count 170 175 176 176 179 178 skip rest
------- ------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 165
------- -------
------- -------
Rm P. 1
------- -------
Count 165
------- -------

New fragment_mass_tolerance = 150 PPM New use_topN_peaks = 150 New minimum_ratio = 0.010000 New intensity_transform = 0 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 32.737 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 150.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = true max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.75 Da. 1065135314 fragments to be searched in 2 slices (15.87 GB total) Operating on slice 1 of 2: Fragment index slice generated in 4.89 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 1.3 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 8.1 s [progress: 19683/19683 (100%) - 38219 spectra/s] 0.5s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 64981 spectra/s] 0.3s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 7.1 s [progress: 26296/26296 (100%) - 50183 spectra/s] 0.5s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 6.9 s [progress: 32846/32846 (100%) - 45683 spectra/s] 0.7s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 41366 spectra/s] 0.7s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.6 s [progress: 27057/27057 (100%) - 43291 spectra/s] 0.6s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.1 s [progress: 9932/9932 (100%) - 23369 spectra/s] 0.4s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.7 s [progress: 16370/16370 (100%) - 37981 spectra/s] 0.4s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32963 spectra/s] 0.1s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.1 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.6 s [progress: 14725/14725 (100%) - 65737 spectra/s] 0.2s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.4 s [progress: 21089/21089 (100%) - 48817 spectra/s] 0.4s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.1 s [progress: 23608/23608 (100%) - 39021 spectra/s] 0.6s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.0 s [progress: 24250/24250 (100%) - 39176 spectra/s] 0.6s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.7 s [progress: 24907/24907 (100%) - 39788 spectra/s] 0.6s Operating on slice 2 of 2: Fragment index slice generated in 4.11 s
  17. DC-DUB-Site-ID-2-E1-f1.mzML 8.4 s [progress: 1070/1070 (100%) - 9554 spectra/s] 0.1s | postprocessing 1.4 s
  18. DC-DUB-Site-ID-2-E1-f2.mzML 7.1 s [progress: 19683/19683 (100%) - 94177 spectra/s] 0.2s | postprocessing 1.7 s
  19. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 93259 spectra/s] 0.2s | postprocessing 1.4 s
  20. DC-DUB-Site-ID-2-E1-f4.mzML 6.7 s [progress: 26296/26296 (100%) - 120073 spectra/s] 0.2s | postprocessing 1.5 s
  21. DC-DUB-Site-ID-2-E1-f5.mzML 7.4 s [progress: 32846/32846 (100%) - 99233 spectra/s] 0.3s | postprocessing 1.7 s
  22. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 93544 spectra/s] 0.3s | postprocessing 1.8 s
  23. DC-DUB-Site-ID-2-E1-f7.mzML 8.7 s [progress: 27057/27057 (100%) - 87000 spectra/s] 0.3s | postprocessing 1.8 s
  24. DC-DUB-Site-ID-2-E1-f8.mzML 38.2 s [progress: 9932/9932 (100%) - 29385 spectra/s] 0.3s | postprocessing 1.9 s
  25. DC-DUB-Site-ID-2-E2-f1.mzML 8.8 s [progress: 16370/16370 (100%) - 73739 spectra/s] 0.2s | postprocessing 1.6 s
  26. DC-DUB-Site-ID-2-E2-f2.mzML 7.3 s [progress: 3560/3560 (100%) - 31504 spectra/s] 0.1s | postprocessing 1.1 s
  27. DC-DUB-Site-ID-2-E2-f3.mzML 5.3 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.9 s
  28. DC-DUB-Site-ID-2-E2-f4.mzML 5.3 s [progress: 14725/14725 (100%) - 136343 spectra/s] 0.1s | postprocessing 1.2 s
  29. DC-DUB-Site-ID-2-E2-f5.mzML 6.7 s [progress: 21089/21089 (100%) - 94147 spectra/s] 0.2s | postprocessing 1.5 s
  30. DC-DUB-Site-ID-2-E2-f6.mzML 7.5 s [progress: 23608/23608 (100%) - 102643 spectra/s] 0.2s | postprocessing 1.5 s
  31. DC-DUB-Site-ID-2-E2-f7.mzML 17.5 s [progress: 24250/24250 (100%) - 70906 spectra/s] 0.3s | postprocessing 1.7 s
  32. DC-DUB-Site-ID-2-E2-f8.mzML 19.1 s [progress: 24907/24907 (100%) - 76402 spectra/s] 0.3s | postprocessing 1.9 s MAIN SEARCH DONE IN 6.276 MIN

***TOTAL TIME 44.943 MIN**** Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML DC-DUB-Site-ID-2-E1-f1.pepXML Done! The execution time is 0.18237 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML DC-DUB-Site-ID-2-E1-f7.pepXML Done! The execution time is 0.18897 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML DC-DUB-Site-ID-2-E2-f4.pepXML Done! The execution time is 0.07557 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML DC-DUB-Site-ID-2-E1-f5.pepXML Done! The execution time is 0.16607 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML DC-DUB-Site-ID-2-E1-f8.pepXML Done! The execution time is 0.69525 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML DC-DUB-Site-ID-2-E2-f3.pepXML Done! The execution time is 0.06227 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML DC-DUB-Site-ID-2-E2-f7.pepXML Done! The execution time is 0.10233 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML DC-DUB-Site-ID-2-E1-f4.pepXML Done! The execution time is 0.16420 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML DC-DUB-Site-ID-2-E2-f1.pepXML Done! The execution time is 0.18342 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML DC-DUB-Site-ID-2-E2-f8.pepXML Done! The execution time is 0.11250 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-10-DC-DUB-Site-ID-2-E2-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML DC-DUB-Site-ID-2-E2-f2.pepXML Done! The execution time is 0.13928 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-11-DC-DUB-Site-ID-2-E1-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML DC-DUB-Site-ID-2-E1-f3.pepXML Done! The execution time is 0.15313 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-12-DC-DUB-Site-ID-2-E1-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML DC-DUB-Site-ID-2-E1-f2.pepXML Done! The execution time is 0.17087 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-13-DC-DUB-Site-ID-2-E2-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML DC-DUB-Site-ID-2-E2-f6.pepXML Done! The execution time is 0.15858 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-14-DC-DUB-Site-ID-2-E1-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML DC-DUB-Site-ID-2-E1-f6.pepXML Done! The execution time is 0.19688 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-15-DC-DUB-Site-ID-2-E2-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML Process 'Crystal-C' finished, exit code: 0 DC-DUB-Site-ID-2-E2-f5.pepXML Done! The execution time is 0.14148 min. PeptideProphet [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas --combine DC-DUB-Site-ID-2-E1-f1_c.pepXML DC-DUB-Site-ID-2-E1-f7_c.pepXML DC-DUB-Site-ID-2-E2-f4_c.pepXML DC-DUB-Site-ID-2-E1-f5_c.pepXML DC-DUB-Site-ID-2-E1-f8_c.pepXML DC-DUB-Site-ID-2-E2-f3_c.pepXML DC-DUB-Site-ID-2-E2-f7_c.pepXML DC-DUB-Site-ID-2-E1-f4_c.pepXML DC-DUB-Site-ID-2-E2-f1_c.pepXML DC-DUB-Site-ID-2-E2-f8_c.pepXML DC-DUB-Site-ID-2-E2-f2_c.pepXML DC-DUB-Site-ID-2-E1-f3_c.pepXML DC-DUB-Site-ID-2-E1-f2_c.pepXML DC-DUB-Site-ID-2-E2-f6_c.pepXML DC-DUB-Site-ID-2-E1-f6_c.pepXML DC-DUB-Site-ID-2-E2-f5_c.pepXML INFO[11:39:17] Executing PeptideProphet v3.3.11
WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f1.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f1.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f1.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f1.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f7.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f7.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f7.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f7.mzXML in msms_run_summary tag... file 1: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1_c.pepXML file 2: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f4.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f4.mzXML in msms_run_summary tag... file 3: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f5.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f5.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f5.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f5.mzXML in msms_run_summary tag... file 4: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f8.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f8.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f8.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f8.mzXML in msms_run_summary tag... file 5: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f3.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f3.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f3.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f3.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f7.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f7.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f7.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f7.mzXML in msms_run_summary tag... file 6: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3_c.pepXML file 7: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f4.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f4.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f4.mzXML in msms_run_summary tag... file 8: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f1.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f1.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f1.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f1.mzXML in msms_run_summary tag... file 9: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f8.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f8.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f8.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f8.mzXML in msms_run_summary tag... file 10: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f2.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f2.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f2.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f2.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f3.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f3.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f3.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f3.mzXML in msms_run_summary tag... file 11: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2_c.pepXML file 12: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f2.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f2.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f2.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f2.mzXML in msms_run_summary tag... file 13: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f6.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f6.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f6.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f6.mzXML in msms_run_summary tag... file 14: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f6.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f6.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f6.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E1-f6.mzXML in msms_run_summary tag... file 15: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6_c.pepXML WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f5.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f5.mzXML in msms_run_summary tag... WARNING: cannot open data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f5.mzML in msms_run_summary tag... trying .mzXML ... WARNING: CANNOT correct data file D:\DanC\DUB10-Site-ID-2\MSFragger-analysis/DC-DUB-Site-ID-2-E2-f5.mzXML in msms_run_summary tag... file 16: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5_c.pepXML processed altogether 102231 results INFO: Results written to file: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml

