Error when running DIA-peptidomics workflow

yishai99 commented 1 year ago

Describe the issue or question: Hi, I got an error when running DIA runs of peptidomics. Below is the error: System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: N/A

Version info: FragPipe version 19.0 MSFragger version 3.6 IonQuant version 1.8.9 Philosopher version 4.7.0

LCMS files: Experiment/Group: B_1

D:\17498\EX1_MB_17498_B1_08122022_DIA.raw DIA Experiment/Group: B_2
D:\17498\EX1_MB_17498_B2_08122022_DIA.raw DIA Experiment/Group: B_3
D:\17498\EX1_MB_17498_B3_08122022_DIA.raw DIA Experiment/Group: C_1
D:\17498\EX1_MB_17498_C1_08122022_DIA.raw DIA Experiment/Group: C_2
D:\17498\EX1_MB_17498_C2_08122022_DIA.raw DIA Experiment/Group: C_3
D:\17498\EX1_MB_17498_C3_08122022_DIA.raw DIA

.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|P70274|SEPP1_MOUSE : UUUUUUUUUU MWRSLGLALALCLLPYGGAESQGQSSACYKAPEWYIGDQNPMLNSEGKVTVVALLQASUYLCLLQASRLEDLRIKLESQGYFNISYIVVNHQGSPSQLKHSHLKKQVSEHIAVYRQEEDGIDVWTLLNGNKDDFLIYDRCGRLVYHLGLPYSFLTFPYVEEAIKIAYCEERCGNCNLTSLEDEDFCKTVTSATANKTAEPSEAHSHHKHHNKHGQEHLGSSKPSENQQPGPSETTLPPSGLHHHHRHRGQHRQGHLESUDTTASEGLHLSLAQRKLURRGCINQLLCKLSKESEAAPSSCCCHCRHLIFEKSGSAIAUQCAENLPSLCSUQGLFAEEKVTESCQCRSPPAAUQNQPMNPMEANPNUSUDNQTRKUKUHSN ..:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:WARNING: Found the following zero-mass residues in protein entry sp|Q80TA1|EPT1_MOUSE : U MAGYEYVSPEQLSGFDKYKYSALDTNPLSLYIMHPFWNTIVKVFPTWLAPNLITFSGFMLLVFNFLLLTYFDPDFYASAPGHKHVPDWVWIVVGILNFAAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILSHWEKYNTGVLFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKSNTLKHKSVYEAMVPFFSPCLLFTLCTVWILWSPSDILEIHPRIFYFMVGTAFANITCQLIVCQMSSTRCPTLNWLLLPLLLVVAAVIVGAATSRLESALLYTLTAAFTLAHIHYGVQVVKQLSRHFQIYPFSLRKPNSDULGMEEQNIGL .........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:..... Total: 37758 Computing degenerate peptides for 1488 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 1536 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1536 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1536 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 1536 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... INFO: mu=8.99553e-06, db_size=41418632 Computing MU for 1536 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO[13:38:01] Done
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\B_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:01] Executing Database v4.7.0
INFO[13:38:01] Annotating the database
INFO[13:38:06] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\C_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:06] Executing Database v4.7.0
INFO[13:38:07] Annotating the database
INFO[13:38:11] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\B_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:11] Executing Database v4.7.0
INFO[13:38:11] Annotating the database
INFO[13:38:16] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\C_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:17] Executing Database v4.7.0
INFO[13:38:17] Annotating the database
INFO[13:38:21] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:22] Executing Database v4.7.0
INFO[13:38:22] Annotating the database
INFO[13:38:26] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\B_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:26] Executing Database v4.7.0
INFO[13:38:26] Annotating the database
INFO[13:38:31] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: D:\17498\MSFragger\C_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe database --annotate D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023adolescentis.fasta.fas --prefix rev INFO[13:38:31] Executing Database v4.7.0
INFO[13:38:31] Annotating the database
