System OS: Windows Server 2016, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A


Version info:
FragPipe version 21.1
MSFragger version 4.0
IonQuant version 1.10.12
Philosopher version 5.1.0


LCMS files:
  Experiment/Group: 
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML	DIA
  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML	DIA


327 commands to execute:
CheckCentroid
Z:\FragPipe-jre-21.1\jre\bin\java.exe -Xmx128G -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;Z:\FragPipe-jre-21.1\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML 16
WorkspaceCleanInit [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\dcb73a88-3d01-471c-abc5-ad9ae23254ee
MSFragger [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx128G Z:\FragPipe-jre-21.1\tools\MSFragger-4.0\MSFragger-4.0.jar \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragger_dia.params \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008.pin
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank1.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank2.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank3.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank4.pepXML
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank5.pepXML
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010.pin
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\e9e5949e-4f0e-481d-b6af-63ca52b3adf8
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\c422ab7f-8413-477d-a86c-11a025320136
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d184f335-1dbe-4b6f-8c3e-48d411a76fe4
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\aedb46b4-5148-4429-9032-ceff40219a49
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\75eae691-307b-4365-b30f-6f94a9d5f18a
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b1b44050-6094-4f7a-acd2-89021374b608
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\f804c033-f40b-4902-8153-f148e736450c
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\7d204d6a-b002-4b91-a853-eb5a77ea247c
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5430494c-6e18-4872-b9f0-8b1aa9f19018
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b0191246-bf19-4983-afb4-6d68de4422b8
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d9354e67-bd15-4d26-8129-0e7a21f30637
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\4ef2adc5-300d-4789-9dd4-85a31c2b9142
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2bf52a4d-89d8-43ca-9efb-f2b720ec284a
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\c1aec70a-cf58-4134-aa5d-c9b014f028e8
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\100b82ca-35e5-4304-b4d2-da94019ee546
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\780661c6-dd6b-4d9b-84af-4f5c087b419d
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d67190d8-f91c-4d85-b14b-a52d08d43929
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\64f95b2a-6335-4741-8274-8d7942faa57a
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\4740f307-9ba9-4bd9-89db-ce1e34d2f6b5
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\397b5a61-5aac-4894-8625-48e4be793fcc
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a538993e-8290-41a4-a2ea-306942e46982
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\060fbc1d-56db-477a-a630-da91131bd111
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\88ba95cd-adb8-40e8-b091-3471d817a3f1
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\da17d9a9-37d9-40a2-9e73-16ab85b767a6
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\50b0e6d1-b097-4d06-b992-57194e068a40
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a2bede30-a23a-4e61-9070-112a6d65f859
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\0e612566-435b-44d8-bad7-ba95c757e478
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\bbe33672-be54-4ed4-97b9-b6d2e0f13064
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\9cb02890-bac7-464d-a0fd-315429d779d2
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5f090d23-fefc-4135-93aa-8b072a2ce0ff
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5a1d1b68-f140-4516-aa96-3b369715d3c0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ce58cb60-ee80-48e1-975c-5151a6f608c6
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\60a5fe66-b7d2-4119-bcad-4e5096f683d0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5fc02f8c-cfeb-4ec7-a593-c3ff4b461562
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\510e8104-83b6-4e91-8b37-2a061fc313d5
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\6739b665-38f2-42ed-9e09-e6533d9294ff
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\efa13f03-8b93-47d6-b3b8-5cddfe5e560e
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\1815951e-aa24-48e3-afae-8ed415dd1ab2
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\14b920c8-a6cf-4fbd-986e-10205dfc7114
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\97aeca55-c0c7-4db3-9f4f-db3e31f1527d
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\7547c678-2853-4f74-b5c1-905528982d72
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\9145105a-8c7f-43dc-94a1-fb2e5df03bea
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b297bdb9-409f-44ef-88bc-6f2dc6d0a107
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2febc165-029c-4cda-950a-e65cc88489fb
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2ab3bf93-b8b6-49a3-9588-177c762842cf
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ecf930ef-adf5-4ccb-9b2e-a8029e4e72e5
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\8027c91d-a82d-4da8-b62c-c0a41f22f72b
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\dfc6e522-ddcf-4a2a-9e34-af0cb676ebb2
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d35851e0-b40c-49fc-8ff1-d8be1b7287f4
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2b5321a3-4233-4362-9fa3-2916e1de4a2a
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\486e4662-8355-4e52-9f06-9beb873fb69b
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\95eca416-42e7-4f50-8bf0-1eacf4e3cd78
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a9ca9542-b17d-462f-98d5-032bd93c2748
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5c51e245-04db-4b70-bc7e-43dbba7f53bc
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b2a6b844-672f-4cb6-bb2f-a93775ae0ae7
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\6ebcc30a-c42c-457e-83b0-e34b3ff60d40
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\97d419ee-a56a-4491-9fa3-3b4b0db37d2a
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\98b5e276-4615-482e-b709-596b20cf970e
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\962f1e18-c5cc-44cc-8ed5-b074704a5029
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ef124aa5-4bb0-49d0-bae5-ce20eafde905
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank5.pepXML
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
ProteinProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --picked --prot 0.01 --tag rev_ --pepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 --protxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\combined.prot.xml --razor
PhilosopherReport [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report --msstats --removecontam
SpecLibGen [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\python.exe -u Z:\FragPipe-jre-21.1\tools\speclib\gen_con_spec_lib.py \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 unused \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 True unused use_easypqp noiRT;noIM 16 "--unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_speclibgen.txt
DIA-NN [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 16 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrix-qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_diann.txt
DIA-NN [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate localization [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\diann-output]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\tools\batmass-io-1.30.0.jar;Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.dmtavt.fragpipe.tools.diann.Localization \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\diann-output]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\commons-io-2.15.1.jar;Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv msstats.csv 0.01 1 0.01 0.01 \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-files.fp-manifest
PTMShepherd [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -Xmx128G -Dlibs.thermo.dir=Z:\FragPipe-jre-21.1\tools\MSFragger-4.0\ext\thermo -cp Z:\FragPipe-jre-21.1\tools\ptmshepherd-2.0.6.jar;Z:\FragPipe-jre-21.1\tools\batmass-io-1.30.0.jar;Z:\FragPipe-jre-21.1\tools\commons-math3-3.6.1.jar;Z:\FragPipe-jre-21.1\tools\hipparchus-1.8\hipparchus-core-1.8.jar;Z:\FragPipe-jre-21.1\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\shepherd.config"
WorkspaceClean [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [CheckCentroid], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [WorkspaceCleanInit], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [MSFragger], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [PeptideProphet], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [ProteinProphet], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [PhilosopherDbAnnotate], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [PhilosopherFilter], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [PhilosopherReport], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [SpecLibGen], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [DIA-NN], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [PTMShepherd], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
    Cmd: [WorkspaceClean], Work dir: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]

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

~~~~~~Sample of \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas~~~~~~~
>Biognosys|iRT-Kit_WR_fusion GN=iRTKit
>rev_sp|O43508|TNF12_HUMAN Tumor necrosis factor ligand superfamily member 12 OS=Homo sapiens OX=9606 GN=TNFSF12 PE=1 SV=1
>rev_sp|P0DML3|CSH2_HUMAN Chorionic somatomammotropin hormone 2 OS=Homo sapiens OX=9606 GN=CSH2 PE=1 SV=1
>rev_sp|P49685|GPR15_HUMAN G-protein coupled receptor 15 OS=Homo sapiens OX=9606 GN=GPR15 PE=2 SV=1
>rev_sp|Q14152|EIF3A_HUMAN Eukaryotic translation initiation factor 3 subunit A OS=Homo sapiens OX=9606 GN=EIF3A PE=1 SV=1
>rev_sp|Q68DQ2|CRBG3_HUMAN Very large A-kinase anchor protein OS=Homo sapiens OX=9606 GN=CRYBG3 PE=1 SV=3
>rev_sp|Q8IWE2|NXP20_HUMAN Protein NOXP20 OS=Homo sapiens OX=9606 GN=FAM114A1 PE=1 SV=2
>rev_sp|Q8WVK7|SKA2_HUMAN Spindle and kinetochore-associated protein 2 OS=Homo sapiens OX=9606 GN=SKA2 PE=1 SV=1
>rev_sp|Q9BRG2|SH23A_HUMAN SH2 domain-containing protein 3A OS=Homo sapiens OX=9606 GN=SH2D3A PE=1 SV=1
>rev_sp|Q9NUQ6|SPS2L_HUMAN SPATS2-like protein OS=Homo sapiens OX=9606 GN=SPATS2L PE=1 SV=2
>rev_sp|Q9Y6N7|ROBO1_HUMAN Roundabout homolog 1 OS=Homo sapiens OX=9606 GN=ROBO1 PE=1 SV=1
>sp|O43665|RGS10_HUMAN Regulator of G-protein signaling 10 OS=Homo sapiens OX=9606 GN=RGS10 PE=1 SV=3
>sp|P0DP06|HVD34_HUMAN Immunoglobulin heavy variable 4-30-4 OS=Homo sapiens OX=9606 GN=IGHV4-30-4 PE=3 SV=1
>sp|P49901|MCSP_HUMAN Sperm mitochondrial-associated cysteine-rich protein OS=Homo sapiens OX=9606 GN=SMCP PE=1 SV=2
>sp|Q14264|ENR1_HUMAN Endogenous retrovirus group 3 member 1 Env polyprotein OS=Homo sapiens OX=9606 GN=ERV3-1 PE=2 SV=2
>sp|Q6B9Z1|IGFL4_HUMAN Insulin growth factor-like family member 4 OS=Homo sapiens OX=9606 GN=IGFL4 PE=2 SV=1
>sp|Q8IWZ8|SUGP1_HUMAN SURP and G-patch domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SUGP1 PE=1 SV=2
>sp|Q8WWF5|ZNRF4_HUMAN E3 ubiquitin-protein ligase ZNRF4 OS=Homo sapiens OX=9606 GN=ZNRF4 PE=1 SV=3
>sp|Q9BRZ2|TRI56_HUMAN E3 ubiquitin-protein ligase TRIM56 OS=Homo sapiens OX=9606 GN=TRIM56 PE=1 SV=3
>sp|Q9NVH2|INT7_HUMAN Integrator complex subunit 7 OS=Homo sapiens OX=9606 GN=INTS7 PE=1 SV=1
>sp|W5XKT8|SACA6_HUMAN Sperm acrosome membrane-associated protein 6 OS=Homo sapiens OX=9606 GN=SPACA6 PE=1 SV=2
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v21.1ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\Wlab_Fragpipe_defaults\\Fasta\\2024-01-17-decoys-reviewed-contam-UP000005640.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=Z\:\\FragPipe-jre-21.1\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=Z\:\\FragPipe-jre-21.1\\tools\\IonQuant-1.10.12.jar
fragpipe-config.bin-msfragger=Z\:\\FragPipe-jre-21.1\\tools\\MSFragger-4.0\\MSFragger-4.0.jar
fragpipe-config.bin-philosopher=Z\:\\FragPipe-jre-21.1\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\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.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
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.group_variable=0
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.mass_offsets_detailed=
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.min_sequence_matches=2
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=2000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=lysc-p
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_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
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.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=K
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=lysc-p
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 13.979265,H,true,2; 31.989828,H,true,2; 31.989828,W,true,2; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=true
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=true
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=128
workflow.threads=16

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
Z:\FragPipe-jre-21.1\jre\bin\java.exe -Xmx128G -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;Z:\FragPipe-jre-21.1\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML 16
Done in 7.2 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[17:48:31] Executing Workspace  v5.1.0                  
INFO[17:48:31] Removing workspace                           
INFO[17:48:31] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\dcb73a88-3d01-471c-abc5-ad9ae23254ee
INFO[17:48:32] Executing Workspace  v5.1.0                  
INFO[17:48:32] Creating workspace                           
INFO[17:48:32] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx128G Z:\FragPipe-jre-21.1\tools\MSFragger-4.0\MSFragger-4.0.jar \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragger_dia.params \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
MSFragger version MSFragger-4.0
Batmass-IO version 1.30.0
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows Server 2016, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 128 GB memory
Checking database...
