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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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Error with ProteinProphet #155

Closed willijas closed 3 years ago

willijas commented 3 years ago

Hey Guys, I am trying to search PTMs in RAW files that came off of an Orbitrap Fusion Lumos. I am certain MSfragger and Philosopher are up-to-date. The couple sample sets I have put in i have started with just trying the defaults but I keep getting errors that cancel out my runs, I am relatively new to proteomic databases searching and don't even know where to start troubleshooting. I am pasting the last section of the log where the error comes up. Any advice would be greatly appreciated. Jason.s.williams@cuanschutz.edu

goroutine 1 [running]:

runtime.throw(0xbf7ee8, 0x5)   | /usr/local/go/src/runtime/panic.go:1116 +0x79 fp=0xc000140018 sp=0xc00013ffe8 pc=0x436459 runtime.sigpanic()   | /usr/local/go/src/runtime/signal_windows.go:249 +0x228 fp=0xc000140048 sp=0xc000140018 pc=0x449c98 bytes.(Buffer).ReadByte(0x6120d9, 0xc000282887, 0xc000289c34, 0x7)   | /usr/local/go/src/bytes/buffer.go:340 +0x28 fp=0xc000140068 sp=0xc000140048 pc=0x4b92b8 compress/flate.(decompressor).huffSym(0xc00023e388, 0xc53, 0x7, 0x0, 0x0)   | /usr/local/go/src/compress/flate/inflate.go:719 +0x8c fp=0xc0001400c0 sp=0xc000140068 pc=0x617bbc compress/flate.(decompressor).huffmanBlock(0xc00023d300)   | /usr/local/go/src/compress/flate/inflate.go:607 +0x8c9 fp=0xc000140148 sp=0xc0001400c0 pc=0x617109 compress/flate.(decompressor).Read(0xc00023d300, 0xc0002a8000, 0x7e00, 0x7e00, 0x8000, 0x69879d9e, 0x0)   | /usr/local/go/src/compress/flate/inflate.go:347 +0x7e fp=0xc000140180 sp=0xc000140148 pc=0x615e9e compress/gzip.(Reader).Read(0xc000017340, 0xc0002a8000, 0x7e00, 0x7e00, 0x200, 0x0, 0x0)   | /usr/local/go/src/compress/gzip/gunzip.go:251 +0x8e fp=0xc000140220 sp=0xc000140180 pc=0x61b4ce bytes.(Buffer).ReadFrom(0xc000231170, 0xdc90a0, 0xc000017340, 0x8960080, 0xc000231170, 0xc000140201)   | /usr/local/go/src/bytes/buffer.go:204 +0xb8 fp=0xc000140290 sp=0xc000140220 pc=0x4b8b18 io.copyBuffer(0xdc9020, 0xc000231170, 0xdc90a0, 0xc000017340, 0x0, 0x0, 0x0, 0x43fc83, 0xc0000ca000, 0x300000002)   | /usr/local/go/src/io/io.go:391 +0x303 fp=0xc000140308 sp=0xc000140290 pc=0x473ae3 io.Copy(...)   | /usr/local/go/src/io/io.go:364 philosopher/lib/ext/peptideprophet/win.bindataRead(0x3e48940, 0xb079b3, 0xb079b3, 0xc0066c, 0x12, 0x86e74a8, 0x4c4ceb, 0xc0066c, 0x12, 0xc4655c)   | /workspace/philosopher/lib/ext/peptideprophet/win/bindata.go:30 +0x1f2 fp=0xc0001403b8 sp=0xc000140308 pc=0x9b69f2 philosopher/lib/ext/peptideprophet/win.interactparserExeBytes(...)   | /workspace/philosopher/lib/ext/peptideprophet/win/bindata.go:77 philosopher/lib/ext/peptideprophet/win.interactparserExe(0xb281c0, 0xc0000e7980, 0xc0066c)   | /workspace/philosopher/lib/ext/peptideprophet/win/bindata.go:84 +0x73 fp=0xc0001404a8 sp=0xc0001403b8 pc=0x9b6ce3 philosopher/lib/ext/peptideprophet/win.Asset(0xc0066c, 0x12, 0xc0000ea540, 0xc0000ea587, 0xc0001405e0, 0xc46628, 0xc000144280)   | /workspace/philosopher/lib/ext/peptideprophet/win/bindata.go:200 +0xcf fp=0xc000140540 sp=0xc0001404a8 pc=0x9b7b1f philosopher/lib/ext/peptideprophet/win.WinInteractParser(0xc0000ea3c0, 0x5a)   | /workspace/philosopher/lib/ext/peptideprophet/win/win.go:14 +0x41 fp=0xc000140590 sp=0xc000140540 pc=0x9b7d61 philosopher/lib/ext/peptideprophet.(PeptideProphet).Deploy(0xc000140890, 0xc000018b60, 0x7, 0xc000018b80, 0x7)   | /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:81 +0x2f3 fp=0xc0001405c8 sp=0xc000140590 pc=0x9b98a3 philosopher/lib/ext/peptideprophet.Run(0xc00001c660, 0x24, 0xc00001a380, 0x3c, 0xc000022410, 0x47, 0xc000022460, 0x4b, 0xc0000224b0, 0x42, ...)   | /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:67 +0x42d fp=0xc000140960 sp=0xc0001405c8 pc=0x9b941d philosopher/cmd.glob..func12(0x86de2c0, 0xc00020a2a0, 0x2, 0xe)   | /workspace/philosopher/cmd/peproph.go:26 +0xf8 fp=0xc000141d98 sp=0xc000140960 pc=0xa798b8 github.com/spf13/cobra.(Command).execute(0x86de2c0, 0xc00020a1c0, 0xe, 0xe, 0x86de2c0, 0xc00020a1c0)   | /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:844 +0x2a4 fp=0xc000141e70 sp=0xc000141d98 pc=0x9934c4 github.com/spf13/cobra.(Command).ExecuteC(0x86defe0, 0x0, 0x0, 0x0)   | /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:945 +0x31e fp=0xc000141f48 sp=0xc000141e70 pc=0x99417e github.com/spf13/cobra.(Command).Execute(...)   | /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:885 philosopher/cmd.Execute()   | /workspace/philosopher/cmd/root.go:35 +0x34 fp=0xc000141f78 sp=0xc000141f48 pc=0xa75ce4 main.main()   | /workspace/philosopher/main.go:22 +0x75 fp=0xc000141f88 sp=0xc000141f78 pc=0xa7b555 runtime.main() Process 'PeptideProphet' finished, exit code: 2 Process returned non-zero exit code, stoppingINFO[17:18:23] Executing PeptideProphet  v3.2.9   |  