INFO[13:38:36] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\B_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\B_1_1 --protxml D:\17498\MSFragger\combined.prot.xml --razor INFO[13:38:36] Executing Filter v4.7.0
INFO[13:38:36] Processing peptide identification files
INFO[13:38:36] Parsing D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q3.pep.xml INFO[13:38:36] Parsing D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q1.pep.xml INFO[13:38:36] Parsing D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q2.pep.xml INFO[13:38:37] 1+ Charge profile decoy=1 target=3 INFO[13:38:37] 2+ Charge profile decoy=35 target=861 INFO[13:38:37] 3+ Charge profile decoy=41 target=1015 INFO[13:38:37] 4+ Charge profile decoy=24 target=647 INFO[13:38:37] 5+ Charge profile decoy=19 target=278 INFO[13:38:37] 6+ Charge profile decoy=0 target=0 INFO[13:38:37] Database search results ions=1894 peptides=1207 psms=2924 INFO[13:38:37] Converged to 0.96 % FDR with 2178 PSMs decoy=21 threshold=0.90407 total=2199 INFO[13:38:37] Converged to 0.93 % FDR with 757 Peptides decoy=7 threshold=0.933613 total=764 INFO[13:38:37] Converged to 0.97 % FDR with 1343 Ions decoy=13 threshold=0.916383 total=1356 INFO[13:38:37] Protein inference results decoy=333 target=712 INFO[13:38:37] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:38:38] Applying sequential FDR estimation ions=1414 peptides=850 psms=2199 INFO[13:38:38] Converged to 0.96 % FDR with 2178 PSMs decoy=21 threshold=0.90407 total=2199 INFO[13:38:38] Converged to 0.93 % FDR with 757 Peptides decoy=7 threshold=0.933613 total=764 INFO[13:38:38] Converged to 0.97 % FDR with 1343 Ions decoy=13 threshold=0.916383 total=1356 INFO[13:38:38] Post processing identifications
INFO[13:38:38] Assigning protein identifications to layers
INFO[13:38:39] Processing protein inference
INFO[13:38:42] Synchronizing PSMs and proteins
INFO[13:38:42] Final report numbers after FDR filtering, and post-processing ions=1343 peptides=757 proteins=105 psms=2178 INFO[13:38:42] Saving
INFO[13:38:42] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\B_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\B_2_2 --protxml D:\17498\MSFragger\combined.prot.xml --razorbin D:\17498\MSFragger\B_1_1.meta\razor.bin INFO[13:38:42] Executing Filter v4.7.0
INFO[13:38:42] Fetching razor assignment from: D:\17498\MSFragger\B_1_1.meta\razor.bin: 3727 razor groups imported. INFO[13:38:42] Processing peptide identification files
INFO[13:38:42] Parsing D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q3.pep.xml INFO[13:38:42] Parsing D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q1.pep.xml INFO[13:38:42] Parsing D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q2.pep.xml INFO[13:38:43] 1+ Charge profile decoy=16 target=24 INFO[13:38:43] 2+ Charge profile decoy=49 target=1535 INFO[13:38:43] 3+ Charge profile decoy=43 target=1699 INFO[13:38:43] 4+ Charge profile decoy=30 target=762 INFO[13:38:43] 5+ Charge profile decoy=7 target=285 INFO[13:38:43] 6+ Charge profile decoy=0 target=0 INFO[13:38:43] Database search results ions=3105 peptides=2101 psms=4450 INFO[13:38:43] Converged to 0.99 % FDR with 3740 PSMs decoy=37 threshold=0.889536 total=3777 INFO[13:38:43] Converged to 0.98 % FDR with 1532 Peptides decoy=15 threshold=0.938457 total=1547 INFO[13:38:43] Converged to 1.00 % FDR with 2507 Ions decoy=25 threshold=0.915868 total=2532 INFO[13:38:43] Protein inference results decoy=333 target=712 INFO[13:38:43] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:38:43] Applying sequential FDR estimation ions=2652 peptides=1745 psms=3777 INFO[13:38:43] Converged to 0.99 % FDR with 3740 PSMs decoy=37 threshold=0.889536 total=3777 INFO[13:38:43] Converged to 0.98 % FDR with 1532 Peptides decoy=15 threshold=0.938457 total=1547 INFO[13:38:43] Converged to 1.00 % FDR with 2507 Ions decoy=25 threshold=0.915868 total=2532 INFO[13:38:43] Post processing identifications