Checking spectral files...
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML: Scans = 86580; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML: Scans = 88170; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML: Scans = 87030; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML: Scans = 87690; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML: Scans = 88350; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML: Scans = 88500; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML: Scans = 87510; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML: Scans = 88800; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML: Scans = 87120; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML: Scans = 88110; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML: Scans = 88980; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML: Scans = 87750; Isolation sizes = [14.0, 14.3, 14.4, 14.5, 15.0, 16.0, 16.1, 16.8, 16.9, 17.0, 17.7, 19.2, 22.0, 22.2, 23.7, 24.4, 26.9, 27.2, 32.6, 34.6, 37.0, 45.3, 67.0, 425.5]
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 16
database_name = \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -10.0
precursor_mass_upper = 10.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 10.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = nonspecific
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
search_enzyme_sense_2 = C
search_enzyme_cut_2 = K
search_enzyme_nocut_2 = 
allowed_missed_cleavage_2 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 2
precursor_charge_high = 3
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 2000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
group_variable = 0
require_precursor = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
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
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Number of unique peptides
	of length 7: 290135
	of length 8: 281157
	of length 9: 280426
	of length 10: 264702
	of length 11: 251299
	of length 12: 240504
	of length 13: 234338
	of length 14: 219666
	of length 15: 207838
	of length 16: 186535
	of length 17: 137645
	of length 18: 73340
	of length 19: 26545
	of length 20: 8478
	of length 21: 2436
	of length 22: 612
	of length 23: 226
	of length 24: 75
	of length 25: 32
	of length 26: 15
	of length 27: 4
	of length 28: 4
	of length 30: 1
In total 2706013 peptides.
Generated 3508648 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
76529948 fragments to be searched in 1 slices (1.14 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.21 s
	001. jhammer_Z_2401_006.mzML 11.4 s | deisotoping 3.3 s
		[progress: 87564/87564 (100%) - 7770 spectra/s] 11.3s | postprocessing 0.6 s
	002. jhammer_Z_2401_007.mzML 11.2 s | deisotoping 3.2 s
		[progress: 88674/88674 (100%) - 9625 spectra/s] 9.2s | postprocessing 0.4 s
	003. jhammer_Z_2401_008.mzML 9.2 s | deisotoping 2.5 s
		[progress: 87426/87426 (100%) - 14768 spectra/s] 5.9s | postprocessing 0.3 s
	004. jhammer_Z_2401_010.mzML 8.9 s | deisotoping 2.3 s
		[progress: 88811/88811 (100%) - 16419 spectra/s] 5.4s | postprocessing 0.3 s
	005. jhammer_Z_2401_011.mzML 10.0 s | deisotoping 3.6 s
		[progress: 88224/88224 (100%) - 12676 spectra/s] 7.0s | postprocessing 0.3 s
	006. jhammer_Z_2401_012.mzML 9.1 s | deisotoping 2.0 s
		[progress: 86725/86725 (100%) - 10694 spectra/s] 8.1s | postprocessing 0.3 s
	007. jhammer_Z_2401_014.mzML 9.2 s | deisotoping 2.0 s
		[progress: 88028/88028 (100%) - 16143 spectra/s] 5.5s | postprocessing 0.3 s
	008. jhammer_Z_2401_015.mzML 8.3 s | deisotoping 2.1 s
		[progress: 87920/87920 (100%) - 10773 spectra/s] 8.2s | postprocessing 0.3 s
	009. jhammer_Z_2401_016.mzML 8.5 s | deisotoping 2.0 s
		[progress: 86227/86227 (100%) - 15486 spectra/s] 5.6s | postprocessing 0.3 s
	010. jhammer_Z_2401_018.mzML 8.6 s | deisotoping 2.1 s
		[progress: 86936/86936 (100%) - 14475 spectra/s] 6.0s | postprocessing 0.3 s
	011. jhammer_Z_2401_019.mzML 8.8 s | deisotoping 2.6 s
		[progress: 87221/87221 (100%) - 13766 spectra/s] 6.3s | postprocessing 0.3 s
	012. jhammer_Z_2401_020.mzML 10.1 s | deisotoping 2.4 s
		[progress: 88170/88170 (100%) - 12769 spectra/s] 6.9s | postprocessing 0.3 s
***************************FIRST SEARCH DONE IN 5.122 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   0.11   0.47 |  -0.00   0.34 |  -0.24   1.21 |   0.01   1.05  
 002 |   0.32   0.48 |   0.02   0.33 |   0.06   1.17 |   0.04   1.04  
 003 |   0.53   0.46 |  -0.00   0.35 |   0.14   1.21 |   0.05   1.08  
 004 |   0.59   0.56 |  -0.01   0.39 |   0.29   1.32 |   0.06   1.15  
 005 |   0.73   0.46 |   0.00   0.37 |   0.48   1.26 |   0.04   1.09  
 006 |   0.96   0.50 |  -0.01   0.36 |   0.55   1.28 |   0.05   1.10  
 007 |   1.39   0.54 |   0.01   0.37 |   0.78   1.35 |   0.05   1.14  
 008 |   1.36   0.52 |  -0.00   0.40 |   0.88   1.37 |   0.07   1.17  
 009 |   1.69   0.45 |  -0.00   0.35 |   1.14   1.34 |   0.07   1.12  
 010 |   1.87   0.51 |   0.03   0.36 |   1.43   1.31 |   0.05   1.10  
 011 |   2.02   0.54 |   0.01   0.38 |   1.80   1.30 |   0.05   1.07  
 012 |   1.61   0.55 |  -0.00   0.36 |   1.44   1.30 |   0.05   1.09  
-----|---------------|---------------|---------------|---------------
New fragment_mass_tolerance = 5.000000 PPM
New precursor_true_tolerance = 2.000000 PPM
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.940 MIN*********

************************************MAIN SEARCH************************************
Checking database...
data_type > 0. Will use the isolation window from the spectral file as precursor tolerance.
Parameters:
num_threads = 16
database_name = \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = isolation window lower
precursor_mass_upper = isolation window upper
precursor_mass_units = isolation window
data_type = 1
precursor_true_tolerance = 2.0
precursor_true_units = 1
fragment_mass_tolerance = 5.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = nonspecific
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
search_enzyme_sense_2 = C
search_enzyme_cut_2 = K
search_enzyme_nocut_2 = 
allowed_missed_cleavage_2 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 5
output_max_expect = 1.7976931348623157E308
report_alternative_proteins = 1
override_charge = 1
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 2000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
group_variable = 0
require_precursor = 0
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = isolation window
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_10 = 13.979265 H 2
variable_mod_11 = 31.989828 H 2
variable_mod_12 = 31.989828 W 2
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Number of unique peptides
	of length 7: 290135
	of length 8: 281157
	of length 9: 280426
	of length 10: 264702
	of length 11: 251299
	of length 12: 240504
	of length 13: 234338
	of length 14: 219666
	of length 15: 207838
	of length 16: 186535
	of length 17: 137645
	of length 18: 73340
	of length 19: 26545
	of length 20: 8478
	of length 21: 2436
	of length 22: 612
	of length 23: 226
	of length 24: 75
	of length 25: 32
	of length 26: 15
	of length 27: 4
	of length 28: 4
	of length 30: 1
In total 2706013 peptides.
Generated 7136581 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.02 Da.
