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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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"library.tsv" file is not found in the Frigepipe16.0 (MSfragger 3.3) because there is no Python installed #470

Closed jinaanna closed 3 years ago

jinaanna commented 3 years ago

Hi,

I want to use the MSfragger to bulid the DDA-based spectral library but found that no “library.tsv” file was generated in the result file. What could be the reason for this ?

I'm sure that spectral library generation term has been checked.

image

Thank you!

Jina

fcyu commented 3 years ago

Hi Jina,

Can you send us the log?

Thanks,

Fengchao

jinaanna commented 3 years ago

Hi Feng chao,

The log has been sent to you in the attachment.

Jina jina

@. | 签名由网易邮箱大师定制 On 9/25/2021 @.> wrote：

Hi Jina,

Can you send us the log?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 16.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421)

LCMS files: Experiment/Group:

69 commands to execute: CheckCentroid D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;D:\software\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw 27 WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G D:\software\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar D:\raw_data\huali_HFD\DDA_lib\fragger.params D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F9_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F9_percolator_decoy_psms.tsv P20200902392_DDA_F9.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F1_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F1_percolator_decoy_psms.tsv P20200902392_DDA_F1.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F2_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F2_percolator_decoy_psms.tsv P20200902392_DDA_F2.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F5_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F5_percolator_decoy_psms.tsv P20200902392_DDA_F5.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F6_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F6_percolator_decoy_psms.tsv P20200902392_DDA_F6.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F10_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F10_percolator_decoy_psms.tsv P20200902392_DDA_F10.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F3_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F3_percolator_decoy_psms.tsv P20200902392_DDA_F3.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F8_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F8_percolator_decoy_psms.tsv P20200902392_DDA_F8.pin Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F7.pin P20200902392_DDA_F7 P20200902392_DDA_F7_percolator_target_psms.tsv P20200902392_DDA_F7_percolator_decoy_psms.tsv interact-P20200902392_DDA_F7 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F4.pin P20200902392_DDA_F4 P20200902392_DDA_F4_percolator_target_psms.tsv P20200902392_DDA_F4_percolator_decoy_psms.tsv interact-P20200902392_DDA_F4 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F9.pin P20200902392_DDA_F9 P20200902392_DDA_F9_percolator_target_psms.tsv P20200902392_DDA_F9_percolator_decoy_psms.tsv interact-P20200902392_DDA_F9 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F1.pin P20200902392_DDA_F1 P20200902392_DDA_F1_percolator_target_psms.tsv P20200902392_DDA_F1_percolator_decoy_psms.tsv interact-P20200902392_DDA_F1 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F2.pin P20200902392_DDA_F2 P20200902392_DDA_F2_percolator_target_psms.tsv P20200902392_DDA_F2_percolator_decoy_psms.tsv interact-P20200902392_DDA_F2 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F5.pin P20200902392_DDA_F5 P20200902392_DDA_F5_percolator_target_psms.tsv P20200902392_DDA_F5_percolator_decoy_psms.tsv interact-P20200902392_DDA_F5 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F6.pin P20200902392_DDA_F6 P20200902392_DDA_F6_percolator_target_psms.tsv P20200902392_DDA_F6_percolator_decoy_psms.tsv interact-P20200902392_DDA_F6 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F10.pin P20200902392_DDA_F10 P20200902392_DDA_F10_percolator_target_psms.tsv P20200902392_DDA_F10_percolator_decoy_psms.tsv interact-P20200902392_DDA_F10 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F3.pin P20200902392_DDA_F3 P20200902392_DDA_F3_percolator_target_psms.tsv P20200902392_DDA_F3_percolator_decoy_psms.tsv interact-P20200902392_DDA_F3 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F8.pin P20200902392_DDA_F8 P20200902392_DDA_F8_percolator_target_psms.tsv P20200902392_DDA_F8_percolator_decoy_psms.tsv interact-P20200902392_DDA_F8 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.7 --output combined D:\raw_data\huali_HFD\DDA_lib\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_1704220200217.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\raw_data\huali_HFD\DDAlib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev --pepxml D:\raw_data\huali_HFD\DDA_lib --protxml D:\raw_data\huali_HFD\DDA_lib\combined.prot.xml --razorbin D:\raw_data\huali_HFD\DDA_lib.meta\razor.bin PhilosopherReport [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [CheckCentroid], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [MSFragger], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [Percolator], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [ProteinProphet], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherFilter], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherReport], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [WorkspaceClean], Work dir: [D:\raw_data\huali_HFD\DDA_lib]