Cancelling   39 remaining tasks
Processing   interrupted, stopping PeptideProphetProcessing interrupted, stopping   PeptideProphetProcessing interrupted, stopping PeptideProphetProcessing   interrupted, stopping PeptideProphetProcessing interrupted, stopping   PeptideProphetProcessing interrupted, stopping PeptideProphetProcessing   interrupted, stopping PeptideProphet
prvst commented 3 years ago

@willijas , That error message looks like a system call to me. In other words, it is not coming from Philosopher, but from your operational system. For us to help you, we will need that you describe the following:

  1. What kind of experiment do you have?
  2. What type of analysis are you trying to do?
  3. Describe your computer system.
  4. Describe how many files and the type of instrument.
  5. Describe what commands you are trying to run.
willijas commented 3 years ago

Hi Felipe, Thank you for the reply,

  1. What kind of experiment do you have? I am trying to process fractionated samples (three Fractions) of multiple tissue types of control and hypoxia conditions. Global LFQ proteomics on an orbitrap Fusion Lumos.
  2. What type of analysis are you trying to do? I have gotten most of what I need just using PD to look at the protein level report. Now I am trying to dive in and learn PTM Sheperd to get some differences in PTMs between Control and my hypoxic samples.
  3. Describe your computer system. Processor: AMD Ryzen Threadripper 3970x 32-core, 3.70Ghz 128GB RAM x64bit operating system windows 10 enterprise.
  4. Describe how many files and the type of instrument. This sample set that failed, was 8 samples 2 fractions all run at the same time.
  5. Describe what commands you are trying to run. -I load in the Uniport bovine database. -Experiment name is Control or Hypoxia -The separate fractions for each sample are giving the same replicate value.
    • The only settings I change from default are MSfragger peptide length to 6, PPM mass tolerance to 10ppm ( same as fusion lumos) VALIDATION I check Generate peptide level summary. LFQ is not applied ( should I check this?) PTMs the only thing I change is checking the Extended output.

Let me know anything else I can elaborate on.

