problem with configuration
Closed this issue · 17 comments
Ale-ksa-ndra commented
the fragpipe doesnt see IonQuant version: 1.10.27...however its not visisble in the config.(see the photos)
it was ok till i started to load dia files..when i got back with dda it was no functional anymore
do you know what i do wrong?
- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)
- Describe the issue or question:
Ale-ksa-ndra commented
log file its empty
fcyu commented
Could you restart FragPipe to see if it resolve your problem?
One more thing, Java 21 has a bug that might crash FragPipe: #1466 (comment) Please use Java 11 or 17.
Best,
Fengchao
Ale-ksa-ndra commented
i acually can not use java (not allowed by UvA)
i use OpenJDK21U-jdk_x64_windows_hotspot_21.0.1_12
fcyu commented
That is also Java, just not Oracle Java. We are also using OpenJDK. Please check our tutorial here https://fragpipe.nesvilab.org/docs/tutorial_setup_fragpipe.html
If you still have issue configuring your computer or installing Java, please contact your local IT deparement.
Best,
Fengchao
Ale-ksa-ndra commented
thank you
Ale-ksa-ndra commented
Hello I have installed OpenJDK17U-jdk_x64_windows_hotspot_17.0.11_9
But it still doesn’t work.
Now I get
java.net.ConnectException: Connection timed out: connect
at java.base/sun.nio.ch.Net.connect0(Native Method)
at java.base/sun.nio.ch.Net.connect(Net.java:579)
at java.base/sun.nio.ch.Net.connect(Net.java:568)
at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:593)
at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:327)
at java.base/java.net.Socket.connect(Socket.java:633)
at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:304)
at java.base/sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:174)
at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:183)
at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:533)
at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:638)
at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:266)
at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:380)
at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:193)
at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1242)
at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1128)
at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:179)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1687)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1611)
at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224)
at java.base/java.net.URL.openStream(URL.java:1161)
at org.apache.commons.io.IOUtils.toString(IOUtils.java:3239)
at org.apache.commons.io.IOUtils.toString(IOUtils.java:3214)
at org.apache.commons.io.IOUtils.toString(IOUtils.java:3330)
at com.dmtavt.fragpipe.tools.ionquant.IonQuantVersionFetcherServer.fetchVersionResponse(IonQuantVersionFetcherServer.java:108)
at com.dmtavt.fragpipe.tools.ionquant.IonQuantVersionFetcherServer.fetchVersion(IonQuantVersionFetcherServer.java:80)
at com.dmtavt.fragpipe.tools.ionquant.IonQuantVersionFetcherServer.autoUpdate(IonQuantVersionFetcherServer.java:123)
at com.dmtavt.fragpipe.tabs.TabConfig.lambda$actionToolsDownload$11(TabConfig.java:516)
at java.base/java.lang.Thread.run(Thread.java:840)
how can I fix it?
Kind regards,
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Wednesday, 26 June 2024 14:30
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Author ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
Could you restart FragPipe to see if it resolve your problem?
One more thing, Java 21 has a bug that might crash FragPipe: #1466 (comment)<#1466 (comment)> Please use Java 11 or 17.
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZ25J4MAWC3JN2IEVDTZJKX6HAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJRGU3TEMBWGI>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
fcyu commented
It is hard for us to trouble the operating system, networking, or java issues remotely. Please contact your local IT department.
Best,
Fengchao
Ale-ksa-ndra commented
Dear Fengchao,
Now it doesn’t look like java problem, but PTMs is not active
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525<tel:(0)20%20525> 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Wednesday, 3 July 2024 17:37
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Author ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
It is hard for us to trouble the operating system, networking, or java issues remotely. Please contact your local IT department.
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZ4UNZOHOWHVMDSGO4DZKQLAPAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBWGU4DSMRXGY>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.11, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A
Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1
LCMS files:
Experiment/Group:
(if "spectral library generation" is enabled, all files will be analyzed together)
- C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML DIA
60 commands to execute:
CheckCentroid
java -Xmx19G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML 23
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\d446c87c-d5a6-458e-9912-f3ae5845602b
UmpireSe
java -Xmx19G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML C:\Users\achojna1\Documents\results32w\umpire-se.params
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\diaumpire_se.log C:\Users\achojna1\Documents\results32w\diaumpire_se.log
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Peak C:\Users\achojna1\Documents\results32w\h16w32w_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.DIAWindowsFS C:\Users\achojna1\Documents\results32w\h16w32w.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.RTidxFS C:\Users\achojna1\Documents\results32w\h16w32w.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanClusterMapping_Q1 C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanClusterMapping_Q2 C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanClusterMapping_Q3 C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanidxFS C:\Users\achojna1\Documents\results32w\h16w32w.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanPosFS C:\Users\achojna1\Documents\results32w\h16w32w.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w.ScanRTFS C:\Users\achojna1\Documents\results32w\h16w32w.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_diasetting.ser C:\Users\achojna1\Documents\results32w\h16w32w_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_params.ser C:\Users\achojna1\Documents\results32w\h16w32w_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q1.mgf C:\Users\achojna1\Documents\results32w\h16w32w_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q2.mgf C:\Users\achojna1\Documents\results32w\h16w32w_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q3.mgf C:\Users\achojna1\Documents\results32w\h16w32w_Q3.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q1.mzML C:\Users\achojna1\Documents\results32w\h16w32w_Q1.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q2.mzML C:\Users\achojna1\Documents\results32w\h16w32w_Q2.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\Documents\sciex\04july24\h16w32w_Q3.mzML C:\Users\achojna1\Documents\results32w\h16w32w_Q3.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q3.mgf
MSFragger [Work dir: C:\Users\achojna1\Documents\results32w]
java -jar -Dfile.encoding=UTF-8 -Xmx19G C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\Users\achojna1\Documents\results32w\fragger_dda.params C:\Users\achojna1\Documents\results32w\h16w32w_Q1.mzML C:\Users\achojna1\Documents\results32w\h16w32w_Q2.mzML C:\Users\achojna1\Documents\results32w\h16w32w_Q3.mzML
MSBooster [Work dir: C:\Users\achojna1\Documents\results32w]
java -Xmx19G -cp C:\Users\achojna1\fragpipe\tools\MSBooster-1.2.31.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\Users\achojna1\Documents\results32w\msbooster_params.txt
Percolator [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms h16w32w_Q2_percolator_target_psms.tsv --decoy-results-psms h16w32w_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ h16w32w_Q2_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms h16w32w_Q1_percolator_target_psms.tsv --decoy-results-psms h16w32w_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ h16w32w_Q1_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms h16w32w_Q3_percolator_target_psms.tsv --decoy-results-psms h16w32w_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ h16w32w_Q3_edited.pin
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\results32w]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML h16w32w_Q2.pin h16w32w_Q2 h16w32w_Q2_percolator_target_psms.tsv h16w32w_Q2_percolator_decoy_psms.tsv interact-h16w32w_Q2 DDA 0.7 C:\Users\achojna1\Documents\results32w\h16w32w_Q2_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q2_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q2_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\results32w]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML h16w32w_Q1.pin h16w32w_Q1 h16w32w_Q1_percolator_target_psms.tsv h16w32w_Q1_percolator_decoy_psms.tsv interact-h16w32w_Q1 DDA 0.7 C:\Users\achojna1\Documents\results32w\h16w32w_Q1_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q1_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\results32w]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML h16w32w_Q3.pin h16w32w_Q3 h16w32w_Q3_percolator_target_psms.tsv h16w32w_Q3_percolator_decoy_psms.tsv interact-h16w32w_Q3 DDA 0.7 C:\Users\achojna1\Documents\results32w\h16w32w_Q3_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q3_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\results32w\h16w32w_Q3_percolator_decoy_psms.tsv
ProteinProphet [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\achojna1\Documents\results32w\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --tag rev_ --pepxml C:\Users\achojna1\Documents\results32w --protxml C:\Users\achojna1\Documents\results32w\combined.prot.xml --razor
PhilosopherReport [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
WorkspaceClean [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
SpecLibGen [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\AppData\Local\Programs\Python\Python39\python -u C:\Users\achojna1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas C:\Users\achojna1\Documents\results32w unused C:\Users\achojna1\Documents\results32w True unused use_easypqp noiRT;noIM 23 "--unimod C:/Users/achojna1/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.01" delete_intermediate_files C:\Users\achojna1\Documents\results32w\filelist_speclibgen.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 23 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg C:\Users\achojna1\Documents\results32w\filelist_diann.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate information [Work dir: C:\Users\achojna1\Documents\results32w\diann-output]
java -cp C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation C:\Users\achojna1\Documents\results32w
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: C:\Users\achojna1\Documents\results32w\diann-output]
java -cp C:\Users\achojna1\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ C:\Users\achojna1\Documents\results32w\psm.tsv 0.01 1 0.01 0.01 C:\Users\achojna1\Documents\results32w\fragpipe-files.fp-manifest
~~~~~~~~~~~~~~~~~~~~~~
Execution order:
Cmd: [START], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [UmpireSe], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [MSBooster], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [Percolator], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [ProteinProphet], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [SpecLibGen], Work dir: [C:\Users\achojna1\Documents\results32w]
Cmd: [DIA-NN], Work dir: [C:\Users\achojna1\Documents\results32w]
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~Sample of C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas~~~~~~~
contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
rev_sp|O43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1
rev_sp|P0DMB2|CH088_HUMAN Uncharacterized protein C8orf88 OS=Homo sapiens OX=9606 GN=C8orf88 PE=4 SV=1
rev_sp|P49642|PRI1_HUMAN DNA primase small subunit OS=Homo sapiens OX=9606 GN=PRIM1 PE=1 SV=1
rev_sp|Q14142|TRI14_HUMAN Tripartite motif-containing protein 14 OS=Homo sapiens OX=9606 GN=TRIM14 PE=1 SV=2
rev_sp|Q68DH5|LMBD2_HUMAN G-protein coupled receptor-associated protein LMBRD2 OS=Homo sapiens OX=9606 GN=LMBRD2 PE=1 SV=1
rev_sp|Q8IWB6|TEX14_HUMAN Inactive serine/threonine-protein kinase TEX14 OS=Homo sapiens OX=9606 GN=TEX14 PE=1 SV=2
rev_sp|Q8WVI0|UQCC5_HUMAN Ubiquinol-cytochrome c reductase complex assembly factor 5 OS=Homo sapiens OX=9606 GN=UQCC5 PE=1 SV=2
rev_sp|Q9BRB3|PIGQ_HUMAN Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q OS=Homo sapiens OX=9606 GN=PIGQ PE=1 SV=3
rev_sp|Q9NUP1|BL1S4_HUMAN Biogenesis of lysosome-related organelles complex 1 subunit 4 OS=Homo sapiens OX=9606 GN=BLOC1S4 PE=1 SV=1
rev_sp|Q9Y6M9|NDUB9_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 OS=Homo sapiens OX=9606 GN=NDUFB9 PE=1 SV=3
sp|O43614|OX2R_HUMAN Orexin receptor type 2 OS=Homo sapiens OX=9606 GN=HCRTR2 PE=1 SV=2
sp|P0DN86|CGB3_HUMAN Choriogonadotropin subunit beta 3 OS=Homo sapiens OX=9606 GN=CGB3 PE=1 SV=1
sp|P49796|RGS3_HUMAN Regulator of G-protein signaling 3 OS=Homo sapiens OX=9606 GN=RGS3 PE=1 SV=2
sp|Q14213|IL27B_HUMAN Interleukin-27 subunit beta OS=Homo sapiens OX=9606 GN=EBI3 PE=1 SV=2
sp|Q6AI12|ANR40_HUMAN Ankyrin repeat domain-containing protein 40 OS=Homo sapiens OX=9606 GN=ANKRD40 PE=1 SV=2
sp|Q8IWV8|UBR2_HUMAN E3 ubiquitin-protein ligase UBR2 OS=Homo sapiens OX=9606 GN=UBR2 PE=1 SV=1
sp|Q8WW43|APH1B_HUMAN Gamma-secretase subunit APH-1B OS=Homo sapiens OX=9606 GN=APH1B PE=1 SV=3
sp|Q9BRT6|LLPH_HUMAN Protein LLP homolog OS=Homo sapiens OX=9606 GN=LLPH PE=1 SV=1
sp|Q9NVC3|S38A7_HUMAN Sodium-coupled neutral amino acid transporter 7 OS=Homo sapiens OX=9606 GN=SLC38A7 PE=1 SV=1
sp|Q9Y6Y0|NS1BP_HUMAN Influenza virus NS1A-binding protein OS=Homo sapiens OX=9606 GN=IVNS1ABP PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache
# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Users\\achojna1\\2024-06-06-decoys-reviewed-contam-UP000005640.fas
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=false
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=true
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=2
diaumpire.SE.MassDefectFilter=false
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=2
diaumpire.run-diaumpire=true
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\achojna1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=
fragpipe-config.bin-msfragger=
fragpipe-config.bin-philosopher=
fragpipe-config.bin-python=C\:\\Users\\achojna1\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\Users\\achojna1\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=2
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=50
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=HCD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=2
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=false
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
ptmshepherd.run-shepherd=true
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=1
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=true
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=true
speclibgen.convert-psm=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-0
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=C\:\\Users\\achojna1\\Documents\\results32w
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=23
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx19G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML 23
Done in 1,7 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="16:21:53" level=info msg="Executing Workspace v5.1.1"
time="16:21:53" level=info msg="Removing workspace"
time="16:21:53" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\results32w]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\d446c87c-d5a6-458e-9912-f3ae5845602b
time="16:21:53" level=info msg="Executing Workspace v5.1.1"
time="16:21:53" level=info msg="Creating workspace"
time="16:21:53" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
java -Xmx19G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML C:\Users\achojna1\Documents\results32w\umpire-se.params
=================================================================================================
DIA-Umpire signal extraction analysis (version: v2.3.2)
(c) University of Michigan
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-07-04 16:21:54,043 INFO [main] Version: v2.3.2
2024-07-04 16:21:54,043 INFO [main] Parameter file:C:\Users\achojna1\Documents\results32w\umpire-se.params
2024-07-04 16:21:54,043 INFO [main] Spectra file:C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] ####################################################################################################
2024-07-04 16:21:54,043 INFO [main] #No of threads
2024-07-04 16:21:54,043 INFO [main] Thread = 23
2024-07-04 16:21:54,043 INFO [main] ####################################################################################################
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] ## omit Thread
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] #Precursor-fragments grouping parameters
2024-07-04 16:21:54,043 INFO [main] RPmax = 25
2024-07-04 16:21:54,043 INFO [main] RFmax = 500
2024-07-04 16:21:54,043 INFO [main] CorrThreshold = 0
2024-07-04 16:21:54,043 INFO [main] DeltaApex = 0.2
2024-07-04 16:21:54,043 INFO [main] RTOverlap = 0.3
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] #Fragment intensity adjustments
2024-07-04 16:21:54,043 INFO [main] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2024-07-04 16:21:54,043 INFO [main] AdjustFragIntensity = true
2024-07-04 16:21:54,043 INFO [main] BoostComplementaryIon = false
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2024-07-04 16:21:54,043 INFO [main] ExportPrecursorPeak = false
2024-07-04 16:21:54,043 INFO [main]
2024-07-04 16:21:54,043 INFO [main] Q1 = true
2024-07-04 16:21:54,059 INFO [main] Q2 = true
2024-07-04 16:21:54,059 INFO [main] Q3 = true
2024-07-04 16:21:54,059 INFO [main]
2024-07-04 16:21:54,059 INFO [main] #Signal extraction: mass accuracy and resolution
2024-07-04 16:21:54,059 INFO [main] # resolution parameter matters only for data generated in profile mode
2024-07-04 16:21:54,059 INFO [main] SE.MS1PPM = 10
2024-07-04 16:21:54,059 INFO [main] SE.MS2PPM = 20
2024-07-04 16:21:54,059 INFO [main] SE.Resolution = 60000
2024-07-04 16:21:54,059 INFO [main]
2024-07-04 16:21:54,059 INFO [main] #Signal extraction: signal to noise filter
2024-07-04 16:21:54,059 INFO [main] SE.SN = 2
2024-07-04 16:21:54,059 INFO [main] SE.MS2SN = 2
2024-07-04 16:21:54,059 INFO [main]
2024-07-04 16:21:54,059 INFO [main] #Signal extraction: minimum signal intensity filter
2024-07-04 16:21:54,059 INFO [main] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2024-07-04 16:21:54,059 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2024-07-04 16:21:54,059 INFO [main] SE.EstimateBG = true
2024-07-04 16:21:54,059 INFO [main] SE.MinMSIntensity = 1
2024-07-04 16:21:54,059 INFO [main] SE.MinMSMSIntensity = 1
2024-07-04 16:21:54,059 INFO [main]
2024-07-04 16:21:54,059 INFO [main] #Signal extraction: peak curve detection and isotope grouping
2024-07-04 16:21:54,059 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2024-07-04 16:21:54,059 INFO [main] SE.NoMissedScan = 1
2024-07-04 16:21:54,059 INFO [main] SE.MaxCurveRTRange = 2
2024-07-04 16:21:54,059 INFO [main] SE.RemoveGroupedPeaks = true
2024-07-04 16:21:54,059 INFO [main] SE.RemoveGroupedPeaksRTOverlap = 0.3
2024-07-04 16:21:54,059 INFO [main] SE.RemoveGroupedPeaksCorr = 0.3
2024-07-04 16:21:54,059 INFO [main] SE.MinNoPeakCluster = 2
2024-07-04 16:21:54,059 INFO [main] SE.MaxNoPeakCluster = 4
2024-07-04 16:21:54,059 INFO [main]
2024-07-04 16:21:54,059 INFO [main] #Signal extraction: filtering of MS1 features
2024-07-04 16:21:54,196 INFO [main] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2024-07-04 16:21:54,196 INFO [main] SE.IsoPattern = 0.3
2024-07-04 16:21:54,196 INFO [main] SE.MassDefectFilter = false
2024-07-04 16:21:54,196 INFO [main] SE.MassDefectOffset = 0.1
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main] #Signal extraction: other
2024-07-04 16:21:54,196 INFO [main] SE.StartCharge = 1
2024-07-04 16:21:54,196 INFO [main] SE.EndCharge = 5
2024-07-04 16:21:54,196 INFO [main] SE.MS2StartCharge = 2
2024-07-04 16:21:54,196 INFO [main] SE.MS2EndCharge = 5
2024-07-04 16:21:54,196 INFO [main] SE.MinFrag = 10
2024-07-04 16:21:54,196 INFO [main] SE.StartRT = 0
2024-07-04 16:21:54,196 INFO [main] SE.EndRT = 9999
2024-07-04 16:21:54,196 INFO [main] SE.MinMZ = 200
2024-07-04 16:21:54,196 INFO [main] SE.MinPrecursorMass = 600
2024-07-04 16:21:54,196 INFO [main] SE.MaxPrecursorMass = 5000
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main] #Isolation window setting
2024-07-04 16:21:54,196 INFO [main] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2024-07-04 16:21:54,196 INFO [main] WindowType = SWATH
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main] #Fix window size (For SWATH)
2024-07-04 16:21:54,196 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-04 16:21:54,196 INFO [main] WindowSize = 10
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2024-07-04 16:21:54,196 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-04 16:21:54,196 INFO [main] ==window setting begin
2024-07-04 16:21:54,196 INFO [main]
2024-07-04 16:21:54,196 INFO [main] =================================================================================================
2024-07-04 16:21:54,196 INFO [main] Processing C:\Users\achojna1\Documents\sciex\04july24\h16w32w.mzML....
2024-07-04 16:21:54,196 INFO [main] Writing DIA setting to file:C:\Users\achojna1\Documents\sciex\04july24\h16w32w_diasetting.ser...
2024-07-04 16:21:54,196 INFO [main] Writing parameter to file:C:\Users\achojna1\Documents\sciex\04july24\h16w32w_params.ser...
2024-07-04 16:21:54,196 INFO [main] Module A: Signal extraction
2024-07-04 16:22:02,554 INFO [main] Writing DIA setting to file:C:\Users\achojna1\Documents\sciex\04july24\h16w32w_diasetting.ser...
2024-07-04 16:22:02,664 INFO [main] Processing MS1 peak detection
2024-07-04 16:22:02,664 INFO [main] MS1 average cycle time : 3.3399596 seconds
2024-07-04 16:22:05,613 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:05,613 INFO [main] Smoothing detected signals......
2024-07-04 16:22:06,556 INFO [main] 366086 Peak curves found (Memory usage:361MB)
2024-07-04 16:22:06,556 INFO [main] Inclusion mz values found: 0/0
2024-07-04 16:22:06,556 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:06,556 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:07,742 INFO [main] No of ion clusters:15839 (Memory usage:214MB)
2024-07-04 16:22:07,742 INFO [main] Writing PeakCluster serialization to file:h16w32w_PeakCluster.serFS...
