Odd Error at end of SpecLibGen #421

DrDee79 · 2021-08-06T15:15:36Z

-Just trying to use the standard Fragpipe tutorial steps to generate a spectral library from DDA files. I get most of it done I believe but the log has an odd trace at the end I'd like to know if it's normal (as some of the files referenced in others don't appear):

Traceback (most recent call last):
File "C:\Users\q-tof\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 212, in
easypqp = get_bin_path('easypqp', 'easypqp')
File "C:\Users\q-tof\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 121, in get_bin_path
if dist.get('files') is None and sys.platform == "win32":
AttributeError: '_PackageInfo' object has no attribute 'get'
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping
log_2021-08-06_11-12-22.txt

Cancelling 2 remaining tasks

The text was updated successfully, but these errors were encountered:

guoci · 2021-08-06T18:22:47Z

Fixed, please try the following
https://drive.google.com/file/d/1kt6Kq-0-BemOwSlfxBsurBxiBQ8OLce8/view?usp=sharing

DrDee79 · 2021-08-06T19:32:04Z

Thank you! It worked on the test file I did, now to see if I can do multiples!

DrDee79 · 2021-08-09T15:29:41Z

Hi, Been testing this newer version and still getting errors though this one is different. Any advice?

Dorothy

easypqp, version 0.1.24
Executing ['C:\Users\q-tof\AppData\Local\Programs\Python\Python39\Scripts\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\interact-20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.pep.xml', '--spectra', 'C:\Users\q-tof\Desktop\DIA\20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.psmpkl', '--peaks', '20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.peakpkl']
Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic.
Info: Reading file C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.psmpkl.
Info: 23026 redundant PSMs identified after filtering with C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\psm.tsv and C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\peptide.tsv
base_name modified_peptide
0 20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL 5309
Info: easypqp_rt_alignment_20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL; Peptide overlap between run and reference: 5309.
Exception in thread Thread-1:
Traceback (most recent call last):
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\threading.py", line 954, in _bootstrap_inner
self.run()
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\site-packages\joblib\externals\loky\process_executor.py", line 555, in run
result_item, is_broken, bpe = self.wait_result_broken_or_wakeup()
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\site-packages\joblib\externals\loky\process_executor.py", line 609, in wait_result_broken_or_wakeup
ready = wait(readers + worker_sentinels)
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\multiprocessing\connection.py", line 884, in wait
ready_handles = _exhaustive_wait(waithandle_to_obj.keys(), timeout)
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\multiprocessing\connection.py", line 816, in _exhaustive_wait
res = _winapi.WaitForMultipleObjects(L, False, timeout)
ValueError: need at most 63 handles, got a sequence of length 65
log_2021-08-09_11-26-37.txt

DrDee79 · 2021-08-09T18:20:39Z

Hi, Been testing this newer version and still getting errors though this one is different. Any advice?

Dorothy

easypqp, version 0.1.24
Executing ['C:\Users\q-tof\AppData\Local\Programs\Python\Python39\Scripts\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\interact-20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.pep.xml', '--spectra', 'C:\Users\q-tof\Desktop\DIA\20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.psmpkl', '--peaks', '20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.peakpkl']
Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic.
Info: Reading file C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL.psmpkl.
Info: 23026 redundant PSMs identified after filtering with C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\psm.tsv and C:\Users\q-tof\Desktop\DIA\PlasmaLib14-PlasmaDDALib\peptide.tsv
base_name modified_peptide
0 20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL 5309
Info: easypqp_rt_alignment_20210625_CUBE_Plasma_5248_FAIMS_90secDE_Test_2uL; Peptide overlap between run and reference: 5309.
Exception in thread Thread-1:
Traceback (most recent call last):
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\threading.py", line 954, in _bootstrap_inner
self.run()
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\site-packages\joblib\externals\loky\process_executor.py", line 555, in run
result_item, is_broken, bpe = self.wait_result_broken_or_wakeup()
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\site-packages\joblib\externals\loky\process_executor.py", line 609, in wait_result_broken_or_wakeup
ready = wait(readers + worker_sentinels)
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\multiprocessing\connection.py", line 884, in wait
ready_handles = _exhaustive_wait(waithandle_to_obj.keys(), timeout)
File "c:\users\q-tof\appdata\local\programs\python\python39\lib\multiprocessing\connection.py", line 816, in _exhaustive_wait
res = _winapi.WaitForMultipleObjects(L, False, timeout)
ValueError: need at most 63 handles, got a sequence of length 65
log_2021-08-09_11-26-37.txt