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 stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 48711 2+, 32566 3+, 13156 4+, 5519 5+, 1978 6+, and 301 7+ spectra. Found 49236 Decoys, and 52995 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 (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 (7+). model complete after 26 iterations Process 'PeptideProphet' finished, exit code: 0 INFO[11:40:41] Done
Rewrite pepxml [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp C:\Users\dconole\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML Fixing pepxml: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml Writing output to: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml16396264751672859388.temp-rewrite Deleting file: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml Moving rewritten file to original location: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml16396264751672859388.temp-rewrite] -> [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\DanC\2020-10-19-decoys-Human proteome_2003219606.fasta.fas --prefix rev INFO[11:40:43] Executing Database v3.3.11
INFO[11:40:43] Processing database
Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[11:40:44] Done
PhilosopherFilter [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev_ --pepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis INFO[11:40:45] Executing Filter v3.3.11
INFO[11:40:45] Processing peptide identification files
INFO[11:40:45] 1+ Charge profile decoy=0 target=0 INFO[11:40:45] 2+ Charge profile decoy=0 target=0 INFO[11:40:45] 3+ Charge profile decoy=0 target=0 INFO[11:40:45] 4+ Charge profile decoy=0 target=0 INFO[11:40:45] 5+ Charge profile decoy=0 target=0 INFO[11:40:45] 6+ Charge profile decoy=28 target=174 INFO[11:40:45] Database search results ions=59 peptides=58 psms=202 INFO[11:40:45] Converged to 0.78 % FDR with 127 PSMs decoy=1 threshold=0.4063 total=128 INFO[11:40:45] Converged to 0.00 % FDR with 7 Peptides decoy=0 threshold=0.4153 total=7 INFO[11:40:45] Converged to 0.00 % FDR with 8 Ions decoy=0 threshold=0.4153 total=8 INFO[11:40:45] Post processing identifications
INFO[11:40:45] Mapping modifications
Process 'PhilosopherFilter' finished, exit code: 0 INFO[11:40:45] Assigning protein identifications to layers
INFO[11:40:45] Updating razor PSM assignment to proteins
INFO[11:40:45] Calculating spectral counts
INFO[11:40:45] Saving
INFO[11:40:45] Done
FreeQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected INFO[11:40:45] Executing Label-free quantification v3.3.11 INFO[11:40:45] Indexing PSM information
INFO[11:40:45] Reading spectra and tracing peaks
INFO[11:40:45] Processing DC-DUB-Site-ID-2-E1-f6
INFO[11:41:35] Processing DC-DUB-Site-ID-2-E1-f7
INFO[11:42:34] Processing DC-DUB-Site-ID-2-E1-f8
INFO[11:44:16] Processing DC-DUB-Site-ID-2-E2-f5
INFO[11:45:01] Processing DC-DUB-Site-ID-2-E2-f7
INFO[11:46:06] Processing DC-DUB-Site-ID-2-E2-f8
Process 'FreeQuant' finished, exit code: 0 LabelQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 6 --annot D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\annotation.txt --brand tmt --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected INFO[11:47:19] Assigning intensities to data layers
INFO[11:47:19] Done
INFO[11:47:19] Executing Isobaric-label quantification v3.3.11 INFO[11:47:19] Calculating intensities and ion interference INFO[11:47:19] Processing DC-DUB-Site-ID-2-E1-f6
INFO[11:48:14] Processing DC-DUB-Site-ID-2-E1-f7
INFO[11:49:10] Processing DC-DUB-Site-ID-2-E1-f8
INFO[11:50:20] Processing DC-DUB-Site-ID-2-E2-f5
INFO[11:51:09] Processing DC-DUB-Site-ID-2-E2-f7
INFO[11:52:03] Processing DC-DUB-Site-ID-2-E2-f8
INFO[11:53:03] Filtering spectra for label quantification
INFO[11:53:03] Removing 0 PSMs from isobaric quantification INFO[11:53:03] Calculating normalized protein levels
INFO[11:53:03] Saving
INFO[11:53:03] Done
Process 'LabelQuant' finished, exit code: 0 PhilosopherReport [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report INFO[11:53:04] Executing Report v3.3.11
INFO[11:53:04] Creating reports
panic: runtime error: index out of range [10] with length 8

goroutine 1 [running]: philosopher/lib/rep.Evidence.MetaIonReport(0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...) /workspace/philosopher/lib/rep/ion.go:193 +0x3797 philosopher/lib/rep.Run(0xc00001a870, 0x24, 0xc00001a8a0, 0x2a, 0xc0000224b0, 0x48, 0xc00001e380, 0x39, 0xc00001a8d0, 0x30, ...) /workspace/philosopher/lib/rep/rep.go:435 +0x331 philosopher/cmd.glob..func16(0x7b9e4e0, 0x7bc5308, 0x0, 0x0) /workspace/philosopher/cmd/report.go:25 +0xb2 github.com/spf13/cobra.(Command).execute(0x7b9e4e0, 0x7bc5308, 0x0, 0x0, 0x7b9e4e0, 0x7bc5308) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:844 +0x2b1 github.com/spf13/cobra.(Command).ExecuteC(0x7b9e780, 0x0, 0x0, 0x0) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:945 +0x31e github.com/spf13/cobra.(*Command).Execute(...) /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:885 philosopher/cmd.Execute() /workspace/philosopher/cmd/root.go:35 +0x34 main.main() /workspace/philosopher/main.go:22 +0x75 Process 'PhilosopherReport' finished, exit code: 2 Process returned non-zero exit code, stoppingTmtIntegrator [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp "C:\Users\dconole\Desktop\fragpipe\tools\tmt-integrator-2.1.5.jar" TMTIntegrator D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\tmt-integrator-conf.yml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\psm.tsv


Cancelling 3 remaining tasks
Processing interrupted, stopping TmtIntegrator
----------------------
## If you're submitting a bug report, please attach log file

The log file can be saved from FragPipe:

- by clicking the `Export Log` button on the `Run` tab.
- or just copy text from the output console on `Run` tab to a text file.
fcyu commented 4 years ago

Hi @hayse1 ,

Is this the same issue you had before? It is also TMT 6 plex.

Best,

Fengchao

prvst commented 4 years ago

I would take another look at the data or the parameters ...

INFO[11:40:45] 1+ Charge profile decoy=0 target=0
INFO[11:40:45] 2+ Charge profile decoy=0 target=0
INFO[11:40:45] 3+ Charge profile decoy=0 target=0
INFO[11:40:45] 4+ Charge profile decoy=0 target=0
INFO[11:40:45] 5+ Charge profile decoy=0 target=0
INFO[11:40:45] 6+ Charge profile decoy=28 target=174
INFO[11:40:45] Database search results ions=59 peptides=58 psms=202
INFO[11:40:45] Converged to 0.78 % FDR with 127 PSMs decoy=1 threshold=0.4063 total=128
INFO[11:40:45] Converged to 0.00 % FDR with 7 Peptides decoy=0 threshold=0.4153 total=7
INFO[11:40:45] Converged to 0.00 % FDR with 8 Ions decoy=0 threshold=0.4153 total=8
anesvi commented 4 years ago

Hi Daniel,

I see you are running an unususual workflow.

First, if you are using narrow precursor tolerance, you do not need Crystal-C Second, I see the following modifications in your main search:

variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1

There is no TMT modification. Assuming this is TMT lkabeled, you need to specify TMT modifications.

So I think you need to tell us about more about your data.

I suggest you load one if the TMT workflows (e.g. TMT10 or TMT10-MS3 if quant from MS3; I suggest you change TMT on n-term from variable to fixed, and also uncheck over labeling on S). Then add your two cysteine modifications.

Best Alexey

From: DanielConole notifications@github.com Sent: Tuesday, October 20, 2020 7:16 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

External Email - Use Caution

Hi there Alexey and team,

I tried to run a site-ID and TMT quant analysis on some files, which went well up until the TMT integrator part. Not sure what went wrong here - can you help?

Log is as below:

System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.3.11 (build 1601497354)

LCMS files: Experiment/Group:

45 commands to execute: WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-10-DC-DUB-Site-ID-2-E2-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-11-DC-DUB-Site-ID-2-E1-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-12-DC-DUB-Site-ID-2-E1-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-13-DC-DUB-Site-ID-2-E2-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-14-DC-DUB-Site-ID-2-E1-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-15-DC-DUB-Site-ID-2-E2-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML PeptideProphet [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas --combine DC-DUB-Site-ID-2-E1-f1_c.pepXML DC-DUB-Site-ID-2-E1-f7_c.pepXML DC-DUB-Site-ID-2-E2-f4_c.pepXML DC-DUB-Site-ID-2-E1-f5_c.pepXML DC-DUB-Site-ID-2-E1-f8_c.pepXML DC-DUB-Site-ID-2-E2-f3_c.pepXML DC-DUB-Site-ID-2-E2-f7_c.pepXML DC-DUB-Site-ID-2-E1-f4_c.pepXML DC-DUB-Site-ID-2-E2-f1_c.pepXML DC-DUB-Site-ID-2-E2-f8_c.pepXML DC-DUB-Site-ID-2-E2-f2_c.pepXML DC-DUB-Site-ID-2-E1-f3_c.pepXML DC-DUB-Site-ID-2-E1-f2_c.pepXML DC-DUB-Site-ID-2-E2-f6_c.pepXML DC-DUB-Site-ID-2-E1-f6_c.pepXML DC-DUB-Site-ID-2-E2-f5_c.pepXML Rewrite pepxml [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp C:\Users\dconole\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML PhilosopherDbAnnotate [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\DanC\2020-10-19-decoys-Human proteome_2003219606.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev_ --pepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis FreeQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected LabelQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 6 --annot D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\annotation.txt --brand tmt --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected PhilosopherReport [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp "C:\Users\dconole\Desktop\fragpipe\tools\tmt-integrator-2.1.5.jar" TMTIntegrator D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\tmt-integrator-conf.yml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\psm.tsv WorkspaceClean [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -cp "C:\Users\dconole\Desktop\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\shepherd.config"

Execution order:

Cmd: [START], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceCleanInit], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [MsFragger], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [Crystal-C], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PeptideProphet], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherDbAnnotate], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherFilter], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [FreeQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [LabelQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherReport], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [TmtIntegrator], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceClean], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PTMShepherd], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

