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Published 20 hours ago • verified publisher icon Nesvilab

Peptideprophet crashes during open search with variable PTM

Open iheremans opened this issue 2 years ago • 11 comments

Dear FragPipe team,

As a new user, I ran into an issue when attempting to run 'open search' using the latest version of Fragpipe. The error occurs during PSM validation using PeptideProphet (see below). I ran the 'open' workflow without changing anything, except adding phosphate-STY variable modification. Since these sample are phosphopeptide-enriched, almost all peptide will have a phosphate Please find the run parameters below the error message.

Best regards, Isaac

Error message

PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1] PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 17_KO_EP_a_c.pepXML C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 18_DKO_CHL_EP_a_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_CHL_EP_2] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 22_KO_EP_b_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 23_DKO_CHL_EP_b_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 28_DKO_CHL_EP_c_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 16_ctrl_EP_a_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 26_ctrl_EP_c_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 21_ctrl_EP_b_c.pepXML PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_CHL_EP_3] C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 27_KO_EP_c_c.pepXML INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
INFO[13:14:15] Executing PeptideProphet v4.2.2
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure[abi:cxx11] >' what(): failed opening file: The system cannot find the file specified.​

: iostream error panic: Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

goroutine 1 [running]: philosopher/lib/msg.callLogrus(0xc00049e070, 0x6c, 0x12ee878, 0x5) /workspace/philosopher/lib/msg/msg.go:319 +0x4c5 philosopher/lib/msg.ExecutingBinary(0x140d1e0, 0xc000094000, 0x12ee878, 0x5) /workspace/philosopher/lib/msg/msg.go:209 +0xb1 philosopher/lib/ext/peptideprophet.interactParser(0xc000138180, 0x5c, 0xc0001381e0, 0x5b, 0xc000146000, 0x62, 0xc000138180, 0x5c, 0xc0001381e0, 0x5b, ...) /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:235 +0x1d37 philosopher/lib/ext/peptideprophet.PeptideProphet.Execute(0xc000138180, 0x5c, 0xc0001381e0, 0x5b, 0xc000146000, 0x62, 0xc000138180, 0x5c, 0xc0001381e0, 0x5b, ...) /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:86 +0x1f0 philosopher/lib/ext/peptideprophet.Run(0xc00001c900, 0x24, 0xc000022690, 0x48, 0xc0000226e0, 0x49, 0xc0000a4480, 0x57, 0xc000022730, 0x4e, ...) /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:67 +0x4e8 philosopher/cmd.glob..func12(0x284caa0, 0xc0001200d0, 0x1, 0xd) /workspace/philosopher/cmd/peproph.go:26 +0xf2 github.com/spf13/cobra.(*Command).execute(0x284caa0, 0xc000120000, 0xd, 0xd, 0x284caa0, 0xc000120000) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:844 +0x2c2 github.com/spf13/cobra.(*Command).ExecuteC(0x284d7c0, 0xb40b60, 0xc0000cff70, 0xc0000cff68) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:945 +0x336 github.com/spf13/cobra.(*Command).Execute(...) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:885 philosopher/cmd.Execute() /workspace/philosopher/cmd/root.go:35 +0x34 main.main() /workspace/philosopher/main.go:25 +0x85 Process 'PeptideProphet' finished, exit code: 2 Process returned non-zero exit code, stopping ERRO[13:14:17] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

Run parameters

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.2.2

LCMS files:
  Experiment/Group: ctrl_CHL_EP_1
  - C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.mzML	DDA
  Experiment/Group: ctrl_CHL_EP_2
  - C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.mzML	DDA
  Experiment/Group: ctrl_CHL_EP_3
  - C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.mzML	DDA
  Experiment/Group: KO_EP_1
  - C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.mzML	DDA
  Experiment/Group: KO_EP_2
  - C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.mzML	DDA
  Experiment/Group: KO_EP_3
  - C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.mzML	DDA
  Experiment/Group: DKO_EP_1
  - C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.mzML	DDA
  Experiment/Group: DKO_EP_2
  - C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.mzML	DDA
  Experiment/Group: DKO_EP_3
  - C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.mzML	DDA