162965908 fragments to be searched in 1 slices (2.43 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 2.50 s
	001. jhammer_Z_2401_006.mzBIN_calibrated 7.2 s
		[progress: 87497/87497 (100%) - 521 spectra/s] 168.0s
		Building spectral index for the mzBIN_calibrated file 17.3 s
		Rescoring with peak tracing 55.0 s
		Picking top PSMs for each precursor 16.1 s
		Rescoring 10.8 s
		Writing results 51.8 s
	002. jhammer_Z_2401_007.mzBIN_calibrated 3.9 s
		[progress: 88639/88639 (100%) - 532 spectra/s] 166.8s
		Building spectral index for the mzBIN_calibrated file 20.3 s
		Rescoring with peak tracing 40.5 s
		Picking top PSMs for each precursor 16.1 s
		Rescoring 6.8 s
		Writing results 51.5 s
	003. jhammer_Z_2401_008.mzBIN_calibrated 3.8 s
		[progress: 87371/87371 (100%) - 551 spectra/s] 158.5s
		Building spectral index for the mzBIN_calibrated file 23.0 s
		Rescoring with peak tracing 40.3 s
		Picking top PSMs for each precursor 11.6 s
		Rescoring 8.7 s
		Writing results 47.1 s
	004. jhammer_Z_2401_010.mzBIN_calibrated 4.2 s
		[progress: 88783/88783 (100%) - 645 spectra/s] 137.7s
		Building spectral index for the mzBIN_calibrated file 21.4 s
		Rescoring with peak tracing 30.8 s
		Picking top PSMs for each precursor 14.1 s
		Rescoring 8.4 s
		Writing results 42.9 s
	005. jhammer_Z_2401_011.mzBIN_calibrated 5.1 s
		[progress: 88183/88183 (100%) - 538 spectra/s] 163.8s
		Building spectral index for the mzBIN_calibrated file 19.6 s
		Rescoring with peak tracing 35.6 s
		Picking top PSMs for each precursor 16.4 s
		Rescoring 9.0 s
		Writing results 42.7 s
	006. jhammer_Z_2401_012.mzBIN_calibrated 4.8 s
		[progress: 86671/86671 (100%) - 573 spectra/s] 151.3s
		Building spectral index for the mzBIN_calibrated file 23.6 s
		Rescoring with peak tracing 32.8 s
		Picking top PSMs for each precursor 12.0 s
		Rescoring 12.1 s
		Writing results 39.6 s
	007. jhammer_Z_2401_014.mzBIN_calibrated 5.0 s
		[progress: 88015/88015 (100%) - 686 spectra/s] 128.3s
		Building spectral index for the mzBIN_calibrated file 19.6 s
		Rescoring with peak tracing 30.3 s
		Picking top PSMs for each precursor 13.1 s
		Rescoring 5.1 s
		Writing results 36.0 s
	008. jhammer_Z_2401_015.mzBIN_calibrated 4.7 s
		[progress: 87883/87883 (100%) - 716 spectra/s] 122.8s
		Building spectral index for the mzBIN_calibrated file 17.8 s
		Rescoring with peak tracing 29.5 s
		Picking top PSMs for each precursor 11.1 s
		Rescoring 6.1 s
		Writing results 33.2 s
	009. jhammer_Z_2401_016.mzBIN_calibrated 4.8 s
		[progress: 86150/86150 (100%) - 620 spectra/s] 138.8s
		Building spectral index for the mzBIN_calibrated file 19.5 s
		Rescoring with peak tracing 33.1 s
		Picking top PSMs for each precursor 13.7 s
		Rescoring 6.0 s
		Writing results 35.4 s
	010. jhammer_Z_2401_018.mzBIN_calibrated 4.9 s
		[progress: 86910/86910 (100%) - 594 spectra/s] 146.3s
		Building spectral index for the mzBIN_calibrated file 19.3 s
		Rescoring with peak tracing 31.8 s
		Picking top PSMs for each precursor 14.4 s
		Rescoring 5.8 s
		Writing results 38.9 s
	011. jhammer_Z_2401_019.mzBIN_calibrated 5.3 s
		[progress: 87159/87159 (100%) - 510 spectra/s] 170.8s
		Building spectral index for the mzBIN_calibrated file 20.1 s
		Rescoring with peak tracing 40.5 s
		Picking top PSMs for each precursor 13.7 s
		Rescoring 10.5 s
		Writing results 44.2 s
	012. jhammer_Z_2401_020.mzBIN_calibrated 5.4 s
		[progress: 88119/88119 (100%) - 540 spectra/s] 163.1s
		Building spectral index for the mzBIN_calibrated file 20.9 s
		Rescoring with peak tracing 41.3 s
		Picking top PSMs for each precursor 13.0 s
		Rescoring 10.9 s
		Writing results 42.3 s
***************************MAIN SEARCH DONE IN 61.687 MIN***************************

*******************************TOTAL TIME 69.749 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank1.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank2.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank3.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank4.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010_rank5.pepXML \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar;/Z:/FragPipe-jre-21.1/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.pin \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010.pin
Process 'MSFragger move pin' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\e9e5949e-4f0e-481d-b6af-63ca52b3adf8
INFO[19:00:11] Executing Workspace  v5.1.0                  
INFO[19:00:11] Creating workspace                           
INFO[19:00:11] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\c422ab7f-8413-477d-a86c-11a025320136
INFO[19:00:12] Executing Workspace  v5.1.0                  
INFO[19:00:12] Creating workspace                           
INFO[19:00:12] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d184f335-1dbe-4b6f-8c3e-48d411a76fe4
INFO[19:00:12] Executing Workspace  v5.1.0                  
INFO[19:00:12] Creating workspace                           
INFO[19:00:12] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\aedb46b4-5148-4429-9032-ceff40219a49
INFO[19:00:13] Executing Workspace  v5.1.0                  
INFO[19:00:13] Creating workspace                           
INFO[19:00:13] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\75eae691-307b-4365-b30f-6f94a9d5f18a
INFO[19:00:13] Executing Workspace  v5.1.0                  
INFO[19:00:13] Creating workspace                           
INFO[19:00:13] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b1b44050-6094-4f7a-acd2-89021374b608
INFO[19:00:14] Executing Workspace  v5.1.0                  
INFO[19:00:14] Creating workspace                           
INFO[19:00:14] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\f804c033-f40b-4902-8153-f148e736450c
INFO[19:00:14] Executing Workspace  v5.1.0                  
INFO[19:00:14] Creating workspace                           
INFO[19:00:14] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\7d204d6a-b002-4b91-a853-eb5a77ea247c
INFO[19:00:15] Executing Workspace  v5.1.0                  
INFO[19:00:15] Creating workspace                           
INFO[19:00:15] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5430494c-6e18-4872-b9f0-8b1aa9f19018
INFO[19:00:15] Executing Workspace  v5.1.0                  
INFO[19:00:15] Creating workspace                           
INFO[19:00:15] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b0191246-bf19-4983-afb4-6d68de4422b8
INFO[19:00:15] Executing Workspace  v5.1.0                  
INFO[19:00:15] Creating workspace                           
INFO[19:00:15] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d9354e67-bd15-4d26-8129-0e7a21f30637
INFO[19:00:16] Executing Workspace  v5.1.0                  
INFO[19:00:16] Creating workspace                           
INFO[19:00:16] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\4ef2adc5-300d-4789-9dd4-85a31c2b9142
INFO[19:00:16] Executing Workspace  v5.1.0                  
INFO[19:00:16] Creating workspace                           
INFO[19:00:16] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2bf52a4d-89d8-43ca-9efb-f2b720ec284a
INFO[19:00:16] Executing Workspace  v5.1.0                  
INFO[19:00:16] Creating workspace                           
INFO[19:00:16] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\c1aec70a-cf58-4134-aa5d-c9b014f028e8
INFO[19:00:17] Executing Workspace  v5.1.0                  
INFO[19:00:17] Creating workspace                           
INFO[19:00:17] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\100b82ca-35e5-4304-b4d2-da94019ee546
INFO[19:00:17] Executing Workspace  v5.1.0                  
INFO[19:00:17] Creating workspace                           
INFO[19:00:17] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\780661c6-dd6b-4d9b-84af-4f5c087b419d
INFO[19:00:18] Executing Workspace  v5.1.0                  
INFO[19:00:18] Creating workspace                           
INFO[19:00:18] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d67190d8-f91c-4d85-b14b-a52d08d43929
INFO[19:00:18] Executing Workspace  v5.1.0                  
INFO[19:00:18] Creating workspace                           
INFO[19:00:18] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\64f95b2a-6335-4741-8274-8d7942faa57a
INFO[19:00:25] Executing Workspace  v5.1.0                  
INFO[19:00:25] Creating workspace                           
INFO[19:00:25] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\4740f307-9ba9-4bd9-89db-ce1e34d2f6b5
INFO[19:00:25] Executing Workspace  v5.1.0                  
INFO[19:00:25] Creating workspace                           
INFO[19:00:25] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\397b5a61-5aac-4894-8625-48e4be793fcc
INFO[19:00:26] Executing Workspace  v5.1.0                  
INFO[19:00:26] Creating workspace                           
INFO[19:00:26] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a538993e-8290-41a4-a2ea-306942e46982
INFO[19:00:26] Executing Workspace  v5.1.0                  
INFO[19:00:26] Creating workspace                           
INFO[19:00:26] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\060fbc1d-56db-477a-a630-da91131bd111
INFO[19:00:27] Executing Workspace  v5.1.0                  
INFO[19:00:27] Creating workspace                           
INFO[19:00:27] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\88ba95cd-adb8-40e8-b091-3471d817a3f1
INFO[19:00:27] Executing Workspace  v5.1.0                  
INFO[19:00:27] Creating workspace                           
INFO[19:00:27] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\da17d9a9-37d9-40a2-9e73-16ab85b767a6
INFO[19:00:28] Executing Workspace  v5.1.0                  
INFO[19:00:28] Creating workspace                           
INFO[19:00:28] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\50b0e6d1-b097-4d06-b992-57194e068a40
INFO[19:00:28] Executing Workspace  v5.1.0                  
INFO[19:00:28] Creating workspace                           
INFO[19:00:28] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a2bede30-a23a-4e61-9070-112a6d65f859
INFO[19:00:29] Executing Workspace  v5.1.0                  
INFO[19:00:29] Creating workspace                           
INFO[19:00:29] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\0e612566-435b-44d8-bad7-ba95c757e478
INFO[19:00:29] Executing Workspace  v5.1.0                  
INFO[19:00:29] Creating workspace                           
INFO[19:00:29] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\bbe33672-be54-4ed4-97b9-b6d2e0f13064
INFO[19:00:30] Executing Workspace  v5.1.0                  
INFO[19:00:30] Creating workspace                           
INFO[19:00:30] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\9cb02890-bac7-464d-a0fd-315429d779d2
INFO[19:00:30] Executing Workspace  v5.1.0                  
INFO[19:00:30] Creating workspace                           
INFO[19:00:30] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5f090d23-fefc-4135-93aa-8b072a2ce0ff
INFO[19:00:31] Executing Workspace  v5.1.0                  
INFO[19:00:31] Creating workspace                           
INFO[19:00:31] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5a1d1b68-f140-4516-aa96-3b369715d3c0
INFO[19:00:31] Executing Workspace  v5.1.0                  
INFO[19:00:31] Creating workspace                           
INFO[19:00:31] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ce58cb60-ee80-48e1-975c-5151a6f608c6
INFO[19:00:32] Executing Workspace  v5.1.0                  
INFO[19:00:32] Creating workspace                           
INFO[19:00:32] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\60a5fe66-b7d2-4119-bcad-4e5096f683d0
INFO[19:00:32] Executing Workspace  v5.1.0                  
INFO[19:00:32] Creating workspace                           
INFO[19:00:32] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5fc02f8c-cfeb-4ec7-a593-c3ff4b461562
INFO[19:00:33] Executing Workspace  v5.1.0                  
INFO[19:00:33] Creating workspace                           
INFO[19:00:33] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\510e8104-83b6-4e91-8b37-2a061fc313d5
INFO[19:00:33] Executing Workspace  v5.1.0                  
INFO[19:00:33] Creating workspace                           
INFO[19:00:33] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\6739b665-38f2-42ed-9e09-e6533d9294ff
INFO[19:00:33] Executing Workspace  v5.1.0                  
INFO[19:00:33] Creating workspace                           
INFO[19:00:33] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\efa13f03-8b93-47d6-b3b8-5cddfe5e560e
INFO[19:00:34] Executing Workspace  v5.1.0                  
INFO[19:00:34] Creating workspace                           
INFO[19:00:34] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\1815951e-aa24-48e3-afae-8ed415dd1ab2
INFO[19:00:35] Executing Workspace  v5.1.0                  
INFO[19:00:35] Creating workspace                           
INFO[19:00:35] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\14b920c8-a6cf-4fbd-986e-10205dfc7114
INFO[19:00:35] Executing Workspace  v5.1.0                  
INFO[19:00:35] Creating workspace                           
INFO[19:00:35] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\97aeca55-c0c7-4db3-9f4f-db3e31f1527d
INFO[19:00:36] Executing Workspace  v5.1.0                  
INFO[19:00:36] Creating workspace                           
INFO[19:00:36] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\7547c678-2853-4f74-b5c1-905528982d72
INFO[19:00:36] Executing Workspace  v5.1.0                  
INFO[19:00:36] Creating workspace                           
INFO[19:00:36] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\9145105a-8c7f-43dc-94a1-fb2e5df03bea
INFO[19:00:36] Executing Workspace  v5.1.0                  
INFO[19:00:36] Creating workspace                           
INFO[19:00:36] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b297bdb9-409f-44ef-88bc-6f2dc6d0a107
INFO[19:00:37] Executing Workspace  v5.1.0                  
INFO[19:00:37] Creating workspace                           
INFO[19:00:37] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2febc165-029c-4cda-950a-e65cc88489fb
INFO[19:00:38] Executing Workspace  v5.1.0                  
INFO[19:00:38] Creating workspace                           
INFO[19:00:38] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2ab3bf93-b8b6-49a3-9588-177c762842cf
INFO[19:00:38] Executing Workspace  v5.1.0                  
INFO[19:00:38] Creating workspace                           
INFO[19:00:38] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ecf930ef-adf5-4ccb-9b2e-a8029e4e72e5
INFO[19:00:39] Executing Workspace  v5.1.0                  
INFO[19:00:39] Creating workspace                           
INFO[19:00:39] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\8027c91d-a82d-4da8-b62c-c0a41f22f72b
INFO[19:00:39] Executing Workspace  v5.1.0                  
INFO[19:00:39] Creating workspace                           
INFO[19:00:39] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\dfc6e522-ddcf-4a2a-9e34-af0cb676ebb2
INFO[19:00:39] Executing Workspace  v5.1.0                  
INFO[19:00:39] Creating workspace                           
INFO[19:00:39] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\d35851e0-b40c-49fc-8ff1-d8be1b7287f4
INFO[19:00:40] Executing Workspace  v5.1.0                  
INFO[19:00:40] Creating workspace                           
INFO[19:00:40] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\2b5321a3-4233-4362-9fa3-2916e1de4a2a
INFO[19:00:40] Executing Workspace  v5.1.0                  
INFO[19:00:40] Creating workspace                           
INFO[19:00:40] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\486e4662-8355-4e52-9f06-9beb873fb69b
INFO[19:00:41] Executing Workspace  v5.1.0                  
INFO[19:00:41] Creating workspace                           
INFO[19:00:41] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\95eca416-42e7-4f50-8bf0-1eacf4e3cd78
INFO[19:00:41] Executing Workspace  v5.1.0                  
INFO[19:00:41] Creating workspace                           
INFO[19:00:41] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\a9ca9542-b17d-462f-98d5-032bd93c2748
INFO[19:00:42] Executing Workspace  v5.1.0                  
INFO[19:00:42] Creating workspace                           
INFO[19:00:42] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\5c51e245-04db-4b70-bc7e-43dbba7f53bc
INFO[19:00:42] Executing Workspace  v5.1.0                  
INFO[19:00:42] Creating workspace                           
INFO[19:00:42] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\b2a6b844-672f-4cb6-bb2f-a93775ae0ae7
INFO[19:00:43] Executing Workspace  v5.1.0                  
INFO[19:00:43] Creating workspace                           
INFO[19:00:43] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\6ebcc30a-c42c-457e-83b0-e34b3ff60d40
INFO[19:00:43] Executing Workspace  v5.1.0                  
INFO[19:00:43] Creating workspace                           
INFO[19:00:43] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\97d419ee-a56a-4491-9fa3-3b4b0db37d2a
INFO[19:00:43] Executing Workspace  v5.1.0                  
INFO[19:00:43] Creating workspace                           
INFO[19:00:44] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\98b5e276-4615-482e-b709-596b20cf970e
INFO[19:00:44] Executing Workspace  v5.1.0                  
INFO[19:00:44] Creating workspace                           
INFO[19:00:44] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\962f1e18-c5cc-44cc-8ed5-b074704a5029
INFO[19:00:44] Executing Workspace  v5.1.0                  
INFO[19:00:44] Creating workspace                           
INFO[19:00:44] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet: Workspace init [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\jhammer\AppData\Local\Temp\12\ef124aa5-4bb0-49d0-bae5-ce20eafde905
INFO[19:00:45] Executing Workspace  v5.1.0                  
INFO[19:00:45] Creating workspace                           
