System OS: Windows Server 2019, Architecture: AMD64
Java Info: 11.0.15, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A


Version info:
FragPipe version 19.0
MSFragger version 3.6
IonQuant version 1.8.9
Philosopher version 4.6.0


LCMS files:
  Experiment/Group: A
  - D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML	DIA
  - D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML	DIA
  - D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML	DIA


45 commands to execute:
CheckCentroid
java -Xmx82G -cp "D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\batmass-io-1.28.8.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML 47
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\sark546\AppData\Local\Temp\15\9e90bd85-abb8-4392-bb1c-b6d0d06686ff
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\sark546\AppData\Local\Temp\15\4039e347-a341-4bda-9a82-3522f976c2eb
MSFragger [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
java -jar -Dfile.encoding=UTF-8 -Xmx82G D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\MSFragger-3.6\MSFragger-3.6.jar D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\fragger_dia.params D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin
MSBooster [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
java -Xmx82G -cp "D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\msbooster-1.1.10.jar;D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\batmass-io-1.28.8.jar" Features.MainClass --paramsList D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\msbooster_params.txt
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe database --annotate D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe database --annotate D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe filter --picked --prot 0.01 --tag rev_ --pepxml D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A --protxml D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe report
SpecLibGen [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
C:\Python39\python.exe -u D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\speclib\gen_con_spec_lib.py D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A unused D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A True unused use_easypqp noiRT;noIM 47 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] " "--rt_lowess_fraction 0.0" delete_intermediate_files D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\filelist_speclibgen.txt
WorkspaceClean [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [CheckCentroid], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
    Cmd: [MSFragger], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [MSBooster], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [Percolator], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [ProteinProphet], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [PhilosopherFilter], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [PhilosopherReport], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [SpecLibGen], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [WorkspaceClean], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
    Cmd: [WorkspaceClean], Work dir: [D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]

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

~~~~~~Sample of D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas~~~~~~~
>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
>rev_sp|O43505|B4GA1_HUMAN Beta-1,4-glucuronyltransferase 1 OS=Homo sapiens OX=9606 GN=B4GAT1 PE=1 SV=1
>rev_sp|P0DME0|SETLP_HUMAN Protein SETSIP OS=Homo sapiens OX=9606 GN=SETSIP PE=1 SV=1
>rev_sp|P49662|CASP4_HUMAN Caspase-4 OS=Homo sapiens OX=9606 GN=CASP4 PE=1 SV=1
>rev_sp|Q14146|URB2_HUMAN Unhealthy ribosome biogenesis protein 2 homolog OS=Homo sapiens OX=9606 GN=URB2 PE=1 SV=2
>rev_sp|Q68DK2|ZFY26_HUMAN Zinc finger FYVE domain-containing protein 26 OS=Homo sapiens OX=9606 GN=ZFYVE26 PE=1 SV=4
>rev_sp|Q8IWB9|TEX2_HUMAN Testis-expressed protein 2 OS=Homo sapiens OX=9606 GN=TEX2 PE=1 SV=2
>rev_sp|Q8WVI7|PPR1C_HUMAN Protein phosphatase 1 regulatory subunit 1C OS=Homo sapiens OX=9606 GN=PPP1R1C PE=1 SV=1
>rev_sp|Q9BRC7|PLCD4_HUMAN 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-4 OS=Homo sapiens OX=9606 GN=PLCD4 PE=1 SV=1
>rev_sp|Q9NUP7|TRM13_HUMAN tRNA:m(4)X modification enzyme TRM13 homolog OS=Homo sapiens OX=9606 GN=TRMT13 PE=1 SV=2
>rev_sp|Q9Y6N1|COX11_HUMAN Cytochrome c oxidase assembly protein COX11, mitochondrial OS=Homo sapiens OX=9606 GN=COX11 PE=1 SV=3
>sp|O43623|SNAI2_HUMAN Zinc finger protein SNAI2 OS=Homo sapiens OX=9606 GN=SNAI2 PE=1 SV=1
>sp|P0DO97|CC192_HUMAN Coiled-coil domain-containing protein 192 OS=Homo sapiens OX=9606 GN=CCDC192 PE=4 SV=1
>sp|P49810|PSN2_HUMAN Presenilin-2 OS=Homo sapiens OX=9606 GN=PSEN2 PE=1 SV=1
>sp|Q14240|IF4A2_HUMAN Eukaryotic initiation factor 4A-II OS=Homo sapiens OX=9606 GN=EIF4A2 PE=1 SV=2
>sp|Q6AW86|Z324B_HUMAN Zinc finger protein 324B OS=Homo sapiens OX=9606 GN=ZNF324B PE=1 SV=1
>sp|Q8IWX5|SGPP2_HUMAN Sphingosine-1-phosphate phosphatase 2 OS=Homo sapiens OX=9606 GN=SGPP2 PE=1 SV=1
>sp|Q8WW59|SPRY4_HUMAN SPRY domain-containing protein 4 OS=Homo sapiens OX=9606 GN=SPRYD4 PE=1 SV=3
>sp|Q9BRT9|SLD5_HUMAN DNA replication complex GINS protein SLD5 OS=Homo sapiens OX=9606 GN=GINS4 PE=1 SV=1
>sp|Q9NVD3|SETD4_HUMAN SET domain-containing protein 4 OS=Homo sapiens OX=9606 GN=SETD4 PE=1 SV=1
>sp|Q9Y6Y8|S23IP_HUMAN SEC23-interacting protein OS=Homo sapiens OX=9606 GN=SEC23IP PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v19.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\2024-04-09-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 accuracy)
diann.run-dia-nn=false
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
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=C\:\\Users\\sark546\\Documents\\FragPipe-jre-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=D\:\\Public\\Snigdha\\Documents\\FragPipe-19.0\\fragpipe\\tools\\IonQuant-1.8.9.jar