2024-07-04 16:22:07,843 INFO [main] ==================================================================================
2024-07-04 16:22:07,843 INFO [main] Processing DIA MS2 (mz range):1174.0_1200.0( 1/32 )
2024-07-04 16:22:07,962 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:07,962 INFO [main] Smoothing detected signals......
2024-07-04 16:22:08,375 INFO [main] 144914 Peak curves found (Memory usage:299MB)
2024-07-04 16:22:08,375 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:08,375 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:08,544 INFO [main] No of ion clusters:0 (Memory usage:311MB)
2024-07-04 16:22:08,544 INFO [main] Writing PeakCluster serialization to file:h16w32w_1174_1200_PeakCluster.serFS...
2024-07-04 16:22:08,544 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:08,685 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:08,762 INFO [main] ==================================================================================
2024-07-04 16:22:08,762 INFO [main] Processing DIA MS2 (mz range):1149.0_1175.0( 2/32 )
2024-07-04 16:22:08,870 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:08,870 INFO [main] Smoothing detected signals......
2024-07-04 16:22:09,245 INFO [main] 148675 Peak curves found (Memory usage:290MB)
2024-07-04 16:22:09,245 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:09,261 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:09,423 INFO [main] No of ion clusters:0 (Memory usage:302MB)
2024-07-04 16:22:09,423 INFO [main] Writing PeakCluster serialization to file:h16w32w_1149_1175_PeakCluster.serFS...
2024-07-04 16:22:09,423 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:09,550 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:09,605 INFO [main] ==================================================================================
2024-07-04 16:22:09,605 INFO [main] Processing DIA MS2 (mz range):1124.0_1150.0( 3/32 )
2024-07-04 16:22:09,713 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:09,713 INFO [main] Smoothing detected signals......
2024-07-04 16:22:10,059 INFO [main] 148340 Peak curves found (Memory usage:290MB)
2024-07-04 16:22:10,059 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:10,059 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:10,260 INFO [main] No of ion clusters:0 (Memory usage:302MB)
2024-07-04 16:22:10,260 INFO [main] Writing PeakCluster serialization to file:h16w32w_1124_1150_PeakCluster.serFS...
2024-07-04 16:22:10,260 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:10,345 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:10,398 INFO [main] ==================================================================================
2024-07-04 16:22:10,398 INFO [main] Processing DIA MS2 (mz range):1099.0_1125.0( 4/32 )
2024-07-04 16:22:10,500 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:10,500 INFO [main] Smoothing detected signals......
2024-07-04 16:22:10,846 INFO [main] 139644 Peak curves found (Memory usage:285MB)
2024-07-04 16:22:10,861 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:10,861 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:11,015 INFO [main] No of ion clusters:0 (Memory usage:297MB)
2024-07-04 16:22:11,015 INFO [main] Writing PeakCluster serialization to file:h16w32w_1099_1125_PeakCluster.serFS...
2024-07-04 16:22:11,015 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:11,099 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:11,147 INFO [main] ==================================================================================
2024-07-04 16:22:11,147 INFO [main] Processing DIA MS2 (mz range):1074.0_1100.0( 5/32 )
2024-07-04 16:22:11,244 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:11,244 INFO [main] Smoothing detected signals......
2024-07-04 16:22:11,581 INFO [main] 134878 Peak curves found (Memory usage:283MB)
2024-07-04 16:22:11,581 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:11,581 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:11,765 INFO [main] No of ion clusters:0 (Memory usage:294MB)
2024-07-04 16:22:11,765 INFO [main] Writing PeakCluster serialization to file:h16w32w_1074_1100_PeakCluster.serFS...
2024-07-04 16:22:11,765 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:11,862 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:11,932 INFO [main] ==================================================================================
2024-07-04 16:22:11,932 INFO [main] Processing DIA MS2 (mz range):1049.0_1075.0( 6/32 )
2024-07-04 16:22:12,000 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:12,000 INFO [main] Smoothing detected signals......
2024-07-04 16:22:12,332 INFO [main] 127848 Peak curves found (Memory usage:279MB)
2024-07-04 16:22:12,332 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:12,332 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:12,495 INFO [main] No of ion clusters:0 (Memory usage:289MB)
2024-07-04 16:22:12,495 INFO [main] Writing PeakCluster serialization to file:h16w32w_1049_1075_PeakCluster.serFS...
2024-07-04 16:22:12,501 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:12,570 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:12,641 INFO [main] ==================================================================================
2024-07-04 16:22:12,641 INFO [main] Processing DIA MS2 (mz range):1024.0_1050.0( 7/32 )
2024-07-04 16:22:12,715 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:12,715 INFO [main] Smoothing detected signals......
2024-07-04 16:22:13,048 INFO [main] 119308 Peak curves found (Memory usage:275MB)
2024-07-04 16:22:13,048 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:13,048 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:13,187 INFO [main] No of ion clusters:0 (Memory usage:284MB)
2024-07-04 16:22:13,187 INFO [main] Writing PeakCluster serialization to file:h16w32w_1024_1050_PeakCluster.serFS...
2024-07-04 16:22:13,187 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:13,283 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:13,349 INFO [main] ==================================================================================
2024-07-04 16:22:13,349 INFO [main] Processing DIA MS2 (mz range):999.0_1025.0( 8/32 )
2024-07-04 16:22:13,410 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:13,410 INFO [main] Smoothing detected signals......
2024-07-04 16:22:13,666 INFO [main] 103314 Peak curves found (Memory usage:267MB)
2024-07-04 16:22:13,666 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:13,666 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:13,803 INFO [main] No of ion clusters:0 (Memory usage:275MB)
2024-07-04 16:22:13,803 INFO [main] Writing PeakCluster serialization to file:h16w32w_999_1025_PeakCluster.serFS...
2024-07-04 16:22:13,803 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:13,851 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:13,919 INFO [main] ==================================================================================
2024-07-04 16:22:13,919 INFO [main] Processing DIA MS2 (mz range):974.0_1000.0( 9/32 )
2024-07-04 16:22:13,970 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:13,970 INFO [main] Smoothing detected signals......
2024-07-04 16:22:14,220 INFO [main] 85753 Peak curves found (Memory usage:258MB)
2024-07-04 16:22:14,220 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:14,220 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:14,351 INFO [main] No of ion clusters:0 (Memory usage:265MB)
2024-07-04 16:22:14,351 INFO [main] Writing PeakCluster serialization to file:h16w32w_974_1000_PeakCluster.serFS...
2024-07-04 16:22:14,351 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:14,404 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:14,451 INFO [main] ==================================================================================
2024-07-04 16:22:14,451 INFO [main] Processing DIA MS2 (mz range):949.0_975.0( 10/32 )
2024-07-04 16:22:14,563 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:14,563 INFO [main] Smoothing detected signals......
2024-07-04 16:22:14,720 INFO [main] 1580 Peak curves found (Memory usage:224MB)
2024-07-04 16:22:14,720 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:14,720 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:14,798 INFO [main] No of ion clusters:0 (Memory usage:224MB)
2024-07-04 16:22:14,798 INFO [main] Writing PeakCluster serialization to file:h16w32w_949_975_PeakCluster.serFS...
2024-07-04 16:22:14,805 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:14,805 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:14,852 INFO [main] ==================================================================================
2024-07-04 16:22:14,852 INFO [main] Processing DIA MS2 (mz range):924.0_950.0( 11/32 )
2024-07-04 16:22:14,913 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:14,913 INFO [main] Smoothing detected signals......
2024-07-04 16:22:15,221 INFO [main] 98466 Peak curves found (Memory usage:261MB)
2024-07-04 16:22:15,221 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:15,221 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:15,352 INFO [main] No of ion clusters:0 (Memory usage:268MB)
2024-07-04 16:22:15,352 INFO [main] Writing PeakCluster serialization to file:h16w32w_924_950_PeakCluster.serFS...
2024-07-04 16:22:15,352 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:15,421 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:15,468 INFO [main] ==================================================================================
2024-07-04 16:22:15,468 INFO [main] Processing DIA MS2 (mz range):899.0_925.0( 12/32 )
2024-07-04 16:22:15,539 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:15,539 INFO [main] Smoothing detected signals......
2024-07-04 16:22:15,769 INFO [main] 106315 Peak curves found (Memory usage:265MB)
2024-07-04 16:22:15,769 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:15,769 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:15,907 INFO [main] No of ion clusters:0 (Memory usage:273MB)
2024-07-04 16:22:15,907 INFO [main] Writing PeakCluster serialization to file:h16w32w_899_925_PeakCluster.serFS...
2024-07-04 16:22:15,907 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:15,988 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:16,054 INFO [main] ==================================================================================
2024-07-04 16:22:16,054 INFO [main] Processing DIA MS2 (mz range):874.0_900.0( 13/32 )
2024-07-04 16:22:16,115 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:16,115 INFO [main] Smoothing detected signals......
2024-07-04 16:22:16,323 INFO [main] 105207 Peak curves found (Memory usage:265MB)
2024-07-04 16:22:16,323 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:16,323 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:16,454 INFO [main] No of ion clusters:1 (Memory usage:273MB)
2024-07-04 16:22:16,454 INFO [main] Writing PeakCluster serialization to file:h16w32w_874_900_PeakCluster.serFS...
2024-07-04 16:22:16,454 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:16,536 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:16,608 INFO [main] ==================================================================================
2024-07-04 16:22:16,608 INFO [main] Processing DIA MS2 (mz range):849.0_875.0( 14/32 )
2024-07-04 16:22:16,670 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:16,670 INFO [main] Smoothing detected signals......
2024-07-04 16:22:16,909 INFO [main] 110802 Peak curves found (Memory usage:268MB)
2024-07-04 16:22:16,909 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:16,909 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:17,041 INFO [main] No of ion clusters:0 (Memory usage:276MB)
2024-07-04 16:22:17,041 INFO [main] Writing PeakCluster serialization to file:h16w32w_849_875_PeakCluster.serFS...
2024-07-04 16:22:17,041 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:17,133 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:17,210 INFO [main] ==================================================================================
2024-07-04 16:22:17,210 INFO [main] Processing DIA MS2 (mz range):824.0_850.0( 15/32 )
2024-07-04 16:22:17,276 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:17,276 INFO [main] Smoothing detected signals......