INFO[13:38:44] Assigning protein identifications to layers
INFO[13:38:44] Processing protein inference
INFO[13:38:47] Synchronizing PSMs and proteins
INFO[13:38:47] Final report numbers after FDR filtering, and post-processing ions=2507 peptides=1532 proteins=335 psms=3740 INFO[13:38:47] Saving
INFO[13:38:47] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\B_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\B_3_3 --protxml D:\17498\MSFragger\combined.prot.xml --razorbin D:\17498\MSFragger\B_1_1.meta\razor.bin INFO[13:38:48] Executing Filter v4.7.0
INFO[13:38:48] Fetching razor assignment from: D:\17498\MSFragger\B_1_1.meta\razor.bin: 3727 razor groups imported. INFO[13:38:48] Processing peptide identification files
INFO[13:38:48] Parsing D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q3.pep.xml INFO[13:38:48] Parsing D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q1.pep.xml INFO[13:38:48] Parsing D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q2.pep.xml INFO[13:38:48] 1+ Charge profile decoy=6 target=9 INFO[13:38:48] 2+ Charge profile decoy=53 target=1211 INFO[13:38:48] 3+ Charge profile decoy=40 target=1319 INFO[13:38:48] 4+ Charge profile decoy=20 target=632 INFO[13:38:48] 5+ Charge profile decoy=12 target=235 INFO[13:38:48] 6+ Charge profile decoy=0 target=0 INFO[13:38:48] Database search results ions=2427 peptides=1643 psms=3537 INFO[13:38:48] Converged to 0.97 % FDR with 2886 PSMs decoy=28 threshold=0.880071 total=2914 INFO[13:38:48] Converged to 0.95 % FDR with 1156 Peptides decoy=11 threshold=0.924314 total=1167 INFO[13:38:48] Converged to 0.96 % FDR with 1883 Ions decoy=18 threshold=0.901144 total=1901 INFO[13:38:48] Protein inference results decoy=333 target=712 INFO[13:38:48] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:38:49] Applying sequential FDR estimation ions=1988 peptides=1305 psms=2914 INFO[13:38:49] Converged to 0.97 % FDR with 2886 PSMs decoy=28 threshold=0.880071 total=2914 INFO[13:38:49] Converged to 0.95 % FDR with 1156 Peptides decoy=11 threshold=0.924314 total=1167 INFO[13:38:49] Converged to 0.96 % FDR with 1883 Ions decoy=18 threshold=0.901144 total=1901 INFO[13:38:49] Post processing identifications
INFO[13:38:49] Assigning protein identifications to layers
INFO[13:38:50] Processing protein inference
INFO[13:38:52] Synchronizing PSMs and proteins
INFO[13:38:53] Final report numbers after FDR filtering, and post-processing ions=1883 peptides=1156 proteins=228 psms=2886 INFO[13:38:53] Saving
INFO[13:38:53] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\C_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\C_1_1 --protxml D:\17498\MSFragger\combined.prot.xml --razorbin D:\17498\MSFragger\B_1_1.meta\razor.bin INFO[13:38:53] Executing Filter v4.7.0
INFO[13:38:53] Fetching razor assignment from: D:\17498\MSFragger\B_1_1.meta\razor.bin: 3727 razor groups imported. INFO[13:38:53] Processing peptide identification files
INFO[13:38:53] Parsing D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q3.pep.xml INFO[13:38:53] Parsing D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q1.pep.xml INFO[13:38:53] Parsing D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q2.pep.xml INFO[13:38:53] 1+ Charge profile decoy=1 target=8 INFO[13:38:53] 2+ Charge profile decoy=25 target=614 INFO[13:38:53] 3+ Charge profile decoy=22 target=719 INFO[13:38:53] 4+ Charge profile decoy=28 target=444 INFO[13:38:53] 5+ Charge profile decoy=10 target=209 INFO[13:38:53] 6+ Charge profile decoy=0 target=0 INFO[13:38:53] Database search results ions=1468 peptides=1047 psms=2080 INFO[13:38:53] Converged to 0.99 % FDR with 1415 PSMs decoy=14 threshold=0.908905 total=1429 INFO[13:38:53] Converged to 0.97 % FDR with 618 Peptides decoy=6 threshold=0.931617 