fragpipe-config.bin-msfragger=D\:\\Public\\Snigdha\\Documents\\FragPipe-19.0\\fragpipe\\tools\\MSFragger-3.6\\MSFragger-3.6.jar
fragpipe-config.bin-philosopher=D\:\\Public\\Snigdha\\Documents\\FragPipe-19.0\\fragpipe\\tools\\philosopher_v4.6.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Python39\\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=10
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=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=4
msfragger.allowed_missed_cleavage_2=1
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=0.0
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=5
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
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=1
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=true
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=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
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; 0.0,site_06,false,1; 0.0,site_07,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 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=300
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=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
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.diagextract_mode=false
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_mode=false
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_mode=false
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=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
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=false
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=false
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.dont-run-fq-lq=false
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=D\:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=47

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx82G -cp "D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\batmass-io-1.28.8.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML 47
Done in 14187 ms.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:16:59] Executing Workspace  v4.6.0                  
INFO[10:16:59] Removing workspace                           
WARN[10:16:59] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[10:16:59] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\sark546\AppData\Local\Temp\15\9e90bd85-abb8-4392-bb1c-b6d0d06686ff
INFO[10:17:00] Executing Workspace  v4.6.0                  
INFO[10:17:00] Creating workspace                           
INFO[10:17:00] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[10:17:00] Executing Workspace  v4.6.0                  
INFO[10:17:00] Removing workspace                           
WARN[10:17:00] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[10:17:00] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\sark546\AppData\Local\Temp\15\4039e347-a341-4bda-9a82-3522f976c2eb
INFO[10:17:01] Executing Workspace  v4.6.0                  
INFO[10:17:01] Creating workspace                           
INFO[10:17:01] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
java -jar -Dfile.encoding=UTF-8 -Xmx82G D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\MSFragger-3.6\MSFragger-3.6.jar D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\fragger_dia.params D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
MSFragger version MSFragger-3.6
Batmass-IO version 1.28.8
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 2019, Architecture: AMD64
Java Info: 11.0.15, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 82 GB memory
data_type > 0 and intensity_transform != 0. Change intensity_transform to 1.
Checking database...
data_type > 0. Will use the isolation window from the spectral file as precursor tolerance.
Checking spectral files...
D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML: Scans = 73294
D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML: Scans = 72728
D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML: Scans = 72340
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 47
database_name = D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -10.0
precursor_mass_upper = 10.0
precursor_mass_units = 1
data_type = 1
precursor_true_tolerance = 10.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 1
use_all_mods_in_first_search = false
write_calibrated_mzml = 0
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 1.7976931348623157E308
report_alternative_proteins = false
override_charge = true
precursor_charge_low = 2
precursor_charge_high = 3
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = true
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 200
minIonsScoring = 2
min_matched_fragments = 5
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
remove_precursor_peak = 0
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 = true
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: 290216
	of length 8: 281208
	of length 9: 280502
	of length 10: 264775
	of length 11: 251346
	of length 12: 240545
	of length 13: 234409
	of length 14: 219696
	of length 15: 208369
	of length 16: 194727
	of length 17: 182215
	of length 18: 174912
	of length 19: 171673
	of length 20: 153762
	of length 21: 147015
	of length 22: 137952
	of length 23: 128673
	of length 24: 122028
	of length 25: 114729
	of length 26: 106882
	of length 27: 101796
	of length 28: 97214
	of length 29: 88421
	of length 30: 83896
	of length 31: 78639
	of length 32: 74510
	of length 33: 69726
	of length 34: 65339
	of length 35: 59162
	of length 36: 57587
	of length 37: 52337
	of length 38: 49259
	of length 39: 44409
	of length 40: 42250
	of length 41: 39353
	of length 42: 36353
	of length 43: 30487
	of length 44: 24692
	of length 45: 18969
	of length 46: 12402
	of length 47: 7841
	of length 48: 4514
	of length 49: 2441
	of length 50: 1488
In total 5048719 peptides.
