danielgeiszler
commented
2 years ago There is no log attached here. Could you please try uploading it again?
Closed iolanda-vendrell closed 2 years ago
danielgeiszler
commented
2 years ago There is no log attached here. Could you please try uploading it again?
iolanda-vendrell
commented
2 years ago Hi, I have now uploaded. Also attached in this email,
Many thanks,
Best wishes, Iolanda
From: danielgeiszler @.> Sent: 25 May 2022 15:19 To: Nesvilab/FragPipe @.> Cc: Iolanda Vendrell @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Percolator failing opening a file (Issue #691)
There is no log attached here. Could you please try uploading it again?
— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/691#issuecomment-1137314898, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZKVD7SDWOK5KKSJOJLPB6TVLYZFBANCNFSM5W5HKWHA. You are receiving this because you authored the thread.Message ID: @.**@.>>
System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info: FragPipe version 17.1 MSFragger version 3.4 Philosopher version 4.1.1 (build 1637179075)
LCMS files: Experiment/Group: TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512
620 commands to execute: CheckCentroid D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -Xmx24G -cp "D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.d 7 WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F1_6_CIR-PSBK-01-2hr_A_p_DDA_S1-F1_36518] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F1_6_CIR-PSBK-01-2hr_A_p_DDA_S1-F1_36518] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G5_39_CIR-PSBK-04-2hr_C_p_DDA_S1-G5_36567] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G5_39_CIR-PSBK-04-2hr_C_p_DDA_S1-G5_36567] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G6_47_CIR-PSBK-04-18hr_C_p_DDA_S1-G6_36569] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G6_47_CIR-PSBK-04-18hr_C_p_DDA_S1-G6_36569] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G2_15_CIR-PSBK-04-18hr_A_p_DDA_S1-G2_36525] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G2_15_CIR-PSBK-04-18hr_A_p_DDA_S1-G2_36525] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H4_32_CIR-PSBK-07-18hr_B_p_DDA_S1-H4_36552] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H4_32_CIR-PSBK-07-18hr_B_p_DDA_S1-H4_36552] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H2_16_CIR-PSBK-07-18hr_A_p_DDA_S1-H2_36530] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H2_16_CIR-PSBK-07-18hr_A_p_DDA_S1-H2_36530] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C6_43_CIR-PSBK-04-6hr_C_p_DDA_S1-C6_36568] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C6_43_CIR-PSBK-04-6hr_C_p_DDA_S1-C6_36568] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G3_23_CIR-PSBK-04-2hr_B_p_DDA_S1-G3_36545] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G3_23_CIR-PSBK-04-2hr_B_p_DDA_S1-G3_36545] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D3_20_CIR-PSBK-07-30min_B_p_DDA_S1-D3_36549] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D3_20_CIR-PSBK-07-30min_B_p_DDA_S1-D3_36549] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C2_11_CIR-PSBK-04-6hr_A_p_DDA_S1-C2_36524] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C2_11_CIR-PSBK-04-6hr_A_p_DDA_S1-C2_36524] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_3_p_DDA_S2-C12_36553] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_3_p_DDA_S2-C12_36553] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E4_29_DMSO-18hr_B_p_DDA_S1-E4_36537] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E4_29_DMSO-18hr_B_p_DDA_S1-E4_36537] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E3_21_DMSO-2hr_B_p_DDA_S1-E3_36535] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E3_21_DMSO-2hr_B_p_DDA_S1-E3_36535] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_2_p_DDA_S2-B12_36531] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_2_p_DDA_S2-B12_36531] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E6_45_DMSO-18hr_C_p_DDA_S1-E6_36559] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E6_45_DMSO-18hr_C_p_DDA_S1-E6_36559] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H6_48_CIR-PSBK-07-18hr_C_p_DDA_S1-H6_36574] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H6_48_CIR-PSBK-07-18hr_C_p_DDA_S1-H6_36574] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F2_14_CIR-PSBK-01-18hr_A_p_DDA_S1-F2_36520] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F2_14_CIR-PSBK-01-18hr_A_p_DDA_S1-F2_36520] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_1_p_DDA_S2-A12_36510] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_1_p_DDA_S2-A12_36510] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C4_27_CIR-PSBK-04-6hr_B_p_DDA_S1-C4_36546] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C4_27_CIR-PSBK-04-6hr_B_p_DDA_S1-C4_36546] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E2_13_DMSO-18hr_A_p_DDA_S1-E2_36515] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E2_13_DMSO-18hr_A_p_DDA_S1-E2_36515] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F4_30_CIR-PSBK-01-18hr_B_p_DDA_S1-F4_36542] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F4_30_CIR-PSBK-01-18hr_B_p_DDA_S1-F4_36542] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_4_p_DDA_S2-D12_36575] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_4_p_DDA_S2-D12_36575] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D1_4_CIR-PSBK-07-30min_A_p_DDA_S1-D1_36527] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D1_4_CIR-PSBK-07-30min_A_p_DDA_S1-D1_36527] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C5_35_CIR-PSBK-04-30min_C_p_DDA_S1-C5_36566] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C5_35_CIR-PSBK-04-30min_C_p_DDA_S1-C5_36566] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C3_19_CIR-PSBK-04-30min_B_p_DDA_S1-C3_36544] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C3_19_CIR-PSBK-04-30min_B_p_DDA_S1-C3_36544] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E5_37_DMSO-2hr_C_p_DDA_S1-E5_36557] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E5_37_DMSO-2hr_C_p_DDA_S1-E5_36557] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D6_44_CIR-PSBK-07-6hr_C_p_DDA_S1-D6_36573] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D6_44_CIR-PSBK-07-6hr_C_p_DDA_S1-D6_36573] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F5_38_CIR-PSBK-01-2hr_C_p_DDA_S1-F5_36562] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F5_38_CIR-PSBK-01-2hr_C_p_DDA_S1-F5_36562] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H3_24_CIR-PSBK-07-2hr_B_p_DDA_S1-H3_36550] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H3_24_CIR-PSBK-07-2hr_B_p_DDA_S1-H3_36550] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F3_22_CIR-PSBK-01-2hr_B_p_DDA_S1-F3_36540] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F3_22_CIR-PSBK-01-2hr_B_p_DDA_S1-F3_36540] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F6_46_CIR-PSBK-01-18hr_C_p_DDA_S1-F6_36564] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F6_46_CIR-PSBK-01-18hr_C_p_DDA_S1-F6_36564] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G4_31_CIR-PSBK-04-18hr_B_p_DDA_S1-G4_36547] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G4_31_CIR-PSBK-04-18hr_B_p_DDA_S1-G4_36547] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G1_7_CIR-PSBK-04-2hr_A_p_DDA_S1-G1_36523] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G1_7_CIR-PSBK-04-2hr_A_p_DDA_S1-G1_36523] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D4_28_CIR-PSBK-07-6hr_B_p_DDA_S1-D4_36551] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D4_28_CIR-PSBK-07-6hr_B_p_DDA_S1-D4_36551] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H5_40_CIR-PSBK-07-2hr_C_p_DDA_S1-H5_36572] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H5_40_CIR-PSBK-07-2hr_C_p_DDA_S1-H5_36572] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D2_12_CIR-PSBK-07-6hr_A_p_DDA_S1-D2_36529] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D2_12_CIR-PSBK-07-6hr_A_p_DDA_S1-D2_36529] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E1_5_DMSO-2hr_A_p_DDA_S1-E1_36513] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E1_5_DMSO-2hr_A_p_DDA_S1-E1_36513] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H1_8_CIR-PSBK-07-2hr_A_p_DDA_S1-H1_36528] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H1_8_CIR-PSBK-07-2hr_A_p_DDA_S1-H1_36528] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C1_3_CIR-PSBK-04-30min_A_p_DDA_S1-C1_36522] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C1_3_CIR-PSBK-04-30min_A_p_DDA_S1-C1_36522] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D5_36_CIR-PSBK-07-30min_C_p_DDA_S1-D5_36571] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D5_36_CIR-PSBK-07-30min_C_p_DDA_S1-D5_36571] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34] D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx24G D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\fragger.params D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C1_3_CIR-PSBK-04-30min_A_p_DDA_S1-C1_36522.