FragPipe v14.0ui state cache

crystalc.run-crystalc=true

database.db-path=D\:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas

database.decoy-tag=rev_

fragpipe-config.bin-msfragger=C\:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar

fragpipe-config.bin-philosopher=C\:\Users\dconole\Desktop\fragpipe\lib\..\tools\philosopher\philosopher.exe

fragpipe-config.bin-python=C\:\Users\dconole\Anaconda3\python.exe

freequant.mz-tol=10

freequant.rt-tol=0.4

freequant.run-freequant=false

ionquant.excludemods=

ionquant.heavy=

ionquant.imtol=0.05

ionquant.ionfdr=0.01

ionquant.light=

ionquant.mbr=0

ionquant.mbrimtol=0.05

ionquant.mbrmincorr=0

ionquant.mbrrttol=1

ionquant.mbrtoprun=10

ionquant.medium=

ionquant.minexps=1

ionquant.minfreq=0.5

ionquant.minions=2

ionquant.minisotopes=2

ionquant.mztol=10

ionquant.normalization=1

ionquant.peptidefdr=1

ionquant.proteinfdr=1

ionquant.proteinquant=2

ionquant.requantify=1

ionquant.rttol=0.4

ionquant.run-ionquant=true

ionquant.tp=3

ionquant.writeindex=0

msfragger.Y_type_masses=

msfragger.add_topN_complementary=0

msfragger.allow_multiple_variable_mods_on_residue=true

msfragger.allowed_missed_cleavage=2

msfragger.calibrate_mass=2

msfragger.clip_nTerm_M=true

msfragger.deisotope=1

msfragger.delta_mass_exclude_ranges=(-1.5,3.5)

msfragger.diagnostic_fragments=

msfragger.diagnostic_intensity_filter=0

msfragger.digest_max_length=50

msfragger.digest_min_length=7

msfragger.fragment_ion_series=b,y

msfragger.fragment_mass_tolerance=20

msfragger.fragment_mass_units=1

msfragger.intensity_transform=0

msfragger.ion_series_definitions=

msfragger.isotope_error=0/1/2

msfragger.labile_search_mode=off

msfragger.localize_delta_mass=false

msfragger.mass_diff_to_variable_mod=0

msfragger.mass_offsets=0

msfragger.max_fragment_charge=2

msfragger.max_variable_mods_combinations=5000

msfragger.max_variable_mods_per_peptide=3

msfragger.min_fragments_modelling=2

msfragger.min_matched_fragments=4

msfragger.minimum_peaks=15

msfragger.minimum_ratio=0.01

msfragger.misc.fragger.clear-mz-hi=0

msfragger.misc.fragger.clear-mz-lo=0

msfragger.misc.fragger.digest-mass-hi=5000

msfragger.misc.fragger.digest-mass-lo=500

msfragger.misc.fragger.enzyme-dropdown=stricttrypsin

msfragger.misc.fragger.precursor-charge-hi=4

msfragger.misc.fragger.precursor-charge-lo=1

msfragger.misc.fragger.remove-precursor-range-hi=1.5

msfragger.misc.fragger.remove-precursor-range-lo=-1.5

msfragger.misc.slice-db=1

msfragger.num_enzyme_termini=2

msfragger.output_format=pepXML

msfragger.output_max_expect=50

msfragger.output_report_topN=1

msfragger.override_charge=false

msfragger.precursor_mass_lower=-20

msfragger.precursor_mass_mode=selected

msfragger.precursor_mass_units=1

msfragger.precursor_mass_upper=20

msfragger.precursor_true_tolerance=20

msfragger.precursor_true_units=1

msfragger.remove_precursor_peak=0

msfragger.report_alternative_proteins=false

msfragger.restrict_deltamass_to=all

msfragger.run-msfragger=true

msfragger.search_enzyme_butnotafter=

msfragger.search_enzyme_cutafter=KR

msfragger.search_enzyme_name=stricttrypsin

msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1

msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 254.105500,C,true,1; 304.088100,C,true,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1

msfragger.track_zero_topN=0

msfragger.use_topN_peaks=150

msfragger.write_calibrated_mgf=false

msfragger.zero_bin_accept_expect=0

msfragger.zero_bin_mult_expect=1

peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2

peptide-prophet.combine-pepxml=true

peptide-prophet.run-peptide-prophet=true

phi-report.dont-use-prot-proph-file=false

phi-report.filter=--sequential --razor --prot 0.01

phi-report.pep-level-summary=false

phi-report.print-decoys=false

phi-report.run-report=true

protein-prophet.cmd-opts=--maxppmdiff 2000000

protein-prophet.run-protein-prophet=false

ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5

ptmprophet.run-ptmprophet=false

ptmshepherd.annotation-common=false

ptmshepherd.annotation-custom=false

ptmshepherd.annotation-unimod=true

ptmshepherd.annotation_file=

ptmshepherd.annotation_tol=0.01

ptmshepherd.cap_y_ions=

ptmshepherd.diag_ions=

ptmshepherd.glyco_mode=false

ptmshepherd.histo_smoothbins=2

ptmshepherd.iontype_a=false

ptmshepherd.iontype_b=true

ptmshepherd.iontype_c=false

ptmshepherd.iontype_x=false

ptmshepherd.iontype_y=true

ptmshepherd.iontype_z=false

ptmshepherd.localization_background=4

ptmshepherd.output_extended=false

ptmshepherd.peakpicking_mass_units=0

ptmshepherd.peakpicking_promRatio=0.3

ptmshepherd.peakpicking_width=0.002

ptmshepherd.precursor_mass_units=0

ptmshepherd.precursor_tol=0.01

ptmshepherd.remainder_masses=

ptmshepherd.run-shepherd=true

ptmshepherd.spectra_maxfragcharge=2

ptmshepherd.varmod_masses=P13_Probe\:254.1055, P14_Probe\:304.0881

quantitation.run-label-free-quant=false

speclibgen.easypqp.extras.rt_lowess_fraction=0.04

speclibgen.easypqp.rt-cal=noiRT

speclibgen.easypqp.select-file.text=

speclibgen.run-speclibgen=false

speclibgen.use-easypqp=false

speclibgen.use-spectrast=true

tmtintegrator.add_Ref=1

tmtintegrator.allow_overlabel=true

tmtintegrator.allow_unlabeled=false

tmtintegrator.best_psm=true

tmtintegrator.channel_num=6

tmtintegrator.dont-run-fq-lq=false

tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated

tmtintegrator.groupby=-1

tmtintegrator.labelquant=--tol 20 --level 2

tmtintegrator.max_pep_prob_thres=0

tmtintegrator.min_ntt=0

tmtintegrator.min_pep_prob=0.9

tmtintegrator.min_percent=0.05

tmtintegrator.min_purity=0.5

tmtintegrator.min_site_prob=-1

tmtintegrator.mod_tag=none

tmtintegrator.ms1_int=true

tmtintegrator.outlier_removal=true

tmtintegrator.print_RefInt=false

tmtintegrator.prot_exclude=none

tmtintegrator.prot_norm=0

tmtintegrator.psm_norm=false

tmtintegrator.ref_tag=pool

tmtintegrator.run-tmtintegrator=true

tmtintegrator.top3_pep=true

tmtintegrator.unique_gene=0

tmtintegrator.unique_pep=false

workdir=D\:\DanC\DUB10-Site-ID-2\MSFragger-analysis

workflow.input.data-type.im-ms=false

workflow.input.data-type.regular-ms=true

workflow.process-exps-separately=true

workflow.ram=0

workflow.threads=11

WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Removing workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Creating workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML... Checking if the data is low resolution MS/MS... The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance. FIRST SEARCH* Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 300.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 1.50 Da. 318866252 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.62 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 8.6 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s | postprocessing 0.0 s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 7.4 s [progress: 19683/19683 (100%) - 41790 spectra/s] 0.5s | postprocessing 0.1 s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 56268 spectra/s] 0.4s | postprocessing 0.0 s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 6.8 s [progress: 26296/26296 (100%) - 59092 spectra/s] 0.4s | postprocessing 0.0 s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 2.1 s [progress: 32846/32846 (100%) - 47329 spectra/s] 0.7s | postprocessing 0.0 s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.9 s [progress: 30776/30776 (100%) - 46986 spectra/s] 0.7s | postprocessing 0.0 s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.2 s [progress: 27057/27057 (100%) - 49555 spectra/s] 0.5s | postprocessing 0.0 s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.8 s [progress: 9932/9932 (100%) - 29126 spectra/s] 0.3s | postprocessing 0.0 s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.6 s [progress: 16370/16370 (100%) - 49757 spectra/s] 0.3s | postprocessing 0.0 s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32661 spectra/s] 0.1s | postprocessing 0.0 s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.2 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.0 s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.5 s [progress: 14725/14725 (100%) - 67237 spectra/s] 0.2s | postprocessing 0.0 s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.6 s [progress: 21089/21089 (100%) - 59406 spectra/s] 0.4s | postprocessing 0.0 s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.7 s [progress: 23608/23608 (100%) - 42614 spectra/s] 0.6s | postprocessing 0.0 s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.3 s [progress: 24250/24250 (100%) - 45158 spectra/s] 0.5s | postprocessing 0.0 s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.8 s [progress: 24907/24907 (100%) - 44319 spectra/s] 0.6s | postprocessing 0.0 s *FIRST SEARCH DONE IN 5.929 MIN
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 Not enough data to perform mass calibration. Using the uncalibrated data.
002 Not enough data to perform mass calibration. Using the uncalibrated data.
003 Not enough data to perform mass calibration. Using the uncalibrated data.
004 Not enough data to perform mass calibration. Using the uncalibrated data.
005 Not enough data to perform mass calibration. Using the uncalibrated data.
006 Not enough data to perform mass calibration. Using the uncalibrated data.
007 Not enough data to perform mass calibration. Using the uncalibrated data.
008 Not enough data to perform mass calibration. Using the uncalibrated data.
009 Not enough data to perform mass calibration. Using the uncalibrated data.
010 Not enough data to perform mass calibration. Using the uncalibrated data.
011 Not enough data to perform mass calibration. Using the uncalibrated data.
012 Not enough data to perform mass calibration. Using the uncalibrated data.
013 Not enough data to perform mass calibration. Using the uncalibrated data.
014 Not enough data to perform mass calibration. Using the uncalibrated data.
015 Not enough data to perform mass calibration. Using the uncalibrated data.
016 Not enough data to perform mass calibration. Using the uncalibrated data.
----- --------------- --------------- --------------- ---------------

Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2

150

200

250

300

350

400

Count

179

121

skip rest

Peaks

500_0

300_0

200_0

175_0

150_1

125_1

Count

170

175

176

176

179

178

Int.