Generated 5048719 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
183344414 fragments to be searched in 1 slices (2.73 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 3.01 s
	001. 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML 7.4 s | deisotoping 6.2 s
		[progress: 70818/70818 (100%) - 2686 spectra/s] 26.4s
	002. 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML 4.6 s | deisotoping 0.8 s
		[progress: 69578/69578 (100%) - 4026 spectra/s] 17.3s
	003. 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML 3.3 s | deisotoping 0.8 s
		[progress: 69864/69864 (100%) - 3810 spectra/s] 18.3s
***************************FIRST SEARCH DONE IN 2.131 MIN**************************

*********************************MASS CALIBRATION**********************************
-----|---------------|---------------
     |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  
 001 |   0.05   1.50 |  -0.03   1.43  
 002 |   0.09   1.44 |  -0.05   1.44  
 003 |  -0.01   1.43 |  -0.02   1.42  
-----|---------------|---------------
New fragment_mass_tolerance = 6 PPM
**************************MASS CALIBRATION DONE IN 0.575 MIN***********************

************************************MAIN SEARCH************************************
data_type > 0 and intensity_transform != 0. Change intensity_transform to 1.
Checking database...
data_type > 0. Will use the isolation window from the spectral file as precursor tolerance.
Parameters:
num_threads = 47
database_name = D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -10.0
precursor_mass_upper = 10.0
precursor_mass_units = 1
data_type = 1
precursor_true_tolerance = 10.0
precursor_true_units = 1
fragment_mass_tolerance = 6.0
fragment_mass_units = 1
calibrate_mass = 1
use_all_mods_in_first_search = false
write_calibrated_mzml = 0
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 4
num_enzyme_termini = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
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 = true
override_charge = true
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = true
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 5
minimum_ratio = 0.0
intensity_transform = 1
activation_types = all
remove_precursor_peak = 0
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 = true
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: 4242276
	of length 8: 4450119
	of length 9: 4479314
	of length 10: 4493717
	of length 11: 4494009
	of length 12: 4480002
	of length 13: 4454400
	of length 14: 4427178
	of length 15: 4389541
	of length 16: 4348247
	of length 17: 4300235
	of length 18: 4235815
	of length 19: 4159314
	of length 20: 4101482
	of length 21: 4022826
	of length 22: 3937805
	of length 23: 3854020
	of length 24: 3764234
	of length 25: 3671472
	of length 26: 3579926
	of length 27: 3483407
	of length 28: 3366444
	of length 29: 3268415
	of length 30: 3169927
	of length 31: 3069620
	of length 32: 2969803
	of length 33: 2871340
	of length 34: 2771230
	of length 35: 2677551
	of length 36: 2580197
	of length 37: 2486105
	of length 38: 2392198
	of length 39: 2304001
	of length 40: 2211337
	of length 41: 2108620
	of length 42: 1962137
	of length 43: 1732728
	of length 44: 1406042
	of length 45: 1031265
	of length 46: 687782
	of length 47: 424158
	of length 48: 246465
	of length 49: 140002
	of length 50: 79751
In total 133326457 peptides.
Generated 223708320 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.03 Da.
10998021012 fragments to be searched in 3 slices (163.88 GB total)
Operating on slice 1 of 3: 
	Fragment index slice generated in 54.41 s
	001. 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 3.8 s
		[progress: 70549/70549 (100%) - 113 spectra/s] 622.2s
	002. 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 5.8 s
		[progress: 69333/69333 (100%) - 118 spectra/s] 588.3s
	003. 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 5.6 s
		[progress: 69631/69631 (100%) - 122 spectra/s] 569.5s
Operating on slice 2 of 3: 
	Fragment index slice generated in 54.97 s
	001. 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 4.7 s
		[progress: 70549/70549 (100%) - 537 spectra/s] 131.5s
	002. 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 3.7 s
		[progress: 69333/69333 (100%) - 556 spectra/s] 124.7s
	003. 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 3.8 s
		[progress: 69631/69631 (100%) - 565 spectra/s] 123.3s
Operating on slice 3 of 3: 
	Fragment index slice generated in 56.96 s
	001. 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 3.5 s
		[progress: 70549/70549 (100%) - 1008 spectra/s] 70.0s
		Building spectral index for 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 38.3 s
		Rescoring with peak tracing 34.4 s
		Picking top PSMs for each precursor 27.7 s
		Rescoring using greedy method 19.5 s
		Writing results 34.7 s
	002. 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 4.4 s
		[progress: 69333/69333 (100%) - 989 spectra/s] 70.1s
		Building spectral index for 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 34.7 s
		Rescoring with peak tracing 17.7 s
		Picking top PSMs for each precursor 22.2 s
		Rescoring using greedy method 14.6 s
		Writing results 32.9 s
	003. 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 5.7 s
		[progress: 69631/69631 (100%) - 958 spectra/s] 72.7s
		Building spectral index for 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzBIN_calibrated 36.3 s
		Rescoring with peak tracing 17.0 s
		Picking top PSMs for each precursor 23.7 s
		Rescoring using greedy method 15.1 s
		Writing results 33.1 s
***************************MAIN SEARCH DONE IN 56.170 MIN***************************

*******************************TOTAL TIME 58.876 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pepxml
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar;/D:/Public/Snigdha/Documents/FragPipe-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
java -Xmx82G -cp "D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\msbooster-1.1.10.jar;D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\batmass-io-1.28.8.jar" Features.MainClass --paramsList D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\msbooster_params.txt
MSBooster v1.1.10
Using 47 threads
Generating input file for DIA-NN
665864 unique peptides from 847081 PSMs
Writing DIA-NN input file
Diann input file generation took 10123 milliseconds
Input file at  D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\spectraRT.tsv
665864 unique peptides from 847081 PSMs
createFull input file generation took 6474 milliseconds
Input file at  D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\spectraRT_full.tsv
Generating DIA-NN predictions
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\spectraRT.tsv --predict --threads 47 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Tue Apr  9 11:16:23 2024
CPU: GenuineIntel Intel(R) Xeon(R) Silver 4214 CPU @ 2.20GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 48
Predicted spectra will be saved in a binary format
Thread number set to 47
DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search
Deep learning predictor will predict 100 fragments
Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed
[0:00] Loading spectral library D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\spectraRT.tsv
[0:04] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:05] Spectral library loaded: 0 protein isoforms, 0 protein groups and 665864 precursors in 645203 elution groups.