# FragPipe v16.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=D\:\\raw_data\\huali_HFD\\P20200902392\\2021-09-23-decoys-Swissprot_mouse_17042_20200217.fasta.fas
database.decoy-tag=rev_
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=D\:\\software\\FragPipe-jre-16.0\\fragpipe\\tools\\MSFragger-3.3\\MSFragger-3.3\\MSFragger-3.3.jar
fragpipe-config.bin-philosopher=D\:\\software\\FragPipe-jre-16.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-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.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
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
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=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=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.minimum_peaks=15
msfragger.minimum_ratio=0.00
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=stricttrypsin
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_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
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,true,1; -18.010600,nE,true,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 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=300
msfragger.write_calibrated_mgf=true
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=--razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.7
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=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.diag_ions=
ptmshepherd.glyco_mode=false
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.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.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-diaumpire=false
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=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=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.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.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\raw_data\\huali_HFD\\DDA_lib
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=27

CheckCentroid D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;D:\software\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw 27 Process 'CheckCentroid' finished, exit code: 0 Done in 0 ms. WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[22:14:43] Executing Workspace v4.0.0
INFO[22:14:43] Removing workspace
WARN[22:14:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[22:14:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[22:14:43] Executing Workspace v4.0.0
INFO[22:14:43] Creating workspace
INFO[22:14:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G D:\software\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar D:\raw_data\huali_HFD\DDA_lib\fragger.params D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw MSFragger version MSFragger-3.3 Batmass-IO version 1.23.4 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... D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw: Scans = 19976 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw: Scans = 53995 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw: Scans = 64240 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw: Scans = 81009 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw: Scans = 80196 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw: Scans = 82757 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw: Scans = 85817 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw: Scans = 86787 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw: Scans = 74837 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw: Scans = 86693 ***FIRST SEARCH**** Parameters: num_threads = 27 database_name = D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_17042_20200217.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 = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 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 = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 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 variable_mod_04 = -17.026500 nQnC 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 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 0.10 Da. 297256776 fragments to be searched in 1 slices (4.43 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.69 s

  1. P20200902392_DDA_F1.raw 101.3 s | deisotoping 0.8 s [progress: 52297/52297 (100%) - 9529 spectra/s] 5.5s | postprocessing 0.2 s
  2. P20200902392_DDA_F10.raw 72.0 s | deisotoping 0.0 s [progress: 18493/18493 (100%) - 87231 spectra/s] 0.2s | postprocessing 0.0 s
  3. P20200902392_DDA_F2.raw 106.6 s | deisotoping 0.1 s [progress: 62028/62028 (100%) - 78219 spectra/s] 0.8s | postprocessing 0.2 s
  4. P20200902392_DDA_F3.raw 133.4 s | deisotoping 0.2 s [progress: 79512/79512 (100%) - 51265 spectra/s] 1.6s | postprocessing 0.2 s
  5. P20200902392_DDA_F4.raw 167.1 s | deisotoping 0.4 s [progress: 86262/86262 (100%) - 40960 spectra/s] 2.1s | postprocessing 0.2 s
  6. P20200902392_DDA_F5.raw 165.0 s | deisotoping 0.4 s [progress: 86331/86331 (100%) - 43079 spectra/s] 2.0s | postprocessing 0.2 s
  7. P20200902392_DDA_F6.raw 166.7 s | deisotoping 0.5 s [progress: 85333/85333 (100%) - 40385 spectra/s] 2.1s | postprocessing 0.2 s
  8. P20200902392_DDA_F7.raw 157.3 s | deisotoping 0.4 s [progress: 82334/82334 (100%) - 40539 spectra/s] 2.0s | postprocessing 0.2 s
  9. P20200902392_DDA_F8.raw 151.0 s | deisotoping 0.4 s [progress: 79586/79586 (100%) - 44437 spectra/s] 1.8s | postprocessing 0.2 s
  10. P20200902392_DDA_F9.raw 125.6 s | deisotoping 0.3 s [progress: 73911/73911 (100%) - 51506 spectra/s] 1.4s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 24.326 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.19 0.90 -0.03 0.60 -0.63 2.89 0.03 2.90
002 0.30 0.76 0.01 0.42 0.14 2.90 0.25 2.82
003 0.13 1.03 0.03 0.77 -0.52 2.61 0.06 2.59
004 -0.38 1.31 -0.01 0.75 -0.63 2.43 -0.01 2.32
005 0.84 0.96 -0.03 0.62 0.73 2.12 0.01 2.06
006 0.55 0.96 -0.03 0.67 0.39 2.19 -0.01 2.18
007 -0.52 0.99 -0.03 0.62 -0.55 2.23 -0.01 2.23
008 0.73 0.98 -0.03 0.64 0.59 2.35 0.03 2.32
009 -0.60 1.17 0.02 0.70 -0.73 2.48 -0.00 2.39
010 0.02 1.03 -0.03 0.72 -0.28 2.55 0.03 2.56
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 36009 37228 37778 37896 37549 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 37896 37896 37831 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 38648
------- -------
------- -------
Rm P. 1
------- -------
Count 38714
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 23.636 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 27 database_name = D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_17042_20200217.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 = 1 isotope_error = 0/1/2 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 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 = 200 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 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 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. 317544780 fragments to be searched in 1 slices (4.73 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.56 s

