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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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TMT10 - MS3 quantification problem #468

Closed merbllab closed 3 years ago

merbllab commented 3 years ago

(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

prvst commented 3 years ago

Does your data contain MS 3 spectra? Where is your database search results? I don't see any fragger log messages.

merbllab commented 3 years ago

HI,

sorry - I attached a log of a rerun when the error return. this is the first run log with the MSFragger

the raw files contains MS3 , I converted the raw files to mzML before running fragpipe

Assaf

From: Felipe da Veiga Leprevost @.***> Sent: Wednesday, September 22, 2021 9:10:30 PM To: Nesvilab/FragPipe Cc: Merbllab; Author Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

Does your data contain MS 3 spectra? Where is your database search results? I don't see any fragger log messages.

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System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_144, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 16.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421)

LCMS files: Experiment/Group: TMT-P-41

170 commands to execute: CheckCentroid java -Xmx16G -cp "D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;D:\FragPipe-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04228_Prot_41_01.mzML 6 WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] java -jar -Dfile.encoding=UTF-8 -Xmx16G D:\FragPipe-16.0\MSFragger-3.3\MSFragger-3.3.jar D:\Gygi-proteomics-cell-line-fragpipe\analysis2\fragger.params D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04228_Prot_41_01.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04229_Prot_41_02.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04230_Prot_41_03.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04231_Prot_41_04.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04232_Prot_41_05.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04233_Prot_41_06.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04234_Prot_41_07.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04235_Prot_41_08.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04236_Prot_41_09.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04237_Prot_41_10.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04238_Prot_41_11.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04239_Prot_41_12.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04168_Prot_42_01.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04169_Prot_42_02.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04170_Prot_42_03.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04171_Prot_42_04.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04172_Prot_42_05.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04173_Prot_42_06.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04174_Prot_42_07.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04175_Prot_42_08.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04176_Prot_42_09.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04177_Prot_42_10.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04178_Prot_42_11.mzML D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04179_Prot_42_12.mzML MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04228_Prot_41_01.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04228_Prot_41_01.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04228_Prot_41_01.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04228_Prot_41_01.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04229_Prot_41_02.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04229_Prot_41_02.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04229_Prot_41_02.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04229_Prot_41_02.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04230_Prot_41_03.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04230_Prot_41_03.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04230_Prot_41_03.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04230_Prot_41_03.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04231_Prot_41_04.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04231_Prot_41_04.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04231_Prot_41_04.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04231_Prot_41_04.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04232_Prot_41_05.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04232_Prot_41_05.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04232_Prot_41_05.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04232_Prot_41_05.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04233_Prot_41_06.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04233_Prot_41_06.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04233_Prot_41_06.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04233_Prot_41_06.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04234_Prot_41_07.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04234_Prot_41_07.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04234_Prot_41_07.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04234_Prot_41_07.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04235_Prot_41_08.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04235_Prot_41_08.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04235_Prot_41_08.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04235_Prot_41_08.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04236_Prot_41_09.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04236_Prot_41_09.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04236_Prot_41_09.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04236_Prot_41_09.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04237_Prot_41_10.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04237_Prot_41_10.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04237_Prot_41_10.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04237_Prot_41_10.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04238_Prot_41_11.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04238_Prot_41_11.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04238_Prot_41_11.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04238_Prot_41_11.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04239_Prot_41_12.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04239_Prot_41_12.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04239_Prot_41_12.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\c04239_Prot_41_12.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04168_Prot_42_01.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04168_Prot_42_01.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04168_Prot_42_01.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04168_Prot_42_01.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04169_Prot_42_02.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04169_Prot_42_02.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04169_Prot_42_02.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04169_Prot_42_02.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04170_Prot_42_03.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04170_Prot_42_03.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04170_Prot_42_03.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04170_Prot_42_03.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04171_Prot_42_04.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04171_Prot_42_04.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04171_Prot_42_04.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04171_Prot_42_04.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04172_Prot_42_05.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04172_Prot_42_05.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04172_Prot_42_05.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04172_Prot_42_05.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04173_Prot_42_06.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04173_Prot_42_06.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04173_Prot_42_06.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04173_Prot_42_06.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04174_Prot_42_07.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04174_Prot_42_07.