[0:05] Encoding peptides for spectra and RTs prediction
[0:07] Predicting spectra and IMs
[13:10] Predicting RTs
[18:06] Decoding predicted spectra and IMs
[18:32] Decoding RTs
[18:33] Saving the list of predictions to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\spectraRT.predicted.bin
Finished
Done generating DIA-NN predictions
Model running took 1120139 milliseconds
Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS]
Loading predicted spectra
Processing 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML
RT regression using 5000 PSMs
Edited pin file at D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Processing 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML
RT regression using 5000 PSMs
Edited pin file at D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Processing 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
RT regression using 5000 PSMs
Edited pin file at D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Done in 113856 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Started Tue Apr  9 11:36:56 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Features:
retentiontime rank log10_intensity abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotopes log10_kl log10_kl_negative_1 log10_kl_negative_2 hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 276527 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 172536 positives and 103991 negatives, size ratio=1.65914 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 28 as initial direction. Could separate 16925 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 28 as initial direction. Could separate 16831 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 28 as initial direction. Could separate 16405 training set positives with q<0.01 in that direction.
Found 24923 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 11.916 cpu seconds or 12 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 44264 PSMs with q<0.01
Iteration 2:	Estimated 48974 PSMs with q<0.01
Iteration 3:	Estimated 50360 PSMs with q<0.01
Iteration 4:	Estimated 50852 PSMs with q<0.01
Iteration 5:	Estimated 50992 PSMs with q<0.01
Iteration 6:	Estimated 51056 PSMs with q<0.01
Iteration 7:	Estimated 51043 PSMs with q<0.01
Iteration 8:	Estimated 51044 PSMs with q<0.01
Iteration 9:	Estimated 51055 PSMs with q<0.01
Iteration 10:	Estimated 51118 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.1008	-0.0974	-0.0829	retentiontime
-0.1191	-0.2112	-0.2130	rank
-0.5808	-0.6546	-0.8992	log10_intensity
-0.4442	-0.5153	-0.7072	abs_ppm
-0.0946	 0.0144	-0.1456	abs_rt_diff
-0.2155	-0.3493	-0.3690	complementary_ions
 0.1474	 0.2213	 0.3449	ion_series
-0.0079	-0.0046	 0.0237	weighted_average_abs_fragment_ppm
-0.2545	-0.4121	-0.4226	weighted_average_fragment_rt_deviation
-0.1078	-0.1875	-0.1071	precursor_rt_deviation
 0.2430	 0.3691	 0.3663	isotopes
-0.0771	-0.0345	-0.0600	log10_kl
 0.0051	-0.0174	-0.0414	log10_kl_negative_1
 0.0095	 0.0192	 0.0553	log10_kl_negative_2
 1.8697	 1.2558	 1.5107	hyperscore
-0.9061	-0.1896	-0.2792	matched_ion_num
 0.1909	 0.2624	 0.2274	peptide_length
 0.3244	 0.4141	 0.4315	ntt
 0.1355	 0.1870	 0.2738	nmc
-0.0847	-0.0485	-0.0522	charge_1
 0.0313	 0.1077	 0.1217	charge_2
 0.1261	 0.1162	 0.1527	charge_3
-0.1242	-0.1899	-0.2361	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
-0.0442	-0.0169	-0.0018	15.9949M
 1.9102	 2.1776	 2.4289	unweighted_spectral_entropy
-0.6500	-0.7461	-0.8980	delta_RT_loess
-3.3563	-3.5187	-3.7140	m0
Found 50722 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 172536 target PSMs and 103991 decoy PSMs.
Calculating q values.
Final list yields 50727 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 43.7 cpu seconds or 44 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Started Tue Apr  9 11:37:56 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Features:
retentiontime rank log10_intensity abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotopes log10_kl log10_kl_negative_1 log10_kl_negative_2 hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 278996 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 175523 positives and 103473 negatives, size ratio=1.69632 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 15 as initial direction. Could separate 16532 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 15 as initial direction. Could separate 16625 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 15 as initial direction. Could separate 16580 training set positives with q<0.01 in that direction.