126 commands to execute:
CheckCentroid
C:\Fragpipe_18.0\jre\bin\java.exe -Xmx45G -cp "C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.mzML 35
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\566d1c1f-a046-4882-af9a-07c9b4685f6e
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\07825582-bad0-432e-9ded-9063ec72ad0b
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\8dbfdff1-1176-4b5f-84f1-37b7413fb317
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\cb708679-b55b-45f5-a727-8c579a57895a
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\5f65dd13-15bd-4833-84d8-fb511ae5c9c8
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\5ecbc656-ce20-4911-af0f-b01f8d532635
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\ac6ad4db-9526-48a0-b961-c8e3a4a9e66d
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\b0ca7682-7269-4d78-819d-61b1f0ad96ed
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\dd8a698f-dab4-4659-9cf6-dfa54e0be1bf
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\GUIDOB~1\AppData\Local\Temp\de5c6df3-7ca1-4b01-a370-e88e3d226895
MSFragger [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx45G C:\Fragpipe_18.0\tools\MSFragger-3.5\MSFragger-3.5.jar C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\fragger.params C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.mzML C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.mzML C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.mzML C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.mzML C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.mzML C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.mzML C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.mzML C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.mzML C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.mzML
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\16_ctrl_EP_a.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\16_ctrl_EP_a.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\16_ctrl_EP_a.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\21_ctrl_EP_b.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\21_ctrl_EP_b.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\21_ctrl_EP_b.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\26_ctrl_EP_c.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\26_ctrl_EP_c.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\26_ctrl_EP_c.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\17_KO_EP_a.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\17_KO_EP_a.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\17_KO_EP_a.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\22_KO_EP_b.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\22_KO_EP_b.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\22_KO_EP_b.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\27_KO_EP_c.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\27_KO_EP_c.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\27_KO_EP_c.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\18_DKO_EP_a.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\18_DKO_EP_a.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\18_DKO_EP_a.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\23_DKO_EP_b.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\23_DKO_EP_b.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\23_DKO_EP_b.pin
MSFragger move pepxml
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.pepXML C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\28_DKO_EP_c.pepXML
MSFragger move tsv
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.tsv C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\28_DKO_EP_c.tsv
MSFragger move pin
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar;/C:/Fragpipe_18.0/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.pin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\28_DKO_EP_c.pin
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\crystalc-0-16_ctrl_EP_a.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\16_ctrl_EP_a.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\crystalc-1-21_ctrl_EP_b.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\21_ctrl_EP_b.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\crystalc-2-26_ctrl_EP_c.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\26_ctrl_EP_c.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\crystalc-3-17_KO_EP_a.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\17_KO_EP_a.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\crystalc-4-22_KO_EP_b.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\22_KO_EP_b.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\crystalc-5-27_KO_EP_c.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\27_KO_EP_c.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\crystalc-6-18_DKO_EP_a.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\18_DKO_EP_a.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\crystalc-7-23_DKO_EP_b.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\23_DKO_EP_b.pepXML
Crystal-C [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -Xmx45G -cp "C:\Fragpipe_18.0\tools\original-crystalc-1.4.4.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\grppr-0.3.23.jar" crystalc.Run C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\crystalc-8-28_DKO_EP_c.pepXML.params C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\28_DKO_EP_c.pepXML
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\crystalc-0-16_ctrl_EP_a.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\crystalc-1-21_ctrl_EP_b.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\crystalc-2-26_ctrl_EP_c.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\crystalc-3-17_KO_EP_a.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\crystalc-4-22_KO_EP_b.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\crystalc-5-27_KO_EP_c.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\crystalc-6-18_DKO_EP_a.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\crystalc-7-23_DKO_EP_b.pepXML.params
Crystal-C: Delete temp
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\crystalc-8-28_DKO_EP_c.pepXML.params
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 17_KO_EP_a_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 18_DKO_EP_a_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 22_KO_EP_b_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 23_DKO_EP_b_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 28_DKO_EP_c_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 16_ctrl_EP_a_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 26_ctrl_EP_c_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 21_ctrl_EP_b_c.pepXML
PeptideProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --combine 27_KO_EP_c_c.pepXML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\16_ctrl_EP_a.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\18_DKO_EP_a.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\17_KO_EP_a.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\22_KO_EP_b.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\27_KO_EP_c.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\23_DKO_EP_b.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\28_DKO_EP_c.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\26_ctrl_EP_c.mzML
Rewrite pepxml [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\jre\bin\java.exe -cp C:\Fragpipe_18.0\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2\interact.pep.xml C:\20220505_Ecoli_KO_3reps_EP\21_ctrl_EP_b.mzML
ProteinProphet [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherDbAnnotate [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe database --annotate C:\Fragpipe_18.0\bin\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razor
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherFilter [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3 --protxml C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\combined.prot.xml --razorbin C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1\.meta\razor.bin
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe report
PhilosopherAbacus [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe abacus --razor --reprint --tag rev_ --protein ctrl_CHL_EP_1 ctrl_CHL_EP_2 ctrl_CHL_EP_3 KO_EP_1 KO_EP_2 KO_EP_3 DKO_EP_1 DKO_EP_2 DKO_EP_3
PTMShepherd [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\jre\bin\java.exe -Xmx45G -Dbatmass.io.libs.thermo.dir="C:\Fragpipe_18.0\tools\MSFragger-3.5\ext\thermo" -cp "C:\Fragpipe_18.0\tools\ptmshepherd-2.0.0.jar;C:\Fragpipe_18.0\tools\batmass-io-1.25.5.jar;C:\Fragpipe_18.0\tools\commons-math3-3.6.1.jar;C:\Fragpipe_18.0\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Fragpipe_18.0\tools\hipparchus-1.8\hipparchus-stat-1.8.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\shepherd.config"
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
C:\Fragpipe_18.0\tools\philosopher_v4.2.2_windows_amd64\philosopher.exe workspace --clean --nocheck