2024-07-04 16:22:17,581 INFO [main] 115564 Peak curves found (Memory usage:272MB)
2024-07-04 16:22:17,597 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:17,597 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:17,711 INFO [main] No of ion clusters:1 (Memory usage:280MB)
2024-07-04 16:22:17,711 INFO [main] Writing PeakCluster serialization to file:h16w32w_824_850_PeakCluster.serFS...
2024-07-04 16:22:17,726 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:17,811 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:17,893 INFO [main] ==================================================================================
2024-07-04 16:22:17,893 INFO [main] Processing DIA MS2 (mz range):799.0_825.0( 16/32 )
2024-07-04 16:22:17,971 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:17,971 INFO [main] Smoothing detected signals......
2024-07-04 16:22:18,285 INFO [main] 118623 Peak curves found (Memory usage:274MB)
2024-07-04 16:22:18,285 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:18,285 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:18,427 INFO [main] No of ion clusters:1 (Memory usage:282MB)
2024-07-04 16:22:18,427 INFO [main] Writing PeakCluster serialization to file:h16w32w_799_825_PeakCluster.serFS...
2024-07-04 16:22:18,427 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:18,545 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:18,612 INFO [main] ==================================================================================
2024-07-04 16:22:18,612 INFO [main] Processing DIA MS2 (mz range):774.0_800.0( 17/32 )
2024-07-04 16:22:18,692 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:18,692 INFO [main] Smoothing detected signals......
2024-07-04 16:22:19,041 INFO [main] 117070 Peak curves found (Memory usage:274MB)
2024-07-04 16:22:19,041 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:19,041 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:19,185 INFO [main] No of ion clusters:1 (Memory usage:283MB)
2024-07-04 16:22:19,185 INFO [main] Writing PeakCluster serialization to file:h16w32w_774_800_PeakCluster.serFS...
2024-07-04 16:22:19,185 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:19,313 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:19,376 INFO [main] ==================================================================================
2024-07-04 16:22:19,376 INFO [main] Processing DIA MS2 (mz range):749.0_775.0( 18/32 )
2024-07-04 16:22:19,460 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:19,460 INFO [main] Smoothing detected signals......
2024-07-04 16:22:19,788 INFO [main] 114648 Peak curves found (Memory usage:272MB)
2024-07-04 16:22:19,788 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:19,788 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:19,920 INFO [main] No of ion clusters:1 (Memory usage:281MB)
2024-07-04 16:22:19,936 INFO [main] Writing PeakCluster serialization to file:h16w32w_749_775_PeakCluster.serFS...
2024-07-04 16:22:19,936 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:20,052 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:20,141 INFO [main] ==================================================================================
2024-07-04 16:22:20,143 INFO [main] Processing DIA MS2 (mz range):724.0_750.0( 19/32 )
2024-07-04 16:22:20,216 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:20,217 INFO [main] Smoothing detected signals......
2024-07-04 16:22:20,596 INFO [main] 120904 Peak curves found (Memory usage:276MB)
2024-07-04 16:22:20,596 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:20,596 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:20,750 INFO [main] No of ion clusters:3 (Memory usage:285MB)
2024-07-04 16:22:20,750 INFO [main] Writing PeakCluster serialization to file:h16w32w_724_750_PeakCluster.serFS...
2024-07-04 16:22:20,750 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:20,887 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:20,997 INFO [main] ==================================================================================
2024-07-04 16:22:20,997 INFO [main] Processing DIA MS2 (mz range):699.0_725.0( 20/32 )
2024-07-04 16:22:21,065 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:21,065 INFO [main] Smoothing detected signals......
2024-07-04 16:22:21,450 INFO [main] 123464 Peak curves found (Memory usage:278MB)
2024-07-04 16:22:21,450 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:21,450 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:21,597 INFO [main] No of ion clusters:3 (Memory usage:287MB)
2024-07-04 16:22:21,597 INFO [main] Writing PeakCluster serialization to file:h16w32w_699_725_PeakCluster.serFS...
2024-07-04 16:22:21,597 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:21,735 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:21,847 INFO [main] ==================================================================================
2024-07-04 16:22:21,847 INFO [main] Processing DIA MS2 (mz range):674.0_700.0( 21/32 )
2024-07-04 16:22:21,931 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:21,931 INFO [main] Smoothing detected signals......
2024-07-04 16:22:22,287 INFO [main] 122354 Peak curves found (Memory usage:278MB)
2024-07-04 16:22:22,287 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:22,287 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:22,455 INFO [main] No of ion clusters:1 (Memory usage:287MB)
2024-07-04 16:22:22,455 INFO [main] Writing PeakCluster serialization to file:h16w32w_674_700_PeakCluster.serFS...
2024-07-04 16:22:22,455 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:22,595 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:22,684 INFO [main] ==================================================================================
2024-07-04 16:22:22,684 INFO [main] Processing DIA MS2 (mz range):649.0_675.0( 22/32 )
2024-07-04 16:22:22,766 INFO [main] Processing all scans to detect possible m/z peak curves and
2024-07-04 16:22:22,766 INFO [main] Smoothing detected signals......
2024-07-04 16:22:23,166 INFO [main] 130384 Peak curves found (Memory usage:283MB)
2024-07-04 16:22:23,166 INFO [main] Grouping isotopic peak curves........
2024-07-04 16:22:23,166 INFO [main] Building PeakCurve Mass-RT KD tree
2024-07-04 16:22:23,309 INFO [main] No of ion clusters:3 (Memory usage:293MB)
2024-07-04 16:22:23,309 INFO [main] Writing PeakCluster serialization to file:h16w32w_649_675_PeakCluster.serFS...
2024-07-04 16:22:23,325 INFO [main] Building precursor-fragment pairs for MS1 features....
2024-07-04 16:22:23,496 INFO [main] Building precursor-fragment pairs for unfragmented ions....
2024-07-04 16:22:23,612 INFO [main] ==============
Ale-ksa-ndra commented
Hello,
I can not get into processing if timstof data, ale not have understanding what goes wrong here.
Please have a look into the log file.
Kind regards,
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.11, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A
Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1
LCMS files:
Experiment/Group:
(if "spectral library generation" is enabled, all files will be analyzed together)
- C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d DIA
61 commands to execute:
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\c75befb7-3e68-49e5-b9cc-4877e028f970
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\diaumpire_se.log C:\Users\achojna1\Documents\brukerReasults1\diaumpire_se.log
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Peak C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.RTidxFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanidxFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanPosFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanRTFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
MSFragger [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\Users\achojna1\Documents\brukerReasults1\fragger_dda.params C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
MSBooster [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -Xmx15G -cp C:\Users\achojna1\fragpipe\tools\MSBooster-1.2.31.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\Users\achojna1\Documents\brukerReasults1\msbooster_params.txt
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q3_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q1_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q2_edited.pin
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q3.pin 060_30SPD_DIA_S1-D4_1_753_Q3 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q3 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q1.pin 060_30SPD_DIA_S1-D4_1_753_Q1 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q1 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q2.pin 060_30SPD_DIA_S1-D4_1_753_Q2 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q2 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\achojna1\Documents\brukerReasults1\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --tag rev_ --pepxml C:\Users\achojna1\Documents\brukerReasults1 --protxml C:\Users\achojna1\Documents\brukerReasults1\combined.prot.xml --razor
PhilosopherReport [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PTMShepherd [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\ptmshepherd-3.0.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\tools\commons-math3-3.6.1.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar;C:\Users\achojna1\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\achojna1\Documents\brukerReasults1\shepherd.config"
WorkspaceClean [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
SpecLibGen [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\AppData\Local\Programs\Python\Python39\python -u C:\Users\achojna1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas C:\Users\achojna1\Documents\brukerReasults1 unused C:\Users\achojna1\Documents\brukerReasults1 True unused use_easypqp ciRT;noIM 23 "--unimod C:/Users/achojna1/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] --decoy_prefix rev_" "--rt_lowess_fraction 0.0" delete_intermediate_files C:\Users\achojna1\Documents\brukerReasults1\filelist_speclibgen.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 23 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg C:\Users\achojna1\Documents\brukerReasults1\filelist_diann.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate information [Work dir: C:\Users\achojna1\Documents\brukerReasults1\diann-output]
java -cp C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation C:\Users\achojna1\Documents\brukerReasults1
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: C:\Users\achojna1\Documents\brukerReasults1\diann-output]
java -cp C:\Users\achojna1\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ C:\Users\achojna1\Documents\brukerReasults1\psm.tsv 0.01 1 0.01 0.01 C:\Users\achojna1\Documents\brukerReasults1\fragpipe-files.fp-manifest
~~~~~~~~~~~~~~~~~~~~~~
Execution order:
Cmd: [START], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [UmpireSe], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [diaTracer], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [MSBooster], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [Percolator], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [ProteinProphet], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PTMShepherd], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [SpecLibGen], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [DIA-NN], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~Sample of C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas~~~~~~~
contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
rev_sp|O43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1
rev_sp|P0DMB2|CH088_HUMAN Uncharacterized protein C8orf88 OS=Homo sapiens OX=9606 GN=C8orf88 PE=4 SV=1
rev_sp|P49642|PRI1_HUMAN DNA primase small subunit OS=Homo sapiens OX=9606 GN=PRIM1 PE=1 SV=1
rev_sp|Q14142|TRI14_HUMAN Tripartite motif-containing protein 14 OS=Homo sapiens OX=9606 GN=TRIM14 PE=1 SV=2
rev_sp|Q68DH5|LMBD2_HUMAN G-protein coupled receptor-associated protein LMBRD2 OS=Homo sapiens OX=9606 GN=LMBRD2 PE=1 SV=1
rev_sp|Q8IWB6|TEX14_HUMAN Inactive serine/threonine-protein kinase TEX14 OS=Homo sapiens OX=9606 GN=TEX14 PE=1 SV=2
rev_sp|Q8WVI0|UQCC5_HUMAN Ubiquinol-cytochrome c reductase complex assembly factor 5 OS=Homo sapiens OX=9606 GN=UQCC5 PE=1 SV=2
rev_sp|Q9BRB3|PIGQ_HUMAN Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q OS=Homo sapiens OX=9606 GN=PIGQ PE=1 SV=3
rev_sp|Q9NUP1|BL1S4_HUMAN Biogenesis of lysosome-related organelles complex 1 subunit 4 OS=Homo sapiens OX=9606 GN=BLOC1S4 PE=1 SV=1
rev_sp|Q9Y6M9|NDUB9_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 OS=Homo sapiens OX=9606 GN=NDUFB9 PE=1 SV=3
sp|O43614|OX2R_HUMAN Orexin receptor type 2 OS=Homo sapiens OX=9606 GN=HCRTR2 PE=1 SV=2
sp|P0DN86|CGB3_HUMAN Choriogonadotropin subunit beta 3 OS=Homo sapiens OX=9606 GN=CGB3 PE=1 SV=1
sp|P49796|RGS3_HUMAN Regulator of G-protein signaling 3 OS=Homo sapiens OX=9606 GN=RGS3 PE=1 SV=2
sp|Q14213|IL27B_HUMAN Interleukin-27 subunit beta OS=Homo sapiens OX=9606 GN=EBI3 PE=1 SV=2
sp|Q6AI12|ANR40_HUMAN Ankyrin repeat domain-containing protein 40 OS=Homo sapiens OX=9606 GN=ANKRD40 PE=1 SV=2
sp|Q8IWV8|UBR2_HUMAN E3 ubiquitin-protein ligase UBR2 OS=Homo sapiens OX=9606 GN=UBR2 PE=1 SV=1
sp|Q8WW43|APH1B_HUMAN Gamma-secretase subunit APH-1B OS=Homo sapiens OX=9606 GN=APH1B PE=1 SV=3
sp|Q9BRT6|LLPH_HUMAN Protein LLP homolog OS=Homo sapiens OX=9606 GN=LLPH PE=1 SV=1
sp|Q9NVC3|S38A7_HUMAN Sodium-coupled neutral amino acid transporter 7 OS=Homo sapiens OX=9606 GN=SLC38A7 PE=1 SV=1
sp|Q9Y6Y0|NS1BP_HUMAN Influenza virus NS1A-binding protein OS=Homo sapiens OX=9606 GN=IVNS1ABP PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache
# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Users\\achojna1\\2024-06-06-decoys-reviewed-contam-UP000005640.fas
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=true
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=true
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\achojna1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=
fragpipe-config.bin-msfragger=
fragpipe-config.bin-philosopher=
fragpipe-config.bin-python=C\:\\Users\\achojna1\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\Users\\achojna1\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=2
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=50
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=HCD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=2
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=false
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
ptmshepherd.run-shepherd=true
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=1
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=true
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=false
speclibgen.convert-psm=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-0
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=C\:\\Users\\achojna1\\Documents\\brukerReasults1
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=23
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="11:26:42" level=info msg="Executing Workspace v5.1.1"
time="11:26:42" level=info msg="Removing workspace"
time="11:26:42" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\c75befb7-3e68-49e5-b9cc-4877e028f970
time="11:26:42" level=info msg="Executing Workspace v5.1.1"
time="11:26:42" level=info msg="Creating workspace"
time="11:26:42" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
=================================================================================================
DIA-Umpire signal extraction analysis (version: v2.3.2)
(c) University of Michigan
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-07-17 11:26:43,596 INFO [main] Version: v2.3.2
2024-07-17 11:26:43,596 INFO [main] Parameter file:C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
2024-07-17 11:26:43,596 INFO [main] Spectra file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] ####################################################################################################
2024-07-17 11:26:43,596 INFO [main] #No of threads
2024-07-17 11:26:43,596 INFO [main] Thread = 23
2024-07-17 11:26:43,596 INFO [main] ####################################################################################################
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] ## omit Thread
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Precursor-fragments grouping parameters
2024-07-17 11:26:43,596 INFO [main] RPmax = 25
2024-07-17 11:26:43,596 INFO [main] RFmax = 500
2024-07-17 11:26:43,596 INFO [main] CorrThreshold = 0
2024-07-17 11:26:43,596 INFO [main] DeltaApex = 0.2
2024-07-17 11:26:43,596 INFO [main] RTOverlap = 0.3
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Fragment intensity adjustments
2024-07-17 11:26:43,596 INFO [main] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2024-07-17 11:26:43,596 INFO [main] AdjustFragIntensity = true
2024-07-17 11:26:43,596 INFO [main] BoostComplementaryIon = false
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2024-07-17 11:26:43,596 INFO [main] ExportPrecursorPeak = false
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] Q1 = true
2024-07-17 11:26:43,596 INFO [main] Q2 = true
2024-07-17 11:26:43,596 INFO [main] Q3 = true
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Signal extraction: mass accuracy and resolution
2024-07-17 11:26:43,596 INFO [main] # resolution parameter matters only for data generated in profile mode
2024-07-17 11:26:43,596 INFO [main] SE.MS1PPM = 10
2024-07-17 11:26:43,596 INFO [main] SE.MS2PPM = 20
2024-07-17 11:26:43,596 INFO [main] SE.Resolution = 60000
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Signal extraction: signal to noise filter
2024-07-17 11:26:43,596 INFO [main] SE.SN = 1.1
2024-07-17 11:26:43,596 INFO [main] SE.MS2SN = 1.1
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Signal extraction: minimum signal intensity filter
2024-07-17 11:26:43,596 INFO [main] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2024-07-17 11:26:43,596 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2024-07-17 11:26:43,596 INFO [main] SE.EstimateBG = false
2024-07-17 11:26:43,596 INFO [main] SE.MinMSIntensity = 1
2024-07-17 11:26:43,596 INFO [main] SE.MinMSMSIntensity = 1
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Signal extraction: peak curve detection and isotope grouping
2024-07-17 11:26:43,596 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2024-07-17 11:26:43,596 INFO [main] SE.NoMissedScan = 1
2024-07-17 11:26:43,596 INFO [main] SE.MaxCurveRTRange = 2
2024-07-17 11:26:43,596 INFO [main] SE.RemoveGroupedPeaks = true
2024-07-17 11:26:43,596 INFO [main] SE.RemoveGroupedPeaksRTOverlap = 0.3
2024-07-17 11:26:43,596 INFO [main] SE.RemoveGroupedPeaksCorr = 0.3
2024-07-17 11:26:43,596 INFO [main] SE.MinNoPeakCluster = 2
2024-07-17 11:26:43,596 INFO [main] SE.MaxNoPeakCluster = 4
2024-07-17 11:26:43,596 INFO [main]
2024-07-17 11:26:43,596 INFO [main] #Signal extraction: filtering of MS1 features
Exception in thread "main" java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
2024-07-17 11:26:43,735 INFO [main] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2024-07-17 11:26:43,735 INFO [main] SE.IsoPattern = 0.3
2024-07-17 11:26:43,735 INFO [main] SE.MassDefectFilter = true
2024-07-17 11:26:43,735 INFO [main] SE.MassDefectOffset = 0.1
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main] #Signal extraction: other
2024-07-17 11:26:43,735 INFO [main] SE.StartCharge = 1
2024-07-17 11:26:43,735 INFO [main] SE.EndCharge = 5
2024-07-17 11:26:43,735 INFO [main] SE.MS2StartCharge = 2
2024-07-17 11:26:43,735 INFO [main] SE.MS2EndCharge = 5
2024-07-17 11:26:43,735 INFO [main] SE.MinFrag = 10
2024-07-17 11:26:43,735 INFO [main] SE.StartRT = 0
2024-07-17 11:26:43,735 INFO [main] SE.EndRT = 9999
2024-07-17 11:26:43,735 INFO [main] SE.MinMZ = 200
2024-07-17 11:26:43,735 INFO [main] SE.MinPrecursorMass = 600
2024-07-17 11:26:43,735 INFO [main] SE.MaxPrecursorMass = 5000
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main] #Isolation window setting
2024-07-17 11:26:43,735 INFO [main] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2024-07-17 11:26:43,735 INFO [main] WindowType = SWATH
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main] #Fix window size (For SWATH)
2024-07-17 11:26:43,735 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-17 11:26:43,735 INFO [main] WindowSize = 10
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2024-07-17 11:26:43,735 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-17 11:26:43,735 INFO [main] ==window setting begin
2024-07-17 11:26:43,735 INFO [main]
2024-07-17 11:26:43,735 INFO [main] =================================================================================================
2024-07-17 11:26:43,735 INFO [main] Processing C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d....
2024-07-17 11:26:43,735 INFO [main] Writing DIA setting to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser...
2024-07-17 11:26:43,735 INFO [main] Writing parameter to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser...
2024-07-17 11:26:43,735 INFO [main] Module A: Signal extraction
2024-07-17 11:26:43,735 ERROR [main] The spectral lfile: C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d is not supported.
2024-07-17 11:26:43,735 ERROR [main] java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
Process 'UmpireSe' finished, exit code: 1
Process returned non-zero exit code, stopping
~~~~~~~~~~~~~~~~~~~~
Cancelling 58 remaining tasks
fcyu commented
You loaded the wrong workflow. Please load the one with key word "PASEF".
Best,
Fengchao
Ale-ksa-ndra commented
Dear ,
I believe it is the same. Please see the log file.
Kind regards,
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Wednesday, July 17, 2024 3:38 PM
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Author ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
You loaded the wrong workflow. Please load the one with key work PASEF.