  1. P20200902392_DDA_F1.mzBIN_calibrated 0.8 s [progress: 51676/51676 (100%) - 76106 spectra/s] 0.7s | postprocessing 1.5 s
  2. P20200902392_DDA_F10.mzBIN_calibrated 0.2 s [progress: 17453/17453 (100%) - 79694 spectra/s] 0.2s | postprocessing 0.2 s
  3. P20200902392_DDA_F2.mzBIN_calibrated 1.1 s [progress: 61566/61566 (100%) - 69961 spectra/s] 0.9s | postprocessing 1.9 s
  4. P20200902392_DDA_F3.mzBIN_calibrated 1.2 s [progress: 79205/79205 (100%) - 43687 spectra/s] 1.8s | postprocessing 2.4 s
  5. P20200902392_DDA_F4.mzBIN_calibrated 1.5 s [progress: 86073/86073 (100%) - 38102 spectra/s] 2.3s | postprocessing 3.5 s
  6. P20200902392_DDA_F5.mzBIN_calibrated 2.2 s [progress: 86175/86175 (100%) - 40668 spectra/s] 2.1s | postprocessing 2.7 s
  7. P20200902392_DDA_F6.mzBIN_calibrated 1.6 s [progress: 85175/85175 (100%) - 38127 spectra/s] 2.2s | postprocessing 2.7 s
  8. P20200902392_DDA_F7.mzBIN_calibrated 1.6 s [progress: 82154/82154 (100%) - 40995 spectra/s] 2.0s | postprocessing 2.5 s
  9. P20200902392_DDA_F8.mzBIN_calibrated 1.5 s [progress: 79381/79381 (100%) - 42067 spectra/s] 1.9s | postprocessing 2.4 s
  10. P20200902392_DDA_F9.mzBIN_calibrated 1.3 s [progress: 73700/73700 (100%) - 47395 spectra/s] 1.6s | postprocessing 2.2 s MAIN SEARCH DONE IN 0.935 MIN