1

Count

165

Rm P.

1

Count

165

New fragment_mass_tolerance = 150 PPM

New use_topN_peaks = 150

New minimum_ratio = 0.010000

New intensity_transform = 0

New remove_precursor_peak = 0

***MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 32.737 MIN

MAIN SEARCH Checking database... Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 150.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = true max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.75 Da. 1065135314 fragments to be searched in 2 slices (15.87 GB total) Operating on slice 1 of 2: Fragment index slice generated in 4.89 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 1.3 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 8.1 s [progress: 19683/19683 (100%) - 38219 spectra/s] 0.5s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 64981 spectra/s] 0.3s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 7.1 s [progress: 26296/26296 (100%) - 50183 spectra/s] 0.5s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 6.9 s [progress: 32846/32846 (100%) - 45683 spectra/s] 0.7s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 41366 spectra/s] 0.7s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.6 s [progress: 27057/27057 (100%) - 43291 spectra/s] 0.6s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.1 s [progress: 9932/9932 (100%) - 23369 spectra/s] 0.4s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.7 s [progress: 16370/16370 (100%) - 37981 spectra/s] 0.4s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32963 spectra/s] 0.1s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.1 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.6 s [progress: 14725/14725 (100%) - 65737 spectra/s] 0.2s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.4 s [progress: 21089/21089 (100%) - 48817 spectra/s] 0.4s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.1 s [progress: 23608/23608 (100%) - 39021 spectra/s] 0.6s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.0 s [progress: 24250/24250 (100%) - 39176 spectra/s] 0.6s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.7 s [progress: 24907/24907 (100%) - 39788 spectra/s] 0.6s Operating on slice 2 of 2: Fragment index slice generated in 4.11 s
  17. DC-DUB-Site-ID-2-E1-f1.mzML 8.4 s [progress: 1070/1070 (100%) - 9554 spectra/s] 0.1s | postprocessing 1.4 s
  18. DC-DUB-Site-ID-2-E1-f2.mzML 7.1 s [progress: 19683/19683 (100%) - 94177 spectra/s] 0.2s | postprocessing 1.7 s
  19. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 93259 spectra/s] 0.2s | postprocessing 1.4 s
  20. DC-DUB-Site-ID-2-E1-f4.mzML 6.7 s [progress: 26296/26296 (100%) - 120073 spectra/s] 0.2s | postprocessing 1.5 s
  21. DC-DUB-Site-ID-2-E1-f5.mzML 7.4 s [progress: 32846/32846 (100%) - 99233 spectra/s] 0.3s | postprocessing 1.7 s
  22. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 93544 spectra/s] 0.3s | postprocessing 1.8 s
  23. DC-DUB-Site-ID-2-E1-f7.mzML 8.7 s [progress: 27057/27057 (100%) - 87000 spectra/s] 0.3s | postprocessing 1.8 s
  24. DC-DUB-Site-ID-2-E1-f8.mzML 38.2 s [progress: 9932/9932 (100%) - 29385 spectra/s] 0.3s | postprocessing 1.9 s
  25. DC-DUB-Site-ID-2-E2-f1.mzML 8.8 s [progress: 16370/16370 (100%) - 73739 spectra/s] 0.2s | postprocessing 1.6 s
  26. DC-DUB-Site-ID-2-E2-f2.mzML 7.3 s [progress: 3560/3560 (100%) - 31504 spectra/s] 0.1s | postprocessing 1.1 s
  27. DC-DUB-Site-ID-2-E2-f3.mzML 5.3 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.9 s
  28. DC-DUB-Site-ID-2-E2-f4.mzML 5.3 s [progress: 14725/14725 (100%) - 136343 spectra/s] 0.1s | postprocessing 1.2 s
  29. DC-DUB-Site-ID-2-E2-f5.mzML 6.7 s [progress: 21089/21089 (100%) - 94147 spectra/s] 0.2s | postprocessing 1.5 s
  30. DC-DUB-Site-ID-2-E2-f6.mzML 7.5 s [progress: 23608/23608 (100%) - 102643 spectra/s] 0.2s | postprocessing 1.5 s
  31. DC-DUB-Site-ID-2-E2-f7.mzML 17.5 s [progress: 24250/24250 (100%) - 70906 spectra/s] 0.3s | postprocessing 1.7 s
  32. DC-DUB-Site-ID-2-E2-f8.mzML 19.1 s [progress: 24907/24907 (100%) - 76402 spectra/s] 0.3s | postprocessing 1.9 s MAIN SEARCH DONE IN 6.276 MIN

TOTAL TIME 44.943 MIN* Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML DC-DUB-Site-ID-2-E1-f1.pepXML Done! The execution time is 0.18237 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML DC-DUB-Site-ID-2-E1-f7.pepXML Done! The execution time is 0.18897 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML DC-DUB-Site-ID-2-E2-f4.pepXML Done! The execution time is 0.07557 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML DC-DUB-Site-ID-2-E1-f5.pepXML Done! The execution time is 0.16607 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML DC-DUB-Site-ID-2-E1-f8.pepXML Done! The execution time is 0.69525 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML DC-DUB-Site-ID-2-E2-f3.pepXML Done! The execution time is 0.06227 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML DC-DUB-Site-ID-2-E2-f7.pepXML Done! The execution time is 0.10233 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML DC-DUB-Site-ID-2-E1-f4.pepXML Done! The execution time is 0.16420 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML DC-DUB-Site-ID-2-E2-f1.pepXML Done! The execution time is 0.18342 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML DC-DUB-Site-ID-2-E2-f8.pepXML Done! The execution time is 0.11250 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\D

DanielConole commented 4 years ago

Thanks Alexey – this makes sense. I accidently replaced the TMT variable mods with my own ones (stupid!).

I have made all the suggested changes and resubmitted – let’s see how this goes.

It’s a Site ID experiment for chemical probe modified peptides, and yes it is TMT labelled to quantify greater labelling with increasing concentrations of the probe. So I need both modifications as you recommend.

I selected a tight tolerance window to try and accurately compare the data with that generated from MaxQuant, but I will stick with the default parameters for now.

Thanks, Dan

From: Alexey Nesvizhskii notifications@github.com Sent: 20 October 2020 14:55 To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Conole, Daniel P T d.conole@imperial.ac.uk; Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

This email from notifications@github.commailto:notifications@github.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Hi Daniel,

I see you are running an unususual workflow.

First, if you are using narrow precursor tolerance, you do not need Crystal-C Second, I see the following modifications in your main search:

variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1

There is no TMT modification. Assuming this is TMT lkabeled, you need to specify TMT modifications.

So I think you need to tell us about more about your data.

I suggest you load one if the TMT workflows (e.g. TMT10 or TMT10-MS3 if quant from MS3; I suggest you change TMT on n-term from variable to fixed, and also uncheck over labeling on S). Then add your two cysteine modifications.

Best Alexey

From: DanielConole notifications@github.com<mailto:notifications@github.com> Sent: Tuesday, October 20, 2020 7:16 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

External Email - Use Caution

Hi there Alexey and team,

I tried to run a site-ID and TMT quant analysis on some files, which went well up until the TMT integrator part. Not sure what went wrong here - can you help?

Log is as below:

System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.3.11 (build 1601497354)

LCMS files: Experiment/Group:

45 commands to execute: WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-10-DC-DUB-Site-ID-2-E2-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-11-DC-DUB-Site-ID-2-E1-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-12-DC-DUB-Site-ID-2-E1-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-13-DC-DUB-Site-ID-2-E2-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-14-DC-DUB-Site-ID-2-E1-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-15-DC-DUB-Site-ID-2-E2-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML PeptideProphet [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas --combine DC-DUB-Site-ID-2-E1-f1_c.pepXML DC-DUB-Site-ID-2-E1-f7_c.pepXML DC-DUB-Site-ID-2-E2-f4_c.pepXML DC-DUB-Site-ID-2-E1-f5_c.pepXML DC-DUB-Site-ID-2-E1-f8_c.pepXML DC-DUB-Site-ID-2-E2-f3_c.pepXML DC-DUB-Site-ID-2-E2-f7_c.pepXML DC-DUB-Site-ID-2-E1-f4_c.pepXML DC-DUB-Site-ID-2-E2-f1_c.pepXML DC-DUB-Site-ID-2-E2-f8_c.pepXML DC-DUB-Site-ID-2-E2-f2_c.pepXML DC-DUB-Site-ID-2-E1-f3_c.pepXML DC-DUB-Site-ID-2-E1-f2_c.pepXML DC-DUB-Site-ID-2-E2-f6_c.pepXML DC-DUB-Site-ID-2-E1-f6_c.pepXML DC-DUB-Site-ID-2-E2-f5_c.pepXML Rewrite pepxml [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp C:\Users\dconole\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML PhilosopherDbAnnotate [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\DanC\2020-10-19-decoys-Human proteome_2003219606.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev_ --pepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis FreeQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected LabelQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 6 --annot D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\annotation.txt --brand tmt --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected PhilosopherReport [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp "C:\Users\dconole\Desktop\fragpipe\tools\tmt-integrator-2.1.5.jar" TMTIntegrator D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\tmt-integrator-conf.yml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\psm.tsv WorkspaceClean [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -cp "C:\Users\dconole\Desktop\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\shepherd.config"

Execution order:

Cmd: [START], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceCleanInit], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [MsFragger], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [Crystal-C], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PeptideProphet], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherDbAnnotate], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherFilter], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [FreeQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [LabelQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherReport], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [TmtIntegrator], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceClean], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PTMShepherd], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