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZ4LYWONFFJ2FPFPCETZMZXUDAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZTGM2TAMZWGI>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.11, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A
Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1
LCMS files:
Experiment/Group:
(if "spectral library generation" is enabled, all files will be analyzed together)
- C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d DIA
61 commands to execute:
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\b6c5e905-6273-4540-b6b9-a2245e1589e4
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\diaumpire_se.log C:\Users\achojna1\Documents\brukerReasults1\diaumpire_se.log
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Peak C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.RTidxFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanidxFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanPosFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanRTFS C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mgf C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
MSFragger [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\Users\achojna1\Documents\brukerReasults1\fragger_dda.params C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
MSBooster [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -Xmx15G -cp C:\Users\achojna1\fragpipe\tools\MSBooster-1.2.31.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\Users\achojna1\Documents\brukerReasults1\msbooster_params.txt
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q3_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q1_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q2_edited.pin
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q3.pin 060_30SPD_DIA_S1-D4_1_753_Q3 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q3 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q1.pin 060_30SPD_DIA_S1-D4_1_753_Q1 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q1 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q2.pin 060_30SPD_DIA_S1-D4_1_753_Q2 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q2 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults1\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\achojna1\Documents\brukerReasults1\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --tag rev_ --pepxml C:\Users\achojna1\Documents\brukerReasults1 --protxml C:\Users\achojna1\Documents\brukerReasults1\combined.prot.xml --razor
PhilosopherReport [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PTMShepherd [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\ptmshepherd-3.0.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\tools\commons-math3-3.6.1.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar;C:\Users\achojna1\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\achojna1\Documents\brukerReasults1\shepherd.config"
WorkspaceClean [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
SpecLibGen [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\AppData\Local\Programs\Python\Python39\python -u C:\Users\achojna1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas C:\Users\achojna1\Documents\brukerReasults1 unused C:\Users\achojna1\Documents\brukerReasults1 True unused use_easypqp ciRT;noIM 23 "--unimod C:/Users/achojna1/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] --decoy_prefix rev_" "--rt_lowess_fraction 0.0" delete_intermediate_files C:\Users\achojna1\Documents\brukerReasults1\filelist_speclibgen.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 23 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg C:\Users\achojna1\Documents\brukerReasults1\filelist_diann.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate information [Work dir: C:\Users\achojna1\Documents\brukerReasults1\diann-output]
java -cp C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation C:\Users\achojna1\Documents\brukerReasults1
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: C:\Users\achojna1\Documents\brukerReasults1\diann-output]
java -cp C:\Users\achojna1\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ C:\Users\achojna1\Documents\brukerReasults1\psm.tsv 0.01 1 0.01 0.01 C:\Users\achojna1\Documents\brukerReasults1\fragpipe-files.fp-manifest
~~~~~~~~~~~~~~~~~~~~~~
Execution order:
Cmd: [START], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [UmpireSe], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [diaTracer], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [MSBooster], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [Percolator], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [ProteinProphet], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [PTMShepherd], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [SpecLibGen], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
Cmd: [DIA-NN], Work dir: [C:\Users\achojna1\Documents\brukerReasults1]
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~Sample of C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas~~~~~~~
contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
rev_sp|O43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1
rev_sp|P0DMB2|CH088_HUMAN Uncharacterized protein C8orf88 OS=Homo sapiens OX=9606 GN=C8orf88 PE=4 SV=1
rev_sp|P49642|PRI1_HUMAN DNA primase small subunit OS=Homo sapiens OX=9606 GN=PRIM1 PE=1 SV=1
rev_sp|Q14142|TRI14_HUMAN Tripartite motif-containing protein 14 OS=Homo sapiens OX=9606 GN=TRIM14 PE=1 SV=2
rev_sp|Q68DH5|LMBD2_HUMAN G-protein coupled receptor-associated protein LMBRD2 OS=Homo sapiens OX=9606 GN=LMBRD2 PE=1 SV=1
rev_sp|Q8IWB6|TEX14_HUMAN Inactive serine/threonine-protein kinase TEX14 OS=Homo sapiens OX=9606 GN=TEX14 PE=1 SV=2
rev_sp|Q8WVI0|UQCC5_HUMAN Ubiquinol-cytochrome c reductase complex assembly factor 5 OS=Homo sapiens OX=9606 GN=UQCC5 PE=1 SV=2
rev_sp|Q9BRB3|PIGQ_HUMAN Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q OS=Homo sapiens OX=9606 GN=PIGQ PE=1 SV=3
rev_sp|Q9NUP1|BL1S4_HUMAN Biogenesis of lysosome-related organelles complex 1 subunit 4 OS=Homo sapiens OX=9606 GN=BLOC1S4 PE=1 SV=1
rev_sp|Q9Y6M9|NDUB9_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 OS=Homo sapiens OX=9606 GN=NDUFB9 PE=1 SV=3
sp|O43614|OX2R_HUMAN Orexin receptor type 2 OS=Homo sapiens OX=9606 GN=HCRTR2 PE=1 SV=2
sp|P0DN86|CGB3_HUMAN Choriogonadotropin subunit beta 3 OS=Homo sapiens OX=9606 GN=CGB3 PE=1 SV=1
sp|P49796|RGS3_HUMAN Regulator of G-protein signaling 3 OS=Homo sapiens OX=9606 GN=RGS3 PE=1 SV=2
sp|Q14213|IL27B_HUMAN Interleukin-27 subunit beta OS=Homo sapiens OX=9606 GN=EBI3 PE=1 SV=2
sp|Q6AI12|ANR40_HUMAN Ankyrin repeat domain-containing protein 40 OS=Homo sapiens OX=9606 GN=ANKRD40 PE=1 SV=2
sp|Q8IWV8|UBR2_HUMAN E3 ubiquitin-protein ligase UBR2 OS=Homo sapiens OX=9606 GN=UBR2 PE=1 SV=1
sp|Q8WW43|APH1B_HUMAN Gamma-secretase subunit APH-1B OS=Homo sapiens OX=9606 GN=APH1B PE=1 SV=3
sp|Q9BRT6|LLPH_HUMAN Protein LLP homolog OS=Homo sapiens OX=9606 GN=LLPH PE=1 SV=1
sp|Q9NVC3|S38A7_HUMAN Sodium-coupled neutral amino acid transporter 7 OS=Homo sapiens OX=9606 GN=SLC38A7 PE=1 SV=1
sp|Q9Y6Y0|NS1BP_HUMAN Influenza virus NS1A-binding protein OS=Homo sapiens OX=9606 GN=IVNS1ABP PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache
# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Users\\achojna1\\2024-06-06-decoys-reviewed-contam-UP000005640.fas
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=true
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=true
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\achojna1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=
fragpipe-config.bin-msfragger=
fragpipe-config.bin-philosopher=
fragpipe-config.bin-python=C\:\\Users\\achojna1\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\Users\\achojna1\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=2
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=50
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=HCD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=2
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=false
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
ptmshepherd.run-shepherd=true
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=1
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=true
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=false
speclibgen.convert-psm=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-0
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=C\:\\Users\\achojna1\\Documents\\brukerReasults1
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=23
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="14:42:59" level=info msg="Executing Workspace v5.1.1"
time="14:42:59" level=info msg="Removing workspace"
time="14:42:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults1]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\b6c5e905-6273-4540-b6b9-a2245e1589e4
time="14:42:59" level=info msg="Executing Workspace v5.1.1"
time="14:42:59" level=info msg="Creating workspace"
time="14:42:59" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
=================================================================================================
DIA-Umpire signal extraction analysis (version: v2.3.2)
(c) University of Michigan
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-07-18 14:43:00,577 INFO [main] Version: v2.3.2
2024-07-18 14:43:00,579 INFO [main] Parameter file:C:\Users\achojna1\Documents\brukerReasults1\umpire-se.params
2024-07-18 14:43:00,579 INFO [main] Spectra file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d
2024-07-18 14:43:00,580 INFO [main]
2024-07-18 14:43:00,580 INFO [main] ####################################################################################################
2024-07-18 14:43:00,580 INFO [main] #No of threads
2024-07-18 14:43:00,580 INFO [main] Thread = 23
2024-07-18 14:43:00,580 INFO [main] ####################################################################################################
2024-07-18 14:43:00,580 INFO [main]
2024-07-18 14:43:00,580 INFO [main] ## omit Thread
2024-07-18 14:43:00,580 INFO [main]
2024-07-18 14:43:00,581 INFO [main] #Precursor-fragments grouping parameters
2024-07-18 14:43:00,581 INFO [main] RPmax = 25
2024-07-18 14:43:00,581 INFO [main] RFmax = 500
2024-07-18 14:43:00,581 INFO [main] CorrThreshold = 0
2024-07-18 14:43:00,581 INFO [main] DeltaApex = 0.2
2024-07-18 14:43:00,581 INFO [main] RTOverlap = 0.3
2024-07-18 14:43:00,581 INFO [main]
2024-07-18 14:43:00,581 INFO [main] #Fragment intensity adjustments
2024-07-18 14:43:00,581 INFO [main] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2024-07-18 14:43:00,581 INFO [main] AdjustFragIntensity = true
2024-07-18 14:43:00,581 INFO [main] BoostComplementaryIon = false
2024-07-18 14:43:00,581 INFO [main]
2024-07-18 14:43:00,581 INFO [main] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2024-07-18 14:43:00,581 INFO [main] ExportPrecursorPeak = false
2024-07-18 14:43:00,581 INFO [main]
2024-07-18 14:43:00,581 INFO [main] Q1 = true
2024-07-18 14:43:00,581 INFO [main] Q2 = true
2024-07-18 14:43:00,582 INFO [main] Q3 = true
2024-07-18 14:43:00,582 INFO [main]
2024-07-18 14:43:00,582 INFO [main] #Signal extraction: mass accuracy and resolution
2024-07-18 14:43:00,582 INFO [main] # resolution parameter matters only for data generated in profile mode
2024-07-18 14:43:00,582 INFO [main] SE.MS1PPM = 10
2024-07-18 14:43:00,582 INFO [main] SE.MS2PPM = 20
2024-07-18 14:43:00,582 INFO [main] SE.Resolution = 60000
2024-07-18 14:43:00,582 INFO [main]
2024-07-18 14:43:00,582 INFO [main] #Signal extraction: signal to noise filter
2024-07-18 14:43:00,582 INFO [main] SE.SN = 1.1
2024-07-18 14:43:00,582 INFO [main] SE.MS2SN = 1.1
2024-07-18 14:43:00,582 INFO [main]
2024-07-18 14:43:00,582 INFO [main] #Signal extraction: minimum signal intensity filter
2024-07-18 14:43:00,582 INFO [main] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2024-07-18 14:43:00,582 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2024-07-18 14:43:00,582 INFO [main] SE.EstimateBG = false
2024-07-18 14:43:00,582 INFO [main] SE.MinMSIntensity = 1
2024-07-18 14:43:00,583 INFO [main] SE.MinMSMSIntensity = 1
2024-07-18 14:43:00,583 INFO [main]
2024-07-18 14:43:00,583 INFO [main] #Signal extraction: peak curve detection and isotope grouping
2024-07-18 14:43:00,583 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2024-07-18 14:43:00,583 INFO [main] SE.NoMissedScan = 1
2024-07-18 14:43:00,583 INFO [main] SE.MaxCurveRTRange = 2
2024-07-18 14:43:00,583 INFO [main] SE.RemoveGroupedPeaks = true
2024-07-18 14:43:00,583 INFO [main] SE.RemoveGroupedPeaksRTOverlap = 0.3
2024-07-18 14:43:00,583 INFO [main] SE.RemoveGroupedPeaksCorr = 0.3
2024-07-18 14:43:00,583 INFO [main] SE.MinNoPeakCluster = 2
2024-07-18 14:43:00,583 INFO [main] SE.MaxNoPeakCluster = 4
2024-07-18 14:43:00,583 INFO [main]
2024-07-18 14:43:00,583 INFO [main] #Signal extraction: filtering of MS1 features
Exception in thread "main" java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
2024-07-18 14:43:00,732 INFO [main] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2024-07-18 14:43:00,733 INFO [main] SE.IsoPattern = 0.3
2024-07-18 14:43:00,733 INFO [main] SE.MassDefectFilter = true
2024-07-18 14:43:00,733 INFO [main] SE.MassDefectOffset = 0.1
2024-07-18 14:43:00,733 INFO [main]
2024-07-18 14:43:00,733 INFO [main] #Signal extraction: other
2024-07-18 14:43:00,734 INFO [main] SE.StartCharge = 1
2024-07-18 14:43:00,734 INFO [main] SE.EndCharge = 5
2024-07-18 14:43:00,734 INFO [main] SE.MS2StartCharge = 2
2024-07-18 14:43:00,734 INFO [main] SE.MS2EndCharge = 5
2024-07-18 14:43:00,734 INFO [main] SE.MinFrag = 10
2024-07-18 14:43:00,734 INFO [main] SE.StartRT = 0
2024-07-18 14:43:00,734 INFO [main] SE.EndRT = 9999
2024-07-18 14:43:00,735 INFO [main] SE.MinMZ = 200
2024-07-18 14:43:00,736 INFO [main] SE.MinPrecursorMass = 600
2024-07-18 14:43:00,736 INFO [main] SE.MaxPrecursorMass = 5000
2024-07-18 14:43:00,736 INFO [main]
2024-07-18 14:43:00,736 INFO [main]
2024-07-18 14:43:00,736 INFO [main] #Isolation window setting
2024-07-18 14:43:00,736 INFO [main] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2024-07-18 14:43:00,736 INFO [main] WindowType = SWATH
2024-07-18 14:43:00,736 INFO [main]
2024-07-18 14:43:00,736 INFO [main] #Fix window size (For SWATH)
2024-07-18 14:43:00,736 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-18 14:43:00,736 INFO [main] WindowSize = 10
2024-07-18 14:43:00,737 INFO [main]
2024-07-18 14:43:00,737 INFO [main] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2024-07-18 14:43:00,737 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-18 14:43:00,737 INFO [main] ==window setting begin
2024-07-18 14:43:00,737 INFO [main]
2024-07-18 14:43:00,737 INFO [main] =================================================================================================
2024-07-18 14:43:00,737 INFO [main] Processing C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d....