Found 24757 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 11.62 cpu seconds or 12 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 46988 PSMs with q<0.01
Iteration 2:	Estimated 51365 PSMs with q<0.01
Iteration 3:	Estimated 52390 PSMs with q<0.01
Iteration 4:	Estimated 52681 PSMs with q<0.01
Iteration 5:	Estimated 52706 PSMs with q<0.01
Iteration 6:	Estimated 52767 PSMs with q<0.01
Iteration 7:	Estimated 52731 PSMs with q<0.01
Iteration 8:	Estimated 52719 PSMs with q<0.01
Iteration 9:	Estimated 52746 PSMs with q<0.01
Iteration 10:	Estimated 52731 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.1377	-0.1338	-0.1092	retentiontime
-0.2438	-0.2232	-0.2069	rank
-0.6993	-0.9009	-0.7135	log10_intensity
-0.4822	-0.5001	-0.5246	abs_ppm
-0.2582	-0.3273	-0.1894	abs_rt_diff
-0.4590	-0.3849	-0.3559	complementary_ions
 0.3463	 0.2352	 0.2686	ion_series
 0.0891	 0.0259	 0.0127	weighted_average_abs_fragment_ppm
-0.3912	-0.2936	-0.3322	weighted_average_fragment_rt_deviation
-0.0873	-0.1010	-0.0809	precursor_rt_deviation
 0.2262	 0.2845	 0.2483	isotopes
-0.0666	-0.0523	-0.0505	log10_kl
 0.0005	-0.0048	 0.0168	log10_kl_negative_1
 0.0113	 0.0016	 0.0078	log10_kl_negative_2
 1.1368	 1.4506	 0.9107	hyperscore
 0.0762	-0.2830	 0.1744	matched_ion_num
 0.2302	 0.1641	 0.1334	peptide_length
 0.5381	 0.4437	 0.4612	ntt
 0.2458	 0.1955	 0.1917	nmc
-0.0289	-0.0318	-0.1020	charge_1
 0.0474	 0.0523	 0.0429	charge_2
 0.1562	 0.0979	 0.1008	charge_3
-0.1832	-0.1298	-0.1038	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0017	-0.0208	 0.0017	15.9949M
 2.4741	 2.1313	 2.0227	unweighted_spectral_entropy
-0.7242	-0.6091	-0.6172	delta_RT_loess
-3.5093	-3.3152	-3.2248	m0
Found 52437 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 175523 target PSMs and 103473 decoy PSMs.
Calculating q values.
Final list yields 52440 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 44.01 cpu seconds or 44 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Percolator version 3.05.0, Build Date May 18 2020 02:35:01
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 47 --results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv --decoy-results-psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Started Tue Apr  9 11:38:56 2024
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_edited.pin
Features:
retentiontime rank log10_intensity abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotopes log10_kl log10_kl_negative_1 log10_kl_negative_2 hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more 15.9949M unweighted_spectral_entropy delta_RT_loess 
Found 291558 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 180989 positives and 110569 negatives, size ratio=1.63689 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 28 as initial direction. Could separate 16784 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 28 as initial direction. Could separate 16430 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 28 as initial direction. Could separate 16465 training set positives with q<0.01 in that direction.
Found 24530 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 11.633 cpu seconds or 12 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 45559 PSMs with q<0.01
Iteration 2:	Estimated 49364 PSMs with q<0.01
Iteration 3:	Estimated 50710 PSMs with q<0.01
Iteration 4:	Estimated 51129 PSMs with q<0.01
Iteration 5:	Estimated 51301 PSMs with q<0.01
Iteration 6:	Estimated 51444 PSMs with q<0.01
Iteration 7:	Estimated 51536 PSMs with q<0.01
Iteration 8:	Estimated 51583 PSMs with q<0.01
Iteration 9:	Estimated 51614 PSMs with q<0.01
Iteration 10:	Estimated 51625 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.1333	-0.1399	-0.1312	retentiontime
-0.1424	-0.1767	-0.1377	rank
-0.8977	-0.7720	-0.7820	log10_intensity
-0.3688	-0.4451	-0.4668	abs_ppm
-0.3005	-0.2485	-0.1459	abs_rt_diff
-0.3817	-0.3496	-0.3077	complementary_ions
 0.1691	 0.1506	 0.1116	ion_series
 0.0251	 0.0161	 0.0029	weighted_average_abs_fragment_ppm
-0.3174	-0.3337	-0.2703	weighted_average_fragment_rt_deviation
-0.1703	-0.0949	-0.1201	precursor_rt_deviation
 0.3812	 0.3701	 0.3670	isotopes
-0.0685	-0.0257	-0.0152	log10_kl
-0.0189	-0.0032	-0.0157	log10_kl_negative_1
 0.0307	 0.0274	 0.0152	log10_kl_negative_2
 2.0168	 1.5998	 1.5339	hyperscore
-0.7429	-0.3755	-0.5255	matched_ion_num
 0.1870	 0.2138	 0.1894	peptide_length
 0.4605	 0.4341	 0.4183	ntt
 0.1989	 0.1695	 0.1460	nmc
 0.0012	-0.0210	-0.0245	charge_1
 0.0826	 0.0696	 0.0696	charge_2
 0.0802	 0.1157	 0.0973	charge_3
-0.1479	-0.1647	-0.1459	charge_4
 0.0000	 0.0000	 0.0000	charge_5
 0.0000	 0.0000	 0.0000	charge_6
 0.0000	 0.0000	 0.0000	charge_7_or_more
 0.0074	-0.0032	-0.0406	15.9949M
 2.2808	 2.3041	 1.9824	unweighted_spectral_entropy
-0.7928	-0.8123	-0.6414	delta_RT_loess
-3.6852	-3.4681	-3.5620	m0
Found 51470 test set PSMs with q<0.01.