INFO[19:00:45] Done                                         
Process 'PeptideProphet: Workspace init' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_006_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank1.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_007_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank3.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank2.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank4.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_008_rank5.pepXML
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank5.pepXML
 processed altogether 52479 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1472 1+, 22329 2+, 20955 3+, 7723 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25071 Decoys, and 27408 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:20:38] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank5.pepXML
 processed altogether 56103 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1584 1+, 23732 2+, 22409 3+, 8378 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26530 Decoys, and 29573 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 22 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:21:55] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank5.pepXML
 processed altogether 56193 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1644 1+, 24663 2+, 21906 3+, 7980 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26707 Decoys, and 29486 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:22:10] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank4.pepXML
 processed altogether 57605 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1696 1+, 24598 2+, 22569 3+, 8742 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27050 Decoys, and 30555 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:22:34] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_010_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank4.pepXML
 processed altogether 61092 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1843 1+, 25777 2+, 24199 3+, 9273 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28351 Decoys, and 32741 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:23:53] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank4.pepXML
 processed altogether 61644 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1949 1+, 27070 2+, 23623 3+, 9002 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28833 Decoys, and 32811 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:23:56] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank3.pepXML
 processed altogether 62568 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1943 1+, 27076 2+, 24068 3+, 9481 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28470 Decoys, and 34098 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:24:27] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank3.pepXML
 processed altogether 65706 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2144 1+, 28418 2+, 25310 3+, 9834 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 29351 Decoys, and 36355 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:25:33] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank3.pepXML
 processed altogether 66660 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2312 1+, 29538 2+, 24997 3+, 9813 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 30047 Decoys, and 36613 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:25:52] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_011_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank2.pepXML
 processed altogether 67466 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2263 1+, 30144 2+, 25072 3+, 9987 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27752 Decoys, and 39714 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:28:22] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank2.pepXML
 processed altogether 70071 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2412 1+, 31182 2+, 26311 3+, 10166 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28164 Decoys, and 41907 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:29:36] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank2.pepXML
 processed altogether 71429 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2637 1+, 32928 2+, 25824 3+, 10040 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 29175 Decoys, and 42254 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:30:07] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank1.pepXML
 processed altogether 68527 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2658 1+, 34071 2+, 23279 3+, 8519 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 22851 Decoys, and 45676 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:31:19] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_008_rank1.pepXML
 processed altogether 72828 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2493 1+, 34675 2+, 26042 3+, 9618 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21645 Decoys, and 51183 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:34:17] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_012_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006_rank1.pepXML
 processed altogether 74523 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2635 1+, 35895 2+, 26530 3+, 9463 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 20993 Decoys, and 53530 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 25 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:35:15] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:00:45] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_007_rank1.pepXML
 processed altogether 76157 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2968 1+, 37310 2+, 26187 3+, 9692 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 22438 Decoys, and 53719 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:35:48] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:22:34] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank5.pepXML
 processed altogether 43620 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1459 1+, 20075 2+, 16267 3+, 5819 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21034 Decoys, and 22586 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 29 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:39:21] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:22:10] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank4.pepXML
 processed altogether 50185 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1694 1+, 22910 2+, 18842 3+, 6739 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 23971 Decoys, and 26214 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:41:16] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:21:55] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank3.pepXML
 processed altogether 56070 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2128 1+, 25781 2+, 20483 3+, 7678 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26493 Decoys, and 29577 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:43:21] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_014_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:20:39] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_010_rank2.pepXML
 processed altogether 61677 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2415 1+, 28622 2+, 22270 3+, 8370 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26967 Decoys, and 34710 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:45:40] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:25:52] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank5.pepXML
 processed altogether 54954 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1592 1+, 24081 2+, 21324 3+, 7957 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26561 Decoys, and 28393 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 29 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:46:51] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:25:34] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank4.pepXML
 processed altogether 60017 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1811 1+, 26078 2+, 23445 3+, 8683 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28270 Decoys, and 31747 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 22 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:48:29] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:24:27] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank3.pepXML
 processed altogether 64560 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2035 1+, 28532 2+, 24503 3+, 9490 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 29230 Decoys, and 35330 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:49:08] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:23:57] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank2.pepXML
 processed altogether 69292 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2393 1+, 31343 2+, 25524 3+, 10032 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28744 Decoys, and 40548 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:52:41] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_015_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:31:20] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank4.pepXML
 processed altogether 55628 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1617 1+, 23584 2+, 21914 3+, 8513 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26170 Decoys, and 29458 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:52:55] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:30:07] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank3.pepXML
 processed altogether 60283 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1832 1+, 25974 2+, 23322 3+, 9155 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27406 Decoys, and 32877 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:53:35] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:34:17] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank5.pepXML
 processed altogether 50662 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1383 1+, 21577 2+, 19953 3+, 7749 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 24362 Decoys, and 26300 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 22 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:53:45] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:29:36] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank2.pepXML
 processed altogether 65084 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2095 1+, 29094 2+, 24278 3+, 9617 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27118 Decoys, and 37966 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:56:57] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:23:53] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_011_rank1.pepXML
 processed altogether 74553 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2464 1+, 36359 2+, 25881 3+, 9849 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 22355 Decoys, and 52198 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:58:25] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_016_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:43:22] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank5.pepXML
 processed altogether 41181 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1131 1+, 18200 2+, 15851 3+, 5999 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 19709 Decoys, and 21472 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 28 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:59:18] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:41:16] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank4.pepXML
 processed altogether 47554 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1426 1+, 21056 2+, 18164 3+, 6908 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 22531 Decoys, and 25023 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:59:34] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:39:21] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank3.pepXML
 processed altogether 53316 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1744 1+, 23527 2+, 20286 3+, 7759 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 24681 Decoys, and 28635 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 29 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[19:59:56] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:35:48] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank2.pepXML
 processed altogether 59137 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2046 1+, 26892 2+, 22059 3+, 8140 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25925 Decoys, and 33212 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:00:07] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:28:22] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_012_rank1.pepXML
 processed altogether 70623 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2303 1+, 33942 2+, 24949 3+, 9429 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21693 Decoys, and 48930 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 25 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:01:31] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_018_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:35:15] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_014_rank1.pepXML
 processed altogether 66364 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2368 1+, 32047 2+, 23563 3+, 8386 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21951 Decoys, and 44413 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:05:52] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:49:08] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank4.pepXML
 processed altogether 45862 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1489 1+, 20450 2+, 17339 3+, 6584 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21971 Decoys, and 23891 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:06:42] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:52:41] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank5.pepXML
 processed altogether 39574 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1278 1+, 17748 2+, 14912 3+, 5636 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 18994 Decoys, and 20580 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 29 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:08:05] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:48:29] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank3.pepXML
 processed altogether 51596 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1877 1+, 23233 2+, 19167 3+, 7319 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 24354 Decoys, and 27242 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:08:12] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:46:52] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank2.pepXML
 processed altogether 57241 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2157 1+, 26572 2+, 20762 3+, 7750 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 24728 Decoys, and 32513 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:10:10] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_019_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:53:46] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank3.pepXML
 processed altogether 55343 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1611 1+, 24076 2+, 21401 3+, 8255 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25231 Decoys, and 30112 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:14:58] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank1.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:45:40] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_015_rank1.pepXML
 processed altogether 64845 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2436 1+, 31813 2+, 22477 3+, 8119 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21148 Decoys, and 43697 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 25 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:15:12] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank2.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:58:26] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank5.pepXML
 processed altogether 44903 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1199 1+, 19217 2+, 17663 3+, 6824 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21597 Decoys, and 23306 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 29 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:15:49] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank3.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:56:57] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank4.pepXML
 processed altogether 50277 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1353 1+, 21669 2+, 19642 3+, 7613 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 23680 Decoys, and 26597 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:16:09] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank4.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[19:53:35] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank2.pepXML
 processed altogether 60617 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1937 1+, 26967 2+, 22860 3+, 8853 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25417 Decoys, and 35200 Non-Decoys
INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: .........10.........20......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:18:28] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev_ --database \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas ..\jhammer_Z_2401_020_rank5.pepXML
Please wait. PeptideProphet is running. It can take a long time.