FragPipe v14.0ui state cache

crystalc.run-crystalc=true

database.db-path=D\:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas

database.decoy-tag=rev_

fragpipe-config.bin-msfragger=C\:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar

fragpipe-config.bin-philosopher=C\:\Users\dconole\Desktop\fragpipe\lib\..\tools\philosopher\philosopher.exe

fragpipe-config.bin-python=C\:\Users\dconole\Anaconda3\python.exe

freequant.mz-tol=10

freequant.rt-tol=0.4

freequant.run-freequant=false

ionquant.excludemods=

ionquant.heavy=

ionquant.imtol=0.05

ionquant.ionfdr=0.01

ionquant.light=

ionquant.mbr=0

ionquant.mbrimtol=0.05

ionquant.mbrmincorr=0

ionquant.mbrrttol=1

ionquant.mbrtoprun=10

ionquant.medium=

ionquant.minexps=1

ionquant.minfreq=0.5

ionquant.minions=2

ionquant.minisotopes=2

ionquant.mztol=10

ionquant.normalization=1

ionquant.peptidefdr=1

ionquant.proteinfdr=1

ionquant.proteinquant=2

ionquant.requantify=1

ionquant.rttol=0.4

ionquant.run-ionquant=true

ionquant.tp=3

ionquant.writeindex=0

msfragger.Y_type_masses=

msfragger.add_topN_complementary=0

msfragger.allow_multiple_variable_mods_on_residue=true

msfragger.allowed_missed_cleavage=2

msfragger.calibrate_mass=2

msfragger.clip_nTerm_M=true

msfragger.deisotope=1

msfragger.delta_mass_exclude_ranges=(-1.5,3.5)

msfragger.diagnostic_fragments=

msfragger.diagnostic_intensity_filter=0

msfragger.digest_max_length=50

msfragger.digest_min_length=7

msfragger.fragment_ion_series=b,y

msfragger.fragment_mass_tolerance=20

msfragger.fragment_mass_units=1

msfragger.intensity_transform=0

msfragger.ion_series_definitions=

msfragger.isotope_error=0/1/2

msfragger.labile_search_mode=off

msfragger.localize_delta_mass=false

msfragger.mass_diff_to_variable_mod=0

msfragger.mass_offsets=0

msfragger.max_fragment_charge=2

msfragger.max_variable_mods_combinations=5000

msfragger.max_variable_mods_per_peptide=3

msfragger.min_fragments_modelling=2

msfragger.min_matched_fragments=4

msfragger.minimum_peaks=15

msfragger.minimum_ratio=0.01

msfragger.misc.fragger.clear-mz-hi=0

msfragger.misc.fragger.clear-mz-lo=0

msfragger.misc.fragger.digest-mass-hi=5000

msfragger.misc.fragger.digest-mass-lo=500

msfragger.misc.fragger.enzyme-dropdown=stricttrypsin

msfragger.misc.fragger.precursor-charge-hi=4

msfragger.misc.fragger.precursor-charge-lo=1

msfragger.misc.fragger.remove-precursor-range-hi=1.5

msfragger.misc.fragger.remove-precursor-range-lo=-1.5

msfragger.misc.slice-db=1

msfragger.num_enzyme_termini=2

msfragger.output_format=pepXML

msfragger.output_max_expect=50

msfragger.output_report_topN=1

msfragger.override_charge=false

msfragger.precursor_mass_lower=-20

msfragger.precursor_mass_mode=selected

msfragger.precursor_mass_units=1

msfragger.precursor_mass_upper=20

msfragger.precursor_true_tolerance=20

msfragger.precursor_true_units=1

msfragger.remove_precursor_peak=0

msfragger.report_alternative_proteins=false

msfragger.restrict_deltamass_to=all

msfragger.run-msfragger=true

msfragger.search_enzyme_butnotafter=

msfragger.search_enzyme_cutafter=KR

msfragger.search_enzyme_name=stricttrypsin

msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1

msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 254.105500,C,true,1; 304.088100,C,true,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1

msfragger.track_zero_topN=0

msfragger.use_topN_peaks=150

msfragger.write_calibrated_mgf=false

msfragger.zero_bin_accept_expect=0

msfragger.zero_bin_mult_expect=1

peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2

peptide-prophet.combine-pepxml=true

peptide-prophet.run-peptide-prophet=true

phi-report.dont-use-prot-proph-file=false

phi-report.filter=--sequential --razor --prot 0.01

phi-report.pep-level-summary=false

phi-report.print-decoys=false

phi-report.run-report=true

protein-prophet.cmd-opts=--maxppmdiff 2000000

protein-prophet.run-protein-prophet=false

ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5

ptmprophet.run-ptmprophet=false

ptmshepherd.annotation-common=false

ptmshepherd.annotation-custom=false

ptmshepherd.annotation-unimod=true

ptmshepherd.annotation_file=

ptmshepherd.annotation_tol=0.01

ptmshepherd.cap_y_ions=

ptmshepherd.diag_ions=

ptmshepherd.glyco_mode=false

ptmshepherd.histo_smoothbins=2

ptmshepherd.iontype_a=false

ptmshepherd.iontype_b=true

ptmshepherd.iontype_c=false

ptmshepherd.iontype_x=false

ptmshepherd.iontype_y=true

ptmshepherd.iontype_z=false

ptmshepherd.localization_background=4

ptmshepherd.output_extended=false

ptmshepherd.peakpicking_mass_units=0

ptmshepherd.peakpicking_promRatio=0.3

ptmshepherd.peakpicking_width=0.002

ptmshepherd.precursor_mass_units=0

ptmshepherd.precursor_tol=0.01

ptmshepherd.remainder_masses=

ptmshepherd.run-shepherd=true

ptmshepherd.spectra_maxfragcharge=2

ptmshepherd.varmod_masses=P13_Probe\:254.1055, P14_Probe\:304.0881

quantitation.run-label-free-quant=false

speclibgen.easypqp.extras.rt_lowess_fraction=0.04

speclibgen.easypqp.rt-cal=noiRT

speclibgen.easypqp.select-file.text=

speclibgen.run-speclibgen=false

speclibgen.use-easypqp=false

speclibgen.use-spectrast=true

tmtintegrator.add_Ref=1

tmtintegrator.allow_overlabel=true

tmtintegrator.allow_unlabeled=false

tmtintegrator.best_psm=true

tmtintegrator.channel_num=6

tmtintegrator.dont-run-fq-lq=false

tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated

tmtintegrator.groupby=-1

tmtintegrator.labelquant=--tol 20 --level 2

tmtintegrator.max_pep_prob_thres=0

tmtintegrator.min_ntt=0

tmtintegrator.min_pep_prob=0.9

tmtintegrator.min_percent=0.05

tmtintegrator.min_purity=0.5

tmtintegrator.min_site_prob=-1

tmtintegrator.mod_tag=none

tmtintegrator.ms1_int=true

tmtintegrator.outlier_removal=true

tmtintegrator.print_RefInt=false

tmtintegrator.prot_exclude=none

tmtintegrator.prot_norm=0

tmtintegrator.psm_norm=false

tmtintegrator.ref_tag=pool

tmtintegrator.run-tmtintegrator=true

tmtintegrator.top3_pep=true

tmtintegrator.unique_gene=0

tmtintegrator.unique_pep=false

workdir=D\:\DanC\DUB10-Site-ID-2\MSFragger-analysis

workflow.input.data-type.im-ms=false

workflow.input.data-type.regular-ms=true

workflow.process-exps-separately=true

workflow.ram=0

workflow.threads=11

WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Removing workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Creating workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML... Checking if the data is low resolution MS/MS... The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance. FIRST SEARCH* Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 300.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 1.50 Da. 318866252 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.62 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 8.6 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s | postprocessing 0.0 s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 7.4 s [progress: 19683/19683 (100%) - 41790 spectra/s] 0.5s | postprocessing 0.1 s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 56268 spectra/s] 0.4s | postprocessing 0.0 s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 6.8 s [progress: 26296/26296 (100%) - 59092 spectra/s] 0.4s | postprocessing 0.0 s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 2.1 s [progress: 32846/32846 (100%) - 47329 spectra/s] 0.7s | postprocessing 0.0 s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.9 s [progress: 30776/30776 (100%) - 46986 spectra/s] 0.7s | postprocessing 0.0 s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.2 s [progress: 27057/27057 (100%) - 49555 spectra/s] 0.5s | postprocessing 0.0 s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.8 s [progress: 9932/9932 (100%) - 29126 spectra/s] 0.3s | postprocessing 0.0 s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.6 s [progress: 16370/16370 (100%) - 49757 spectra/s] 0.3s | postprocessing 0.0 s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32661 spectra/s] 0.1s | postprocessing 0.0 s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.2 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.0 s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.5 s [progress: 14725/14725 (100%) - 67237 spectra/s] 0.2s | postprocessing 0.0 s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.6 s [progress: 21089/21089 (100%) - 59406 spectra/s] 0.4s | postprocessing 0.0 s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.7 s [progress: 23608/23608 (100%) - 42614 spectra/s] 0.6s | postprocessing 0.0 s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.3 s [progress: 24250/24250 (100%) - 45158 spectra/s] 0.5s | postprocessing 0.0 s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.8 s [progress: 24907/24907 (100%) - 44319 spectra/s] 0.6s | postprocessing 0.0 s *FIRST SEARCH DONE IN 5.929 MIN
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 Not enough data to perform mass calibration. Using the uncalibrated data.
002 Not enough data to perform mass calibration. Using the uncalibrated data.
003 Not enough data to perform mass calibration. Using the uncalibrated data.
004 Not enough data to perform mass calibration. Using the uncalibrated data.
005 Not enough data to perform mass calibration. Using the uncalibrated data.
006 Not enough data to perform mass calibration. Using the uncalibrated data.
007 Not enough data to perform mass calibration. Using the uncalibrated data.
008 Not enough data to perform mass calibration. Using the uncalibrated data.
009 Not enough data to perform mass calibration. Using the uncalibrated data.
010 Not enough data to perform mass calibration. Using the uncalibrated data.
011 Not enough data to perform mass calibration. Using the uncalibrated data.
012 Not enough data to perform mass calibration. Using the uncalibrated data.
013 Not enough data to perform mass calibration. Using the uncalibrated data.
014 Not enough data to perform mass calibration. Using the uncalibrated data.
015 Not enough data to perform mass calibration. Using the uncalibrated data.
016 Not enough data to perform mass calibration. Using the uncalibrated data.
----- --------------- --------------- --------------- ---------------

Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2

150

200

250

300

350

400

Count

179

121

skip rest

Peaks

500_0

300_0

200_0

175_0

150_1

125_1

Count

170

175

176

176

179

178

Int.