2024-07-18 14:43:00,739 INFO [main] Writing DIA setting to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser...
2024-07-18 14:43:00,742 INFO [main] Writing parameter to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser...
2024-07-18 14:43:00,743 INFO [main] Module A: Signal extraction
2024-07-18 14:43:00,744 ERROR [main] The spectral lfile: C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d is not supported.
2024-07-18 14:43:00,745 ERROR [main] java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
Process 'UmpireSe' finished, exit code: 1
Process returned non-zero exit code, stopping
~~~~~~~~~~~~~~~~~~~~
Cancelling 58 remaining tasks
fcyu commented
@Ale-ksa-ndra , may I ask which workflow you loaded? I don't think you loaded the one with DIA and pasef because your log has diaumpire.run-diaumpire=true and diatracer.run-diatracer=false.
Best,
Fengchao
Ale-ksa-ndra commented
Dear ,
I have loaded DIA_SpecLib_Quant_diaPASEF.
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Thursday, July 18, 2024 3:02 PM
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Mention ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
@Ale-ksa-ndra<https://github.com/Ale-ksa-ndra> , may I ask which workflow you loaded? I don't think you loaded the one with DIA and pasef because your log has diaumpire.run-diaumpire=true and diatracer.run-diatracer=false.
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZZOXVJRW4MHDO42ENLZM64DDAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGQZTOOJUGM>.
You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>
fcyu commented
Well, your log file says you did not.
Just in case, have you clicked "load" after select the workflow?
Best,
Fengchao
Ale-ksa-ndra commented
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Thursday, July 18, 2024 3:02 PM
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Mention ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
@Ale-ksa-ndra<https://github.com/Ale-ksa-ndra> , may I ask which workflow you loaded? I don't think you loaded the one with DIA and pasef because your log has diaumpire.run-diaumpire=true and diatracer.run-diatracer=false.
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZZOXVJRW4MHDO42ENLZM64DDAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGQZTOOJUGM>.
You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.11, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A
Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1
LCMS files:
Experiment/Group:
(if "spectral library generation" is enabled, all files will be analyzed together)
- C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d DIA
61 commands to execute:
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\e6c97b0e-753d-46f7-8710-4dd9bb4ed9a6
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults3\umpire-se.params
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\diaumpire_se.log C:\Users\achojna1\Documents\brukerReasults3\diaumpire_se.log
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Peak C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.RTidxFS C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanidxFS C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanPosFS C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.ScanRTFS C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mgf C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mgf C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mgf C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/achojna1/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_Q3.mzML C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Peak
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.DIAWindowsFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.RTidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanidxFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanPosFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753.ScanRTFS
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_diasetting.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_params.ser
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2.mgf
UmpireSe
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3.mgf
MSFragger [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -jar -Dfile.encoding=UTF-8 -Xmx15G C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\Users\achojna1\Documents\brukerReasults3\fragger_dda.params C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1.mzML C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2.mzML C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3.mzML
MSBooster [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -Xmx15G -cp C:\Users\achojna1\fragpipe\tools\MSBooster-1.2.31.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList C:\Users\achojna1\Documents\brukerReasults3\msbooster_params.txt
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q3_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q1_edited.pin
Percolator [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv --decoy-results-psms 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ 060_30SPD_DIA_S1-D4_1_753_Q2_edited.pin
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q3.pin 060_30SPD_DIA_S1-D4_1_753_Q3 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q3 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q3_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q1.pin 060_30SPD_DIA_S1-D4_1_753_Q1 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q1 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -cp C:\Users\achojna1\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 060_30SPD_DIA_S1-D4_1_753_Q2.pin 060_30SPD_DIA_S1-D4_1_753_Q2 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv 060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv interact-060_30SPD_DIA_S1-D4_1_753_Q2 DDA 0.7 C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2_calibrated.mzML
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_target_psms.tsv
Percolator: Delete temp
java -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete C:\Users\achojna1\Documents\brukerReasults3\060_30SPD_DIA_S1-D4_1_753_Q2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\Users\achojna1\Documents\brukerReasults3\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --picked --prot 0.01 --tag rev_ --pepxml C:\Users\achojna1\Documents\brukerReasults3 --protxml C:\Users\achojna1\Documents\brukerReasults3\combined.prot.xml --razor
PhilosopherReport [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
PTMShepherd [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\ptmshepherd-3.0.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\tools\commons-math3-3.6.1.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\achojna1\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar;C:\Users\achojna1\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\achojna1\Documents\brukerReasults3\shepherd.config"
WorkspaceClean [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
SpecLibGen [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\AppData\Local\Programs\Python\Python39\python -u C:\Users\achojna1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas C:\Users\achojna1\Documents\brukerReasults3 unused C:\Users\achojna1\Documents\brukerReasults3 True unused use_easypqp ciRT;noIM 23 "--unimod C:/Users/achojna1/fragpipe/tools/unimod_old.xml --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] --decoy_prefix rev_" "--rt_lowess_fraction 0.0" delete_intermediate_files C:\Users\achojna1\Documents\brukerReasults3\filelist_speclibgen.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 23 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --cfg C:\Users\achojna1\Documents\brukerReasults3\filelist_diann.txt
DIA-NN [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate information [Work dir: C:\Users\achojna1\Documents\brukerReasults3\diann-output]
java -cp C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation C:\Users\achojna1\Documents\brukerReasults3
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: C:\Users\achojna1\Documents\brukerReasults3\diann-output]
java -cp C:\Users\achojna1\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ C:\Users\achojna1\Documents\brukerReasults3\psm.tsv 0.01 1 0.01 0.01 C:\Users\achojna1\Documents\brukerReasults3\fragpipe-files.fp-manifest
~~~~~~~~~~~~~~~~~~~~~~
Execution order:
Cmd: [START], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [CheckCentroid], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [UmpireSe], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [diaTracer], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [MSFragger], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [MSBooster], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [Percolator], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [ProteinProphet], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [PhilosopherFilter], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [PhilosopherReport], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [PTMShepherd], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [WorkspaceClean], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [SpecLibGen], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
Cmd: [DIA-NN], Work dir: [C:\Users\achojna1\Documents\brukerReasults3]
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~Sample of C:\Users\achojna1\2024-06-06-decoys-reviewed-contam-UP000005640.fas~~~~~~~
contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
rev_sp|O43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 OS=Homo sapiens OX=9606 GN=RAD51C PE=1 SV=1
rev_sp|P0DMB2|CH088_HUMAN Uncharacterized protein C8orf88 OS=Homo sapiens OX=9606 GN=C8orf88 PE=4 SV=1
rev_sp|P49642|PRI1_HUMAN DNA primase small subunit OS=Homo sapiens OX=9606 GN=PRIM1 PE=1 SV=1
rev_sp|Q14142|TRI14_HUMAN Tripartite motif-containing protein 14 OS=Homo sapiens OX=9606 GN=TRIM14 PE=1 SV=2
rev_sp|Q68DH5|LMBD2_HUMAN G-protein coupled receptor-associated protein LMBRD2 OS=Homo sapiens OX=9606 GN=LMBRD2 PE=1 SV=1
rev_sp|Q8IWB6|TEX14_HUMAN Inactive serine/threonine-protein kinase TEX14 OS=Homo sapiens OX=9606 GN=TEX14 PE=1 SV=2
rev_sp|Q8WVI0|UQCC5_HUMAN Ubiquinol-cytochrome c reductase complex assembly factor 5 OS=Homo sapiens OX=9606 GN=UQCC5 PE=1 SV=2
rev_sp|Q9BRB3|PIGQ_HUMAN Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q OS=Homo sapiens OX=9606 GN=PIGQ PE=1 SV=3
rev_sp|Q9NUP1|BL1S4_HUMAN Biogenesis of lysosome-related organelles complex 1 subunit 4 OS=Homo sapiens OX=9606 GN=BLOC1S4 PE=1 SV=1
rev_sp|Q9Y6M9|NDUB9_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 OS=Homo sapiens OX=9606 GN=NDUFB9 PE=1 SV=3
sp|O43614|OX2R_HUMAN Orexin receptor type 2 OS=Homo sapiens OX=9606 GN=HCRTR2 PE=1 SV=2
sp|P0DN86|CGB3_HUMAN Choriogonadotropin subunit beta 3 OS=Homo sapiens OX=9606 GN=CGB3 PE=1 SV=1