From: Felipe Leprevost notifications@github.com Sent: Tuesday, September 15, 2020 2:21 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU; Mention mention@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

@willijashttps://github.com/willijas , That error message looks like a system call to me. In other words, it is not coming from Philosopher, but from your operational system. For us to help you, we will need that you describe the following:

  1. What kind of experiment do you have?
  2. What type of analysis are you trying to do?
  3. Describe your computer system.
  4. Describe how many files and the type of instrument.
  5. Describe what commands you are trying to run.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/155#issuecomment-692957608, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ5OTK7SAKI3UW7MO52JI73SF7EFFANCNFSM4RNV7H3Q.

prvst commented 3 years ago

Are you running the command line version or FragPipe?

willijas commented 3 years ago

Fragpipe (v13.0).

And I can get you the full export log if you need it, I just included the last bit that I figured had the error in it.

From: Felipe Leprevost notifications@github.com Sent: Thursday, September 17, 2020 1:31 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU; Mention mention@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Are you running the command line version or FragPipe?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/155#issuecomment-694452910, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ5OTK3IFLYLIY5JGNWBZDLSGJPXZANCNFSM4RNV7H3Q.

anesvi commented 3 years ago

Please send us the full log

From: willijas notifications@github.com Sent: Thursday, September 17, 2020 3:55 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

External Email - Use Caution Fragpipe (v13.0).

And I can get you the full export log if you need it, I just included the last bit that I figured had the error in it.

From: Felipe Leprevost notifications@github.com<mailto:notifications@github.com> Sent: Thursday, September 17, 2020 1:31 PM To: Nesvilab/philosopher philosopher@noreply.github.com<mailto:philosopher@noreply.github.com> Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU<mailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Are you running the command line version or FragPipe?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/155#issuecomment-694452910, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ5OTK3IFLYLIY5JGNWBZDLSGJPXZANCNFSM4RNV7H3Q.

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willijas commented 3 years ago

Here is the full Log that I exported for that analysis. Also to note, I have gotten 1 sample set to run to completion. what's odd is these are run on the same mass spec, they are the exact same thermo RAW files that the other samples sets that have failed, just a different tissue set.

From: Alexey Nesvizhskii notifications@github.com Sent: Thursday, September 17, 2020 1:59 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU; Mention mention@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Please send us the full log

From: willijas notifications@github.com Sent: Thursday, September 17, 2020 3:55 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

External Email - Use Caution Fragpipe (v13.0).

And I can get you the full export log if you need it, I just included the last bit that I figured had the error in it.

From: Felipe Leprevost notifications@github.com<mailto:notifications@github.com> Sent: Thursday, September 17, 2020 1:31 PM To: Nesvilab/philosopher philosopher@noreply.github.com<mailto:philosopher@noreply.github.com> Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU<mailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Are you running the command line version or FragPipe?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/155#issuecomment-694452910, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ5OTK3IFLYLIY5JGNWBZDLSGJPXZANCNFSM4RNV7H3Q.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/155#issuecomment-694464694, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM65Q5DO26QTS2D4HX7DSGJSQHANCNFSM4RNV7H3Q.

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System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 13.0 MSFragger version 3.0 Philosopher version 3.2.9 (build 1593192429)

LCMS files: Experiment/Group: Control_1

113 commands to execute: WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx123G C:\Users\PeaksX\Downloads\MSFragger-3.0\MSFragger-3.0.jar D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\fragger.params D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.raw MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.tsv Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\crystalc-0-Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\crystalc-1-Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\crystalc-2-Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\crystalc-3-Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\crystalc-4-Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\crystalc-5-Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\crystalc-6-Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\crystalc-7-Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\crystalc-8-Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\crystalc-9-Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\crystalc-10-Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\crystalc-11-Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\crystalc-12-Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\crystalc-13-Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\crystalc-14-Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\crystalc-15-Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_230_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_230_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_228_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_228_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_227_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_227_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_11_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_11_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_229_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_229_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_13_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_13_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_12_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_12_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_10_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_10_c.pepXML ProteinProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\interact.pep.xml PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report iProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 63 D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\interact.pep.xml PhilosopherAbacus [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein --peptide PH_7 Control_2 Control_5 PH_4 Control_6 Control_1 PH_3 PH_8 WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Xmx123G -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\ptmshepherd-0.3.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\shepherd.config"


Execution order:

    Cmd: [START], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1]
    Cmd: [MsFragger], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [Crystal-C], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [PeptideProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [ProteinProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [PhilosopherFilter], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [PhilosopherReport], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [iProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [PhilosopherAbacus], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2]
    Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1]
    Cmd: [PTMShepherd], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]