This seems to be only happening when I try to use the SpecLib with DDA files- I am able to get through the workflow with DIA 4 m/z files. I hope it's an easy fix!

guoci · 2021-08-10T16:44:11Z

Please install my version of EasyPQP and try again by using the following commands in Anaconda prompt:

pip uninstall -y easypqp
pip install git+https://github.com/guoci/easypqp@joblib_thread_fix

The issue is documented at joblib/loky#192

DrDee79 · 2021-08-11T16:34:37Z

Having a bit of trouble cloning from that link, can you double-check it?

Collecting git+https://github.com/guoci/easypqp@joblib_thread_fix
Cloning https://github.com/guoci/easypqp (to revision joblib_thread_fix) to c:\users\q-tof\appdata\local\temp\pip-req-build-3heqv7b0
Running command git clone -q https://github.com/guoci/easypqp 'C:\Users\q-tof\AppData\Local\Temp\pip-req-build-3heqv7b0'
ERROR: Error [WinError 2] The system cannot find the file specified while executing command git clone -q https://github.com/guoci/easypqp 'C:\Users\q-tof\AppData\Local\Temp\pip-req-build-3heqv7b0'

guoci · 2021-08-11T16:41:34Z

Is the error the same every time you run it?
I have tested it on a Windows computer.

DrDee79 · 2021-08-11T16:57:55Z

It's very odd as the easypqp is recognized as present by Fragpipe, but uninstalling says "Skipping easypqp as it is not installed."

Then the installation error is the same every time.

DrDee79 · 2021-08-11T17:09:19Z

So I was able to install using a different link git+https://github.com/grosenberger/easypqp.git@master, but keep getting the error with the one you had provided. Are both versions the same?

guoci · 2021-08-11T17:23:46Z

no, they are not the same

DrDee79 · 2021-08-11T17:28:29Z

Still not having luck with your link sorry.

guoci · 2021-08-11T17:55:45Z

Can you set RT lowess fraction to a non-zero value e.g. 0.05 and try again?

DrDee79 · 2021-08-11T20:01:08Z

That seemed to help with the errors!

giorgiolivi · 2021-10-18T12:11:40Z

Hi There,
I get the same error
Could you please help me how you figure out?
Thanks in advance.
Giorgio
File list provided
Traceback (most recent call last):
File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 212, in
easypqp = get_bin_path('easypqp', 'easypqp')
File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 121, in get_bin_path
if dist.get('files') is None and sys.platform == "win32":
AttributeError: '_PackageInfo' object has no attribute 'get'
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

fcyu · 2021-10-18T13:40:57Z

@guoci Can you take a look when you have time?

Thanks,

Fengchao

guoci · 2021-10-18T18:41:57Z

@giorgiolivi that has been fixed, download link to the fixed version:
https://drive.google.com/drive/folders/1yLxJmXjN8tHpOos_eFRRfz4WjlMoAtV7?usp=sharing

giorgiolivi · 2021-10-19T09:46:25Z

Hi Goucci, I am thinking we almost there to fix but not yet, here the error: SpecLibGen [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\anaconda3\python.exe -u C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas F:\TEST F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_uncalibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_uncalibrated.mgf F:\TEST True unused use_easypqp iRT 16 "--rt_lowess_fraction 0.01" Traceback (most recent call last): File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 428, in <module> raise RuntimeError('missing spectra files') RuntimeError: missing spectra files Using (un)calibrated.mgfs. Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping Please cite: (Regular searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020) (Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. bioRxiv. DOI: 10.1101/2020.07.08.192583 (2020) (Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods DOI: 10.1101/2020.05.18.10266 (2020) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19: 1575 (2020) (PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020) (DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015) ==================================================================================DONE============================================================ ~~~~~~~~~~~~~~~~~~~~ Cancelling 0 remaining tasks 10:39:57 ERROR: Error writing log to file java.nio.channels.ClosedByInterruptException: null at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202) at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:216) at java.nio.channels.Channels.writeFullyImpl(Channels.java:78) at java.nio.channels.Channels.writeFully(Channels.java:101) at java.nio.channels.Channels.access$000(Channels.java:61) at java.nio.channels.Channels$1.write(Channels.java:174) at java.nio.file.Files.write(Files.java:3297) at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:354) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:308) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510) at org.greenrobot.eventbus.EventBus.postToSubscription(EventBus.java:447) at org.greenrobot.eventbus.EventBus.postSingleEventForEventType(EventBus.java:414) at org.greenrobot.eventbus.EventBus.postSingleEvent(EventBus.java:387) at org.greenrobot.eventbus.EventBus.post(EventBus.java:268) at com.dmtavt.fragpipe.api.Bus.post(Bus.java:51) at com.dmtavt.fragpipe.FragpipeRun.lambda$run$6(FragpipeRun.java:283) at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1640) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

