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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Perocolator stopped_TimsTOF DDA data #520

Closed domthe closed 2 years ago

domthe commented 3 years ago

Hi all, I was running six data files from timsTOF for DDA LFQ analysis and ended up halting at Percolator step.

Does anyone have a clue on whats this is? Thanks,

Issued command: C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_4B_RD5_1_644_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_4B_RD5_1_644_percolator_decoy_psms.tsv 061121_KP_M_4B_RD5_1_644_edited.pin Started Tue Nov 9 11:45:05 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 061121_KP_M_4B_RD5_1_644_edited.pin ERROR: Cannot open data stream. ERROR: Failed to read in file, check if the correct file-format was used. Process 'Percolator' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 53 remaining tasks
yangkl96 commented 3 years ago

Hi @domthe,

Could you please attach your entire log file?

Thanks, Kevin

domthe commented 3 years ago

Hello there, error log file attached. Thanks,

log_2021-11-09_16-26-10.txt

yangkl96 commented 3 years ago

Is one of your uncalibrated mgf files ~2GB or greater?

domthe commented 3 years ago

Yes, that's right, some of the uncalibrated mgf files are greater than 2GB. Would that be an issue and if so is there a way out? Thanks

yangkl96 commented 3 years ago

No worries, we are working to fix the issue and should be fine in the update we release soon

fcyu commented 3 years ago

Hi @domthe ,

Here (https://www.dropbox.com/s/s8wlt6camz5wrhq/FragPipe-17.1-build2.zip?dl=0) is the fixed version. Can you try to see if it fixes your problem?

Thanks,

Fengchao

domthe commented 3 years ago

Hi Fengchao, That's great, Shall try and let you know how it goes, Thanks for this Dom

On Tue, Nov 9, 2021 at 5:17 PM Fengchao @.***> wrote:

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

Here ( https://www.dropbox.com/s/s8wlt6camz5wrhq/FragPipe-17.1-build2.zip?dl=0) is the fixed version. Can you try to see if it fixes your problem?

Thanks,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/520#issuecomment-964361805, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALG5BIDJ6CMBQU6UTUOUYE3ULFJRRANCNFSM5HVEVT4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

domthe commented 2 years ago

Hi Fegchao, Unfortunately, 1.7 build 2 throws another error. Logfile attached, Would you be able to look into this, whenever possible? Many thanks Dominic

On Tue, Nov 9, 2021 at 6:08 PM Dominic Kurian @.***> wrote:

Hi Fengchao, That's great, Shall try and let you know how it goes, Thanks for this Dom

On Tue, Nov 9, 2021 at 5:17 PM Fengchao @.***> wrote:

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

Here ( https://www.dropbox.com/s/s8wlt6camz5wrhq/FragPipe-17.1-build2.zip?dl=0) is the fixed version. Can you try to see if it fixes your problem?

Thanks,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/520#issuecomment-964361805, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALG5BIDJ6CMBQU6UTUOUYE3ULFJRRANCNFSM5HVEVT4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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

Version info: FragPipe version 17.1-build2 MSFragger version 3.4 Philosopher version 4.1.0 (build 1635640020)