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04174_Prot_42_07.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04174_Prot_42_07.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04175_Prot_42_08.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04175_Prot_42_08.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04175_Prot_42_08.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04175_Prot_42_08.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04176_Prot_42_09.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04176_Prot_42_09.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04176_Prot_42_09.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04176_Prot_42_09.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04177_Prot_42_10.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04177_Prot_42_10.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04177_Prot_42_10.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04177_Prot_42_10.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04178_Prot_42_11.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04178_Prot_42_11.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04178_Prot_42_11.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04178_Prot_42_11.pin MSFragger move pepxml java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04179_Prot_42_12.pepXML D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04179_Prot_42_12.pepXML MSFragger move pin java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04179_Prot_42_12.pin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\c04179_Prot_42_12.pin PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04228_Prot_41_01.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04229_Prot_41_02.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04230_Prot_41_03.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04231_Prot_41_04.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04232_Prot_41_05.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04233_Prot_41_06.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04234_Prot_41_07.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04235_Prot_41_08.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04236_Prot_41_09.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04237_Prot_41_10.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04238_Prot_41_11.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04239_Prot_41_12.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04168_Prot_42_01.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04169_Prot_42_02.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04170_Prot_42_03.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04171_Prot_42_04.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04172_Prot_42_05.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04173_Prot_42_06.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04174_Prot_42_07.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04175_Prot_42_08.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04176_Prot_42_09.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04177_Prot_42_10.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04178_Prot_42_11.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04179_Prot_42_12.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04228_Prot_41_01.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04228_Prot_41_01.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04229_Prot_41_02.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04229_Prot_41_02.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04230_Prot_41_03.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04230_Prot_41_03.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04231_Prot_41_04.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04231_Prot_41_04.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04232_Prot_41_05.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04232_Prot_41_05.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04233_Prot_41_06.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04233_Prot_41_06.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04234_Prot_41_07.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04234_Prot_41_07.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04235_Prot_41_08.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04235_Prot_41_08.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04236_Prot_41_09.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04236_Prot_41_09.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04237_Prot_41_10.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04237_Prot_41_10.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04238_Prot_41_11.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04238_Prot_41_11.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04239_Prot_41_12.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04239_Prot_41_12.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04168_Prot_42_01.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04168_Prot_42_01.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04169_Prot_42_02.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04169_Prot_42_02.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04170_Prot_42_03.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04170_Prot_42_03.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04171_Prot_42_04.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04171_Prot_42_04.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04172_Prot_42_05.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04172_Prot_42_05.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04173_Prot_42_06.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04173_Prot_42_06.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04174_Prot_42_07.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04174_Prot_42_07.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04175_Prot_42_08.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04175_Prot_42_08.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04176_Prot_42_09.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04176_Prot_42_09.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04177_Prot_42_10.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04177_Prot_42_10.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04178_Prot_42_11.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04178_Prot_42_11.pepXML PeptideProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04179_Prot_42_12.pepXML-temp] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database X:\assafk\database\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas ..\c04179_Prot_42_12.pepXML PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04228_Prot_41_01.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04229_Prot_41_02.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04230_Prot_41_03.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04231_Prot_41_04.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04232_Prot_41_05.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04233_Prot_41_06.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04234_Prot_41_07.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04235_Prot_41_08.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04236_Prot_41_09.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04237_Prot_41_10.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04238_Prot_41_11.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\fragpipe-c04239_Prot_41_12.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04168_Prot_42_01.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04169_Prot_42_02.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04170_Prot_42_03.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04171_Prot_42_04.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04172_Prot_42_05.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04173_Prot_42_06.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04174_Prot_42_07.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04175_Prot_42_08.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04176_Prot_42_09.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04177_Prot_42_10.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04178_Prot_42_11.pepXML-temp PeptideProphet: Delete temp java -cp D:\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\fragpipe-c04179_Prot_42_12.pepXML-temp Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04235_Prot_41_08.