INFO[20:01:31] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank5.pepXML
 processed altogether 48649 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1152 1+, 20915 2+, 19326 3+, 7256 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 23227 Decoys, and 25422 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 22 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:20:10] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:00:07] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank4.pepXML
 processed altogether 53526 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1395 1+, 22924 2+, 21170 3+, 8037 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25172 Decoys, and 28354 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:20:35] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[19:59:56] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank3.pepXML
 processed altogether 58038 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1656 1+, 25042 2+, 22684 3+, 8656 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26484 Decoys, and 31554 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:22:12] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[19:52:55] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_016_rank1.pepXML
 processed altogether 67036 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2077 1+, 32011 2+, 23835 3+, 9113 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 20635 Decoys, and 46401 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

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

WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:23:53] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[19:59:35] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank2.pepXML
 processed altogether 62820 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1990 1+, 28216 2+, 23423 3+, 9191 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 25994 Decoys, and 36826 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:25:37] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[19:59:19] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_018_rank1.pepXML
 processed altogether 68492 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2075 1+, 33068 2+, 24248 3+, 9101 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 20309 Decoys, and 48183 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:30:08] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:08:12] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank4.pepXML
 processed altogether 61804 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1836 1+, 26193 2+, 24614 3+, 9161 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28824 Decoys, and 32980 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:30:35] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:10:10] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank5.pepXML
 processed altogether 57720 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1583 1+, 24159 2+, 23332 3+, 8646 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27307 Decoys, and 30413 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:31:06] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:08:05] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank3.pepXML
 processed altogether 65550 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2175 1+, 28219 2+, 25351 3+, 9805 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 29085 Decoys, and 36465 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:32:01] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:06:43] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank2.pepXML
 processed altogether 69418 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2540 1+, 30913 2+, 25884 3+, 10081 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 27389 Decoys, and 42029 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:34:17] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:16:09] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank4.pepXML
 processed altogether 61365 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1898 1+, 26868 2+, 23664 3+, 8935 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28921 Decoys, and 32444 Non-Decoys
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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:37:03] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:18:28] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank5.pepXML
 processed altogether 56518 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 1691 1+, 24683 2+, 22044 3+, 8100 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 26781 Decoys, and 29737 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:37:48] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:15:49] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank3.pepXML
 processed altogether 65708 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2209 1+, 29006 2+, 24719 3+, 9774 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 29642 Decoys, and 36066 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 (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:38:21] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:05:52] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_019_rank1.pepXML
 processed altogether 73617 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2508 1+, 35540 2+, 26059 3+, 9510 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 20395 Decoys, and 53222 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:38:27] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:15:12] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank2.pepXML
 processed altogether 69793 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2481 1+, 31800 2+, 25466 3+, 10046 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 28657 Decoys, and 41136 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 (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:40:34] Done                                         
Process 'PeptideProphet' finished, exit code: 0
INFO[20:14:58] Executing PeptideProphet  v5.1.0             
 file 1: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_020_rank1.pepXML
 processed altogether 74165 results
INFO: Results written to file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml

  - \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml
  - Building Commentz-Walter keyword tree...'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

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

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem nonspecific 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 2612 1+, 36368 2+, 25610 3+, 9575 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 21675 Decoys, and 52490 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 (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
INFO[20:43:56] Done                                         
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_006_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_007_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_008_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_010_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_011_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_012_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_014_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_015_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_016_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_018_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_019_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank1.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank2.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank3.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank4.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
PeptideProphet: Delete temp
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib\fragpipe-21.1.jar com.github.chhh.utils.FileDelete \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\fragpipe-jhammer_Z_2401_020_rank5.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml4213508721897690072.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml4213508721897690072.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml13689319984458204466.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml13689319984458204466.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml17814224888963578445.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml17814224888963578445.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml3055406573532754547.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml3055406573532754547.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml13924627842630306387.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml13924627842630306387.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml2844109441562820076.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml2844109441562820076.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml14612214500425860714.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml14612214500425860714.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml12713111549462369365.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml12713111549462369365.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml4537964364509139013.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml4537964364509139013.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml9430504889698008005.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml9430504889698008005.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml15433761778107970994.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml15433761778107970994.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml17074605455364064100.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml17074605455364064100.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml126819992337310244.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml126819992337310244.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml1573439483469970045.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml1573439483469970045.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml4029561552135679499.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml4029561552135679499.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml5663123908674917677.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml5663123908674917677.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml9386707290670040255.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml9386707290670040255.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml16761232840010215958.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml16761232840010215958.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml7230523922876658326.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml7230523922876658326.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml15470487599545738151.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml15470487599545738151.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml15976735842645516293.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml15976735842645516293.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml7988619659663042710.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml7988619659663042710.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml134590828401941412.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml134590828401941412.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml10062748998120213681.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml10062748998120213681.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml2230685773841787406.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml2230685773841787406.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml123467957813426878.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml123467957813426878.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml14633857935274163292.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml14633857935274163292.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml3403292516456869396.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml3403292516456869396.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml10513293371445785879.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml10513293371445785879.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml3069145522399882859.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml3069145522399882859.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml5596663270082757255.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml5596663270082757255.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml9472820103260892221.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml9472820103260892221.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml18266644882428552183.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml18266644882428552183.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml9814278444130908213.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml9814278444130908213.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml10260358653686010561.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml10260358653686010561.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml7555424466087844407.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml7555424466087844407.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml7127968612088972884.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml7127968612088972884.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml6255922719894928428.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml6255922719894928428.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml16816533472206027267.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml16816533472206027267.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml15459847258499314477.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml15459847258499314477.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml8377425771870595944.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml8377425771870595944.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml10734142026756577003.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml10734142026756577003.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml14245755466805719093.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml14245755466805719093.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml2660039866685688686.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml2660039866685688686.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml12798367521301750239.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml12798367521301750239.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml2335279456465659768.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml2335279456465659768.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml11169536814449806707.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml11169536814449806707.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml12306708670489464026.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml12306708670489464026.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml11205128156040978948.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml11205128156040978948.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml4472155645052856399.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml4472155645052856399.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml14542602632755647613.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml14542602632755647613.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml12738543552501205023.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml12738543552501205023.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml12864680038975863731.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml12864680038975863731.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml6297190435117140072.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml6297190435117140072.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml12237709917194157521.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml12237709917194157521.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml18033195496562843316.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml18033195496562843316.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml7852025935627821504.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml7852025935627821504.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml15366023052157243105.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml15366023052157243105.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml14990656366304166818.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml14990656366304166818.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
Rewrite pepxml [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\jre\bin\java.exe -cp Z:\FragPipe-jre-21.1\lib/* com.dmtavt.fragpipe.util.RewritePepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML
Fixing pepxml: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml
Writing output to: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml16934305616838218825.temp-rewrite
Deleting file: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml
Moving rewritten file to original location: [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml16934305616838218825.temp-rewrite] -> [\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
ProteinProphet [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_proteinprophet.txt
INFO[20:46:58] Executing ProteinProphet  v5.1.0             
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml...