total=624 INFO[13:38:53] Converged to 0.96 % FDR with 942 Ions decoy=9 threshold=0.923266 total=951 INFO[13:38:53] Protein inference results decoy=333 target=712 INFO[13:38:53] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:38:53] Applying sequential FDR estimation ions=1003 peptides=691 psms=1429 INFO[13:38:53] Converged to 0.99 % FDR with 1415 PSMs decoy=14 threshold=0.908905 total=1429 INFO[13:38:53] Converged to 0.97 % FDR with 618 Peptides decoy=6 threshold=0.931617 total=624 INFO[13:38:53] Converged to 0.96 % FDR with 942 Ions decoy=9 threshold=0.923266 total=951 INFO[13:38:53] Post processing identifications
INFO[13:38:54] Assigning protein identifications to layers
INFO[13:38:54] Processing protein inference
INFO[13:38:57] Synchronizing PSMs and proteins
INFO[13:38:57] Final report numbers after FDR filtering, and post-processing ions=942 peptides=618 proteins=159 psms=1415 INFO[13:38:57] Saving
INFO[13:38:57] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\C_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\C_2_2 --protxml D:\17498\MSFragger\combined.prot.xml --razorbin D:\17498\MSFragger\B_1_1.meta\razor.bin INFO[13:38:57] Executing Filter v4.7.0
INFO[13:38:58] Fetching razor assignment from: D:\17498\MSFragger\B_1_1.meta\razor.bin: 3727 razor groups imported. INFO[13:38:58] Processing peptide identification files
INFO[13:38:58] Parsing D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q3.pep.xml INFO[13:38:58] Parsing D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q1.pep.xml INFO[13:38:58] Parsing D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q2.pep.xml INFO[13:38:58] 1+ Charge profile decoy=3 target=5 INFO[13:38:58] 2+ Charge profile decoy=40 target=795 INFO[13:38:58] 3+ Charge profile decoy=26 target=779 INFO[13:38:58] 4+ Charge profile decoy=18 target=490 INFO[13:38:58] 5+ Charge profile decoy=15 target=261 INFO[13:38:58] 6+ Charge profile decoy=0 target=0 INFO[13:38:58] Database search results ions=1744 peptides=1237 psms=2432 INFO[13:38:58] Converged to 0.99 % FDR with 1812 PSMs decoy=18 threshold=0.899164 total=1830 INFO[13:38:58] Converged to 0.90 % FDR with 779 Peptides decoy=7 threshold=0.928716 total=786 INFO[13:38:58] Converged to 0.95 % FDR with 1269 Ions decoy=12 threshold=0.903256 total=1281 INFO[13:38:58] Protein inference results decoy=333 target=712 INFO[13:38:58] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:38:58] Applying sequential FDR estimation ions=1300 peptides=880 psms=1830 INFO[13:38:58] Converged to 0.99 % FDR with 1812 PSMs decoy=18 threshold=0.899164 total=1830 INFO[13:38:58] Converged to 0.90 % FDR with 779 Peptides decoy=7 threshold=0.928716 total=786 INFO[13:38:58] Converged to 0.95 % FDR with 1269 Ions decoy=12 threshold=0.903256 total=1281 INFO[13:38:58] Post processing identifications
INFO[13:38:59] Assigning protein identifications to layers
INFO[13:38:59] Processing protein inference
INFO[13:39:02] Synchronizing PSMs and proteins
INFO[13:39:02] Final report numbers after FDR filtering, and post-processing ions=1269 peptides=779 proteins=176 psms=1812 INFO[13:39:02] Saving
INFO[13:39:02] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: D:\17498\MSFragger\C_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe filter --sequential --prot 1 --tag rev --pepxml D:\17498\MSFragger\C_3_3 --protxml D:\17498\MSFragger\combined.prot.xml --razorbin D:\17498\MSFragger\B_1_1.meta\razor.bin INFO[13:39:02] Executing Filter v4.7.0
INFO[13:39:02] Fetching razor assignment from: D:\17498\MSFragger\B_1_1.meta\razor.bin: 3727 razor groups imported. INFO[13:39:02] Processing peptide identification files