LCMS files: Experiment/Group: Calcified_1

82 commands to execute: CheckCentroid C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d 35 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\fragger.params \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.d MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643.pin MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4B_RD5_1_644.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4B_RD5_1_644.pin MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3\061121_KP_M_4C_RD6_1_645.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3\061121_KP_M_4C_RD6_1_645.pin MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1\061121_KP_M_2A_RD1_1_639.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1\061121_KP_M_2A_RD1_1_639.pin MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2\061121_KP_M_2B_RD2_1_640.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2\061121_KP_M_2B_RD2_1_640.pin MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3\061121_KP_M_2C_RD3_1_641.pepXML MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3\061121_KP_M_2C_RD3_1_641.pin MSBooster [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\msbooster-1.0.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\smile-core-2.6.0.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\smile-math-2.6.0.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\batmass-io-1.23.6.jar" Features.MainClass --paramsList E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\msbooster_params.txt Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_2C_RD3_1_641_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_2C_RD3_1_641_percolator_decoy_psms.tsv 061121_KP_M_2C_RD3_1_641_edited.pin Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_4C_RD6_1_645_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_4C_RD6_1_645_percolator_decoy_psms.tsv 061121_KP_M_4C_RD6_1_645_edited.pin Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_2B_RD2_1_640_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_2B_RD2_1_640_percolator_decoy_psms.tsv 061121_KP_M_2B_RD2_1_640_edited.pin Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_4B_RD5_1_644_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_4B_RD5_1_644_percolator_decoy_psms.tsv 061121_KP_M_4B_RD5_1_644_edited.pin Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_2A_RD1_1_639_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_2A_RD1_1_639_percolator_decoy_psms.tsv 061121_KP_M_2A_RD1_1_639_edited.pin Percolator [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 35 --results-psms 061121_KP_M_4A_RD4_1_643_percolator_target_psms.tsv --decoy-results-psms 061121_KP_M_4A_RD4_1_643_percolator_decoy_psms.tsv 061121_KP_M_4A_RD4_1_643_edited.pin Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_2C_RD3_1_641.pin 061121_KP_M_2C_RD3_1_641 061121_KP_M_2C_RD3_1_641_percolator_target_psms.tsv 061121_KP_M_2C_RD3_1_641_percolator_decoy_psms.tsv interact-061121_KP_M_2C_RD3_1_641 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3\061121_KP_M_2C_RD3_1_641_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3\061121_KP_M_2C_RD3_1_641_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_4C_RD6_1_645.pin 061121_KP_M_4C_RD6_1_645 061121_KP_M_4C_RD6_1_645_percolator_target_psms.tsv 061121_KP_M_4C_RD6_1_645_percolator_decoy_psms.tsv interact-061121_KP_M_4C_RD6_1_645 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3\061121_KP_M_4C_RD6_1_645_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3\061121_KP_M_4C_RD6_1_645_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_2B_RD2_1_640.pin 061121_KP_M_2B_RD2_1_640 061121_KP_M_2B_RD2_1_640_percolator_target_psms.tsv 061121_KP_M_2B_RD2_1_640_percolator_decoy_psms.tsv interact-061121_KP_M_2B_RD2_1_640 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2\061121_KP_M_2B_RD2_1_640_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2\061121_KP_M_2B_RD2_1_640_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_4B_RD5_1_644.pin 061121_KP_M_4B_RD5_1_644 061121_KP_M_4B_RD5_1_644_percolator_target_psms.tsv 061121_KP_M_4B_RD5_1_644_percolator_decoy_psms.tsv interact-061121_KP_M_4B_RD5_1_644 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4B_RD5_1_644_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4B_RD5_1_644_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_2A_RD1_1_639.pin 061121_KP_M_2A_RD1_1_639 061121_KP_M_2A_RD1_1_639_percolator_target_psms.tsv 061121_KP_M_2A_RD1_1_639_percolator_decoy_psms.tsv interact-061121_KP_M_2A_RD1_1_639 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1\061121_KP_M_2A_RD1_1_639_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1\061121_KP_M_2A_RD1_1_639_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 061121_KP_M_4A_RD4_1_643.pin 061121_KP_M_4A_RD4_1_643 061121_KP_M_4A_RD4_1_643_percolator_target_psms.tsv 061121_KP_M_4A_RD4_1_643_percolator_decoy_psms.tsv interact-061121_KP_M_4A_RD4_1_643 DDA Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643_percolator_target_psms.tsv Percolator: Delete temp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar com.github.chhh.utils.FileDelete E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643_percolator_decoy_psms.tsv ProteinProphet [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP04-11-21.fasta.fas --prefix rev PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razor PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razorbin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1.meta\razor.bin PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razorbin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1.meta\razor.bin PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razorbin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1.meta\razor.bin PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razorbin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1.meta\razor.bin PhilosopherFilter [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3 --protxml E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\combined.prot.xml --razorbin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1.meta\razor.bin PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherReport [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe report --decoys PhilosopherAbacus [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipelocal\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe abacus --picked --razor --reprint --tag rev --protein Calcified_1 Calcified_2 Calcified_3 Control_1 Control_2 Control_3 WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -Xmx116G -Dlibs.bruker.dir="C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\MSFragger-3.4\ext\bruker" -Dlibs.thermo.dir="C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\ionquant-1.7.16.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\smile-core-2.6.0.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\smile-math-2.6.0.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\javacpp.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\javacpp-windows-x86_64.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\javacpp-linux-x86_64.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\openblas.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\openblas-windows-x86_64.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\javacpp-presets-platform-1.5.6-bin\openblas-linux-x86_64.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\batmass-io-1.23.6.jar" ionquant.IonQuant --threads 35 --ionmobility 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 3 --minfreq 0.5 --minions 2 --minexps 1 --locprob 0.75 --multidir . --filelist E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\filelist_ionquant.txt


Execution order:

    Cmd: [START], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [CheckCentroid], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2]
    Cmd: [MSFragger], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [MSBooster], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [Percolator], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [ProteinProphet], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [PhilosopherDbAnnotate], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [PhilosopherFilter], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [PhilosopherReport], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [PhilosopherAbacus], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]
    Cmd: [WorkspaceClean], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2]
    Cmd: [IonQuant], Work dir: [E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1]

