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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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2GB free memory is too little to do anything #931

Closed SharmaGautam1 closed 1 year ago

SharmaGautam1 commented 1 year ago 

Cancelling 85 remaining tasks
[log_2022-12-16_07-20-04.txt](https://github.com/Nesvilab/FragPipe/files/10242076/log_2022-12-16_07-20-04.txt)

How to resolve this issue?

- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)
fcyu commented 1 year ago

Hi @Gauatm11 ,

Can you send the whole log file?

Thanks,

Fengchao

SharmaGautam1 commented 1 year ago

Hi Fengchao, Please find attached the log file:

Best Regards Gautam Sharma

On Fri, 16 Dec 2022 at 07:39, Fengchao @.***> wrote:

Hi @Gauatm11 https://github.com/Gauatm11 ,

Can you send the whole log file?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/931#issuecomment-1354079888, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4Y22LVZ4L4MJUW6GTANI3DWNPFPDANCNFSM6AAAAAATAMOUQQ . You are receiving this because you were mentioned.Message ID: @.***>

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

Version info: FragPipe version 18.0 MSFragger version 3.6 Philosopher version 4.6.0

LCMS files: Experiment/Group: Diseased_1

104 commands to execute: CheckCentroid D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx2G -cp "D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;D:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.raw 7 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\d52df01b-95df-4a3d-8151-c275ad4accc7 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\d2634e84-f249-463f-959e-f101b2bfb154 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\2ac377b0-909e-4ae4-b78f-2b0e09a60287 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\760f794f-69ee-4420-ae32-64669242be72 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\57cc3279-80ab-4492-97eb-3184b3582a6d WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\b5d96281-38f1-440e-8c4e-b95ce995b4d5 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\70c456fd-86bd-464a-9e79-8fb743111965 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\24361804-2b5d-42e3-86ff-a4712c701c89 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\29261139-8436-49c5-a33b-a96aa216dc1c MSFragger [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx2G D:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\MSFragger-3.6.jar D:\FragpipeTest_HCT116\COPD\fragger.params D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC2.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC3.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC4.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC5.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT1.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT2.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT3.raw MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.pepXML D:\FragpipeTest_HCT116\COPD\Diseased_1\23092021_Fusion_Gautam_DC1.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.pin D:\FragpipeTest_HCT116\COPD\Diseased_1\23092021_Fusion_Gautam_DC1.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC2.pepXML D:\FragpipeTest_HCT116\COPD\Diseased_2\24092021_Fusion_Gautam_DC2.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC2.pin D:\FragpipeTest_HCT116\COPD\Diseased_2\24092021_Fusion_Gautam_DC2.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC3.pepXML D:\FragpipeTest_HCT116\COPD\Diseased_3\24092021_Fusion_Gautam_DC3.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC3.pin D:\FragpipeTest_HCT116\COPD\Diseased_3\24092021_Fusion_Gautam_DC3.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC4.pepXML D:\FragpipeTest_HCT116\COPD\Diseased_4\24092021_Fusion_Gautam_DC4.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC4.pin D:\FragpipeTest_HCT116\COPD\Diseased_4\24092021_Fusion_Gautam_DC4.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC5.pepXML D:\FragpipeTest_HCT116\COPD\Diseased_5\24092021_Fusion_Gautam_DC5.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC5.pin D:\FragpipeTest_HCT116\COPD\Diseased_5\24092021_Fusion_Gautam_DC5.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT1.pepXML D:\FragpipeTest_HCT116\COPD\Normal_1\23092021_Fusion_Gautam_NT1.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT1.pin D:\FragpipeTest_HCT116\COPD\Normal_1\23092021_Fusion_Gautam_NT1.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT2.pepXML D:\FragpipeTest_HCT116\COPD\Normal_2\23092021_Fusion_Gautam_NT2.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT2.pin D:\FragpipeTest_HCT116\COPD\Normal_2\23092021_Fusion_Gautam_NT2.pin MSFragger move pepxml D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT3.pepXML D:\FragpipeTest_HCT116\COPD\Normal_3\23092021_Fusion_Gautam_NT3.pepXML MSFragger move pin D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/D:/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT3.pin D:\FragpipeTest_HCT116\COPD\Normal_3\23092021_Fusion_Gautam_NT3.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 24092021_Fusion_Gautam_DC2_percolator_target_psms.tsv --decoy-results-psms 24092021_Fusion_Gautam_DC2_percolator_decoy_psms.tsv 24092021_Fusion_Gautam_DC2.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 24092021_Fusion_Gautam_DC3_percolator_target_psms.tsv --decoy-results-psms 24092021_Fusion_Gautam_DC3_percolator_decoy_psms.tsv 24092021_Fusion_Gautam_DC3.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 24092021_Fusion_Gautam_DC4_percolator_target_psms.tsv --decoy-results-psms 24092021_Fusion_Gautam_DC4_percolator_decoy_psms.tsv 24092021_Fusion_Gautam_DC4.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 24092021_Fusion_Gautam_DC5_percolator_target_psms.tsv --decoy-results-psms 24092021_Fusion_Gautam_DC5_percolator_decoy_psms.tsv 24092021_Fusion_Gautam_DC5.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 23092021_Fusion_Gautam_DC1_percolator_target_psms.tsv --decoy-results-psms 23092021_Fusion_Gautam_DC1_percolator_decoy_psms.tsv 23092021_Fusion_Gautam_DC1.