INFO[13:39:02] Parsing D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q3.pep.xml INFO[13:39:02] Parsing D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q1.pep.xml INFO[13:39:02] Parsing D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q2.pep.xml INFO[13:39:03] 1+ Charge profile decoy=2 target=2 INFO[13:39:03] 2+ Charge profile decoy=17 target=171 INFO[13:39:03] 3+ Charge profile decoy=11 target=211 INFO[13:39:03] 4+ Charge profile decoy=9 target=203 INFO[13:39:03] 5+ Charge profile decoy=7 target=122 INFO[13:39:03] 6+ Charge profile decoy=0 target=0 INFO[13:39:03] Database search results ions=571 peptides=437 psms=755 INFO[13:39:03] Converged to 0.86 % FDR with 348 PSMs decoy=3 threshold=0.945082 total=351 INFO[13:39:03] Converged to 0.65 % FDR with 155 Peptides decoy=1 threshold=0.968361 total=156 INFO[13:39:03] Converged to 0.74 % FDR with 270 Ions decoy=2 threshold=0.948072 total=272 INFO[13:39:03] Protein inference results decoy=333 target=712 INFO[13:39:03] Converged to 47.94 % FDR with 680 Proteins decoy=326 threshold=0.6997 total=1006 INFO[13:39:03] Applying sequential FDR estimation ions=280 peptides=207 psms=351 INFO[13:39:03] Converged to 0.86 % FDR with 348 PSMs decoy=3 threshold=0.945082 total=351 INFO[13:39:03] Converged to 0.65 % FDR with 155 Peptides decoy=1 threshold=0.968361 total=156 INFO[13:39:03] Converged to 0.74 % FDR with 270 Ions decoy=2 threshold=0.948072 total=272 INFO[13:39:03] Post processing identifications
INFO[13:39:03] Assigning protein identifications to layers
INFO[13:39:04] Processing protein inference
INFO[13:39:07] Synchronizing PSMs and proteins
INFO[13:39:07] Final report numbers after FDR filtering, and post-processing ions=270 peptides=155 proteins=64 psms=348 INFO[13:39:07] Saving
INFO[13:39:07] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\B_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:07] Executing Report v4.7.0
INFO[13:39:07] Creating reports
INFO[13:39:07] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\C_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:07] Executing Report v4.7.0
INFO[13:39:07] Creating reports
INFO[13:39:07] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\B_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:08] Executing Report v4.7.0
INFO[13:39:08] Creating reports
INFO[13:39:08] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\C_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:08] Executing Report v4.7.0
INFO[13:39:08] Creating reports
INFO[13:39:08] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\B_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:08] Executing Report v4.7.0
INFO[13:39:08] Creating reports
INFO[13:39:09] Done
Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: D:\17498\MSFragger\C_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe report INFO[13:39:09] Executing Report v4.7.0
INFO[13:39:09] Creating reports
INFO[13:39:09] Done
Process 'PhilosopherReport' finished, exit code: 0 iProphet [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windowsamd64\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 30 D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\B_1_1\interact-EX1_MB_17498_B1_08122022_DIA_Q3.pep.xml D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\B_2_2\interact-EX1_MB_17498_B2_08122022_DIA_Q3.pep.xml D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\B_3_3\interact-EX1_MB_17498_B3_08122022_DIA_Q3.pep.xml D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\C_1_1\interact-EX1_MB_17498_C1_08122022_DIA_Q3.pep.xml D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\C_2_2\interact-EX1_MB_17498_C2_08122022_DIA_Q3.pep.xml D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q1.pep.xml D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q2.pep.xml D:\17498\MSFragger\C_3_3\interact-EX1_MB_17498_C3_08122022_DIA_Q3.pep.xml INFO[13:39:09] Executing InterProphet v4.7.0
Running FPKM NSS NRS NSE NSI NSM Model EM: Computing NSS values ...