Selected best-scoring PSM per scan+expMass (target-decoy competition): 180989 target PSMs and 110569 decoy PSMs.
Calculating q values.
Final list yields 51473 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 45.66 cpu seconds or 45 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.pin 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13 DIA 0.7
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\filelist_proteinprophet.txt
INFO[11:40:42] Executing ProteinProphet  v4.6.0             
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 D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml...
...read in 1453 1+, 13899 2+, 13610 3+, 7212 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml...
...read in 426 1+, 6082 2+, 5129 3+, 3095 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml...
...read in 120 1+, 2409 2+, 2065 3+, 1256 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml...
...read in 36 1+, 1093 2+, 921 3+, 533 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml...
...read in 17 1+, 536 2+, 438 3+, 255 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml...
...read in 1251 1+, 13346 2+, 13517 3+, 6917 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml...
...read in 303 1+, 6170 2+, 5326 3+, 2982 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml...
...read in 80 1+, 2483 2+, 2129 3+, 1220 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml...
...read in 29 1+, 1067 2+, 928 3+, 486 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml...
...read in 14 1+, 525 2+, 481 3+, 241 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml...
...read in 1414 1+, 13263 2+, 14162 3+, 7676 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml...
...read in 375 1+, 6071 2+, 5514 3+, 3479 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml...
...read in 91 1+, 2449 2+, 2319 3+, 1526 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml...
...read in 22 1+, 1030 2+, 1011 3+, 602 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Reading in D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml...
...read in 13 1+, 491 2+, 456 3+, 315 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.5

Initializing 95272 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:....WARNING: Found the following zero-mass residues in protein entry rev_sp|Q8IZQ5|SELH_HUMAN : U
MSLYKKLEEVVEQPEPFKLKRPPGKKIGTWLEASSGDPRLLTVEFSGRRPKTPNVKVPLEPAELRLAQSLAAANRGYVRUSTCHEIVVTAEEMGEGGNALKERKEAVAVVAAEAKRKRGRPA
.....:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BVL4|SELO_HUMAN : U
MSSUTVCLEAAWLPPKSSYSRQRGDAGDAETAEADTAAGAECHYPTELLKLVRRVESFDGREAAEIANQAIYNRLVYKPNNAHMVRVHEAQWAAADGAGELDKDLRARYAQLWDAWHGQNRSQLEAASLQELRSQQEVRELERAIGARTGMLAFLQPNSQALMLMMSLQRPDMQPRFALRLEELSACQEMLRALFEALGPSELEVPFSSLLYFTNTFDAGTLHMTELLKSVLAGDEELEVQVLGLKRRMKQLYHRQFEADFEEALIAEGLELPLEPQLAEALKRLNWRCVEPQKSYAYRGTNDSANCVHDPDYRDLFGFPGYDITLGLISMNDTLNVGHCFGVCQWEAVMRATRRTVERFFAANRQVSDSAHAAQIEPYFSSIVYDLLQVRIDNRGVSPGARGTHEDASKFIEFSGFRIFTSAVRLVVTCQEYKPNGDYFVDRVVTSESTVCAGARTTPVGLHFMAESCLFERISSRLVKRGDAQRSFPTPGAGKLQLEWREGTATCVEGLYMAAGDGLQGAFQGFQHGCYCHAAPEAGPLLANGSFFLAAEAEAERAPPAGLGLLALAPESLAVLRPQRLPTPQVRTFCAGPVPRPASPAGEPGPPPAEVPLARLARNDFRLGALWRPAPEMAAGSLTSRPAPSPSCRGLPLLRAAALSAGLAARYVA
.......:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5|SELN_HUMAN : UU
MPQLLPLGRRLGEKLFQMYTATSPDEFTSSFSFLNSEIEEPKVSTIDLFYNANIHHVVTGNPLCIMMEVPFSYKELHLGALKQHSSNEQNNQLEELEKVLSWTSIFSENLLTLIPSSELVTERLTRGSGUCSQDDLAGWLLISHVLKNEAKARDFAETFPLYSVKKFPYMAVELRRAAEEWSLEQQWKIEEFVFQLPEGSPLHSDIMSGDEDLIVSPVSPGTAELEMQPIYGIDVEMNSSESAGYLWEMDVNLSRHNPVFLRFDRVHTADKSLIIHGTFQAPSFWFPFDPPESLQFEAHIRFMVTYYFDSIATLCAVAGQPAFRTKVFPRPHFMSLLRHIIVEKGKPPPPYFRNNSLYGTFMSLESPIIWWPEGLEQGPPPLFPQFHRTAFVASPSAAATWNRLGSLALRSVGLFGDKSKTMTEPLLPQFRAEITLTEESPDPPLEEEECSAAPTSRLLSLCSSUNLWPLQPQLSSHSCWQVGTQTVSCSGTLKEAIPKFEEPSIYMDGDTDLSSFLFLGDTGLTKLALEQRAAAQAEAHRACVRVAAAAAAALLAGLLALSRARRRPPAPPQAAPGPSPPGRQGPRARG
WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV6|MSRB1_HUMAN : U
MHGQSASTEKGKPVFKLSSSFIUFRSQGPKPGDNLFEHGLGNGCKGCSVKLAESRNHEPRKAVSDAHITETFAPWPSSHAYKSRSSFLEYGCKACVYVGPEFHNQFVEGGFFSCFS
.......:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|O60613|SEP15_HUMAN : U
MVAMAAGPSGCLVPAFGLRLLLATVLQAVSAFGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEELSILKWNTDSVEEFLSEKLERI
......:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U
MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA
..:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P18283|GPX2_HUMAN : U
MAFIAKSFYDLSAISLDGEKVDFNTFRGRAVLIENVASLUGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLKVAI
..:.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U
MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK
:.........:.........:.........:.........:.........:.........26000
........WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U
MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
.:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|P49908|SEPP1_HUMAN : UUUUUUUUUU
MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASUYLCILQASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDRCGRLVYHLGLPFSFLTFPYVEEAIKIAYCEKKCGNCSLTTLKDEDFCKRVSLATVDKTVETPSPHYHHEHHHNHGHQHLGSSELSENQQPGAPNAPTHPAPPGLHHHHKHKGQHRQGHPENRDMPASEDLQDLQKKLCRKRCINQLLCKLPTDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAUQISQQLIPTEASASURUKNQAKKUEUPSN
........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........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
.........:.........:.........:.........:.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|Q8WWX9|SELM_HUMAN : U
MSLLLPPLALLLLLAALVAPATAATAYRPDWNRLSGLTRARVETCGGUQLNRLKEVKAFVTQDIPFYHNLVMKHLPGADPELVLLGRRYEELERIPLSEMTREEINALVQELGFYRKAAPDAQVPPEYVWAPAKPPEETSDHADL
.......:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|Q99611|SPS2_HUMAN : U