1

Count

165

Rm P.

1

Count

165

New fragment_mass_tolerance = 150 PPM

New use_topN_peaks = 150

New minimum_ratio = 0.010000

New intensity_transform = 0

New remove_precursor_peak = 0

***MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 32.737 MIN

MAIN SEARCH Checking database... Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 150.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = true max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.75 Da. 1065135314 fragments to be searched in 2 slices (15.87 GB total) Operating on slice 1 of 2: Fragment index slice generated in 4.89 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 1.3 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 8.1 s [progress: 19683/19683 (100%) - 38219 spectra/s] 0.5s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 64981 spectra/s] 0.3s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 7.1 s [progress: 26296/26296 (100%) - 50183 spectra/s] 0.5s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 6.9 s [progress: 32846/32846 (100%) - 45683 spectra/s] 0.7s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 41366 spectra/s] 0.7s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.6 s [progress: 27057/27057 (100%) - 43291 spectra/s] 0.6s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.1 s [progress: 9932/9932 (100%) - 23369 spectra/s] 0.4s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.7 s [progress: 16370/16370 (100%) - 37981 spectra/s] 0.4s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32963 spectra/s] 0.1s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.1 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.6 s [progress: 14725/14725 (100%) - 65737 spectra/s] 0.2s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.4 s [progress: 21089/21089 (100%) - 48817 spectra/s] 0.4s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.1 s [progress: 23608/23608 (100%) - 39021 spectra/s] 0.6s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.0 s [progress: 24250/24250 (100%) - 39176 spectra/s] 0.6s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.7 s [progress: 24907/24907 (100%) - 39788 spectra/s] 0.6s Operating on slice 2 of 2: Fragment index slice generated in 4.11 s
  17. DC-DUB-Site-ID-2-E1-f1.mzML 8.4 s [progress: 1070/1070 (100%) - 9554 spectra/s] 0.1s | postprocessing 1.4 s
  18. DC-DUB-Site-ID-2-E1-f2.mzML 7.1 s [progress: 19683/19683 (100%) - 94177 spectra/s] 0.2s | postprocessing 1.7 s
  19. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 93259 spectra/s] 0.2s | postprocessing 1.4 s
  20. DC-DUB-Site-ID-2-E1-f4.mzML 6.7 s [progress: 26296/26296 (100%) - 120073 spectra/s] 0.2s | postprocessing 1.5 s
  21. DC-DUB-Site-ID-2-E1-f5.mzML 7.4 s [progress: 32846/32846 (100%) - 99233 spectra/s] 0.3s | postprocessing 1.7 s
  22. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 93544 spectra/s] 0.3s | postprocessing 1.8 s
  23. DC-DUB-Site-ID-2-E1-f7.mzML 8.7 s [progress: 27057/27057 (100%) - 87000 spectra/s] 0.3s | postprocessing 1.8 s
  24. DC-DUB-Site-ID-2-E1-f8.mzML 38.2 s [progress: 9932/9932 (100%) - 29385 spectra/s] 0.3s | postprocessing 1.9 s
  25. DC-DUB-Site-ID-2-E2-f1.mzML 8.8 s [progress: 16370/16370 (100%) - 73739 spectra/s] 0.2s | postprocessing 1.6 s
  26. DC-DUB-Site-ID-2-E2-f2.mzML 7.3 s [progress: 3560/3560 (100%) - 31504 spectra/s] 0.1s | postprocessing 1.1 s
  27. DC-DUB-Site-ID-2-E2-f3.mzML 5.3 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.9 s
  28. DC-DUB-Site-ID-2-E2-f4.mzML 5.3 s [progress: 14725/14725 (100%) - 136343 spectra/s] 0.1s | postprocessing 1.2 s
  29. DC-DUB-Site-ID-2-E2-f5.mzML 6.7 s [progress: 21089/21089 (100%) - 94147 spectra/s] 0.2s | postprocessing 1.5 s
  30. DC-DUB-Site-ID-2-E2-f6.mzML 7.5 s [progress: 23608/23608 (100%) - 102643 spectra/s] 0.2s | postprocessing 1.5 s
  31. DC-DUB-Site-ID-2-E2-f7.mzML 17.5 s [progress: 24250/24250 (100%) - 70906 spectra/s] 0.3s | postprocessing 1.7 s
  32. DC-DUB-Site-ID-2-E2-f8.mzML 19.1 s [progress: 24907/24907 (100%) - 76402 spectra/s] 0.3s | postprocessing 1.9 s MAIN SEARCH DONE IN 6.276 MIN

TOTAL TIME 44.943 MIN* Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML DC-DUB-Site-ID-2-E1-f1.pepXML Done! The execution time is 0.18237 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML DC-DUB-Site-ID-2-E1-f7.pepXML Done! The execution time is 0.18897 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML DC-DUB-Site-ID-2-E2-f4.pepXML Done! The execution time is 0.07557 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML DC-DUB-Site-ID-2-E1-f5.pepXML Done! The execution time is 0.16607 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML DC-DUB-Site-ID-2-E1-f8.pepXML Done! The execution time is 0.69525 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML DC-DUB-Site-ID-2-E2-f3.pepXML Done! The execution time is 0.06227 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML DC-DUB-Site-ID-2-E2-f7.pepXML Done! The execution time is 0.10233 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML DC-DUB-Site-ID-2-E1-f4.pepXML Done! The execution time is 0.16420 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\

anesvi commented 4 years ago

Feel free to contact us directly and also share some mzML files, so we can test and help optimize the workflow, if you like

From: DanielConole notifications@github.com Sent: Tuesday, October 20, 2020 10:49 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

External Email - Use Caution Thanks Alexey – this makes sense. I accidently replaced the TMT variable mods with my own ones (stupid!).

I have made all the suggested changes and resubmitted – let’s see how this goes.

It’s a Site ID experiment for chemical probe modified peptides, and yes it is TMT labelled to quantify greater labelling with increasing concentrations of the probe. So I need both modifications as you recommend.

I selected a tight tolerance window to try and accurately compare the data with that generated from MaxQuant, but I will stick with the default parameters for now.

Thanks, Dan

From: Alexey Nesvizhskii notifications@github.com<mailto:notifications@github.com> Sent: 20 October 2020 14:55 To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Conole, Daniel P T d.conole@imperial.ac.uk<mailto:d.conole@imperial.ac.uk>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

This email from notifications@github.commailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Hi Daniel,

I see you are running an unususual workflow.

First, if you are using narrow precursor tolerance, you do not need Crystal-C Second, I see the following modifications in your main search:

variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1

There is no TMT modification. Assuming this is TMT lkabeled, you need to specify TMT modifications.

So I think you need to tell us about more about your data.

I suggest you load one if the TMT workflows (e.g. TMT10 or TMT10-MS3 if quant from MS3; I suggest you change TMT on n-term from variable to fixed, and also uncheck over labeling on S). Then add your two cysteine modifications.

Best Alexey

From: DanielConole notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> Sent: Tuesday, October 20, 2020 7:16 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com%3cmailto:FragPipe@noreply.github.com>> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com<mailto:subscribed@noreply.github.com%3cmailto:subscribed@noreply.github.com>> Subject: [Nesvilab/FragPipe] Process returned non-zero exit code, stoppingTmtIntegrator (#250)

External Email - Use Caution

Hi there Alexey and team,

I tried to run a site-ID and TMT quant analysis on some files, which went well up until the TMT integrator part. Not sure what went wrong here - can you help?

Log is as below:

System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.3.11 (build 1601497354)

LCMS files: Experiment/Group:

45 commands to execute: WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-7-DC-DUB-Site-ID-2-E1-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-8-DC-DUB-Site-ID-2-E2-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-9-DC-DUB-Site-ID-2-E2-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-10-DC-DUB-Site-ID-2-E2-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-11-DC-DUB-Site-ID-2-E1-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-12-DC-DUB-Site-ID-2-E1-f2.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-13-DC-DUB-Site-ID-2-E2-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-14-DC-DUB-Site-ID-2-E1-f6.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-15-DC-DUB-Site-ID-2-E2-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML PeptideProphet [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas --combine DC-DUB-Site-ID-2-E1-f1_c.pepXML DC-DUB-Site-ID-2-E1-f7_c.pepXML DC-DUB-Site-ID-2-E2-f4_c.pepXML DC-DUB-Site-ID-2-E1-f5_c.pepXML DC-DUB-Site-ID-2-E1-f8_c.pepXML DC-DUB-Site-ID-2-E2-f3_c.pepXML DC-DUB-Site-ID-2-E2-f7_c.pepXML DC-DUB-Site-ID-2-E1-f4_c.pepXML DC-DUB-Site-ID-2-E2-f1_c.pepXML DC-DUB-Site-ID-2-E2-f8_c.pepXML DC-DUB-Site-ID-2-E2-f2_c.pepXML DC-DUB-Site-ID-2-E1-f3_c.pepXML DC-DUB-Site-ID-2-E1-f2_c.pepXML DC-DUB-Site-ID-2-E2-f6_c.pepXML DC-DUB-Site-ID-2-E1-f6_c.pepXML DC-DUB-Site-ID-2-E2-f5_c.pepXML Rewrite pepxml [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp C:\Users\dconole\Desktop\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\interact.pep.xml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML PhilosopherDbAnnotate [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\DanC\2020-10-19-decoys-Human proteome_2003219606.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev_ --pepxml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis FreeQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected LabelQuant [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 6 --annot D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\annotation.txt --brand tmt --dir D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected PhilosopherReport [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -cp "C:\Users\dconole\Desktop\fragpipe\tools\tmt-integrator-2.1.5.jar" TMTIntegrator D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\tmt-integrator-conf.yml D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\psm.tsv WorkspaceClean [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -cp "C:\Users\dconole\Desktop\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\shepherd.config"