# FragPipe v13.0ui state cache

Table.editor=P
crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=true
database.db-path=D\:\\Databases\\2020-08-17-decoys-contam-UP000009136.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\PeaksX\\Downloads\\MSFragger-3.0\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=C\:\\Users\\PeaksX\\Downloads\\FragPipe-jre-13.0\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.5
ionquant.mbrrttol=1
ionquant.mbrtoprun=3
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=1
ionquant.requantify=0
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=1
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 126.055 163.060096 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=10
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=trypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=tsv_pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.00000,C-Term Peptide,true,-1; 0.00000,N-Term Peptide,true,-1; 0.00000,C-Term Protein,true,-1; 0.00000,N-Term Protein,true,-1; 0.00000,G (glycine),true,-1; 0.00000,A (alanine),true,-1; 0.00000,S (serine),true,-1; 0.00000,P (proline),true,-1; 0.00000,V (valine),true,-1; 0.00000,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.00000,L (leucine),true,-1; 0.00000,I (isoleucine),true,-1; 0.00000,N (asparagine),true,-1; 0.00000,D (aspartic acid),true,-1; 0.00000,Q (glutamine),true,-1; 0.00000,K (lysine),true,-1; 0.00000,E (glutamic acid),true,-1; 0.00000,M (methionine),true,-1; 0.00000,H (histidine),true,-1; 0.00000,F (phenylalanine),true,-1; 0.00000,R (arginine),true,-1; 0.00000,Y (tyrosine),true,-1; 0.00000,W (tryptophan),true,-1; 0.00000,B ,true,-1; 0.00000,J,true,-1; 0.00000,O,true,-1; 0.00000,U,true,-1; 0.00000,X,true,-1; 0.00000,Z,true,-1
msfragger.table.var-mods=15.99490,M,true,3; 42.01060,[^,true,1; 79.96633,STY,false,3; -17.02650,nQnC,true,1; -18.01060,nE,false,1; 57.02146,NQ,true,3; 15.99490,P,true,1; -17.02655,nQ,true,1; 0.00000,site_09,false,1; 0.00000,site_10,false,1; 0.00000,site_11,false,1; 0.00000,site_12,false,1; 0.00000,site_13,false,1; 0.00000,site_14,false,1; 0.00000,site_15,false,1; 0.00000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=true
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmshepherd.annotation_tol=0.01
ptmshepherd.histo_smoothbins=2
ptmshepherd.localization_background=4
ptmshepherd.output_extended=true
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.run-shepherd=true
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\Data\\JasonW\\DPAs\\Neonate_DPA_Fractions_Together
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=123
workflow.threads=63

WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:41] Executing Workspace v3.2.9
INFO[11:03:41] Removing workspace
WARN[11:03:41] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:41] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:41] Executing Workspace v3.2.9
INFO[11:03:41] Creating workspace
INFO[11:03:41] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9
INFO[11:03:42] Removing workspace
WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:42] Executing Workspace v3.2.9
INFO[11:03:42] Creating workspace
INFO[11:03:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9
INFO[11:03:42] Removing workspace
WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:42] Executing Workspace v3.2.9
INFO[11:03:42] Creating workspace
INFO[11:03:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9
INFO[11:03:42] Removing workspace
WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9
INFO[11:03:43] Creating workspace
INFO[11:03:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:43] Executing Workspace v3.2.9
INFO[11:03:43] Removing workspace
WARN[11:03:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9
INFO[11:03:43] Creating workspace
INFO[11:03:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:43] Executing Workspace v3.2.9
INFO[11:03:43] Removing workspace
WARN[11:03:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9
INFO[11:03:43] Creating workspace
INFO[11:03:43] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:44] Executing Workspace v3.2.9
INFO[11:03:44] Removing workspace
WARN[11:03:44] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:44] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceClea

anesvi commented 3 years ago

Github truncates the log

Please send to me by email nesvi at med.umich.edu

From: willijas notifications@github.com Sent: Thursday, September 17, 2020 4:07 PM To: Nesvilab/philosopher philosopher@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

External Email - Use Caution Here is the full Log that I exported for that analysis. Also to note, I have gotten 1 sample set to run to completion. what's odd is these are run on the same mass spec, they are the exact same thermo RAW files that the other samples sets that have failed, just a different tissue set.

From: Alexey Nesvizhskii notifications@github.com<mailto:notifications@github.com> Sent: Thursday, September 17, 2020 1:59 PM To: Nesvilab/philosopher philosopher@noreply.github.com<mailto:philosopher@noreply.github.com> Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU<mailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Please send us the full log

From: willijas notifications@github.com<mailto:notifications@github.com> Sent: Thursday, September 17, 2020 3:55 PM To: Nesvilab/philosopher philosopher@noreply.github.com<mailto:philosopher@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

External Email - Use Caution Fragpipe (v13.0).