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C2_11_CIR-PSBK-04-6hr_A_p_DDA_S1-C2_36524.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C3_19_CIR-PSBK-04-30min_B_p_DDA_S1-C3_36544.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C4_27_CIR-PSBK-04-6hr_B_p_DDA_S1-C4_36546.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C5_35_CIR-PSBK-04-30min_C_p_DDA_S1-C5_36566.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_C6_43_CIR-PSBK-04-6hr_C_p_DDA_S1-C6_36568.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D1_4_CIR-PSBK-07-30min_A_p_DDA_S1-D1_36527.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D2_12_CIR-PSBK-07-6hr_A_p_DDA_S1-D2_36529.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D3_20_CIR-PSBK-07-30min_B_p_DDA_S1-D3_36549.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D4_28_CIR-PSBK-07-6hr_B_p_DDA_S1-D4_36551.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D5_36_CIR-PSBK-07-30min_C_p_DDA_S1-D5_36571.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_D6_44_CIR-PSBK-07-6hr_C_p_DDA_S1-D6_36573.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E1_5_DMSO-2hr_A_p_DDA_S1-E1_36513.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E2_13_DMSO-18hr_A_p_DDA_S1-E2_36515.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E3_21_DMSO-2hr_B_p_DDA_S1-E3_36535.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E4_29_DMSO-18hr_B_p_DDA_S1-E4_36537.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E5_37_DMSO-2hr_C_p_DDA_S1-E5_36557.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_E6_45_DMSO-18hr_C_p_DDA_S1-E6_36559.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F1_6_CIR-PSBK-01-2hr_A_p_DDA_S1-F1_36518.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F2_14_CIR-PSBK-01-18hr_A_p_DDA_S1-F2_36520.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F3_22_CIR-PSBK-01-2hr_B_p_DDA_S1-F3_36540.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F4_30_CIR-PSBK-01-18hr_B_p_DDA_S1-F4_36542.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F5_38_CIR-PSBK-01-2hr_C_p_DDA_S1-F5_36562.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_F6_46_CIR-PSBK-01-18hr_C_p_DDA_S1-F6_36564.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G1_7_CIR-PSBK-04-2hr_A_p_DDA_S1-G1_36523.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G2_15_CIR-PSBK-04-18hr_A_p_DDA_S1-G2_36525.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G3_23_CIR-PSBK-04-2hr_B_p_DDA_S1-G3_36545.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G4_31_CIR-PSBK-04-18hr_B_p_DDA_S1-G4_36547.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G5_39_CIR-PSBK-04-2hr_C_p_DDA_S1-G5_36567.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_G6_47_CIR-PSBK-04-18hr_C_p_DDA_S1-G6_36569.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H1_8_CIR-PSBK-07-2hr_A_p_DDA_S1-H1_36528.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H2_16_CIR-PSBK-07-18hr_A_p_DDA_S1-H2_36530.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H3_24_CIR-PSBK-07-2hr_B_p_DDA_S1-H3_36550.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H4_32_CIR-PSBK-07-18hr_B_p_DDA_S1-H4_36552.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H5_40_CIR-PSBK-07-2hr_C_p_DDA_S1-H5_36572.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_H6_48_CIR-PSBK-07-18hr_C_p_DDA_S1-H6_36574.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_1_p_DDA_S2-A12_36510.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_2_p_DDA_S2-B12_36531.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_3_p_DDA_S2-C12_36553.d D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_p-pept_pool_4_p_DDA_S2-D12_36575.d MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A1_1_DMSO-30min_A_p_DDA_S1-A1_36512.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A2_9_DMSO-6hr_A_p_DDA_S1-A2_36514.