sp|P49796|RGS3_HUMAN Regulator of G-protein signaling 3 OS=Homo sapiens OX=9606 GN=RGS3 PE=1 SV=2
sp|Q14213|IL27B_HUMAN Interleukin-27 subunit beta OS=Homo sapiens OX=9606 GN=EBI3 PE=1 SV=2
sp|Q6AI12|ANR40_HUMAN Ankyrin repeat domain-containing protein 40 OS=Homo sapiens OX=9606 GN=ANKRD40 PE=1 SV=2
sp|Q8IWV8|UBR2_HUMAN E3 ubiquitin-protein ligase UBR2 OS=Homo sapiens OX=9606 GN=UBR2 PE=1 SV=1
sp|Q8WW43|APH1B_HUMAN Gamma-secretase subunit APH-1B OS=Homo sapiens OX=9606 GN=APH1B PE=1 SV=3
sp|Q9BRT6|LLPH_HUMAN Protein LLP homolog OS=Homo sapiens OX=9606 GN=LLPH PE=1 SV=1
sp|Q9NVC3|S38A7_HUMAN Sodium-coupled neutral amino acid transporter 7 OS=Homo sapiens OX=9606 GN=SLC38A7 PE=1 SV=1
sp|Q9Y6Y0|NS1BP_HUMAN Influenza virus NS1A-binding protein OS=Homo sapiens OX=9606 GN=IVNS1ABP PE=1 SV=3
~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache
# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\Users\\achojna1\\2024-06-06-decoys-reviewed-contam-UP000005640.fas
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=true
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=true
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=true
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\achojna1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=
fragpipe-config.bin-msfragger=
fragpipe-config.bin-philosopher=
fragpipe-config.bin-python=C\:\\Users\\achojna1\\AppData\\Local\\Programs\\Python\\Python39\\python
fragpipe-config.tools-folder=C\:\\Users\\achojna1\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=2
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=50
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=HCD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=2
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=false
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
ptmshepherd.run-shepherd=true
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=1
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=true
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=false
speclibgen.convert-psm=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-0
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
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.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=C\:\\Users\\achojna1\\Documents\\brukerReasults3
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=23
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx15G -cp C:\Users\achojna1\fragpipe\lib\fragpipe-22.0.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d 23
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="15:07:44" level=info msg="Executing Workspace v5.1.1"
time="15:07:44" level=info msg="Removing workspace"
time="15:07:44" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\achojna1\Documents\brukerReasults3]
C:\Users\achojna1\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\achojna1\AppData\Local\Temp\e6c97b0e-753d-46f7-8710-4dd9bb4ed9a6
time="15:07:44" level=info msg="Executing Workspace v5.1.1"
time="15:07:44" level=info msg="Creating workspace"
time="15:07:44" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
java -Xmx15G -Dlibs.thermo.dir=C:\Users\achojna1\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\achojna1\fragpipe\tools\DIA_Umpire_SE-2.3.2.jar;C:\Users\achojna1\fragpipe\tools\batmass-io-1.33.4.jar dia_umpire_se.DIA_Umpire_SE C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d C:\Users\achojna1\Documents\brukerReasults3\umpire-se.params
=================================================================================================
DIA-Umpire signal extraction analysis (version: v2.3.2)
(c) University of Michigan
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
2024-07-18 15:07:45,540 INFO [main] Version: v2.3.2
2024-07-18 15:07:45,540 INFO [main] Parameter file:C:\Users\achojna1\Documents\brukerReasults3\umpire-se.params
2024-07-18 15:07:45,540 INFO [main] Spectra file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] ####################################################################################################
2024-07-18 15:07:45,540 INFO [main] #No of threads
2024-07-18 15:07:45,540 INFO [main] Thread = 23
2024-07-18 15:07:45,540 INFO [main] ####################################################################################################
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] ## omit Thread
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Precursor-fragments grouping parameters
2024-07-18 15:07:45,540 INFO [main] RPmax = 25
2024-07-18 15:07:45,540 INFO [main] RFmax = 500
2024-07-18 15:07:45,540 INFO [main] CorrThreshold = 0
2024-07-18 15:07:45,540 INFO [main] DeltaApex = 0.2
2024-07-18 15:07:45,540 INFO [main] RTOverlap = 0.3
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Fragment intensity adjustments
2024-07-18 15:07:45,540 INFO [main] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2024-07-18 15:07:45,540 INFO [main] AdjustFragIntensity = true
2024-07-18 15:07:45,540 INFO [main] BoostComplementaryIon = false
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2024-07-18 15:07:45,540 INFO [main] ExportPrecursorPeak = false
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] Q1 = true
2024-07-18 15:07:45,540 INFO [main] Q2 = true
2024-07-18 15:07:45,540 INFO [main] Q3 = true
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Signal extraction: mass accuracy and resolution
2024-07-18 15:07:45,540 INFO [main] # resolution parameter matters only for data generated in profile mode
2024-07-18 15:07:45,540 INFO [main] SE.MS1PPM = 10
2024-07-18 15:07:45,540 INFO [main] SE.MS2PPM = 20
2024-07-18 15:07:45,540 INFO [main] SE.Resolution = 60000
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Signal extraction: signal to noise filter
2024-07-18 15:07:45,540 INFO [main] SE.SN = 1.1
2024-07-18 15:07:45,540 INFO [main] SE.MS2SN = 1.1
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Signal extraction: minimum signal intensity filter
2024-07-18 15:07:45,540 INFO [main] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2024-07-18 15:07:45,540 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2024-07-18 15:07:45,540 INFO [main] SE.EstimateBG = false
2024-07-18 15:07:45,540 INFO [main] SE.MinMSIntensity = 1
2024-07-18 15:07:45,540 INFO [main] SE.MinMSMSIntensity = 1
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Signal extraction: peak curve detection and isotope grouping
2024-07-18 15:07:45,540 INFO [main] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2024-07-18 15:07:45,540 INFO [main] SE.NoMissedScan = 1
2024-07-18 15:07:45,540 INFO [main] SE.MaxCurveRTRange = 2
2024-07-18 15:07:45,540 INFO [main] SE.RemoveGroupedPeaks = true
2024-07-18 15:07:45,540 INFO [main] SE.RemoveGroupedPeaksRTOverlap = 0.3
2024-07-18 15:07:45,540 INFO [main] SE.RemoveGroupedPeaksCorr = 0.3
2024-07-18 15:07:45,540 INFO [main] SE.MinNoPeakCluster = 2
2024-07-18 15:07:45,540 INFO [main] SE.MaxNoPeakCluster = 4
2024-07-18 15:07:45,540 INFO [main]
2024-07-18 15:07:45,540 INFO [main] #Signal extraction: filtering of MS1 features
Exception in thread "main" java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
2024-07-18 15:07:45,689 INFO [main] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2024-07-18 15:07:45,689 INFO [main] SE.IsoPattern = 0.3
2024-07-18 15:07:45,689 INFO [main] SE.MassDefectFilter = true
2024-07-18 15:07:45,689 INFO [main] SE.MassDefectOffset = 0.1
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main] #Signal extraction: other
2024-07-18 15:07:45,689 INFO [main] SE.StartCharge = 1
2024-07-18 15:07:45,689 INFO [main] SE.EndCharge = 5
2024-07-18 15:07:45,689 INFO [main] SE.MS2StartCharge = 2
2024-07-18 15:07:45,689 INFO [main] SE.MS2EndCharge = 5
2024-07-18 15:07:45,689 INFO [main] SE.MinFrag = 10
2024-07-18 15:07:45,689 INFO [main] SE.StartRT = 0
2024-07-18 15:07:45,689 INFO [main] SE.EndRT = 9999
2024-07-18 15:07:45,689 INFO [main] SE.MinMZ = 200
2024-07-18 15:07:45,689 INFO [main] SE.MinPrecursorMass = 600
2024-07-18 15:07:45,689 INFO [main] SE.MaxPrecursorMass = 5000
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main] #Isolation window setting
2024-07-18 15:07:45,689 INFO [main] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2024-07-18 15:07:45,689 INFO [main] WindowType = SWATH
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main] #Fix window size (For SWATH)
2024-07-18 15:07:45,689 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-18 15:07:45,689 INFO [main] WindowSize = 10
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2024-07-18 15:07:45,689 INFO [main] # for Thermo data, this will be determined from raw data automatically
2024-07-18 15:07:45,689 INFO [main] ==window setting begin
2024-07-18 15:07:45,689 INFO [main]
2024-07-18 15:07:45,689 INFO [main] =================================================================================================
2024-07-18 15:07:45,689 INFO [main] Processing C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d....
2024-07-18 15:07:45,689 INFO [main] Writing DIA setting to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_diasetting.ser...
2024-07-18 15:07:45,689 INFO [main] Writing parameter to file:C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753_params.ser...
2024-07-18 15:07:45,689 INFO [main] Module A: Signal extraction
2024-07-18 15:07:45,689 ERROR [main] The spectral lfile: C:\Users\achojna1\bruker5\060_30SPD_DIA_S1-D4_1_753.d is not supported.
2024-07-18 15:07:45,689 ERROR [main] java.lang.NullPointerException: Cannot read field "dIA_Setting" because "this.SpectrumParser" is null
at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:169)
at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:185)
at MSUmpire.DIA.DIAPack.process(DIAPack.java:177)
at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:379)
Process 'UmpireSe' finished, exit code: 1
Process returned non-zero exit code, stopping
~~~~~~~~~~~~~~~~~~~~
Cancelling 58 remaining tasks
Ale-ksa-ndra commented
I am sorry you are correct
I did not
Very sorry to waste your time
A.Chojnacka, PhD│Van 't Hoff Institute for Molecular Sciences (HIMS)│University of Amsterdam│Science Park 904│1098 XH Amsterdam│The Netherlands│+31 (0)20 525 6486│room ***@***.******@***.***>
From: Fengchao ***@***.***>
Sent: Thursday, July 18, 2024 3:07 PM
To: Nesvilab/FragPipe ***@***.***>
Cc: Aleksandra Chojnacka ***@***.***>; Mention ***@***.***>
Subject: Re: [Nesvilab/FragPipe] problem with configuration (Issue #1650)
Well, your log file says you did not.
Just in case, have you clicked "load" after select the workflow?
Best,
Fengchao
—
Reply to this email directly, view it on GitHub<#1650 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDCCSZ6P5GXYLNCZMHD57WTZM64XTAVCNFSM6AAAAABJ5YPZXKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGQ2DQNJRGY>.
You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>