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 23092021_Fusion_Gautam_NT1_percolator_target_psms.tsv --decoy-results-psms 23092021_Fusion_Gautam_NT1_percolator_decoy_psms.tsv 23092021_Fusion_Gautam_NT1.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 23092021_Fusion_Gautam_NT2_percolator_target_psms.tsv --decoy-results-psms 23092021_Fusion_Gautam_NT2_percolator_decoy_psms.tsv 23092021_Fusion_Gautam_NT2.pin Percolator [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 23092021_Fusion_Gautam_NT3_percolator_target_psms.tsv --decoy-results-psms 23092021_Fusion_Gautam_NT3_percolator_decoy_psms.tsv 23092021_Fusion_Gautam_NT3.pin Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 24092021_Fusion_Gautam_DC2.pin 24092021_Fusion_Gautam_DC2 24092021_Fusion_Gautam_DC2_percolator_target_psms.tsv 24092021_Fusion_Gautam_DC2_percolator_decoy_psms.tsv interact-24092021_Fusion_Gautam_DC2 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_2\24092021_Fusion_Gautam_DC2_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_2\24092021_Fusion_Gautam_DC2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 24092021_Fusion_Gautam_DC3.pin 24092021_Fusion_Gautam_DC3 24092021_Fusion_Gautam_DC3_percolator_target_psms.tsv 24092021_Fusion_Gautam_DC3_percolator_decoy_psms.tsv interact-24092021_Fusion_Gautam_DC3 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_3\24092021_Fusion_Gautam_DC3_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_3\24092021_Fusion_Gautam_DC3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 24092021_Fusion_Gautam_DC4.pin 24092021_Fusion_Gautam_DC4 24092021_Fusion_Gautam_DC4_percolator_target_psms.tsv 24092021_Fusion_Gautam_DC4_percolator_decoy_psms.tsv interact-24092021_Fusion_Gautam_DC4 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_4\24092021_Fusion_Gautam_DC4_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_4\24092021_Fusion_Gautam_DC4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 24092021_Fusion_Gautam_DC5.pin 24092021_Fusion_Gautam_DC5 24092021_Fusion_Gautam_DC5_percolator_target_psms.tsv 24092021_Fusion_Gautam_DC5_percolator_decoy_psms.tsv interact-24092021_Fusion_Gautam_DC5 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_5\24092021_Fusion_Gautam_DC5_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_5\24092021_Fusion_Gautam_DC5_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23092021_Fusion_Gautam_DC1.pin 23092021_Fusion_Gautam_DC1 23092021_Fusion_Gautam_DC1_percolator_target_psms.tsv 23092021_Fusion_Gautam_DC1_percolator_decoy_psms.tsv interact-23092021_Fusion_Gautam_DC1 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_1\23092021_Fusion_Gautam_DC1_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Diseased_1\23092021_Fusion_Gautam_DC1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23092021_Fusion_Gautam_NT1.pin 23092021_Fusion_Gautam_NT1 23092021_Fusion_Gautam_NT1_percolator_target_psms.tsv 23092021_Fusion_Gautam_NT1_percolator_decoy_psms.tsv interact-23092021_Fusion_Gautam_NT1 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_1\23092021_Fusion_Gautam_NT1_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_1\23092021_Fusion_Gautam_NT1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23092021_Fusion_Gautam_NT2.pin 23092021_Fusion_Gautam_NT2 23092021_Fusion_Gautam_NT2_percolator_target_psms.tsv 23092021_Fusion_Gautam_NT2_percolator_decoy_psms.tsv interact-23092021_Fusion_Gautam_NT2 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_2\23092021_Fusion_Gautam_NT2_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_2\23092021_Fusion_Gautam_NT2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 23092021_Fusion_Gautam_NT3.pin 23092021_Fusion_Gautam_NT3 23092021_Fusion_Gautam_NT3_percolator_target_psms.tsv 23092021_Fusion_Gautam_NT3_percolator_decoy_psms.tsv interact-23092021_Fusion_Gautam_NT3 DDA 0.5 Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_3\23092021_Fusion_Gautam_NT3_percolator_target_psms.tsv Percolator: Delete temp D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete D:\FragpipeTest_HCT116\COPD\Normal_3\23092021_Fusion_Gautam_NT3_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\FragpipeTest_HCT116\COPD\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe database --annotate D:\FragpipeTestHCT116\COPD\2022-12-16-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Diseased_1 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razor PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Diseased_2 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Diseased_3 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Diseased_4 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Diseased_5 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Normal1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Normal_1 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Normal2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Normal_2 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherFilter [Work dir: D:\FragpipeTest_HCT116\COPD\Normal3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe filter --sequential --prot 0.01 --tag rev --pepxml D:\FragpipeTest_HCT116\COPD\Normal_3 --protxml D:\FragpipeTest_HCT116\COPD\combined.prot.xml --razorbin D:\FragpipeTest_HCT116\COPD\Diseased_1.meta\razor.bin PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report PhilosopherReport [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe report WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx2G -Dlibs.bruker.dir="D:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\bruker" -Dlibs.thermo.dir="D:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "D:\FragPipe-jre-18.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar;D:\FragPipe-jre-18.0\fragpipe\tools\IonQuant-1.8.9.jar" ionquant.IonQuant --threads 7 --ionmobility 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100000 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\FragpipeTest_HCT116\COPD\filelist_ionquant.txt