Execution order:

    Cmd: [START], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [CheckCentroid], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]
    Cmd: [MSFragger], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [Crystal-C], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PeptideProphet], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [ProteinProphet], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PhilosopherFilter], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PhilosopherReport], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PhilosopherAbacus], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [PTMShepherd], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_2]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_1]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_3]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_2]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\DKO_EP_1]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\KO_EP_3]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_2]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_3]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP]
    Cmd: [WorkspaceClean], Work dir: [C:\20220505_Ecoli_KO_3reps_EP\MSfragger_open_EP\ctrl_CHL_EP_1]


>ProteinCenter:sp_canonical|A0A385XJ53 Insertion element IS1 9 protein InsA [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P0A7A9 Inorganic pyrophosphatase [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P0ABB8 Magnesium-transporting ATPase, P-type 1 [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P0AF18 N-acetylglucosamine-6-phosphate deacetylase [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P11866 Threonine dehydratase operon activator protein [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P28912 H repeat-associated putative transposase YhhI [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P37665 Probable lipoprotein YiaD [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P56579 PTS system glucitol/sorbitol-specific EIIC component [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P76000 Putative uncharacterized protein YcgI [OS=Escherichia coli (strain K12)]
>ProteinCenter:sp_canonical|P77454 Glutaminase 1 [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P00561 Bifunctional aspartokinase/homoserine dehydrogenase 1 [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P0A800 DNA-directed RNA polymerase subunit omega [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P0ABV2 Biopolymer transport protein ExbD [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P0AFJ1 Protein YjdM [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P15070 Flagellar motor switch protein FliN [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P31068 Flagellar assembly protein FliH [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P38506 Flap endonuclease Xni [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P62558 Protein SopB [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P76108 Bifunctional polyhydroxybutyrate synthase / ABC transporter periplasmic binding protein [OS=Escherichia coli (strain K12)]
>rev_ProteinCenter:sp_canonical|P77624 Carbamate kinase-like protein YahI [OS=Escherichia coli (strain K12)]
>sp|Q14525|KT33B_HUMAN Keratin, type I cuticular Ha3-II OS=Homo sapiens GN=KRT33B PE=1 SV=3