Creating 30 threads Wait for threads to finish ... ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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done Computing NRS values ...

Creating 30 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSE values ...

Creating 30 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSI values ...

Creating 30 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done Computing NSM values ...

Creating 30 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% ..................................................................................................... done FPKM values are unavailable ... Iterations: .........10......done INFO[13:39:54] Done
Process 'iProphet' finished, exit code: 0 SpecLibGen [Work dir: D:\17498\MSFragger\B_1_1] C:\ProgramData\Anaconda3\python.exe -u C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\speclib\gen_con_spec_lib.py D:\17498\2023-01-04-decoys-contam-Mouse_SP_Jan2023_adolescentis.fasta.fas D:\17498\MSFragger\B_1_1 unused D:\17498\MSFragger\B_1_1 True unused use_easypqp noiRT;noIM 30 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] " "--rt_lowess_fraction 0.0" delete_intermediate_files D:\17498\MSFragger\B_1_1\filelist_speclibgen.txt Traceback (most recent call last): File "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 117, in filelist_str = pathlib.Path(spectra_files0[0]).read_text('utf-8').splitlines() File "C:\ProgramData\Anaconda3\lib\pathlib.py", line 1266, in read_text with self.open(mode='r', encoding=encoding, errors=errors) as f: File "C:\ProgramData\Anaconda3\lib\pathlib.py", line 1252, in open return io.open(self, mode, buffering, encoding, errors, newline, File "C:\ProgramData\Anaconda3\lib\pathlib.py", line 1120, in _opener return self._accessor.open(self, flags, mode) FileNotFoundError: [Errno 2] No such file or directory: 'D:\17498\MSFragger\B_1_1\filelist_speclibgen.txt' Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 26 remaining tasks

fcyu commented 1 year ago

Can you share the whole log file?

Thanks,

Fengchao

yishai99 commented 1 year ago

Attached.

On 4 Jan 2023, at 15:37, Fengchao @.***> wrote:

Can you share the whole log file?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/950#issuecomment-1370939396, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5PDY62G277MNXLB4PDYBLWQV4KPANCNFSM6AAAAAATQXMJSA. You are receiving this because you authored the thread.

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: N/A

Version info: FragPipe version 19.0 MSFragger version 3.6 IonQuant version 1.8.9 Philosopher version 4.7.0

LCMS files: Experiment/Group: B_1

D:\17498\EX1_MB_17498_B1_08122022_DIA.raw DIA Experiment/Group: B_2
D:\17498\EX1_MB_17498_B2_08122022_DIA.raw DIA Experiment/Group: B_3
D:\17498\EX1_MB_17498_B3_08122022_DIA.raw DIA Experiment/Group: C_1
D:\17498\EX1_MB_17498_C1_08122022_DIA.raw DIA Experiment/Group: C_2
D:\17498\EX1_MB_17498_C2_08122022_DIA.raw DIA Experiment/Group: C_3
D:\17498\EX1_MB_17498_C3_08122022_DIA.raw DIA

370 commands to execute: CheckCentroid C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\17498\EX1_MB_17498_B1_08122022_DIA.raw 30 WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\b954c6f4-2e86-4de2-958b-3fed2170d736

WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\8f2218e6-bdfc-4ce4-9a80-a08d70266909

WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_1_1] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\73c5162f-c40f-4619-8efd-f3ff97591e83

WorkspaceCleanInit [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\76adebae-0081-4c00-ab79-3ed161f0ddf0

WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_3_3] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\ce14276e-d392-48e4-b8e1-59d2195f7523

WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\B_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\864c8824-1358-4b3e-b14f-2e595dadac92

WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger\C_2_2] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\972266b6-e87f-46fd-be5f-28946edc8b28

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B1_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\B_1\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Peak D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.RTidxFS D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanidxFS D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanPosFS D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanRTFS D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_diasetting.ser D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_params.ser D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q1.mgf D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q2.mgf D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q3.mgf D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q1.mzML D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q2.mzML D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q3.mzML D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_1\EX1_MB_17498_B1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B2_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\B_2\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Peak D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.RTidxFS D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanidxFS D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanPosFS D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanRTFS D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_diasetting.ser D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_params.ser D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q1.mgf D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q2.mgf D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q3.mgf D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q1.mzML D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q2.mzML D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q3.mzML D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_2\EX1_MB_17498_B2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B3_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\B_3\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Peak D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.RTidxFS D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanidxFS D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanPosFS D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanRTFS D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_diasetting.ser D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_params.ser D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q1.mgf D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q2.mgf D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q3.mgf D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q1.mzML D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q2.mzML D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q3.mzML D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\B_3\EX1_MB_17498_B3_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C1_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\C_1\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Peak D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.RTidxFS D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanidxFS D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanPosFS D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanRTFS D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_diasetting.ser D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_params.ser D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q1.mgf D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q2.mgf D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q3.mgf D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q1.mzML D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q2.mzML D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q3.mzML D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_1\EX1_MB_17498_C1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C2_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\C_2\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Peak D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.RTidxFS D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanidxFS D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanPosFS D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanRTFS D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_diasetting.ser D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_params.ser D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q1.mgf D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q2.mgf D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q3.mgf D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q1.mzML D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q2.mzML D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q3.mzML D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\C_2\EX1_MB_17498_C2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C3_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\C_3\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Peak D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.RTidxFS D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q1