MAEASATGACGEAMAAAEGSSGPAGLTLGRSFSNYRPFEPQALGLSPSWRLTGFSGMKGUGCKVPQEALLKLLAGLTRPDVRPPLGRGLVGGQEEASQEAGLPAGAGPSPTFPALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATAAVLAPDSSNASSEPSS
....:.........:.........:.........:.........37000
....WARNING: Found the following zero-mass residues in protein entry sp|Q9BVL4|SELO_HUMAN : U
MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS
.....:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U
MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:...  Total: 40934
Computing degenerate peptides for 12488 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 12780 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=8.53042e-05, db_size=45676118
Computing MU for 12780 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[11:41:32] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe database --annotate D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas --prefix rev_
INFO[11:41:32] Executing Database  v4.6.0                   
INFO[11:41:32] Annotating the database                      
INFO[11:41:37] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe database --annotate D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas --prefix rev_
INFO[11:41:38] Executing Database  v4.6.0                   
INFO[11:41:38] Annotating the database                      
INFO[11:41:43] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe filter --picked --prot 0.01 --tag rev_ --pepxml D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A --protxml D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\combined.prot.xml --razor
INFO[11:41:43] Executing Filter  v4.6.0                     
INFO[11:41:43] Processing peptide identification files      
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml 
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml 
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml 
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml 
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml 
INFO[11:41:43] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml 
INFO[11:41:44] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml 
INFO[11:41:44] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml 
INFO[11:41:44] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml 
INFO[11:41:45] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml 
INFO[11:41:45] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml 
INFO[11:41:45] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml 
INFO[11:41:45] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml 
INFO[11:41:46] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml 
INFO[11:41:46] Parsing D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml 
INFO[11:41:52] 1+ Charge profile                             decoy=365 target=5279
INFO[11:41:52] 2+ Charge profile                             decoy=1570 target=69344
INFO[11:41:52] 3+ Charge profile                             decoy=2011 target=65995
INFO[11:41:52] 4+ Charge profile                             decoy=1838 target=35957
INFO[11:41:52] 5+ Charge profile                             decoy=0 target=0
INFO[11:41:52] 6+ Charge profile                             decoy=0 target=0
INFO[11:41:53] Database search results                       ions=95199 peptides=83619 psms=182359
INFO[11:41:53] Converged to 1.00 % FDR with 154846 PSMs      decoy=1549 threshold=0.897099 total=156395
INFO[11:41:53] Converged to 1.00 % FDR with 64256 Peptides   decoy=642 threshold=0.945068 total=64898
INFO[11:41:53] Converged to 1.00 % FDR with 75200 Ions       decoy=752 threshold=0.937297 total=75952
INFO[11:42:01] Protein inference results                     decoy=3876 target=8081
INFO[11:42:02] Converged to 1.02 % FDR with 4536 Proteins    decoy=47 threshold=0.992 total=4583
INFO[11:42:05] 2D FDR estimation: Protein mirror image       decoy=4536 target=4536
INFO[11:42:06] Second filtering results                      ions=87529 peptides=75999 psms=173467
INFO[11:42:06] Converged to 1.00 % FDR with 170737 PSMs      decoy=1707 threshold=0.713133 total=172444
INFO[11:42:06] Converged to 1.00 % FDR with 69728 Peptides   decoy=697 threshold=0.842324 total=70425
INFO[11:42:06] Converged to 1.00 % FDR with 81527 Ions       decoy=815 threshold=0.823397 total=82342
INFO[11:42:18] Post processing identifications              
INFO[11:42:29] Assigning protein identifications to layers  
INFO[11:42:31] Processing protein inference                 
INFO[11:42:48] Synchronizing PSMs and proteins              
INFO[11:42:51] Final report numbers after FDR filtering, and post-processing  ions=81511 peptides=69713 proteins=4536 psms=170708
INFO[11:42:51] Saving                                       
INFO[11:42:53] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe report
INFO[11:42:54] Executing Report  v4.6.0                     
INFO[11:42:54] Creating reports                             
INFO[11:43:07] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
SpecLibGen [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
C:\Python39\python.exe -u D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\speclib\gen_con_spec_lib.py D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\2024-04-09-decoys-reviewed-contam-UP000005640.fas D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A unused D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A True unused use_easypqp noiRT;noIM 47 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] " "--rt_lowess_fraction 0.0" delete_intermediate_files D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\filelist_speclibgen.txt
File list provided
Spectral library building
Commands to execute:
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl --peaks 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl --peaks 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl --peaks 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl --peaks 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl --peaks 1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl --peaks 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl --peaks 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl --peaks 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl --peaks 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl --peaks 1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl --peaks 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl --peaks 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl --peaks 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl --peaks 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl
'C:\Python39\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml' --spectra 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML' --exclude-range -1.5,3.5 --psms 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl --peaks 1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl
'C:\Python39\Scripts\easypqp.exe' library --psmtsv 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\psm.tsv' --peptidetsv 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\peptide.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 'D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\filelist_easypqp_library.txt'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easypqp, version 0.1.36
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl', '--peaks', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl', '--peaks', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl', '--peaks', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl', '--peaks', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl', '--peaks', '1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl', '--peaks', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl', '--peaks', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl', '--peaks', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl', '--peaks', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl', '--peaks', '1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl', '--peaks', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl', '--peaks', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl', '--peaks', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl', '--peaks', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl']
Executing ['C:\\Python39\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\A\\interact-1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.pep.xml', '--spectra', 'D:\\Public\\Snigdha\\Lung_macro\\DIA\\DIA_MZML\\DIA_DD_MZML\\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML', '--exclude-range', '-1.5,3.5', '--psms', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl', '--peaks', '1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl']
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.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.psmpkl.
Info: Reading file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.psmpkl.
Info: 165856 redundant PSMs identified after filtering with D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\psm.tsv and D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\peptide.tsv
                                           base_name  modified_peptide
0  1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan...             48089
1  1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan...             47691
2  1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan...             47638
Info: easypqp_rt_alignment_1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13; Peptide overlap between run and reference: 48089.
Info: easypqp_rt_alignment_1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13; Lowess fraction used: 0.08.
Info: easypqp_rt_alignment_1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13; Peptide overlap between run and reference: 34326.
Info: easypqp_rt_alignment_1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13; Lowess fraction used: 0.02.
Info: easypqp_rt_alignment_1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13; Peptide overlap between run and reference: 23725.
Info: easypqp_rt_alignment_1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13; Lowess fraction used: 0.01.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank1.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank2.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank3.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank4.peakpkl.
Info: Parsing file D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13_rank5.peakpkl.
Info: Library successfully generated.
Done generating spectral library
2024-04-09 12:02:55,231:INFO:took 0:19:30.489586
Process 'SpecLibGen' finished, exit code: 0
WorkspaceClean [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[12:02:55] Executing Workspace  v4.6.0                  
INFO[12:02:55] Removing workspace                           
INFO[12:02:55] Done                                         
Process 'WorkspaceClean' finished, exit code: 0
WorkspaceClean [Work dir: D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\A]
D:\Public\Snigdha\Documents\FragPipe-19.0\fragpipe\tools\philosopher_v4.6.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[12:02:56] Executing Workspace  v4.6.0                  
INFO[12:02:56] Removing workspace                           
INFO[12:02:56] Done                                         
Process 'WorkspaceClean' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003)
(FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(Visualization with FP-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)

=============================================================ALL JOBS DONE IN 106.2 MINUTES=============================================================