*****TOTAL TIME 48.897 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll *@.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Started Sat Sep 25 23:03:49 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile P20200902392_DDA_F7.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 64248 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 51773 positives and 12475 negatives, size ratio=4.15014 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 23901 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 23941 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 23924 training set positives with q<0.01 in that direction. Found 35855 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.701 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 36999 PSMs with q<0.01 Iteration 2: Estimated 37262 PSMs with q<0.01 Iteration 3: Estimated 37305 PSMs with q<0.01 Iteration 4: Estimated 37360 PSMs with q<0.01 Iteration 5: Estimated 37380 PSMs with q<0.01 Iteration 6: Estimated 37379 PSMs with q<0.01 Iteration 7: Estimated 37367 PSMs with q<0.01 Iteration 8: Estimated 37375 PSMs with q<0.01 Iteration 9: Estimated 37367 PSMs with q<0.01 Iteration 10: Estimated 37368 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.1491 -0.2290 -0.1806 retentiontime 0.0000 0.0000 0.0000 rank -0.5870 -0.6787 -0.8945 abs_ppm -0.1550 -0.2427 -0.2419 isotope_errors -2.2833 -2.3731 -2.8787 log10_evalue 1.1168 0.8056 1.0900 hyperscore 0.9412 1.1118 0.9993 delta_hyperscore 0.5264 1.2296 0.8904 matched_ion_num -0.3512 -0.3466 -0.4540 peptide_length 0.0000 0.0000 0.0000 ntt -0.2316 -0.2633 -0.1869 nmc -0.3228 -0.3943 -0.3859 charge_1 -0.1463 -0.1510 -0.2062 charge_2 0.1435 0.1724 0.1775 charge_3 0.1882 0.2055 0.2683 charge_4 0.0851 0.1381 0.1086 charge_5 0.0975 0.1056 0.1412 charge_6 0.1135 -0.0979 0.0298 charge_7 2.0027 2.5589 2.7156 m0 Found 37296 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 51773 target PSMs and 12475 decoy PSMs. Calculating q values. Final list yields 37300 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.18 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Started Sat Sep 25 23:04:04 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile P20200902392_DDA_F4.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 68941 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 55257 positives and 13684 negatives, size ratio=4.03807 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 25175 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 25074 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 25436 training set positives with q<0.01 in that direction. Found 37866 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.719 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 38900 PSMs with q<0.01 Iteration 2: Estimated 39144 PSMs with q<0.01 Iteration 3: Estimated 39228 PSMs with q<0.01 Iteration 4: Estimated 39283 PSMs with q<0.01 Iteration 5: Estimated 39291 PSMs with q<0.01 Iteration 6: Estimated 39310 PSMs with q<0.01 Iteration 7: Estimated 39301 PSMs with q<0.01 Iteration 8: Estimated 39297 PSMs with q<0.01 Iteration 9: Estimated 39295 PSMs with q<0.01 Iteration 10: Estimated 39300 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0558 -0.0151 -0.0237 retentiontime 0.0000 0.0000 0.0000 rank -0.3299 -0.2922 -0.3667 abs_ppm -0.1508 -0.0834 -0.1597 isotope_errors -1.7822 -1.5175 -2.1973 log10_evalue 1.1416 1.5105 1.0887 hyperscore 1.0675 1.0471 0.8822 delta_hyperscore 0.9545 0.2387 0.6646 matched_ion_num -0.6725 -0.5977 -0.6032 peptide_length 0.0000 0.0000 0.0000 ntt -0.2017 -0.1669 -0.1768 nmc -0.4186 -0.3642 -0.3827 charge_1 -0.1312 -0.1118 -0.1460 charge_2 0.2275 0.1684 0.2133 charge_3 0.2434 0.2470 0.2575 charge_4 0.1359 0.1254 0.1172 charge_5 0.0405 0.0734 0.0767 charge_6 -0.0236 -0.0175 -0.0237 charge_7 2.1898 1.6226 2.1997 m0 Found 39255 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 55257 target PSMs and 13684 decoy PSMs. Calculating q values. Final list yields 39268 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.22 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F9_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F9_percolator_decoy_psms.tsv P20200902392_DDA_F9.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --po

fcyu commented 3 years ago

GitHub truncates the text file. Please zip it.

jinaanna commented 3 years ago
jina

@. | 签名由网易邮箱大师定制 On 9/26/2021 @.> wrote：

GitHub truncates the text file. Please zip it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

fcyu commented 3 years ago

Still no file attached. Can you send it to yufe@umich.edu?

jinaanna commented 3 years ago

OK, does it work?

jina

@. | 签名由网易邮箱大师定制 On 9/26/2021 @.> wrote：

Still no file attached. Can you send it to @.***?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

fcyu commented 3 years ago

Thanks for your file. You didn't run spectral library generation. Please use SpecLib workflow and try again.

Best,

Fengchao

jinaanna commented 3 years ago

OK, got it.

jina

@. | 签名由网易邮箱大师定制 On 9/26/2021 @.> wrote：

Thanks for your file. You didn't run spectral library generation. Please use SpecLib workflow and try again.

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

jinaanna commented 3 years ago

Hi, I'm sorry to tell you that there is no "library.tsv" file in the output result eve though I have selected the "Speclib" Workflow. What should I do in this condition?

jina

@. | 签名由网易邮箱大师定制 On 9/26/2021 @.> wrote： OK, got it.

jina

@. | 签名由网易邮箱大师定制 On 9/26/2021 @.> wrote：

Thanks for your file. You didn't run spectral library generation. Please use SpecLib workflow and try again.

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

fcyu commented 3 years ago

Can you send me your log?