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04235_Prot_41_08.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04173_Prot_42_06.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04173_Prot_42_06.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04230_Prot_41_03.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04230_Prot_41_03.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04229_Prot_41_02.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04229_Prot_41_02.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04177_Prot_42_10.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04177_Prot_42_10.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04239_Prot_41_12.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04239_Prot_41_12.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04172_Prot_42_05.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04172_Prot_42_05.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04234_Prot_41_07.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04234_Prot_41_07.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04169_Prot_42_02.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04169_Prot_42_02.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04233_Prot_41_06.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04233_Prot_41_06.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04171_Prot_42_04.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04171_Prot_42_04.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04168_Prot_42_01.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04168_Prot_42_01.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04176_Prot_42_09.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04176_Prot_42_09.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04178_Prot_42_11.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04178_Prot_42_11.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04170_Prot_42_03.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04170_Prot_42_03.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04175_Prot_42_08.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04175_Prot_42_08.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04179_Prot_42_12.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04179_Prot_42_12.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04232_Prot_41_05.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04232_Prot_41_05.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04237_Prot_41_10.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04237_Prot_41_10.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04174_Prot_42_07.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\c04174_Prot_42_07.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04228_Prot_41_01.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04228_Prot_41_01.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04238_Prot_41_11.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04238_Prot_41_11.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04231_Prot_41_04.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04231_Prot_41_04.mzML Rewrite pepxml [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] java -cp D:\FragPipe-16.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04236_Prot_41_09.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\c04236_Prot_41_09.mzML ProteinProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined D:\Gygi-proteomics-cell-line-fragpipe\analysis2\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate X:\assafk\database\2021-03-10-decoys-contam-Human_SP27042020.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate X:\assafk\database\2021-03-10-decoys-contam-Human_SP27042020.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe database --annotate X:\assafk\database\2021-03-10-decoys-contam-Human_SP27042020.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41 --protxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\combined.prot.xml --razorbin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41.meta\razor.bin PhilosopherFilter [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42 --protxml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\combined.prot.xml --razorbin D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41.meta\razor.bin FreeQuant [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41 FreeQuant [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42 Quant (Isobaric) [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe labelquant --tol 20 --level 3 --plex 10 --annot D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41\annotation.txt --brand tmt --dir D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-41 Quant (Isobaric) [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe labelquant --tol 20 --level 3 --plex 10 --annot D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42\annotation.txt --brand tmt --dir D:\Gygi-proteomics-cell-line-fragpipe\TMT-P-42 PhilosopherReport [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe report iProphet [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 6 D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04228_Prot_41_01.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04229_Prot_41_02.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04230_Prot_41_03.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04231_Prot_41_04.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04232_Prot_41_05.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04233_Prot_41_06.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04234_Prot_41_07.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04235_Prot_41_08.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04236_Prot_41_09.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04237_Prot_41_10.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04238_Prot_41_11.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\interact-c04239_Prot_41_12.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04168_Prot_42_01.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04169_Prot_42_02.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04170_Prot_42_03.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04171_Prot_42_04.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04172_Prot_42_05.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04173_Prot_42_06.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04174_Prot_42_07.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04175_Prot_42_08.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04176_Prot_42_09.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04177_Prot_42_10.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04178_Prot_42_11.pep.xml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\interact-c04179_Prot_42_12.pep.xml PhilosopherAbacus [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windowsamd64\philosopher.exe abacus --razor --picked --reprint --tag rev --protein --peptide TMT-P-41 TMT-P-42 TmtIntegrator [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] java -Xmx16G -cp "D:\FragPipe-16.0\fragpipe\tools\tmt-integrator-3.0.0.jar" TMTIntegrator D:\Gygi-proteomics-cell-line-fragpipe\analysis2\tmt-integrator-conf.yml D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41\psm.tsv D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42\psm.tsv WorkspaceClean [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42] D:\FragPipe-16.0\philosopher_v4.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [CheckCentroid], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42]
    Cmd: [MSFragger], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [PeptideProphet], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [ProteinProphet], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [PhilosopherFilter], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [FreeQuant], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [Quant (Isobaric)], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [PhilosopherReport], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [iProphet], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [PhilosopherAbacus], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [TmtIntegrator], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [WorkspaceClean], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2]
    Cmd: [WorkspaceClean], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-41]
    Cmd: [WorkspaceClean], Work dir: [D:\Gygi-proteomics-cell-line-fragpipe\analysis2\TMT-P-42]