# FragPipe v18.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Fragpipe_18.0\\bin\\2022-06-20-decoys-contam-Ecoli_K12_sp83333.fasta.fas

crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=0.01
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\Fragpipe_18.0\\tools\\IonQuant-1.8.0.jar
fragpipe-config.bin-msfragger=C\:\\Fragpipe_18.0\\tools\\MSFragger-3.5\\MSFragger-3.5.jar
fragpipe-config.bin-philosopher=C\:\\Fragpipe_18.0\\tools\\philosopher_v4.2.2_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=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
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=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
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.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=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=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
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.restrict_deltamass_to=all
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=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,true,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 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=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01 --mapmods
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
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_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
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=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=-1
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=-1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
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=C\:\\20220505_Ecoli_KO_3reps_EP\\MSfragger_open_EP
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=35

iheremans avatar Jun 21 '22 14:06 iheremans

Hi Isaac,

The log was truncated by GitHub. Can you zip your log file and drag it to https://github.com/Nesvilab/FragPipe/issues/727 to upload?

Thanks,

Fengchao

fcyu avatar Jun 21 '22 14:06 fcyu

FragpipeLog_IH.zip

Please find the complete log here. Thanks!

iheremans avatar Jun 21 '22 14:06 iheremans

I have no idea about the cause. Need Felipe's @prvst help. The error message is as following

terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'

: iostream error
panic: Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

goroutine 1 [running]:
philosopher/lib/msg.callLogrus(0xc00049e070, 0x6c, 0x12ee878, 0x5)
	/workspace/philosopher/lib/msg/msg.go:319 +0x4c5
philosopher/lib/msg.ExecutingBinary(0x140d1e0, 0xc000094000, 0x12ee878, 0x5)
	/workspace/philosopher/lib/msg/msg.go:209 +0xb1
philosopher/lib/ext/peptideprophet.interactParser(0xc000138180, 0x5c, 0xc0001381e0, 0x5b, 0xc000146000, 0x62, 0xc000138180, 0x5c, 0xc0001381e0, 0x5b, ...)
	/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:235 +0x1d37
philosopher/lib/ext/peptideprophet.PeptideProphet.Execute(0xc000138180, 0x5c, 0xc0001381e0, 0x5b, 0xc000146000, 0x62, 0xc000138180, 0x5c, 0xc0001381e0, 0x5b, ...)
	/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:86 +0x1f0
philosopher/lib/ext/peptideprophet.Run(0xc00001c900, 0x24, 0xc000022690, 0x48, 0xc0000226e0, 0x49, 0xc0000a4480, 0x57, 0xc000022730, 0x4e, ...)
	/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:67 +0x4e8
philosopher/cmd.glob..func12(0x284caa0, 0xc0001200d0, 0x1, 0xd)
	/workspace/philosopher/cmd/peproph.go:26 +0xf2
github.com/spf13/cobra.(*Command).execute(0x284caa0, 0xc000120000, 0xd, 0xd, 0x284caa0, 0xc000120000)
	/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:844 +0x2c2
github.com/spf13/cobra.(*Command).ExecuteC(0x284d7c0, 0xb40b60, 0xc0000cff70, 0xc0000cff68)
	/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:945 +0x336
github.com/spf13/cobra.(*Command).Execute(...)
	/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:885
philosopher/cmd.Execute()
	/workspace/philosopher/cmd/root.go:35 +0x34
main.main()
	/workspace/philosopher/main.go:25 +0x85
Process 'PeptideProphet' finished, exit code: 2
Process returned non-zero exit code, stopping
ERRO[13:14:17] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files