Thanks,

Fengchao

jinaanna commented 3 years ago

OK.

jina

@. | 签名由网易邮箱大师定制 On 9/27/2021 @.> wrote：

Can you send me your log?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 16.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421)

LCMS files: Experiment/Group:

69 commands to execute: CheckCentroid D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;D:\software\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw 27 WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G D:\software\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar D:\raw_data\huali_HFD\DDA_lib\fragger.params D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pin MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pepXML MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F9_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F9_percolator_decoy_psms.tsv P20200902392_DDA_F9.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F1_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F1_percolator_decoy_psms.tsv P20200902392_DDA_F1.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F2_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F2_percolator_decoy_psms.tsv P20200902392_DDA_F2.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F5_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F5_percolator_decoy_psms.tsv P20200902392_DDA_F5.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F6_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F6_percolator_decoy_psms.tsv P20200902392_DDA_F6.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F10_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F10_percolator_decoy_psms.tsv P20200902392_DDA_F10.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F3_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F3_percolator_decoy_psms.tsv P20200902392_DDA_F3.pin Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F8_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F8_percolator_decoy_psms.tsv P20200902392_DDA_F8.pin Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F7.pin P20200902392_DDA_F7 P20200902392_DDA_F7_percolator_target_psms.tsv P20200902392_DDA_F7_percolator_decoy_psms.tsv interact-P20200902392_DDA_F7 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F4.pin P20200902392_DDA_F4 P20200902392_DDA_F4_percolator_target_psms.tsv P20200902392_DDA_F4_percolator_decoy_psms.tsv interact-P20200902392_DDA_F4 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F9.pin P20200902392_DDA_F9 P20200902392_DDA_F9_percolator_target_psms.tsv P20200902392_DDA_F9_percolator_decoy_psms.tsv interact-P20200902392_DDA_F9 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F1.pin P20200902392_DDA_F1 P20200902392_DDA_F1_percolator_target_psms.tsv P20200902392_DDA_F1_percolator_decoy_psms.tsv interact-P20200902392_DDA_F1 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F2.pin P20200902392_DDA_F2 P20200902392_DDA_F2_percolator_target_psms.tsv P20200902392_DDA_F2_percolator_decoy_psms.tsv interact-P20200902392_DDA_F2 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F5.pin P20200902392_DDA_F5 P20200902392_DDA_F5_percolator_target_psms.tsv P20200902392_DDA_F5_percolator_decoy_psms.tsv interact-P20200902392_DDA_F5 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F6.pin P20200902392_DDA_F6 P20200902392_DDA_F6_percolator_target_psms.tsv P20200902392_DDA_F6_percolator_decoy_psms.tsv interact-P20200902392_DDA_F6 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F10.pin P20200902392_DDA_F10 P20200902392_DDA_F10_percolator_target_psms.tsv P20200902392_DDA_F10_percolator_decoy_psms.tsv interact-P20200902392_DDA_F10 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F3.pin P20200902392_DDA_F3 P20200902392_DDA_F3_percolator_target_psms.tsv P20200902392_DDA_F3_percolator_decoy_psms.tsv interact-P20200902392_DDA_F3 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML P20200902392_DDA_F8.pin P20200902392_DDA_F8 P20200902392_DDA_F8_percolator_target_psms.tsv P20200902392_DDA_F8_percolator_decoy_psms.tsv interact-P20200902392_DDA_F8 DDA Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8_percolator_target_psms.tsv Percolator: Delete temp D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8_percolator_decoy_psms.tsv ProteinProphet [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.7 --output combined D:\raw_data\huali_HFD\DDA_lib\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_1704220200217.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\raw_data\huali_HFD\DDAlib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev --pepxml D:\raw_data\huali_HFD\DDA_lib --protxml D:\raw_data\huali_HFD\DDA_lib\combined.prot.xml --razorbin D:\raw_data\huali_HFD\DDA_lib.meta\razor.bin PhilosopherReport [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [CheckCentroid], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [MSFragger], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [Percolator], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [ProteinProphet], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherFilter], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [PhilosopherReport], Work dir: [D:\raw_data\huali_HFD\DDA_lib]
    Cmd: [WorkspaceClean], Work dir: [D:\raw_data\huali_HFD\DDA_lib]