# FragPipe v16.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=79.96633
crystalc.run-crystalc=false
database.db-path=X\:\\assafk\\database\\2021-03-10-decoys-contam-Human_SP_27042020.fasta.fas
database.decoy-tag=rev_
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
fragpipe-config.bin-msfragger=D\:\\FragPipe-16.0\\MSFragger-3.3\\MSFragger-3.3.jar
fragpipe-config.bin-philosopher=D\:\\FragPipe-16.0\\philosopher_v4.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
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=0.6
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=131.5
msfragger.misc.fragger.clear-mz-lo=125.5
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 229.162930,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,true,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 229.162930,n^,true,1; 229.162930,S,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=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.diag_ions=
ptmshepherd.glyco_mode=false
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
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
prvst commented 3 years ago

using msconvert? If so, can you tell the version you used?

anesvi commented 3 years ago

I see this if from Gygi’s cell line paper in NBT. Most likely mzML were converted using an old version of msconvert. Philosopher is not compatible with some older versions. Please reconvert using the latest msconvert and try again. Alexey

From: merbllab @.> Sent: Wednesday, September 22, 2021 2:03 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

External Email - Use Caution

(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/468, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62XEKFUHE2TVS6JZRTUDIK6LANCNFSM5ER4MDMQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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merbllab commented 3 years ago

Version: 3.0.20075-2311d38a2 (developer build)

From: Felipe da Veiga Leprevost @.***> Sent: Wednesday, September 22, 2021 9:26:42 PM To: Nesvilab/FragPipe Cc: Merbllab; Author Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

using msconvert? If so, can you tell the version you used?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/468#issuecomment-925179234, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APGKVN7X7D3E3MUPYM6ENZLUDINWFANCNFSM5ER4MDMQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

merbllab commented 3 years ago

yes - this is the data. I will try with a newer version of MSConvert

will update

Assaf

From: Alexey Nesvizhskii @.***> Sent: Wednesday, September 22, 2021 9:27:51 PM To: Nesvilab/FragPipe Cc: Merbllab; Author Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

I see this if from Gygi’s cell line paper in NBT. Most likely mzML were converted using an old version of msconvert. Philosopher is not compatible with some older versions. Please reconvert using the latest msconvert and try again. Alexey

From: merbllab @.> Sent: Wednesday, September 22, 2021 2:03 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

External Email - Use Caution

(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/468, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62XEKFUHE2TVS6JZRTUDIK6LANCNFSM5ER4MDMQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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anesvi commented 3 years ago

Felipe, see log file they attached. Everything is fine until philosopher labelquant This is likely incompatible mzML issue.

From: Felipe da Veiga Leprevost @.> Sent: Wednesday, September 22, 2021 2:11 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Assign @.> Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

External Email - Use Caution

Does your data contain MS 3 spectra? Where is your database search results? I don't see any fragger log messages.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/468#issuecomment-925164677, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63VTSKEG5MXAQJGJL3UDILZNANCNFSM5ER4MDMQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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merbllab commented 3 years ago

it works! . converting the raw files using MSConvert version 3.0.21261-a57bf91 allow the fragpipe to successfully complete the run.

thanks

From: Alexey Nesvizhskii @.***> Sent: Wednesday, September 22, 2021 9:32:22 PM To: Nesvilab/FragPipe Cc: Merbllab; Author Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

Felipe, see log file they attached. Everything is fine until philosopher labelquant This is likely incompatible mzML issue.

From: Felipe da Veiga Leprevost @.> Sent: Wednesday, September 22, 2021 2:11 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Assign @.> Subject: Re: [Nesvilab/FragPipe] TMT10 - MS3 quantification problem (#468)

External Email - Use Caution

Does your data contain MS 3 spectra? Where is your database search results? I don't see any fragger log messages.

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