…

On Mon, 18 Oct 2021 at 18:42, guoci ***@***.***> wrote: @giorgiolivi <https://github.com/giorgiolivi> that has been fixed, download link to the fixed version: https://drive.google.com/drive/folders/1yLxJmXjN8tHpOos_eFRRfz4WjlMoAtV7?usp=sharing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASNT4C3I5M7MAT7ZJJUOCZLUHRS77ANCNFSM5BWDA3DA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

guoci · 2021-10-19T19:13:57Z

@giorgiolivi can you post the full log?

giorgiolivi · 2021-10-19T20:14:43Z

Dear Gouci, Log 1 , using fragpipe v14 ( link you send me before); Log 2, using fragpipe v16. I’ve tried to uninstall and install different python versions plus different packages of Panda etc.. but unfortunately I didn’t succeed so far. Thanks for your help Regards

On Tue, 19 Oct 2021 at 19:14, guoci ***@***.***> wrote: @giorgiolivi <https://github.com/giorgiolivi> can you post the full log? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASNT4C5FGASROSEYJ5JKAQ3UHW7QBANCNFSM5BWDA3DA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK Version info: FragPipe version 14.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421) LCMS files: Experiment/Group: - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d 19 commands to execute: WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx21G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML PeptideProphet: Workspace init [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas ..\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML PeptideProphet [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas ..\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML PeptideProphet: Delete temp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp PeptideProphet: Delete temp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp Rewrite pepxml [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d Rewrite pepxml [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d ProteinProphet [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml PhilosopherDbAnnotate [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev_ --pepxml F:\TEST --protxml F:\TEST\combined.prot.xml PhilosopherReport [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\anaconda3\python.exe -u C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas F:\TEST F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_uncalibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_uncalibrated.mgf F:\TEST True unused use_easypqp iRT 16 "--rt_lowess_fraction 0.01" ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [F:\TEST] Cmd: [WorkspaceCleanInit], Work dir: [F:\TEST] Cmd: [MsFragger], Work dir: [F:\TEST] Cmd: [PeptideProphet], Work dir: [F:\TEST] Cmd: [ProteinProphet], Work dir: [F:\TEST] Cmd: [PhilosopherDbAnnotate], Work dir: [F:\TEST] Cmd: [PhilosopherFilter], Work dir: [F:\TEST] Cmd: [PhilosopherReport], Work dir: [F:\TEST] Cmd: [WorkspaceClean], Work dir: [F:\TEST] Cmd: [SpecLibGen], Work dir: [F:\TEST] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v14.0ui state cache AdjustFragIntensity=true BoostComplementaryIon=true CorrThreshold=0 DeltaApex=0.2 ExportPrecursorPeak=true RFmax=500 RPmax=25 RTOverlap=0.3 SE.EstimateBG=true SE.IsoPattern=0.3 SE.MS1PPM=10 SE.MS2PPM=20 SE.MS2SN=1.1 SE.MassDefectFilter=true SE.MassDefectOffset=0.1 SE.NoMissedScan=1 SE.SN=1.1 Table.editor=-18.0106 crystalc.correct_isotope_error=false crystalc.isotope_number=3 crystalc.max-charge=6 crystalc.precursor_isolation_window=0.7 crystalc.precursor_mass=20 crystalc.run-crystalc=false database.db-path=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Desktop\\fasta\\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas database.decoy-tag=rev_ diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fragpipe-config.bin-msfragger=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Downloads\\FragPipe-15.0\\fragpipe\\tools\\MSFragger-3.3\\MSFragger-3.3.jar fragpipe-config.bin-philosopher=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Downloads\\FragPipe-16.0\\fragpipe\\tools\\philosopher\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\anaconda3\\python.exe freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.label= ionquant.light= ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minexps=1 ionquant.minfreq=0.5 ionquant.minions=1 ionquant.minisotopes=1 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.proteinquant=2 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=3 ionquant.writeindex=0 msfragger.Y_type_masses= msfragger.add_topN_complementary=0 msfragger.allow_multiple_variable_mods_on_residue=true msfragger.allowed_missed_cleavage=2 msfragger.calibrate_mass=2 msfragger.clip_nTerm_M=true msfragger.data_type=0 msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deltamass_allowed_residues=ST msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown=stricttrypsin msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remove_precursor_peak=0 msfragger.report_alternative_proteins=false msfragger.restrict_deltamass_to=all msfragger.run-msfragger=true msfragger.search_enzyme_butnotafter= msfragger.search_enzyme_cutafter=KR