# FragPipe v16.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
crystalc.run-crystalc=false
database.db-path=D\:\\raw_data\\huali_HFD\\P20200902392\\2021-09-23-decoys-Swissprot_mouse_17042_20200217.fasta.fas
database.decoy-tag=rev_
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=D\:\\software\\FragPipe-jre-16.0\\fragpipe\\tools\\MSFragger-3.3\\MSFragger-3.3\\MSFragger-3.3.jar
fragpipe-config.bin-philosopher=D\:\\software\\FragPipe-jre-16.0\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-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.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
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
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage=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=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.minimum_peaks=15
msfragger.minimum_ratio=0.00
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=stricttrypsin
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_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
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,true,1; -18.010600,nE,true,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 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=300
msfragger.write_calibrated_mgf=true
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=--razor --picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.7
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=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.diag_ions=
ptmshepherd.glyco_mode=false
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.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.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-diaumpire=false
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=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=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.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.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\raw_data\\huali_HFD\\DDA_lib
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=27

CheckCentroid D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -Xmx116G -cp "D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;D:\software\FragPipe-jre-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw 27 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[22:56:47] Executing Workspace v4.0.0
INFO[22:56:47] Removing workspace
WARN[22:56:47] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[22:56:47] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[22:56:48] Executing Workspace v4.0.0
INFO[22:56:48] Creating workspace
INFO[22:56:48] Done
MSFragger [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx116G D:\software\FragPipe-jre-16.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar D:\raw_data\huali_HFD\DDA_lib\fragger.params D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw MSFragger version MSFragger-3.3 Batmass-IO version 1.23.4 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... D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.raw: Scans = 19976 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.raw: Scans = 53995 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.raw: Scans = 64240 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.raw: Scans = 81009 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.raw: Scans = 80196 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.raw: Scans = 82757 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.raw: Scans = 85817 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.raw: Scans = 86787 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.raw: Scans = 74837 D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.raw: Scans = 86693 ***FIRST SEARCH**** Parameters: num_threads = 27 database_name = D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_17042_20200217.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 = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 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 = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 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 variable_mod_04 = -17.026500 nQnC 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 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 0.10 Da. 297256776 fragments to be searched in 1 slices (4.43 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.78 s

  1. P20200902392_DDA_F1.raw 98.0 s | deisotoping 0.8 s [progress: 52297/52297 (100%) - 23389 spectra/s] 2.2s | postprocessing 0.2 s
  2. P20200902392_DDA_F10.raw 68.1 s | deisotoping 0.0 s [progress: 18493/18493 (100%) - 87645 spectra/s] 0.2s | postprocessing 0.0 s
  3. P20200902392_DDA_F2.raw 105.3 s | deisotoping 0.1 s [progress: 62028/62028 (100%) - 80661 spectra/s] 0.8s | postprocessing 0.3 s
  4. P20200902392_DDA_F3.raw 130.0 s | deisotoping 0.2 s [progress: 79512/79512 (100%) - 53724 spectra/s] 1.5s | postprocessing 0.2 s
  5. P20200902392_DDA_F4.raw 162.6 s | deisotoping 0.4 s [progress: 86262/86262 (100%) - 38735 spectra/s] 2.2s | postprocessing 0.2 s
  6. P20200902392_DDA_F5.raw 161.3 s | deisotoping 0.3 s [progress: 86331/86331 (100%) - 42010 spectra/s] 2.1s | postprocessing 0.2 s
  7. P20200902392_DDA_F6.raw 162.2 s | deisotoping 0.5 s [progress: 85333/85333 (100%) - 37345 spectra/s] 2.3s | postprocessing 0.3 s
  8. P20200902392_DDA_F7.raw 152.8 s | deisotoping 0.5 s [progress: 82334/82334 (100%) - 40881 spectra/s] 2.0s | postprocessing 0.2 s
  9. P20200902392_DDA_F8.raw 152.2 s | deisotoping 0.4 s [progress: 79586/79586 (100%) - 40481 spectra/s] 2.0s | postprocessing 0.2 s
  10. P20200902392_DDA_F9.raw 123.7 s | deisotoping 0.3 s [progress: 73911/73911 (100%) - 45907 spectra/s] 1.6s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 23.758 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 0.19 0.90 -0.03 0.60 -0.63 2.89 0.03 2.90
002 0.30 0.76 0.01 0.42 0.14 2.90 0.25 2.82
003 0.13 1.03 0.03 0.77 -0.52 2.61 0.06 2.59
004 -0.38 1.31 -0.01 0.75 -0.63 2.43 -0.01 2.32
005 0.84 0.96 -0.03 0.62 0.73 2.12 0.01 2.06
006 0.55 0.96 -0.03 0.67 0.39 2.19 -0.01 2.18
007 -0.52 0.99 -0.03 0.62 -0.55 2.23 -0.01 2.23
008 0.73 0.98 -0.03 0.64 0.59 2.35 0.03 2.32
009 -0.60 1.17 0.02 0.70 -0.73 2.48 -0.00 2.39
010 0.02 1.03 -0.03 0.72 -0.28 2.55 0.03 2.56
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 36009 37228 37778 37896 37549 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 37896 37896 37831 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 38648
------- -------
------- -------
Rm P. 1
------- -------
Count 38714
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 22.588 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 27 database_name = D:\raw_data\huali_HFD\P20200902392\2021-09-23-decoys-Swissprot_mouse_17042_20200217.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 = 1 isotope_error = 0/1/2 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_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 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 = 200 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 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 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. 317544780 fragments to be searched in 1 slices (4.73 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.72 s