Best,

Fengchao

fcyu avatar Jun 21 '22 14:06 fcyu

'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure[abi:cxx11] >' what(): failed opening file: The system cannot find the file specified.​

This is basically a "file cannot be found" error. Check your folders, file paths, and see if the MSFragger finished correctly.

prvst avatar Jun 21 '22 14:06 prvst

The log looks OK

I noticed that you assigned files to different experiments. With Open search, one would typically not assigned files to experiments

Can you try with just 1 file, 22_KO_EP_b, and not assigned to experiments ?

From: Felipe da Veiga Leprevost @.> Sent: Tuesday, June 21, 2022 10:25 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] Peptideprophet crashes during open search with variable PTM (Issue #727)

External Email - Use Caution

'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure[abi:cxx11] >' what(): failed opening file: The system cannot find the file specified.​

This is basically a "file cannot be found" error. Check your folders, file paths, and see if the MSFragger finished correctly.

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/727#issuecomment-1161818874, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62PZT26POITZIIXE7DVQHGFLANCNFSM5ZMO7VMQ. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

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anesvi avatar Jun 21 '22 14:06 anesvi

Thank you for your help! With a single file, it works very well now. However, loading 3 biological replicates gives an error. I will try loading them as fractions of the same experiment.

Best regards, Isaac

iheremans avatar Jun 21 '22 18:06 iheremans

Ok. But I am not sure what causes the error though. Can you try with …_c file alone (you have _a, _b, and _c replicates)? I wonder if there is something about your files ending with _c because Crystal-C also adds _c to the file names

From: iheremans @.> Sent: Tuesday, June 21, 2022 2:15 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] Peptideprophet crashes during open search with variable PTM (Issue #727)

External Email - Use Caution

Thank you for your help! With a single file, it works very well now. However, loading 3 biological replicates gives an error. I will try loading them as fractions of the same experiment.

Best regards, Isaac

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/727#issuecomment-1162142234, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6ZZPCZERLHRC2UWH63VQIBBBANCNFSM5ZMO7VMQ. You are receiving this because you commented.Message ID: @.@.>>

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anesvi avatar Jun 21 '22 18:06 anesvi

Good point! It might be related to an known issue of Crystal-C: https://github.com/Nesvilab/FragPipe/issues/636

Best,

Fengchao

fcyu avatar Jun 21 '22 18:06 fcyu

Iheremans: For now, please rename the files to get rid of ‘_c’ And what do you want to do? To see the differences in PTMs between two conditions? Then assigned replicates of the same condition to the same experiment. If you do not care about differences, just want to see the overall mass shift profile, assign all files to the same experiment .

Fengchao: should we ask Hui-yin to make a change in Crystal-C?

Alexey

From: Fengchao @.> Sent: Tuesday, June 21, 2022 2:24 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Comment @.> Subject: Re: [Nesvilab/FragPipe] Peptideprophet crashes during open search with variable PTM (Issue #727)

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Good point! It might be related to an known issue of Crystal-C: #636https://github.com/Nesvilab/FragPipe/issues/636

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/727#issuecomment-1162154926, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6YKGSJS2Y5FQ7ZUOZLVQICFXANCNFSM5ZMO7VMQ. You are receiving this because you commented.Message ID: @.@.>>

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anesvi avatar Jun 21 '22 18:06 anesvi

We have received two reports, so I think we should ask Hui-Yin to fix this bug in Crystal-C.

Best,

Fengchao

fcyu avatar Jun 21 '22 18:06 fcyu

Running a single file ending with "_c" indeed produces the error. Thanks for all your help!

iheremans avatar Jun 22 '22 09:06 iheremans