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A3_17_DMSO-30min_B_p_DDA_S1-A3_36534.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A4_25_DMSO-6hr_B_p_DDA_S1-A4_36536.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A5_33_DMSO-30min_C_p_DDA_S1-A5_36556.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_A6_41_DMSO-6hr_C_p_DDA_S1-A6_36558.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B1_2_CIR-PSBK-01-30min_A_p_DDA_S1-B1_36517.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B2_10_CIR-PSBK-01-6hr_A_p_DDA_S1-B2_36519.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B3_18_CIR-PSBK-01-30min_B_p_DDA_S1-B3_36539.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B4_26_CIR-PSBK-01-6hr_B_p_DDA_S1-B4_36541.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563.pepXML D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563.pepXML MSFragger move pin D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\0_Raw_files\MSQ2237b_TTP416_CGleason\set1_phospho\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563.pin D:\3_Fragpipe\MSQ2237b_TTP0416_CGleason_phospho\FP_phospho_noS34\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563\TTP0416_MSQ2237b_20220429_IV_SF_CGleeson_B6_42_CIR-PSBK-01-6hr_C_p_DDA_S1-B6_36563.pin MSFragger move pepxml D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\jre\bin\java.exe -cp D:\software\Fragpipe\FragPipe-jre-17.1\fragpipe\lib\fragpipe-17.1.jar;/D:/software/Fragpipe/FragPipe-jre-17.1/fragpipe/lib/commons-
fcyu
commented
2 years ago It looks like something was wrong with your file system. Can you restart everything and try again? For this type of error, it is difficult for us to troubleshot since we cannot reproduce it.
Best,
Fengchao
iolanda-vendrell
commented
2 years ago Hi Fengchao, I have done the analysis few times, closing fragpipe and starting it again. What I haven’t done is to restart the PC, which I will do in half an hour or so… Do you think that the file path is too long? I can try to change that.
Many thanks,
Iolanda
From: Fengchao @.> Sent: 25 May 2022 15:24 To: Nesvilab/FragPipe @.> Cc: Iolanda Vendrell @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Percolator failing opening a file (Issue #691)
It looks like something was wrong with your file system. Can you restart everything and try again? For this type of error, it is difficult for us to troubleshot since we cannot reproduce it.
Best,
Fengchao
— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/691#issuecomment-1137322169, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZKVD7UZQHOBLGDSTIWPYLLVLYZWLANCNFSM5W5HKWHA. You are receiving this because you authored the thread.Message ID: @.**@.>>
fcyu
commented
2 years ago Hi Iolanda,
Do you think that the file path is too long? I can try to change that.
This is also one of the possibilities.
Best,
Fengchao
iolanda-vendrell
commented
2 years ago Good morning Fenchao,
I managed to get It working. The problem it was the folder path were I was saving the fragpipe output. It was too long Thanks for you help. Much appreciated,
Best wishes,
Iolanda
From: Fengchao @.> Sent: 27 May 2022 19:28 To: Nesvilab/FragPipe @.> Cc: Iolanda Vendrell @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Percolator failing opening a file (Issue #691)
Closed #691https://github.com/Nesvilab/FragPipe/issues/691 as completed.
— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/691#event-6694657711, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZKVD7VDPDEABTFRB6ONGCDVMEHZVANCNFSM5W5HKWHA. You are receiving this because you authored the thread.Message ID: @.**@.>>
Hi all, i have been experiencing problems when analysing DDA TIMS-TOF data from a set including 52 mass spec files. Percolator keeps crashing reporting it is unable to open a specific error "ERROR: Could not open the file xxx_psms.tsv for writing. Check if the folder exists and if you have permission to write." Initially this happens with one file, so I double checked that the file wasn't corrupted and ran it through Fragpipe alone and worked. Next, I removed that file and the FP crashed again with same error saying couldn't open another file. The error log is attached. I would appreciate if you could help.
Many thanks in advance,
best wishes,
FP_error_log_2022-05-25_14-47-19.txt