  1. P20200902392_DDA_F1.mzBIN_calibrated 0.7 s [progress: 51676/51676 (100%) - 95168 spectra/s] 0.5s | postprocessing 1.7 s
  2. P20200902392_DDA_F10.mzBIN_calibrated 0.2 s [progress: 17453/17453 (100%) - 53210 spectra/s] 0.3s | postprocessing 0.3 s
  3. P20200902392_DDA_F2.mzBIN_calibrated 1.1 s [progress: 61566/61566 (100%) - 60896 spectra/s] 1.0s | postprocessing 2.0 s
  4. P20200902392_DDA_F3.mzBIN_calibrated 1.2 s [progress: 79205/79205 (100%) - 43376 spectra/s] 1.8s | postprocessing 2.6 s
  5. P20200902392_DDA_F4.mzBIN_calibrated 1.5 s [progress: 86073/86073 (100%) - 36272 spectra/s] 2.4s | postprocessing 2.9 s
  6. P20200902392_DDA_F5.mzBIN_calibrated 1.6 s [progress: 86175/86175 (100%) - 38800 spectra/s] 2.2s | postprocessing 2.7 s
  7. P20200902392_DDA_F6.mzBIN_calibrated 1.6 s [progress: 85175/85175 (100%) - 37940 spectra/s] 2.2s | postprocessing 2.7 s
  8. P20200902392_DDA_F7.mzBIN_calibrated 1.5 s [progress: 82154/82154 (100%) - 38679 spectra/s] 2.1s | postprocessing 2.6 s
  9. P20200902392_DDA_F8.mzBIN_calibrated 1.4 s [progress: 79381/79381 (100%) - 39143 spectra/s] 2.0s | postprocessing 2.5 s
  10. P20200902392_DDA_F9.mzBIN_calibrated 1.2 s [progress: 73700/73700 (100%) - 45354 spectra/s] 1.6s | postprocessing 2.3 s MAIN SEARCH DONE IN 0.935 MIN