...read in 436 1+, 14211 2+, 7497 3+, 773 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml...
...read in 0 1+, 5130 2+, 1712 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml...
...read in 536 1+, 14526 2+, 6538 3+, 529 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml...
...read in 0 1+, 5053 2+, 1436 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml...
...read in 329 1+, 13597 2+, 6798 3+, 623 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml...
...read in 0 1+, 4512 2+, 1450 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml...
...read in 300 1+, 10587 2+, 4114 3+, 345 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml...
...read in 0 1+, 2576 2+, 662 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml...
...read in 328 1+, 14188 2+, 6322 3+, 536 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml...
...read in 0 1+, 4762 2+, 1365 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml...
...read in 248 1+, 12785 2+, 6069 3+, 470 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml...
...read in 0 1+, 3932 2+, 1237 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml...
...read in 152 1+, 10090 2+, 5035 3+, 432 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml...
...read in 0 1+, 2583 2+, 818 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml...
...read in 199 1+, 10168 2+, 4663 3+, 426 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml...
...read in 0 1+, 2628 2+, 738 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml...
...read in 0 1+, 11432 2+, 5966 3+, 516 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml...
...read in 0 1+, 3460 2+, 1239 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml...
...read in 132 1+, 12845 2+, 6328 3+, 508 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml...
...read in 0 1+, 4263 2+, 1259 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml...
...read in 294 1+, 14888 2+, 7652 3+, 740 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml...
...read in 0 1+, 5762 2+, 2003 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml...
...read in 360 1+, 14816 2+, 6692 3+, 553 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml...
...read in 0 1+, 5086 2+, 1420 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Initializing 56191 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database //nas22.ethz.ch/biol_imsb_wollscheid_1/Wlab_Fragpipe_defaults/Fasta/2024-01-17-decoys-reviewed-contam-UP000005640.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U
MGUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTVEGANPGLIHFGIVRDHDFKNCIIKAYCTNNERGAVTWELPWFLTHYIELNEKKYVEIAKEESLGCCGYELPTFVTTPVNIYDCKELSAGFLRQALLKGSQIAVPTLEPKDELIDGVAYVYPVNTQEVDNVPIKGSKENIKVGIKELGIKRTCSDRGIALLVTNYVGEITETGETSKALVKLKGPSGKELQQVMVPIFKRLFKVGHQEMYSGVKEAMEQDFGRLLISRVMVTVDLGFGALFGACELAVYSAGVVLTKGPCYPLSFLDDSITCYEKDGQIGLYRPREGTAIVFQAATYYTEQGKKNTAKIKHHEVFEGYSNVYAVAKERLSLRYGWNLSSIHNQIAKTMTEWNHRVQQNYEWGFKRSDCLAQGLLAAQHMLKKPICGVNVCTGGLGWSTGQPSPVVFDLVMVKKGLIAAEKACSLGGSGGGIIILDYDYALDEQLLKQLLGSQYAQFTQDCGGVHVKNVFINPVTKQNTIESLVEQVRAGDDVQDLELVNCEVGLSSFLEKVRTSHPCYSKSFIVVRSREILGVLHRRLEERAESSRSPGPSSLRARRGPPSLVRAGRVHGSRRNPADGAKGPGPSQPPSRE
........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q92813|IOD2_HUMAN : UU
MGALRTKKURKSFNKELWHRVEQLNYSFPGKGGLYAIKQRQVICVREFAVGYAINANNDMRDAVVRCQPPLSFRELLQQAAACRDEQNQHKKVEFSLSSDGPIAWGDSPHAEDIYVLLFDAVSSFEEVLKRFAPLQTSFPPUTASGFNVVLPREPSAFDLLHCTAGEAIKEQTGNGSNDGGETSSVHVVSSNPADEGLKVQKYADLLFSKWVCRLGESTLMRRWEGRTSKSRSLLLVVHKLLIVSDYLALFLCNSFFVPLIQLTILLDVSLIG
...:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U
MSSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTLNVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVA
........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NNW7|TRXR2_HUMAN : U
MGUCGTVTPDLGSRKSIRLKVVEESCTPHIGVTRMVQAYSAGCKIGLAFGQTVEGANPGLFHLGLVLQPPERLCVMKVYCQSADRGAVTFELPKYHAHYVEVHEQGHRAVAEEESLGVCGYELPTFVTTPVNDYDMLDSSGGFLRQVLLRGAMIAIPTLEPRGEVVDGIAYIHPVSTAERSDVLIKQTDPSTDVGAKELNLSRTDPVRGIAWLVTDFTGTDEKGTTSDEWTVQLQGDPLRRVRSPACGRLFRTGHSAMHEIVMSSMQQDFGRLPISRMMITTDLGIGTLFGACELAVYSAGVVLTKGPSEKLWFIDDSTIGYELAGEIHTPYRPRGGTAIIIHDASLLIEKGGKAVGCVTHEDVFSAKINFYKVKRDQLQVRHGWNLSKVHNQVAEAMKRWDHPVPQAVEWGYNPADQILGGLLAAQHMLKKPICGVNVCTGGLGWRTGQPSPEVYDVVAVKRGLQAAEKACALGGSGGGVVLLDYDRQGAAAGRAAGRVGGAVAQTRWRFRGGLGRLAVAMAA
.18000
.........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV6|MSRB1_HUMAN : U
MHGQSASTEKGKPVFKLSSSFIUFRSQGPKPGDNLFEHGLGNGCKGCSVKLAESRNHEPRKAVSDAHITETFAPWPSSHAYKSRSSFLEYGCKACVYVGPEFHNQFVEGGFFSCFS
........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.......WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U
MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
..:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|P62341|SELT_HUMAN : U
MRLLLLLLVAASAMVRSEASANLGGVPSKRLKMQYATGPLLKFQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS
.:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U
MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG
..:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U
MERSPPQSPGPGKAGDAPNRRSGHVRGARVLSPPGRRARLSSPGPSRSSEAREELRRHLVGLIERSRVVIFSKSYCPHSTRVKELFSSLGVECNVLELDQVDDGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQAYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAKEAAILGKKVMVLDFVVPSPQGTSWGLGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIKATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMVQQLEKGSPGKLKVLAKSTEGTETIEGVYNTVLLAIGRDSCTRKIGLEKIGVKINEKSGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLEIYHTLFWPLEWTVAGRENNTCYAKIICNKFDHDRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG
.......:.........:.........:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U
MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS
....33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9BQE4|SELS_HUMAN : U
MERQEESLSARPALETEGLRFLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGUG
......:.........:.........37000
...WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U
MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS
......:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U
MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL
.....:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U
MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6D0|SELK_HUMAN : U
MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR
.......:..  Total: 40924
Computing degenerate peptides for 12646 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 13053 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=0.000150256, db_size=45657246
Computing MU for 13053 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[20:48:06] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas --prefix rev_
INFO[20:48:06] Executing Database  v5.1.0                   
INFO[20:48:06] Annotating the database                      
INFO[20:48:07] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --picked --prot 0.01 --tag rev_ --pepxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 --protxml \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\combined.prot.xml --razor
INFO[20:48:08] Executing Filter  v5.1.0                     
INFO[20:48:08] Processing peptide identification files      
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml 
WARN[20:48:08] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml 
INFO[20:48:08] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml 
WARN[20:48:09] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml 
INFO[20:48:09] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml 
INFO[20:48:10] Parsing \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml 
WARN[20:48:10] No PSM was found in data set. \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml 
INFO[20:48:13] 1+ Charge profile                             decoy=608 target=3983
INFO[20:48:13] 2+ Charge profile                             decoy=20656 target=246938
INFO[20:48:13] 3+ Charge profile                             decoy=8051 target=116577
INFO[20:48:13] 4+ Charge profile                             decoy=970 target=10547
INFO[20:48:13] 5+ Charge profile                             decoy=0 target=0
INFO[20:48:13] 6+ Charge profile                             decoy=0 target=0
INFO[20:48:15] Database search results                       ions=93711 peptides=76758 psms=408330
INFO[20:48:16] Converged to 1.00 % FDR with 258062 PSMs      decoy=2582 threshold=0.6909 total=260644
INFO[20:48:16] Converged to 0.99 % FDR with 24170 Peptides   decoy=241 threshold=0.9482 total=24411
INFO[20:48:16] Converged to 1.00 % FDR with 32301 Ions       decoy=324 threshold=0.9316 total=32625
INFO[20:48:16] Protein inference results                     decoy=4068 target=7872
INFO[20:48:17] Converged to 0.98 % FDR with 3352 Proteins    decoy=33 threshold=0.9884 total=3385
INFO[20:48:18] 2D FDR estimation: Protein mirror image       decoy=3352 target=3352
INFO[20:48:20] Second filtering results                      ions=55938 peptides=42216 psms=353449
INFO[20:48:20] Converged to 1.00 % FDR with 322717 PSMs      decoy=3229 threshold=0.1317 total=325946
INFO[20:48:20] Converged to 0.99 % FDR with 29127 Peptides   decoy=291 threshold=0.7725 total=29418
INFO[20:48:20] Converged to 1.00 % FDR with 39495 Ions       decoy=395 threshold=0.7105 total=39890
INFO[20:48:20] Post processing identifications              
INFO[20:48:25] Assigning protein identifications to layers  
INFO[20:49:24] Processing protein inference                 
INFO[20:49:25] Synchronizing PSMs and proteins              
INFO[20:49:27] Final report numbers after FDR filtering, and post-processing  ions=39479 peptides=29115 proteins=3352 psms=322605
INFO[20:49:27] Saving                                       
INFO[20:49:48] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
Z:\FragPipe-jre-21.1\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report --msstats --removecontam
INFO[20:49:48] Executing Report  v5.1.0                     
INFO[20:49:48] Creating reports                             
INFO[20:52:17] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
SpecLibGen [Work dir: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3]
\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\python.exe -u Z:\FragPipe-jre-21.1\tools\speclib\gen_con_spec_lib.py \\nas22.ethz.ch\biol_imsb_wollscheid_1\Wlab_Fragpipe_defaults\Fasta\2024-01-17-decoys-reviewed-contam-UP000005640.fas \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 unused \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3 True unused use_easypqp noiRT;noIM 16 "--unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.0" delete_intermediate_files \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_speclibgen.txt
File list provided
Spectral library building
Commands to execute:
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_006.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_006.psmpkl --peaks jhammer_Z_2401_006.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_007.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_007.psmpkl --peaks jhammer_Z_2401_007.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_008.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_008.psmpkl --peaks jhammer_Z_2401_008.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_010.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_010.psmpkl --peaks jhammer_Z_2401_010.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_011.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_011.psmpkl --peaks jhammer_Z_2401_011.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_012.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_012.psmpkl --peaks jhammer_Z_2401_012.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_014.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_014.psmpkl --peaks jhammer_Z_2401_014.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_015.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_015.psmpkl --peaks jhammer_Z_2401_015.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_016.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_016.psmpkl --peaks jhammer_Z_2401_016.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_018.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_018.psmpkl --peaks jhammer_Z_2401_018.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_019.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_019.psmpkl --peaks jhammer_Z_2401_019.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' convert --unimod Z:/FragPipe-jre-21.1/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank1.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank2.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank3.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank4.pep.xml'"'"', '"'"'\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank5.pep.xml'"'"']' --spectra '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\1-12\jhammer_Z_2401_020.mzML' --exclude-range -1.5,3.5 --psms jhammer_Z_2401_020.psmpkl --peaks jhammer_Z_2401_020.peakpkl
'\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe' library --psmtsv '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\psm.tsv' --peptidetsv '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\peptide.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\filelist_easypqp_library.txt'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easypqp, version 0.1.42
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_006_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_006_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_006_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_006_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_006_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_006.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_006.psmpkl', '--peaks', 'jhammer_Z_2401_006.peakpkl']
2024-01-17 20:55:58 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_006_rank5.pep.xml'].
2024-01-17 20:55:58 - Info: Parsing run jhammer_Z_2401_006.
2024-01-17 20:55:59 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank1.pep.xml
2024-01-17 20:56:05 - Info: 28416 PSMs parsed.
2024-01-17 20:56:05 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank2.pep.xml
2024-01-17 20:56:07 - Info: 11068 PSMs parsed.
2024-01-17 20:56:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank3.pep.xml
2024-01-17 20:56:07 - Info: 0 PSMs parsed.
2024-01-17 20:56:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank4.pep.xml
2024-01-17 20:56:07 - Info: 0 PSMs parsed.
2024-01-17 20:56:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_006_rank5.pep.xml
2024-01-17 20:56:07 - Info: 0 PSMs parsed.
2024-01-17 20:56:07 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_007_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_007_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_007_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_007_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_007_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_007.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_007.psmpkl', '--peaks', 'jhammer_Z_2401_007.peakpkl']
2024-01-17 20:57:14 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_007_rank5.pep.xml'].
2024-01-17 20:57:14 - Info: Parsing run jhammer_Z_2401_007.
2024-01-17 20:57:14 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank1.pep.xml
2024-01-17 20:57:20 - Info: 27190 PSMs parsed.
2024-01-17 20:57:20 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank2.pep.xml
2024-01-17 20:57:22 - Info: 10463 PSMs parsed.
2024-01-17 20:57:22 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank3.pep.xml
2024-01-17 20:57:22 - Info: 0 PSMs parsed.
2024-01-17 20:57:22 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank4.pep.xml
2024-01-17 20:57:22 - Info: 0 PSMs parsed.
2024-01-17 20:57:22 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_007_rank5.pep.xml
2024-01-17 20:57:22 - Info: 0 PSMs parsed.
2024-01-17 20:57:22 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_008_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_008_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_008_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_008_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_008_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_008.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_008.psmpkl', '--peaks', 'jhammer_Z_2401_008.peakpkl']
2024-01-17 20:58:30 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_008_rank5.pep.xml'].
2024-01-17 20:58:30 - Info: Parsing run jhammer_Z_2401_008.
2024-01-17 20:58:31 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank1.pep.xml
2024-01-17 20:58:36 - Info: 26672 PSMs parsed.
2024-01-17 20:58:36 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank2.pep.xml
2024-01-17 20:58:38 - Info: 9419 PSMs parsed.
2024-01-17 20:58:38 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank3.pep.xml
2024-01-17 20:58:38 - Info: 0 PSMs parsed.
2024-01-17 20:58:38 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank4.pep.xml
2024-01-17 20:58:38 - Info: 0 PSMs parsed.
2024-01-17 20:58:38 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_008_rank5.pep.xml
2024-01-17 20:58:38 - Info: 0 PSMs parsed.
2024-01-17 20:58:38 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_010_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_010_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_010_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_010_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_010_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_010.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_010.psmpkl', '--peaks', 'jhammer_Z_2401_010.peakpkl']
2024-01-17 20:59:44 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_010_rank5.pep.xml'].
2024-01-17 20:59:44 - Info: Parsing run jhammer_Z_2401_010.
2024-01-17 20:59:45 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank1.pep.xml
2024-01-17 20:59:49 - Info: 20737 PSMs parsed.
2024-01-17 20:59:49 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank2.pep.xml
2024-01-17 20:59:50 - Info: 6117 PSMs parsed.
2024-01-17 20:59:50 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank3.pep.xml
2024-01-17 20:59:50 - Info: 0 PSMs parsed.
2024-01-17 20:59:50 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank4.pep.xml
2024-01-17 20:59:50 - Info: 0 PSMs parsed.
2024-01-17 20:59:50 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_010_rank5.pep.xml
2024-01-17 20:59:50 - Info: 0 PSMs parsed.
2024-01-17 20:59:50 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_011_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_011_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_011_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_011_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_011_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_011.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_011.psmpkl', '--peaks', 'jhammer_Z_2401_011.peakpkl']
2024-01-17 21:00:55 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_011_rank5.pep.xml'].
2024-01-17 21:00:55 - Info: Parsing run jhammer_Z_2401_011.
2024-01-17 21:00:56 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank1.pep.xml
2024-01-17 21:01:01 - Info: 26776 PSMs parsed.
2024-01-17 21:01:01 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank2.pep.xml
2024-01-17 21:01:03 - Info: 10181 PSMs parsed.
2024-01-17 21:01:03 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank3.pep.xml
2024-01-17 21:01:03 - Info: 0 PSMs parsed.
2024-01-17 21:01:03 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank4.pep.xml
2024-01-17 21:01:03 - Info: 0 PSMs parsed.
2024-01-17 21:01:03 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_011_rank5.pep.xml
2024-01-17 21:01:03 - Info: 0 PSMs parsed.
2024-01-17 21:01:04 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_012_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_012_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_012_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_012_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_012_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_012.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_012.psmpkl', '--peaks', 'jhammer_Z_2401_012.peakpkl']
2024-01-17 21:02:09 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_012_rank5.pep.xml'].
2024-01-17 21:02:09 - Info: Parsing run jhammer_Z_2401_012.
2024-01-17 21:02:10 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank1.pep.xml
2024-01-17 21:02:15 - Info: 24757 PSMs parsed.
2024-01-17 21:02:15 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank2.pep.xml
2024-01-17 21:02:17 - Info: 8760 PSMs parsed.
2024-01-17 21:02:17 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank3.pep.xml
2024-01-17 21:02:17 - Info: 0 PSMs parsed.
2024-01-17 21:02:17 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank4.pep.xml
2024-01-17 21:02:17 - Info: 0 PSMs parsed.
2024-01-17 21:02:17 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_012_rank5.pep.xml
2024-01-17 21:02:17 - Info: 0 PSMs parsed.
2024-01-17 21:02:17 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_014_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_014_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_014_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_014_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_014_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_014.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_014.psmpkl', '--peaks', 'jhammer_Z_2401_014.peakpkl']
2024-01-17 21:03:21 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_014_rank5.pep.xml'].
2024-01-17 21:03:21 - Info: Parsing run jhammer_Z_2401_014.
2024-01-17 21:03:22 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank1.pep.xml
2024-01-17 21:03:26 - Info: 21334 PSMs parsed.
2024-01-17 21:03:26 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank2.pep.xml
2024-01-17 21:03:27 - Info: 6257 PSMs parsed.
2024-01-17 21:03:27 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank3.pep.xml
2024-01-17 21:03:27 - Info: 0 PSMs parsed.
2024-01-17 21:03:27 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank4.pep.xml
2024-01-17 21:03:27 - Info: 0 PSMs parsed.