Execution order:

Cmd: [START], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceCleanInit], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [MsFragger], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [Crystal-C], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PeptideProphet], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherDbAnnotate], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherFilter], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [FreeQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [LabelQuant], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PhilosopherReport], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [TmtIntegrator], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [WorkspaceClean], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

Cmd: [PTMShepherd], Work dir: [D:\DanC\DUB10-Site-ID-2\MSFragger-analysis]

FragPipe v14.0ui state cache

crystalc.run-crystalc=true

database.db-path=D\:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas

database.decoy-tag=rev_

fragpipe-config.bin-msfragger=C\:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar

fragpipe-config.bin-philosopher=C\:\Users\dconole\Desktop\fragpipe\lib\..\tools\philosopher\philosopher.exe

fragpipe-config.bin-python=C\:\Users\dconole\Anaconda3\python.exe

freequant.mz-tol=10

freequant.rt-tol=0.4

freequant.run-freequant=false

ionquant.excludemods=

ionquant.heavy=

ionquant.imtol=0.05

ionquant.ionfdr=0.01

ionquant.light=

ionquant.mbr=0

ionquant.mbrimtol=0.05

ionquant.mbrmincorr=0

ionquant.mbrrttol=1

ionquant.mbrtoprun=10

ionquant.medium=

ionquant.minexps=1

ionquant.minfreq=0.5

ionquant.minions=2

ionquant.minisotopes=2

ionquant.mztol=10

ionquant.normalization=1

ionquant.peptidefdr=1

ionquant.proteinfdr=1

ionquant.proteinquant=2

ionquant.requantify=1

ionquant.rttol=0.4

ionquant.run-ionquant=true

ionquant.tp=3

ionquant.writeindex=0

msfragger.Y_type_masses=

msfragger.add_topN_complementary=0

msfragger.allow_multiple_variable_mods_on_residue=true

msfragger.allowed_missed_cleavage=2

msfragger.calibrate_mass=2

msfragger.clip_nTerm_M=true

msfragger.deisotope=1

msfragger.delta_mass_exclude_ranges=(-1.5,3.5)

msfragger.diagnostic_fragments=

msfragger.diagnostic_intensity_filter=0

msfragger.digest_max_length=50

msfragger.digest_min_length=7

msfragger.fragment_ion_series=b,y

msfragger.fragment_mass_tolerance=20

msfragger.fragment_mass_units=1

msfragger.intensity_transform=0

msfragger.ion_series_definitions=

msfragger.isotope_error=0/1/2

msfragger.labile_search_mode=off

msfragger.localize_delta_mass=false

msfragger.mass_diff_to_variable_mod=0

msfragger.mass_offsets=0

msfragger.max_fragment_charge=2

msfragger.max_variable_mods_combinations=5000

msfragger.max_variable_mods_per_peptide=3

msfragger.min_fragments_modelling=2

msfragger.min_matched_fragments=4

msfragger.minimum_peaks=15

msfragger.minimum_ratio=0.01

msfragger.misc.fragger.clear-mz-hi=0

msfragger.misc.fragger.clear-mz-lo=0

msfragger.misc.fragger.digest-mass-hi=5000

msfragger.misc.fragger.digest-mass-lo=500

msfragger.misc.fragger.enzyme-dropdown=stricttrypsin

msfragger.misc.fragger.precursor-charge-hi=4

msfragger.misc.fragger.precursor-charge-lo=1

msfragger.misc.fragger.remove-precursor-range-hi=1.5

msfragger.misc.fragger.remove-precursor-range-lo=-1.5

msfragger.misc.slice-db=1

msfragger.num_enzyme_termini=2

msfragger.output_format=pepXML

msfragger.output_max_expect=50

msfragger.output_report_topN=1

msfragger.override_charge=false

msfragger.precursor_mass_lower=-20

msfragger.precursor_mass_mode=selected

msfragger.precursor_mass_units=1

msfragger.precursor_mass_upper=20

msfragger.precursor_true_tolerance=20

msfragger.precursor_true_units=1

msfragger.remove_precursor_peak=0

msfragger.report_alternative_proteins=false

msfragger.restrict_deltamass_to=all

msfragger.run-msfragger=true

msfragger.search_enzyme_butnotafter=

msfragger.search_enzyme_cutafter=KR

msfragger.search_enzyme_name=stricttrypsin

msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1

msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 254.105500,C,true,1; 304.088100,C,true,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1

msfragger.track_zero_topN=0

msfragger.use_topN_peaks=150

msfragger.write_calibrated_mgf=false

msfragger.zero_bin_accept_expect=0

msfragger.zero_bin_mult_expect=1

peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2

peptide-prophet.combine-pepxml=true

peptide-prophet.run-peptide-prophet=true

phi-report.dont-use-prot-proph-file=false

phi-report.filter=--sequential --razor --prot 0.01

phi-report.pep-level-summary=false

phi-report.print-decoys=false

phi-report.run-report=true

protein-prophet.cmd-opts=--maxppmdiff 2000000

protein-prophet.run-protein-prophet=false

ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5

ptmprophet.run-ptmprophet=false

ptmshepherd.annotation-common=false

ptmshepherd.annotation-custom=false

ptmshepherd.annotation-unimod=true

ptmshepherd.annotation_file=

ptmshepherd.annotation_tol=0.01

ptmshepherd.cap_y_ions=

ptmshepherd.diag_ions=

ptmshepherd.glyco_mode=false

ptmshepherd.histo_smoothbins=2

ptmshepherd.iontype_a=false

ptmshepherd.iontype_b=true

ptmshepherd.iontype_c=false

ptmshepherd.iontype_x=false

ptmshepherd.iontype_y=true

ptmshepherd.iontype_z=false

ptmshepherd.localization_background=4

ptmshepherd.output_extended=false

ptmshepherd.peakpicking_mass_units=0

ptmshepherd.peakpicking_promRatio=0.3

ptmshepherd.peakpicking_width=0.002

ptmshepherd.precursor_mass_units=0

ptmshepherd.precursor_tol=0.01

ptmshepherd.remainder_masses=

ptmshepherd.run-shepherd=true

ptmshepherd.spectra_maxfragcharge=2

ptmshepherd.varmod_masses=P13_Probe\:254.1055, P14_Probe\:304.0881

quantitation.run-label-free-quant=false

speclibgen.easypqp.extras.rt_lowess_fraction=0.04

speclibgen.easypqp.rt-cal=noiRT

speclibgen.easypqp.select-file.text=

speclibgen.run-speclibgen=false

speclibgen.use-easypqp=false

speclibgen.use-spectrast=true

tmtintegrator.add_Ref=1

tmtintegrator.allow_overlabel=true

tmtintegrator.allow_unlabeled=false

tmtintegrator.best_psm=true

tmtintegrator.channel_num=6

tmtintegrator.dont-run-fq-lq=false

tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated

tmtintegrator.groupby=-1

tmtintegrator.labelquant=--tol 20 --level 2

tmtintegrator.max_pep_prob_thres=0

tmtintegrator.min_ntt=0

tmtintegrator.min_pep_prob=0.9

tmtintegrator.min_percent=0.05

tmtintegrator.min_purity=0.5

tmtintegrator.min_site_prob=-1

tmtintegrator.mod_tag=none

tmtintegrator.ms1_int=true

tmtintegrator.outlier_removal=true

tmtintegrator.print_RefInt=false

tmtintegrator.prot_exclude=none

tmtintegrator.prot_norm=0

tmtintegrator.psm_norm=false

tmtintegrator.ref_tag=pool

tmtintegrator.run-tmtintegrator=true

tmtintegrator.top3_pep=true

tmtintegrator.unique_gene=0

tmtintegrator.unique_pep=false

workdir=D\:\DanC\DUB10-Site-ID-2\MSFragger-analysis

workflow.input.data-type.im-ms=false

workflow.input.data-type.regular-ms=true

workflow.process-exps-separately=true

workflow.ram=0

workflow.threads=11

WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Removing workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] C:\Users\dconole\Desktop\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:50:53] Executing Workspace v3.3.11 INFO[10:50:53] Creating workspace INFO[10:50:53] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -jar -Dfile.encoding=UTF-8 -Xmx17G C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\fragger.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 14.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.mzML... Checking D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.mzML... Checking if the data is low resolution MS/MS... The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance. FIRST SEARCH* Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 300.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 1.50 Da. 318866252 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.62 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 8.6 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s | postprocessing 0.0 s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 7.4 s [progress: 19683/19683 (100%) - 41790 spectra/s] 0.5s | postprocessing 0.1 s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 56268 spectra/s] 0.4s | postprocessing 0.0 s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 6.8 s [progress: 26296/26296 (100%) - 59092 spectra/s] 0.4s | postprocessing 0.0 s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 2.1 s [progress: 32846/32846 (100%) - 47329 spectra/s] 0.7s | postprocessing 0.0 s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.9 s [progress: 30776/30776 (100%) - 46986 spectra/s] 0.7s | postprocessing 0.0 s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.2 s [progress: 27057/27057 (100%) - 49555 spectra/s] 0.5s | postprocessing 0.0 s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.8 s [progress: 9932/9932 (100%) - 29126 spectra/s] 0.3s | postprocessing 0.0 s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.6 s [progress: 16370/16370 (100%) - 49757 spectra/s] 0.3s | postprocessing 0.0 s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32661 spectra/s] 0.1s | postprocessing 0.0 s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.2 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.0 s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.5 s [progress: 14725/14725 (100%) - 67237 spectra/s] 0.2s | postprocessing 0.0 s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.6 s [progress: 21089/21089 (100%) - 59406 spectra/s] 0.4s | postprocessing 0.0 s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.7 s [progress: 23608/23608 (100%) - 42614 spectra/s] 0.6s | postprocessing 0.0 s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.3 s [progress: 24250/24250 (100%) - 45158 spectra/s] 0.5s | postprocessing 0.0 s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.8 s [progress: 24907/24907 (100%) - 44319 spectra/s] 0.6s | postprocessing 0.0 s *FIRST SEARCH DONE IN 5.929 MIN
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 Not enough data to perform mass calibration. Using the uncalibrated data.
002 Not enough data to perform mass calibration. Using the uncalibrated data.
003 Not enough data to perform mass calibration. Using the uncalibrated data.
004 Not enough data to perform mass calibration. Using the uncalibrated data.
005 Not enough data to perform mass calibration. Using the uncalibrated data.
006 Not enough data to perform mass calibration. Using the uncalibrated data.
007 Not enough data to perform mass calibration. Using the uncalibrated data.
008 Not enough data to perform mass calibration. Using the uncalibrated data.
009 Not enough data to perform mass calibration. Using the uncalibrated data.
010 Not enough data to perform mass calibration. Using the uncalibrated data.
011 Not enough data to perform mass calibration. Using the uncalibrated data.
012 Not enough data to perform mass calibration. Using the uncalibrated data.
013 Not enough data to perform mass calibration. Using the uncalibrated data.
014 Not enough data to perform mass calibration. Using the uncalibrated data.
015 Not enough data to perform mass calibration. Using the uncalibrated data.
016 Not enough data to perform mass calibration. Using the uncalibrated data.
----- --------------- --------------- --------------- ---------------

Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2

150

200

250

300

350

400

Count

179

121

skip rest

Peaks

500_0

300_0

200_0

175_0

150_1

125_1

Count

170

175

176

176

179

178

Int.

1

Count

165

Rm P.

1

Count

165

New fragment_mass_tolerance = 150 PPM

New use_topN_peaks = 150

New minimum_ratio = 0.010000

New intensity_transform = 0

New remove_precursor_peak = 0

***MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 32.737 MIN

MAIN SEARCH Checking database... Parameters: num_threads = 11 database_name = D:\DanC\2020-10-19-decoys-Human proteome_200321_9606.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 150.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = true max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 0 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_06 = 254.105500 C 1 variable_mod_07 = 304.088100 C 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.75 Da. 1065135314 fragments to be searched in 2 slices (15.87 GB total) Operating on slice 1 of 2: Fragment index slice generated in 4.89 s

  1. DC-DUB-Site-ID-2-E1-f1.mzML 1.3 s [progress: 1070/1070 (100%) - 10288 spectra/s] 0.1s
  2. DC-DUB-Site-ID-2-E1-f2.mzML 8.1 s [progress: 19683/19683 (100%) - 38219 spectra/s] 0.5s
  3. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 64981 spectra/s] 0.3s
  4. DC-DUB-Site-ID-2-E1-f4.mzML 7.1 s [progress: 26296/26296 (100%) - 50183 spectra/s] 0.5s
  5. DC-DUB-Site-ID-2-E1-f5.mzML 6.9 s [progress: 32846/32846 (100%) - 45683 spectra/s] 0.7s
  6. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 41366 spectra/s] 0.7s
  7. DC-DUB-Site-ID-2-E1-f7.mzML 8.6 s [progress: 27057/27057 (100%) - 43291 spectra/s] 0.6s
  8. DC-DUB-Site-ID-2-E1-f8.mzML 37.1 s [progress: 9932/9932 (100%) - 23369 spectra/s] 0.4s
  9. DC-DUB-Site-ID-2-E2-f1.mzML 8.7 s [progress: 16370/16370 (100%) - 37981 spectra/s] 0.4s
  10. DC-DUB-Site-ID-2-E2-f2.mzML 7.0 s [progress: 3560/3560 (100%) - 32963 spectra/s] 0.1s
  11. DC-DUB-Site-ID-2-E2-f3.mzML 5.1 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s
  12. DC-DUB-Site-ID-2-E2-f4.mzML 5.6 s [progress: 14725/14725 (100%) - 65737 spectra/s] 0.2s
  13. DC-DUB-Site-ID-2-E2-f5.mzML 6.4 s [progress: 21089/21089 (100%) - 48817 spectra/s] 0.4s
  14. DC-DUB-Site-ID-2-E2-f6.mzML 7.1 s [progress: 23608/23608 (100%) - 39021 spectra/s] 0.6s
  15. DC-DUB-Site-ID-2-E2-f7.mzML 17.0 s [progress: 24250/24250 (100%) - 39176 spectra/s] 0.6s
  16. DC-DUB-Site-ID-2-E2-f8.mzML 18.7 s [progress: 24907/24907 (100%) - 39788 spectra/s] 0.6s Operating on slice 2 of 2: Fragment index slice generated in 4.11 s
  17. DC-DUB-Site-ID-2-E1-f1.mzML 8.4 s [progress: 1070/1070 (100%) - 9554 spectra/s] 0.1s | postprocessing 1.4 s
  18. DC-DUB-Site-ID-2-E1-f2.mzML 7.1 s [progress: 19683/19683 (100%) - 94177 spectra/s] 0.2s | postprocessing 1.7 s
  19. DC-DUB-Site-ID-2-E1-f3.mzML 6.7 s [progress: 20144/20144 (100%) - 93259 spectra/s] 0.2s | postprocessing 1.4 s
  20. DC-DUB-Site-ID-2-E1-f4.mzML 6.7 s [progress: 26296/26296 (100%) - 120073 spectra/s] 0.2s | postprocessing 1.5 s
  21. DC-DUB-Site-ID-2-E1-f5.mzML 7.4 s [progress: 32846/32846 (100%) - 99233 spectra/s] 0.3s | postprocessing 1.7 s
  22. DC-DUB-Site-ID-2-E1-f6.mzML 8.3 s [progress: 30776/30776 (100%) - 93544 spectra/s] 0.3s | postprocessing 1.8 s
  23. DC-DUB-Site-ID-2-E1-f7.mzML 8.7 s [progress: 27057/27057 (100%) - 87000 spectra/s] 0.3s | postprocessing 1.8 s
  24. DC-DUB-Site-ID-2-E1-f8.mzML 38.2 s [progress: 9932/9932 (100%) - 29385 spectra/s] 0.3s | postprocessing 1.9 s
  25. DC-DUB-Site-ID-2-E2-f1.mzML 8.8 s [progress: 16370/16370 (100%) - 73739 spectra/s] 0.2s | postprocessing 1.6 s
  26. DC-DUB-Site-ID-2-E2-f2.mzML 7.3 s [progress: 3560/3560 (100%) - 31504 spectra/s] 0.1s | postprocessing 1.1 s
  27. DC-DUB-Site-ID-2-E2-f3.mzML 5.3 s [progress: 494/494 (100%) - 4259 spectra/s] 0.1s | postprocessing 0.9 s
  28. DC-DUB-Site-ID-2-E2-f4.mzML 5.3 s [progress: 14725/14725 (100%) - 136343 spectra/s] 0.1s | postprocessing 1.2 s
  29. DC-DUB-Site-ID-2-E2-f5.mzML 6.7 s [progress: 21089/21089 (100%) - 94147 spectra/s] 0.2s | postprocessing 1.5 s
  30. DC-DUB-Site-ID-2-E2-f6.mzML 7.5 s [progress: 23608/23608 (100%) - 102643 spectra/s] 0.2s | postprocessing 1.5 s
  31. DC-DUB-Site-ID-2-E2-f7.mzML 17.5 s [progress: 24250/24250 (100%) - 70906 spectra/s] 0.3s | postprocessing 1.7 s
  32. DC-DUB-Site-ID-2-E2-f8.mzML 19.1 s [progress: 24907/24907 (100%) - 76402 spectra/s] 0.3s | postprocessing 1.9 s MAIN SEARCH DONE IN 6.276 MIN

TOTAL TIME 44.943 MIN* Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E1-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f1.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f1.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f2.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f2.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f3.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f4.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f5.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f5.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f6.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f6.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f7.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml java -cp C:\Users\dconole\Desktop\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DUB10-Site-ID-data-for-MSFragger-selected\DC-DUB-Site-ID-2-E2-f8.pepXML D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f8.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-0-DC-DUB-Site-ID-2-E1-f1.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f1.pepXML DC-DUB-Site-ID-2-E1-f1.pepXML Done! The execution time is 0.18237 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-1-DC-DUB-Site-ID-2-E1-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f7.pepXML DC-DUB-Site-ID-2-E1-f7.pepXML Done! The execution time is 0.18897 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-2-DC-DUB-Site-ID-2-E2-f4.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f4.pepXML DC-DUB-Site-ID-2-E2-f4.pepXML Done! The execution time is 0.07557 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-3-DC-DUB-Site-ID-2-E1-f5.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f5.pepXML DC-DUB-Site-ID-2-E1-f5.pepXML Done! The execution time is 0.16607 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-4-DC-DUB-Site-ID-2-E1-f8.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E1-f8.pepXML DC-DUB-Site-ID-2-E1-f8.pepXML Done! The execution time is 0.69525 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-5-DC-DUB-Site-ID-2-E2-f3.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f3.pepXML DC-DUB-Site-ID-2-E2-f3.pepXML Done! The execution time is 0.06227 min. Process 'Crystal-C' finished, exit code: 0 Crystal-C [Work dir: D:\DanC\DUB10-Site-ID-2\MSFragger-analysis] java -Dbatmass.io.libs.thermo.dir="C:\Users\dconole\Desktop\MSFragger-3.1.1\MSFragger-3.1.1\ext\thermo" -Xmx17G -cp "C:\Users\dconole\Desktop\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\dconole\Desktop\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\dconole\Desktop\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\crystalc-6-DC-DUB-Site-ID-2-E2-f7.pepXML.params D:\DanC\DUB10-Site-ID-2\MSFragger-analysis\DC-DUB-Site-ID-2-E2-f7.