*****TOTAL TIME 47.281 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F1.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F10.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F10.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F2.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F3.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F4.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F5.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F5.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F6.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F6.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F7.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F7.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F8.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F8.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pepXML D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin D:\software\FragPipe-jre-16.0\fragpipe\jre\bin\java.exe -cp D:\software\FragPipe-jre-16.0\fragpipe\lib\fragpipe-16.0.jar;/D:/software/FragPipe-jre-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err D:\raw_data\huali_HFD\P20200902392\DDA\P20200902392_DDA_F9.pin D:\raw_data\huali_HFD\DDA_lib\P20200902392_DDA_F9.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll *@.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F7_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F7_percolator_decoy_psms.tsv P20200902392_DDA_F7.pin Started Sun Sep 26 23:44:16 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile P20200902392_DDA_F7.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 64248 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 51773 positives and 12475 negatives, size ratio=4.15014 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 23901 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 23941 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 23924 training set positives with q<0.01 in that direction. Found 35855 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.785 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 36999 PSMs with q<0.01 Iteration 2: Estimated 37262 PSMs with q<0.01 Iteration 3: Estimated 37305 PSMs with q<0.01 Iteration 4: Estimated 37360 PSMs with q<0.01 Iteration 5: Estimated 37380 PSMs with q<0.01 Iteration 6: Estimated 37379 PSMs with q<0.01 Iteration 7: Estimated 37367 PSMs with q<0.01 Iteration 8: Estimated 37375 PSMs with q<0.01 Iteration 9: Estimated 37367 PSMs with q<0.01 Iteration 10: Estimated 37368 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.1491 -0.2290 -0.1806 retentiontime 0.0000 0.0000 0.0000 rank -0.5870 -0.6787 -0.8945 abs_ppm -0.1550 -0.2427 -0.2419 isotope_errors -2.2833 -2.3731 -2.8787 log10_evalue 1.1168 0.8056 1.0900 hyperscore 0.9412 1.1118 0.9993 delta_hyperscore 0.5264 1.2296 0.8904 matched_ion_num -0.3512 -0.3466 -0.4540 peptide_length 0.0000 0.0000 0.0000 ntt -0.2316 -0.2633 -0.1869 nmc -0.3228 -0.3943 -0.3859 charge_1 -0.1463 -0.1510 -0.2062 charge_2 0.1435 0.1724 0.1775 charge_3 0.1882 0.2055 0.2683 charge_4 0.0851 0.1381 0.1086 charge_5 0.0975 0.1056 0.1412 charge_6 0.1135 -0.0979 0.0298 charge_7 2.0027 2.5589 2.7156 m0 Found 37296 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 51773 target PSMs and 12475 decoy PSMs. Calculating q values. Final list yields 37300 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.68 cpu seconds or 15 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F4_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F4_percolator_decoy_psms.tsv P20200902392_DDA_F4.pin Started Sun Sep 26 23:44:33 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile P20200902392_DDA_F4.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 68941 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 55257 positives and 13684 negatives, size ratio=4.03807 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 25175 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 25074 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 25436 training set positives with q<0.01 in that direction. Found 37866 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.837 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 38900 PSMs with q<0.01 Iteration 2: Estimated 39144 PSMs with q<0.01 Iteration 3: Estimated 39228 PSMs with q<0.01 Iteration 4: Estimated 39283 PSMs with q<0.01 Iteration 5: Estimated 39291 PSMs with q<0.01 Iteration 6: Estimated 39310 PSMs with q<0.01 Iteration 7: Estimated 39301 PSMs with q<0.01 Iteration 8: Estimated 39297 PSMs with q<0.01 Iteration 9: Estimated 39295 PSMs with q<0.01 Iteration 10: Estimated 39300 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0558 -0.0151 -0.0237 retentiontime 0.0000 0.0000 0.0000 rank -0.3299 -0.2922 -0.3667 abs_ppm -0.1508 -0.0834 -0.1597 isotope_errors -1.7822 -1.5175 -2.1973 log10_evalue 1.1416 1.5105 1.0887 hyperscore 1.0675 1.0471 0.8822 delta_hyperscore 0.9545 0.2387 0.6646 matched_ion_num -0.6725 -0.5977 -0.6032 peptide_length 0.0000 0.0000 0.0000 ntt -0.2017 -0.1669 -0.1768 nmc -0.4186 -0.3642 -0.3827 charge_1 -0.1312 -0.1118 -0.1460 charge_2 0.2275 0.1684 0.2133 charge_3 0.2434 0.2470 0.2575 charge_4 0.1359 0.1254 0.1172 charge_5 0.0405 0.0734 0.0767 charge_6 -0.0236 -0.0175 -0.0237 charge_7 2.1898 1.6226 2.1997 m0 Found 39255 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 55257 target PSMs and 13684 decoy PSMs. Calculating q values. Final list yields 39268 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 6.478 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: D:\raw_data\huali_HFD\DDA_lib] D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F9_percolator_target_psms.tsv --decoy-results-psms P20200902392_DDA_F9_percolator_decoy_psms.tsv P20200902392_DDA_F9.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: D:\software\FragPipe-jre-16.0\fragpipe\lib..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 27 --results-psms P20200902392_DDA_F9_per

fcyu commented 3 years ago

Also, can you send me the screenshot of the config tab?

Thanks,

Fengchao

fcyu commented 3 years ago

When sending the log fine, can you zip it and send it to yufe@umich.edu? GitHub truncates the text file.

fcyu commented 3 years ago

Thanks for your files. But what I want it the screenshot of the config tab of FragPipe like the following one, not the config file. image

Please also remember to zip and send it to yufe@umich.edu.

Best,

Fengchao

fcyu commented 3 years ago

You did not install Python and some packages, which are required by speclib. Please read the tutorial (https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#configure-fragpipe) regarding installing the python and the packages.

Here (https://github.com/Nesvilab/FragPipe) contains various of tutorials regarding configuration and using FragPipe in case you need it.

Best,

Fengchao