# FragPipe v17.1-build2ui state cache

crystalc.run-crystalc=false
database.db-path=C\:\\inetpub\\mascot\\sequence\\Uniprot-Mouse\\2021-11-08-decoys-Uniprot-Mouse_OGOP_04-11-21.fasta.fas
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=0
diann.run-dia-nn=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-msfragger=C\:\\Fragpipe_local\\FragPipe-jre-17.0\\fragpipe\\tools\\MSFragger-3.4\\MSFragger-3.4.jar
fragpipe-config.bin-philosopher=C\:\\Fragpipe_local\\FragPipe-jre-17.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\dkurian\\Anaconda3\\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.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.06
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=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=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=stricttrypsin
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,false,-1; 0.000000,N-Term Peptide,false,-1; 0.000000,C-Term Protein,false,-1; 0.000000,N-Term Protein,false,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--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.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=true
phi-report.print-decoys=true
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=false
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
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=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_allowed_res=
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=false
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
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.groupby=-1
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=E\:\\Fragpipe\\KP_Mito_expt_Nov-2021_version17.1
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.ram=0
workflow.threads=35

CheckCentroid C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -Xmx116G -cp "C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d 35 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:22] Executing Workspace v4.1.0
INFO[18:20:22] Removing workspace
WARN[18:20:22] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:22] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:24] Executing Workspace v4.1.0
INFO[18:20:24] Creating workspace
INFO[18:20:24] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[18:20:26] Executing Workspace v4.1.0
INFO[18:20:26] Removing workspace
WARN[18:20:26] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:26] Done
WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:28] Executing Workspace v4.1.0
INFO[18:20:28] Creating workspace
INFO[18:20:28] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:30] Executing Workspace v4.1.0
INFO[18:20:30] Removing workspace
WARN[18:20:30] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:30] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:32] Executing Workspace v4.1.0
INFO[18:20:32] Creating workspace
INFO[18:20:32] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:34] Executing Workspace v4.1.0
INFO[18:20:34] Removing workspace
WARN[18:20:34] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:34] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:36] Executing Workspace v4.1.0
INFO[18:20:36] Creating workspace
INFO[18:20:36] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:38] Executing Workspace v4.1.0
INFO[18:20:38] Removing workspace
WARN[18:20:38] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:38] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_3] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:40] Executing Workspace v4.1.0
INFO[18:20:40] Creating workspace
INFO[18:20:40] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:42] Executing Workspace v4.1.0
INFO[18:20:42] Removing workspace
WARN[18:20:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[18:20:44] Executing Workspace v4.1.0
INFO[18:20:44] Creating workspace
INFO[18:20:44] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[18:20:46] Executing Workspace v4.1.0
INFO[18:20:46] Removing workspace
WARN[18:20:46] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[18:20:46] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Control_2] C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[18:20:48] Executing Workspace v4.1.0
INFO[18:20:48] Creating workspace
INFO[18:20:48] Done
MSFragger [Work dir: E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1] C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G C:\Fragpipe_local\FragPipe-jre-17.0\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\fragger.params \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.d \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.d MSFragger version MSFragger-3.4 Batmass-IO version 1.23.6 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 116 GB memory Checking database... Checking spectral files... \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.d: Scans = 56301 \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.d: Scans = 56380 \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.d: Scans = 56567 \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d: Scans = 56527 \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.d: Scans = 56278 \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.d: Scans = 56562 There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2A_RD1_1_639.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2B_RD2_1_640.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_2C_RD3_1_641.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4C_RD6_1_645.d converted with timsdata-2-8-7-1. Will use this mzBIN file. ***FIRST SEARCH**** Parameters: num_threads = 35 database_name = C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP_04-11-21.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 60.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.30 Da. 332379898 fragments to be searched in 1 slices (4.95 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.69 s