Execution order:

    Cmd: [START], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [CheckCentroid], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_5]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_4]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_3]
    Cmd: [MSFragger], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [Percolator], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [ProteinProphet], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [PhilosopherFilter], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [PhilosopherReport], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_2]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_3]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_1]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_2]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Normal_1]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_5]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_4]
    Cmd: [WorkspaceClean], Work dir: [D:\FragpipeTest_HCT116\COPD\Diseased_3]
    Cmd: [IonQuant], Work dir: [D:\FragpipeTest_HCT116\COPD]

>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
>rev_sp|O43593|HAIR_HUMAN Lysine-specific demethylase hairless OS=Homo sapiens OX=9606 GN=HR PE=1 SV=5
>rev_sp|P0DMW2|PYDC4_HUMAN NLR family pyrin domain-containing protein 2B OS=Homo sapiens OX=9606 GN=NLRP2B PE=2 SV=1
>rev_sp|P49763|PLGF_HUMAN Placenta growth factor OS=Homo sapiens OX=9606 GN=PGF PE=1 SV=2
>rev_sp|Q14186|TFDP1_HUMAN Transcription factor Dp-1 OS=Homo sapiens OX=9606 GN=TFDP1 PE=1 SV=1
>rev_sp|Q693B1|KCD11_HUMAN BTB/POZ domain-containing protein KCTD11 OS=Homo sapiens OX=9606 GN=KCTD11 PE=1 SV=1
>rev_sp|Q8IWK6|AGRA3_HUMAN Adhesion G protein-coupled receptor A3 OS=Homo sapiens OX=9606 GN=ADGRA3 PE=1 SV=2
>rev_sp|Q8WVN6|SCTM1_HUMAN Secreted and transmembrane protein 1 OS=Homo sapiens OX=9606 GN=SECTM1 PE=1 SV=2
>rev_sp|Q9BRI3|ZNT2_HUMAN Proton-coupled zinc antiporter SLC30A2 OS=Homo sapiens OX=9606 GN=SLC30A2 PE=1 SV=2
>rev_sp|Q9NUQ3|TXLNG_HUMAN Gamma-taxilin OS=Homo sapiens OX=9606 GN=TXLNG PE=1 SV=2
>rev_sp|Q9Y6N1|COX11_HUMAN Cytochrome c oxidase assembly protein COX11, mitochondrial OS=Homo sapiens OX=9606 GN=COX11 PE=1 SV=3
>sp|O43716|GATC_HUMAN Glutamyl-tRNA(Gln) amidotransferase subunit C, mitochondrial OS=Homo sapiens OX=9606 GN=GATC PE=1 SV=1
>sp|P0DPA3|SNH28_HUMAN Putative uncharacterized protein SNHG28 OS=Homo sapiens OX=9606 GN=SNHG28 PE=5 SV=1
>sp|P50120|RET2_HUMAN Retinol-binding protein 2 OS=Homo sapiens OX=9606 GN=RBP2 PE=1 SV=3
>sp|Q14353|GAMT_HUMAN Guanidinoacetate N-methyltransferase OS=Homo sapiens OX=9606 GN=GAMT PE=1 SV=1
>sp|Q6DHV5|C2D2B_HUMAN Protein CC2D2B OS=Homo sapiens OX=9606 GN=CC2D2B PE=2 SV=4
>sp|Q8IX05|CD302_HUMAN CD302 antigen OS=Homo sapiens OX=9606 GN=CD302 PE=1 SV=1
>sp|Q8WWF3|SSMM1_HUMAN Serine-rich single-pass membrane protein 1 OS=Homo sapiens OX=9606 GN=SSMEM1 PE=1 SV=1
>sp|Q9BRX5|PSF3_HUMAN DNA replication complex GINS protein PSF3 OS=Homo sapiens OX=9606 GN=GINS3 PE=1 SV=1
>sp|Q9NVE5|UBP40_HUMAN Ubiquitin carboxyl-terminal hydrolase 40 OS=Homo sapiens OX=9606 GN=USP40 PE=1 SV=3
>sp|Q9Y6Y8|S23IP_HUMAN SEC23-interacting protein OS=Homo sapiens OX=9606 GN=SEC23IP PE=1 SV=1
# FragPipe v18.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\FragpipeTest_HCT116\\COPD\\2022-12-16-decoys-reviewed-contam-UP000005640.fas