And I can get you the full export log if you need it, I just included the last bit that I figured had the error in it.

From: Felipe Leprevost notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> Sent: Thursday, September 17, 2020 1:31 PM To: Nesvilab/philosopher philosopher@noreply.github.com<mailto:philosopher@noreply.github.com<mailto:philosopher@noreply.github.com%3cmailto:philosopher@noreply.github.com>> Cc: Williams, Jason (SOP) JASON.S.WILLIAMS@CUANSCHUTZ.EDU<mailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU<mailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU%3cmailto:JASON.S.WILLIAMS@CUANSCHUTZ.EDU>>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com<mailto:mention@noreply.github.com%3cmailto:mention@noreply.github.com>> Subject: Re: [Nesvilab/philosopher] Error with ProteinProphet (#155)

Are you running the command line version or FragPipe?

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System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 13.0 MSFragger version 3.0 Philosopher version 3.2.9 (build 1593192429)

LCMS files: Experiment/Group: Control_1

113 commands to execute: WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx123G C:\Users\PeaksX\Downloads\MSFragger-3.0\MSFragger-3.0.jar D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\fragger.params D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.raw D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.raw MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_10.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_10.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_11.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_11.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_229.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_229.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_230.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_230.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_12.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_12.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_13.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_13.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_227.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_227.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_Cell_228.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.tsv MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML MsFragger C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -cp C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib\fragpipe-13.0.jar com.github.chhh.utils.FileMove --no-err D:\Data\JasonW\DPAs\Raw_Files\Fusion_20191004_DPA_CID_Stenmark_ECM_228.tsv D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.tsv Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\crystalc-0-Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_Cell_228.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\crystalc-1-Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_ECM_11.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\crystalc-2-Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_ECM_229.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\crystalc-3-Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_Cell_12.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\crystalc-4-Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_Cell_230.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\crystalc-5-Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_Cell_227.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\crystalc-6-Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\Fusion_20191004_DPA_CID_Stenmark_ECM_230.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\crystalc-7-Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\Fusion_20191004_DPA_CID_Stenmark_ECM_227.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\crystalc-8-Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\Fusion_20191004_DPA_CID_Stenmark_ECM_228.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\crystalc-9-Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\Fusion_20191004_DPA_CID_Stenmark_Cell_11.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\crystalc-10-Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\Fusion_20191004_DPA_CID_Stenmark_Cell_229.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\crystalc-11-Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_ECM_13.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\crystalc-12-Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\Fusion_20191004_DPA_CID_Stenmark_ECM_12.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\crystalc-13-Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\Fusion_20191004_DPA_CID_Stenmark_Cell_13.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\crystalc-14-Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_Cell_10.pepXML Crystal-C [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\original-crystalc-1.2.1.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\crystalc-15-Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML.params D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\Fusion_20191004_DPA_CID_Stenmark_ECM_10.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_230_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_230_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_228_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_228_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_227_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_227_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_11_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_11_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_229_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_229_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_ECM_13_c.pepXML Fusion_20191004_DPA_CID_Stenmark_Cell_13_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_12_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_12_c.pepXML PeptideProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --combine Fusion_20191004_DPA_CID_Stenmark_Cell_10_c.pepXML Fusion_20191004_DPA_CID_Stenmark_ECM_10_c.pepXML ProteinProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\interact.pep.xml PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate D:\Databases\2020-08-17-decoys-contam-UP000009136.fas --prefix rev PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherFilter [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8 --protxml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\combined.prot.xml PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe report iProphet [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe iprophet --decoy rev --nonsp --output combined --threads 63 D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4\interact.pep.xml D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1\interact.pep.xml PhilosopherAbacus [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_FractionsTogether] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein --peptide PH_7 Control_2 Control_5 PH_4 Control_6 Control_1 PH_3 PH_8 WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\jre\bin\java.exe -Xmx123G -Dbatmass.io.libs.thermo.dir="C:\Users\PeaksX\Downloads\MSFragger-3.0\ext\thermo" -Xmx123G -cp "C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\ptmshepherd-0.3.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\batmass-io-1.17.4.jar;C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\shepherd.config"


Execution order:

Cmd: [START], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1]
Cmd: [MsFragger], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [Crystal-C], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [PeptideProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [ProteinProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [PhilosopherFilter], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [PhilosopherReport], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [iProphet], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [PhilosopherAbacus], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_2]
Cmd: [WorkspaceClean], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_1]
Cmd: [PTMShepherd], Work dir: [D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together]