msfragger.search_enzyme_name=stricttrypsin msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1 msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,true,1; -18.010600,nE,true,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_topN_peaks=300 msfragger.write_calibrated_mgf=true msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=true percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--razor --picked --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.run-report=true phi-report.write-mzid=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.9 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.run-ptmprophet=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.diag_ions= ptmshepherd.glyco_mode=false ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.remainder_masses= ptmshepherd.run-shepherd=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464 quantitation.run-label-free-quant=false run-diaumpire=false run-psm-validation=true speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0.01 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.rt-cal=iRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=true speclibgen.use-easypqp=true speclibgen.use-spectrast=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=6 tmtintegrator.dont-run-fq-lq=false tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated tmtintegrator.groupby=0 tmtintegrator.labelquant=--tol 20 --level 2 tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false workdir=F\:\\TEST workflow.input.data-type.im-ms=true workflow.input.data-type.regular-ms=false workflow.process-exps-separately=false workflow.ram=0 workflow.threads=16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:29:41] Executing Workspace v4.0.0 INFO[10:29:41] Removing workspace WARN[10:29:41] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[10:29:41] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:29:41] Executing Workspace v4.0.0 INFO[10:29:41] Creating workspace INFO[10:29:41] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MsFragger [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx21G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d MSFragger version MSFragger-3.3 Batmass-IO version 1.23.4 Parameter 'data_type' was not supplied. Using default value: 0 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, JVM started with 18 GB memory Checking database... Parameter 'deneutralloss' was not supplied. Using default value: 1 Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 Checking spectral files... F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d: Scans = 42614 F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d: Scans = 42489 There is a mzBIN file from F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d converted with timsdata-2-8-7-1. Will use this mzBIN file. There is a mzBIN file from F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d converted with timsdata-2-8-7-1. Will use this mzBIN file. ***********************************FIRST SEARCH************************************ Parameters: num_threads = 16 database_name = C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 365738238 fragments to be searched in 1 slices (5.45 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.26 s 001. 201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.mzBIN 38.6 s | deisotoping 3.4 s [progress: 117724/117724 (100%) - 8651 spectra/s] 13.6s | postprocessing 0.4 s 002. 201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.mzBIN 40.3 s | deisotoping 3.0 s [progress: 93773/93773 (100%) - 13630 spectra/s] 6.9s | postprocessing 0.2 s ***************************FIRST SEARCH DONE IN 1.927 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 1.35 4.02 | -0.64 3.93 | 0.55 8.20 | -0.16 8.13 002 | 1.32 4.11 | -0.68 4.10 | 0.46 8.38 | -0.17 8.29 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | skip | skip | 63608| 64352| 64433| 64350 -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 64433| 64344| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 66082 -------|------- -------|------- Rm P. | 1 -------|------- Count Parameter 'data_type' was not supplied. Using default value: 0 | 66359 -------|------- New fragment_mass_tolerance = 30 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.944 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameter 'deneutralloss' was not supplied. Using default value: 1 Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 Parameters: num_threads = 16 database_name = C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 30.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = true max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.15 Da. 394902600 fragments to be searched in 1 slices (5.88 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.09 s 001. 201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.mzBIN_calibrated 1.6 s [progress: 117724/117724 (100%) - 9935 spectra/s] 11.8s | postprocessing 6.1 s 002. 