Table.editor=[^K
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=0.01
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=false
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=
diaumpire.DeltaApex=
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=false
diaumpire.Q2=false
diaumpire.Q3=false
diaumpire.RFmax=
diaumpire.RPmax=
diaumpire.RTOverlap=
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=
diaumpire.SE.MS1PPM=
diaumpire.SE.MS2PPM=
diaumpire.SE.MS2SN=
diaumpire.SE.MassDefectFilter=false
diaumpire.SE.MassDefectOffset=
diaumpire.SE.NoMissedScan=
diaumpire.SE.SN=
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=D\:\\FragPipe-jre-18.0\\fragpipe\\tools\\IonQuant-1.8.9.jar
fragpipe-config.bin-msfragger=D\:\\FragPipe-jre-18.0\\fragpipe\\tools\\MSFragger-3.6\\MSFragger-3.6.jar
fragpipe-config.bin-philosopher=D\:\\FragPipe-jre-18.0\\fragpipe\\tools\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\Gautam Sharma\\AppData\\Local\\Programs\\Python\\Python310\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=0
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=trypsin
msfragger.misc.fragger.enzyme-dropdown-2=trypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\FragpipeTest_HCT116\\COPD
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

CheckCentroid D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx2G -cp "D:\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;D:\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.raw 7 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:28] Executing Workspace v4.6.0
INFO[07:17:28] Removing workspace
WARN[07:17:28] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:28] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\d52df01b-95df-4a3d-8151-c275ad4accc7 INFO[07:17:28] Executing Workspace v4.6.0
INFO[07:17:28] Creating workspace
INFO[07:17:28] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:29] Executing Workspace v4.6.0
INFO[07:17:29] Removing workspace
WARN[07:17:29] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:29] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\d2634e84-f249-463f-959e-f101b2bfb154 INFO[07:17:29] Executing Workspace v4.6.0
INFO[07:17:29] Creating workspace
INFO[07:17:29] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:29] Executing Workspace v4.6.0
INFO[07:17:29] Removing workspace
WARN[07:17:29] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:29] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\2ac377b0-909e-4ae4-b78f-2b0e09a60287 INFO[07:17:30] Executing Workspace v4.6.0
INFO[07:17:30] Creating workspace
INFO[07:17:30] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:30] Executing Workspace v4.6.0
INFO[07:17:30] Removing workspace
WARN[07:17:30] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:30] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_2] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\760f794f-69ee-4420-ae32-64669242be72 INFO[07:17:31] Executing Workspace v4.6.0
INFO[07:17:31] Creating workspace
INFO[07:17:31] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:31] Executing Workspace v4.6.0
INFO[07:17:31] Removing workspace
WARN[07:17:31] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:31] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Normal_1] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\57cc3279-80ab-4492-97eb-3184b3582a6d INFO[07:17:31] Executing Workspace v4.6.0
INFO[07:17:31] Creating workspace
INFO[07:17:31] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:32] Executing Workspace v4.6.0
INFO[07:17:32] Removing workspace
WARN[07:17:32] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:32] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\b5d96281-38f1-440e-8c4e-b95ce995b4d5 INFO[07:17:32] Executing Workspace v4.6.0
INFO[07:17:32] Creating workspace
INFO[07:17:32] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[07:17:33] Executing Workspace v4.6.0
INFO[07:17:33] Removing workspace
WARN[07:17:33] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:33] Done
WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_5] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\70c456fd-86bd-464a-9e79-8fb743111965 INFO[07:17:33] Executing Workspace v4.6.0