# FragPipe v13.0ui state cache

Table.editor=P
crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=true
database.db-path=D\:\\Databases\\2020-08-17-decoys-contam-UP000009136.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\Users\\PeaksX\\Downloads\\MSFragger-3.0\\MSFragger-3.0.jar
fragpipe-config.bin-philosopher=C\:\\Users\\PeaksX\\Downloads\\FragPipe-jre-13.0\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.label=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.5
ionquant.mbrrttol=1
ionquant.mbrtoprun=3
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=1
ionquant.requantify=0
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=1
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 126.055 163.060096 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=6
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=10
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=trypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=tsv_pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
msfragger.table.fix-mods=0.00000,C-Term Peptide,true,-1; 0.00000,N-Term Peptide,true,-1; 0.00000,C-Term Protein,true,-1; 0.00000,N-Term Protein,true,-1; 0.00000,G (glycine),true,-1; 0.00000,A (alanine),true,-1; 0.00000,S (serine),true,-1; 0.00000,P (proline),true,-1; 0.00000,V (valine),true,-1; 0.00000,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.00000,L (leucine),true,-1; 0.00000,I (isoleucine),true,-1; 0.00000,N (asparagine),true,-1; 0.00000,D (aspartic acid),true,-1; 0.00000,Q (glutamine),true,-1; 0.00000,K (lysine),true,-1; 0.00000,E (glutamic acid),true,-1; 0.00000,M (methionine),true,-1; 0.00000,H (histidine),true,-1; 0.00000,F (phenylalanine),true,-1; 0.00000,R (arginine),true,-1; 0.00000,Y (tyrosine),true,-1; 0.00000,W (tryptophan),true,-1; 0.00000,B ,true,-1; 0.00000,J,true,-1; 0.00000,O,true,-1; 0.00000,U,true,-1; 0.00000,X,true,-1; 0.00000,Z,true,-1
msfragger.table.var-mods=15.99490,M,true,3; 42.01060,[^,true,1; 79.96633,STY,false,3; -17.02650,nQnC,true,1; -18.01060,nE,false,1; 57.02146,NQ,true,3; 15.99490,P,true,1; -17.02655,nQ,true,1; 0.00000,site_09,false,1; 0.00000,site_10,false,1; 0.00000,site_11,false,1; 0.00000,site_12,false,1; 0.00000,site_13,false,1; 0.00000,site_14,false,1; 0.00000,site_15,false,1; 0.00000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0.00
msfragger.zero_bin_mult_expect=1.00
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=true
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmshepherd.annotation_tol=0.01
ptmshepherd.histo_smoothbins=2
ptmshepherd.localization_background=4
ptmshepherd.output_extended=true
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.run-shepherd=true
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\Data\\JasonW\\DPAs\\Neonate_DPA_Fractions_Together
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=123
workflow.threads=63

WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:41] Executing Workspace v3.2.9 INFO[11:03:41] Removing workspace WARN[11:03:41] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:41] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_4] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:41] Executing Workspace v3.2.9 INFO[11:03:41] Creating workspace INFO[11:03:41] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9 INFO[11:03:42] Removing workspace WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_6] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:42] Executing Workspace v3.2.9 INFO[11:03:42] Creating workspace INFO[11:03:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9 INFO[11:03:42] Removing workspace WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_3] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:42] Executing Workspace v3.2.9 INFO[11:03:42] Creating workspace INFO[11:03:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:42] Executing Workspace v3.2.9 INFO[11:03:42] Removing workspace WARN[11:03:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:42] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\Control_5] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9 INFO[11:03:43] Creating workspace INFO[11:03:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:43] Executing Workspace v3.2.9 INFO[11:03:43] Removing workspace WARN[11:03:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9 INFO[11:03:43] Creating workspace INFO[11:03:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:43] Executing Workspace v3.2.9 INFO[11:03:43] Removing workspace WARN[11:03:43] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_8] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[11:03:43] Executing Workspace v3.2.9 INFO[11:03:43] Creating workspace INFO[11:03:43] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Data\JasonW\DPAs\Neonate_DPA_Fractions_Together\PH_7] C:\Users\PeaksX\Downloads\FragPipe-jre-13.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[11:03:44] Executing Workspace v3.2.9 INFO[11:03:44] Removing workspace WARN[11:03:44] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:03:44] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceClea

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