2024-01-17 21:03:27 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_014_rank5.pep.xml
2024-01-17 21:03:27 - Info: 0 PSMs parsed.
2024-01-17 21:03:27 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_015_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_015_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_015_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_015_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_015_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_015.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_015.psmpkl', '--peaks', 'jhammer_Z_2401_015.peakpkl']
2024-01-17 21:04:36 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_015_rank5.pep.xml'].
2024-01-17 21:04:36 - Info: Parsing run jhammer_Z_2401_015.
2024-01-17 21:04:36 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank1.pep.xml
2024-01-17 21:04:40 - Info: 20876 PSMs parsed.
2024-01-17 21:04:40 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank2.pep.xml
2024-01-17 21:04:42 - Info: 5742 PSMs parsed.
2024-01-17 21:04:42 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank3.pep.xml
2024-01-17 21:04:42 - Info: 0 PSMs parsed.
2024-01-17 21:04:42 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank4.pep.xml
2024-01-17 21:04:42 - Info: 0 PSMs parsed.
2024-01-17 21:04:42 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_015_rank5.pep.xml
2024-01-17 21:04:42 - Info: 0 PSMs parsed.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
2024-01-17 21:04:42 - Info: Generate theoretical spectra.
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_016_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_016_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_016_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_016_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_016_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_016.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_016.psmpkl', '--peaks', 'jhammer_Z_2401_016.peakpkl']
2024-01-17 21:05:47 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_016_rank5.pep.xml'].
2024-01-17 21:05:47 - Info: Parsing run jhammer_Z_2401_016.
2024-01-17 21:05:47 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank1.pep.xml
2024-01-17 21:05:52 - Info: 22875 PSMs parsed.
2024-01-17 21:05:52 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank2.pep.xml
2024-01-17 21:05:54 - Info: 8011 PSMs parsed.
2024-01-17 21:05:54 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank3.pep.xml
2024-01-17 21:05:54 - Info: 0 PSMs parsed.
2024-01-17 21:05:54 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank4.pep.xml
2024-01-17 21:05:54 - Info: 0 PSMs parsed.
2024-01-17 21:05:54 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_016_rank5.pep.xml
2024-01-17 21:05:54 - Info: 0 PSMs parsed.
2024-01-17 21:05:54 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_018_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_018_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_018_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_018_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_018_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_018.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_018.psmpkl', '--peaks', 'jhammer_Z_2401_018.peakpkl']
2024-01-17 21:06:59 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_018_rank5.pep.xml'].
2024-01-17 21:06:59 - Info: Parsing run jhammer_Z_2401_018.
2024-01-17 21:07:00 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank1.pep.xml
2024-01-17 21:07:05 - Info: 24589 PSMs parsed.
2024-01-17 21:07:05 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank2.pep.xml
2024-01-17 21:07:07 - Info: 8985 PSMs parsed.
2024-01-17 21:07:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank3.pep.xml
2024-01-17 21:07:07 - Info: 0 PSMs parsed.
2024-01-17 21:07:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank4.pep.xml
2024-01-17 21:07:07 - Info: 0 PSMs parsed.
2024-01-17 21:07:07 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_018_rank5.pep.xml
2024-01-17 21:07:07 - Info: 0 PSMs parsed.
2024-01-17 21:07:07 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_019_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_019_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_019_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_019_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_019_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_019.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_019.psmpkl', '--peaks', 'jhammer_Z_2401_019.peakpkl']
2024-01-17 21:08:14 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_019_rank5.pep.xml'].
2024-01-17 21:08:14 - Info: Parsing run jhammer_Z_2401_019.
2024-01-17 21:08:14 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank1.pep.xml
2024-01-17 21:08:20 - Info: 28984 PSMs parsed.
2024-01-17 21:08:20 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank2.pep.xml
2024-01-17 21:08:23 - Info: 12308 PSMs parsed.
2024-01-17 21:08:23 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank3.pep.xml
2024-01-17 21:08:23 - Info: 0 PSMs parsed.
2024-01-17 21:08:23 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank4.pep.xml
2024-01-17 21:08:23 - Info: 0 PSMs parsed.
2024-01-17 21:08:23 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_019_rank5.pep.xml
2024-01-17 21:08:23 - Info: 0 PSMs parsed.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
2024-01-17 21:08:23 - Info: Generate theoretical spectra.
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Executing ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\software\\fragpipe_v20.0\\Python\\Scripts\\easypqp.exe', 'convert', '--unimod', 'Z:/FragPipe-jre-21.1/tools/unimod_old.xml', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', "['\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_020_rank1.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_020_rank2.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_020_rank3.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_020_rank4.pep.xml', '\\\\\\\\nas22.ethz.ch\\\\biol_imsb_wollscheid_1\\\\jhammer_nas22\\\\SF16\\\\Fragpipe_3\\\\interact-jhammer_Z_2401_020_rank5.pep.xml']", '--spectra', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\1-12\\jhammer_Z_2401_020.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'jhammer_Z_2401_020.psmpkl', '--peaks', 'jhammer_Z_2401_020.peakpkl']
2024-01-17 21:09:26 - Info: Converting ['\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank1.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank2.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank3.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank4.pep.xml', '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\interact-jhammer_Z_2401_020_rank5.pep.xml'].
2024-01-17 21:09:26 - Info: Parsing run jhammer_Z_2401_020.
2024-01-17 21:09:26 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank1.pep.xml
2024-01-17 21:09:32 - Info: 27609 PSMs parsed.
2024-01-17 21:09:32 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank2.pep.xml
2024-01-17 21:09:34 - Info: 10204 PSMs parsed.
2024-01-17 21:09:34 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank3.pep.xml
2024-01-17 21:09:34 - Info: 0 PSMs parsed.
2024-01-17 21:09:34 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank4.pep.xml
2024-01-17 21:09:34 - Info: 0 PSMs parsed.
2024-01-17 21:09:34 - Info: Parsing pepXML: \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\interact-jhammer_Z_2401_020_rank5.pep.xml
2024-01-17 21:09:34 - Info: 0 PSMs parsed.
2024-01-17 21:09:34 - Info: Generate theoretical spectra.
D:\a\OpenMS\OpenMS\OpenMS\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this.
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 90, in convert
    psms, peaks = conversion(pepxmlfile_list, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses, max_psm_pep, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 737, in conversion
    psms, theoretical = parse_pepxmls(pepxmlfile_list, um, base_name, exclude_range, enable_unannotated, enable_massdiff, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 704, in parse_pepxmls
    theoretical.setdefault(modified_peptide, {})[precursor_charge] = generate_ionseries(modified_peptide, precursor_charge, fragment_charges, fragment_types, enable_specific_losses, enable_unspecific_losses, precision_digits)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\convert.py", line 604, in generate_ionseries
    peptide = po.AASequence.fromString(po.String(peptide_sequence))
  File "pyopenms\\_pyopenms_1.pyx", line 31, in pyopenms._pyopenms_1.__static_AASequence_fromString
RuntimeError: While loading '//nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml': unable to open primary document entity '\\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3///nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml'
Probable cause: The file suffix (xml) does not match the file content (unknown). Rename the file to fix this. in: //nas22.ethz.ch/biol_imsb_wollscheid_1/software/fragpipe_v20.0/Python/lib/site-packages/pyopenms/share/OpenMS/CHEMISTRY/unimod.xml
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
2024-01-17 21:10:41 - Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic.
2024-01-17 21:10:41 - Info: Reading file \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006.psmpkl.
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 135, in library
    generate(infiles, outfile, psmtsv, peptidetsv, perform_rt_calibration, rt_referencefile, rt_reference_run_path, rt_filter, perform_im_calibration, im_referencefile, im_reference_run_path, im_filter, psm_fdr_threshold, peptide_fdr_threshold, protein_fdr_threshold, rt_lowess_fraction, rt_psm_fdr_threshold, im_lowess_fraction, im_psm_fdr_threshold, pi0_lambda, peptide_plot_path, protein_plot_path, min_peptides, proteotypic, consensus, nofdr)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\library.py", line 338, in generate
    psm_tab = pd.read_pickle(psm_file)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\pandas\io\pickle.py", line 187, in read_pickle
    with get_handle(
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\pandas\io\common.py", line 798, in get_handle
    handle = open(handle, ioargs.mode)
FileNotFoundError: [Errno 2] No such file or directory: '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\jhammer_Z_2401_006.psmpkl'
Not enough peptides could be found for alignment.
Using ciRT for alignment
Traceback (most recent call last):
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1128, in __call__
2024-01-17 21:11:49 - Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic.
2024-01-17 21:11:49 - Info: Reading file \\nas22.ethz.ch\biol_imsb_wollscheid_1\jhammer_nas22\SF16\Fragpipe_3\jhammer_Z_2401_006.psmpkl.
    return self.main(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1690, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\click\core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\main.py", line 135, in library
    generate(infiles, outfile, psmtsv, peptidetsv, perform_rt_calibration, rt_referencefile, rt_reference_run_path, rt_filter, perform_im_calibration, im_referencefile, im_reference_run_path, im_filter, psm_fdr_threshold, peptide_fdr_threshold, protein_fdr_threshold, rt_lowess_fraction, rt_psm_fdr_threshold, im_lowess_fraction, im_psm_fdr_threshold, pi0_lambda, peptide_plot_path, protein_plot_path, min_peptides, proteotypic, consensus, nofdr)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\easypqp\library.py", line 338, in generate
    psm_tab = pd.read_pickle(psm_file)
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\pandas\io\pickle.py", line 187, in read_pickle
    with get_handle(
  File "\\nas22.ethz.ch\biol_imsb_wollscheid_1\software\fragpipe_v20.0\Python\lib\site-packages\pandas\io\common.py", line 798, in get_handle
    handle = open(handle, ioargs.mode)
FileNotFoundError: [Errno 2] No such file or directory: '\\\\nas22.ethz.ch\\biol_imsb_wollscheid_1\\jhammer_nas22\\SF16\\Fragpipe_3\\jhammer_Z_2401_006.psmpkl'
Library not generated, not enough peptides could be found for alignment.
Library not generated, not enough peptides could be found for alignment.
Please try using other options for alignment (e.g. ciRT if used other options)
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 7 remaining tasks