INFO[07:17:33] Creating workspace
INFO[07:17:33] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:33] Executing Workspace v4.6.0
INFO[07:17:33] Removing workspace
WARN[07:17:33] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:33] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_4] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\24361804-2b5d-42e3-86ff-a4712c701c89 INFO[07:17:34] Executing Workspace v4.6.0
INFO[07:17:34] Creating workspace
INFO[07:17:34] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --clean --nocheck INFO[07:17:34] Executing Workspace v4.6.0
INFO[07:17:34] Removing workspace
WARN[07:17:34] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:17:34] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\FragpipeTest_HCT116\COPD\Diseased_3] D:\FragPipe-jre-18.0\fragpipe\tools\philosopher.exe workspace --init --nocheck --temp C:\Users\GAUTAM~1\AppData\Local\Temp\29261139-8436-49c5-a33b-a96aa216dc1c INFO[07:17:35] Executing Workspace v4.6.0
INFO[07:17:35] Creating workspace
INFO[07:17:35] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\FragpipeTest_HCT116\COPD] D:\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx2G D:\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\MSFragger-3.6.jar D:\FragpipeTest_HCT116\COPD\fragger.params D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_DC1.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC2.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC3.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC4.raw D:\FragpipeTest_HCT116\24092021_Fusion_Gautam_DC5.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT1.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT2.raw D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT3.raw MSFragger version MSFragger-3.6 Batmass-IO version 1.28.8 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 2 GB memory Checking database... Checking spectral files... java.lang.OutOfMemoryError: Java heap space java.lang.OutOfMemoryError: Java heap space Failed in checking D:\FragpipeTest_HCT116\23092021_Fusion_Gautam_NT1.raw. Will ignore it. CANCELLED: Failed to read message. Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 85 remaining tasks
fcyu commented 1 year ago

Hi @Gauatm11 ,

Thanks for your log file. Your computer only has 2 GB free memory, which is not enough to do anything. The minimum requirement is 8 GB free memory, the recommended requirement is 32 GB - 64 GB.

BTW, you need to upgrade FragPipe to the latest version (version 19.0).

Best,

Fengchao

SharmaGautam1 commented 1 year ago

Hi Fengchao, Thanks for the quick response. The drive which I selected as my directory has more than 100 GB free space.

So, which memory is it actually talking about?

Best Regards Gautam Sharma

On Fri, 16 Dec, 2022, 08:16 Fengchao, @.***> wrote:

Hi @Gauatm11 https://github.com/Gauatm11 ,

Thanks for your log file. Your computer only has 2 GB free memory, which is not enough to do anything. The minimum requirement is 8 GB free memory, the recommended requirement is 32 GB - 64 GB.

BTW, you need to upgrade FragPipe to the latest version (version 19.0).

Best,

Fengchao

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fcyu commented 1 year ago

I am talking about memory (RAM), not the storage (drive, SSD or HDD) space.

Best,

Fengchao

SharmaGautam1 commented 1 year ago

Ok. Thanks for the clarification.

Best Regards Gautam Sharma

On Fri, 16 Dec, 2022, 08:23 Fengchao, @.***> wrote:

I am talking about memory (RAM), not the storage (drive, SSD or HDD) space.

Best,

Fengchao

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fcyu commented 1 year ago

No problem. Please feel free to contact us if you have any questions after using a computer with more memory.

Best,

Fengchao

SharmaGautam1 commented 1 year ago

Sure. Thank you very much.

Best Regards Gautam Sharma

On Fri, 16 Dec, 2022, 20:20 Fengchao, @.***> wrote:

No problem. Please feel free to contact us if you have any questions after using a computer with more memory.

Best,

Fengchao

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