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q2

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q3

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanidxFS D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanPosFS D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanRTFS D:\17498\MSFragger\C_3\EX1_MB_17498_C3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498C3

fcyu commented 1 year ago

Thanks for your log file. For the DIA-related workflow, there should be no experiment or bioreplicate groups for your files because FragPipe needs to build a single spectral library using all files.

Can you clear all groups and try again?

Thanks,

Fengchao

yishai99 commented 1 year ago

Hi Fengchao, I tried it and still get an error. Here it is:

On 4 Jan 2023, at 15:48, Fengchao @.***> wrote:

Thanks for your log file. For the DIA-related workflow, there should be no experiment or bioreplicate groups for your files because FragPipe needs to build a single spectral library using all files.

Can you clear all groups and try again?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/950#issuecomment-1370951338, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5PDYZJRJN5MAYUFZO52ZDWQV5UBANCNFSM6AAAAAATQXMJSA. You are receiving this because you authored the thread.

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: N/A

Version info: FragPipe version 19.0 MSFragger version 3.6 IonQuant version 1.8.9 Philosopher version 4.7.0

LCMS files: Experiment/Group:

D:\17498\EX1_MB_17498_B1_08122022_DIA.raw DIA
D:\17498\EX1_MB_17498_B2_08122022_DIA.raw DIA
D:\17498\EX1_MB_17498_B3_08122022_DIA.raw DIA
D:\17498\EX1_MB_17498_C1_08122022_DIA.raw DIA
D:\17498\EX1_MB_17498_C2_08122022_DIA.raw DIA
D:\17498\EX1_MB_17498_C3_08122022_DIA.raw DIA

283 commands to execute: CheckCentroid C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\17498\EX1_MB_17498_B1_08122022_DIA.raw 30 WorkspaceCleanInit [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\17498\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\philosopher_v4.7.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\cc10df03-8e63-4e53-b070-f5f3832a59d6

UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B1_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B1_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B2_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B2_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_B3_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_B3_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_B3_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C1_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C1_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C1_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C2_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C2_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C2_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\DIA_Umpire_SE-2.3.1.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" dia_umpire_se.DIA_Umpire_SE D:\17498\EX1_MB_17498_C3_08122022_DIA.raw D:\17498\MSFragger\umpire-se.params UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\diaumpire_se.log D:\17498\MSFragger\diaumpire_se.log UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Peak D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.DIAWindowsFS D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.RTidxFS D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.RTidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q1 D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q1 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q2 D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q2 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q3 D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanClusterMapping_Q3 UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanidxFS D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanidxFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanPosFS D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanPosFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA.ScanRTFS D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.ScanRTFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_diasetting.ser D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_diasetting.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_params.ser D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_params.ser UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q1.mgf D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q1.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q2.mgf D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q2.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q3.mgf D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q3.mgf UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q1.mzML D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q1.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q2.mzML D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q2.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\17498\EX1_MB_17498_C3_08122022_DIA_Q3.mzML D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Q3.mzML UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA_Peak UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\17498\MSFragger\EX1_MB_17498_C3_08122022_DIA.DIAWindowsFS UmpireSe C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\User

fcyu commented 1 year ago

Sorry to hear that. The log shows that it was due to the temp file in the D:\17498\ folder. Could you delete all temp files except for the *.raw and try again?

Best,

Fengchao

Nesvilab / FragPipe

Error when running DIA-peptidomics workflow #950