  1. 061121_KP_M_2A_RD1_1_639.mzBIN 1230.3 s | deisotoping 5.8 s [progress: 254856/254856 (100%) - 36387 spectra/s] 7.0s | postprocessing 8.0 s
  2. 061121_KP_M_2B_RD2_1_640.mzBIN 2440.8 s | deisotoping 3.3 s [progress: 221220/221220 (100%) - 39788 spectra/s] 5.6s | postprocessing 6.8 s
  3. 061121_KP_M_2C_RD3_1_641.mzBIN 1339.1 s | deisotoping 3.5 s [progress: 235530/235530 (100%) - 43560 spectra/s] 5.4s | postprocessing 7.0 s
  4. 061121_KP_M_4A_RD4_1_643.mzBIN 1861.1 s | deisotoping 4.2 s [progress: 252818/252818 (100%) - 35953 spectra/s] 7.0s | postprocessing 7.9 s
  5. 061121_KP_M_4B_RD5_1_644.mzBIN 2210.4 s | deisotoping 3.5 s [progress: 236459/236459 (100%) - 41785 spectra/s] 5.7s | postprocessing 7.2 s
  6. 061121_KP_M_4C_RD6_1_645.mzBIN 1030.2 s | deisotoping 4.0 s [progress: 250964/250964 (100%) - 39342 spectra/s] 6.4s | postprocessing 7.5 s ***FIRST SEARCH DONE IN 171.438 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 2.13 3.02 0.03 2.47 -0.29 4.87 -0.12 4.35
002 2.23 2.79 0.04 2.45 0.32 5.08 -0.10 4.56
003 3.22 2.91 0.02 2.46 1.05 5.04 -0.06 4.50
004 3.92 3.05 0.03 2.44 1.48 4.97 -0.02 4.40
005 3.76 2.91 0.04 2.44 1.54 5.04 -0.03 4.46
006 4.08 2.95 0.04 2.43 1.69 5.00 -0.01 4.41
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count skip skip 151254 151530 150809 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 153052 153615 153636 151530 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 154277
------- -------
------- -------
Rm P. 1
------- -------
Count 154596
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 175 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 53.973 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 35 database_name = C:\inetpub\mascot\sequence\Uniprot-Mouse\2021-11-08-decoys-Uniprot-Mouse_OGOP_04-11-21.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 15.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 175 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.08 Da. 332379898 fragments to be searched in 1 slices (4.95 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.13 s

  1. 061121_KP_M_2A_RD1_1_639.mzBIN_calibrated 85.2 s [progress: 250239/250239 (100%) - 27854 spectra/s] 9.0s | postprocessing 74.3 s
  2. 061121_KP_M_2B_RD2_1_640.mzBIN_calibrated 72.8 s [progress: 218769/218769 (100%) - 29228 spectra/s] 7.5s | postprocessing 64.8 s
  3. 061121_KP_M_2C_RD3_1_641.mzBIN_calibrated 74.3 s [progress: 232207/232207 (100%) - 28917 spectra/s] 8.0s | postprocessing 67.3 s
  4. 061121_KP_M_4A_RD4_1_643.mzBIN_calibrated 82.4 s [progress: 249061/249061 (100%) - 28823 spectra/s] 8.6s | postprocessing 73.5 s
  5. 061121_KP_M_4B_RD5_1_644.mzBIN_calibrated 85.5 s [progress: 233432/233432 (100%) - 28723 spectra/s] 8.1s | postprocessing 68.5 s
  6. 061121_KP_M_4C_RD6_1_645.mzBIN_calibrated 82.7 s [progress: 247317/247317 (100%) - 28882 spectra/s] 8.6s | postprocessing 72.2 s MAIN SEARCH DONE IN 16.820 MIN

***TOTAL TIME 242.231 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4A_RD4_1_643.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_1\061121_KP_M_4A_RD4_1_643.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.pepXML E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4B_RD5_1_644.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\jre\bin\java.exe -cp C:\Fragpipe_local\FragPipe-17.1-build2\fragpipe\lib\fragpipe-17.1-build2.jar;/C:/Fragpipe_local/FragPipe-17.1-build2/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err \cmvm.datastore.ed.ac.uk\cmvm\eb\groups\PMR\PMR-4\KP_Nov2021\061121_KP_M_4B_RD5_1_644.pin E:\Fragpipe\KP_Mito_expt_Nov-2021_version17.1\Calcified_2\061121_KP_M_4BRD5

fcyu commented 2 years ago

Hi Dominic,

The log file was truncated by GitHub, can you send it to yufe@umich.edu ?

Thanks,

Fengchao

fcyu commented 2 years ago

Dominic confirmed that the previous error was due to a network issue. It works well now.

gozzdzik commented 2 years ago

can You please share the FragPipe-17.1-build2 once more? I have same issue with timsTOF DDA data Best regards, Tomasz log_2022-04-02_18-29-03.txt .

fcyu commented 2 years ago

We have new one: FragPipe-17.2-build33 https://www.dropbox.com/s/l7mdwc97lhj4gnl/FragPipe-17.2-build33.zip?dl=1

Best,

Fengchao

gozzdzik commented 2 years ago

Thanks for blazing fast response ;) I will check and let You know!