201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.mzBIN_calibrated 1.2 s [progress: 93773/93773 (100%) - 10710 spectra/s] 8.8s | postprocessing 4.7 s ***************************MAIN SEARCH DONE IN 0.653 MIN*************************** *******************************TOTAL TIME 5.525 MIN******************************** Process 'MsFragger' finished, exit code: 0 MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML Process 'MsFragger move pepxml' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[10:35:15] Executing Workspace v4.0.0 INFO[10:35:15] Creating workspace INFO[10:35:15] Done PeptideProphet: Workspace init [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:35:16] Executing Workspace v4.0.0 INFO[10:35:16] Creating workspace INFO[10:35:16] Done Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas ..\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML PeptideProphet [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas ..\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML INFO[10:35:16] Executing PeptideProphet v4.0.0 INFO[10:35:16] Executing PeptideProphet v4.0.0 Unknown file type. No file loaded.F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d WARNING: cannot open data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.mzML in msms_run_summary tag... Unknown file type. No file loaded.F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d WARNING: cannot open data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.mzML in msms_run_summary tag... file 1: F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML Unknown file type. No file loaded.F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d WARNING: cannot open data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.mzML in msms_run_summary tag... Unknown file type. No file loaded.F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d WARNING: cannot open data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ... WARNING: CANNOT correct data file F:\TEST/201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.mzML in msms_run_summary tag... file 1: F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML processed altogether 80809 results processed altogether 110872 results INFO: Results written to file: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml - F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml INFO: Results written to file: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml - F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) ***@***.*** read in 0 1+, 33224 2+, 30328 3+, 13439 4+, 3818 5+, 0 6+, and 0 7+ spectra. Found 20436 Decoys, and 60373 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin Iterations: . PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) ***@***.*** read in 0 1+, 47206 2+, 42483 3+, 16676 4+, 4507 5+, 0 6+, and 0 7+ spectra. Found 19884 Decoys, and 90988 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... ..Iterations: ...........10...........10...20.........WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations ..INFO[10:37:23] Done Process 'PeptideProphet' finished, exit code: 0 ..20.....WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations Process 'PeptideProphet' finished, exit code: 0 INFO[10:38:16] Done PeptideProphet: Delete temp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.d Fixing pepxml: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml Writing output to: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml4885408110259737899.temp-rewrite Deleting file: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml Moving rewritten file to original location: [F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml4885408110259737899.temp-rewrite] -> [F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d Fixing pepxml: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml Writing output to: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml5827898373306067448.temp-rewrite Deleting file: F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml Moving rewritten file to original location: [F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml5827898373306067448.temp-rewrite] -> [F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml INFO[10:38:28] Executing ProteinProphet v4.0.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in F:/TEST/interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646.pep.xml... ...read in 0 1+, 18366 2+, 12116 3+, 3899 4+, 575 5+, 0 6+, 0 7+ spectra with min prob 0.9 Reading in F:/TEST/interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml... ...read in 0 1+, 28511 2+, 26404 3+, 7845 4+, 1155 5+, 0 6+, 0 7+ spectra with min prob 0.9 Initializing 32708 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: ...100% Calculating protein lengths and molecular weights from database c:/Users/giorgio.DESKTOP-OR8T69I/Desktop/fasta/2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:..WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U GUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTVEGANPGLIHFGIVRDHDFKNCIIKAYCTNNERGAVTWELPWFLTHYIELNEKKYVEIAKEESLGCCGYELPTFVTTPVNIYDCKELSAGFLRQALLKGSQIAVPTLEPKDELIDGVAYVYPVNTQEVDNVPIKGSKENIKVGIKELGIKRTCSDRGIALLVTNYVGEITETGETSKALVKLKGPSGKELQQVMVPIFKRLFKVGHQEMYSGVKEAMEQDFGRLLISRVMVTVDLGFGALFGACELAVYSAGVVLTKGPCYPLSFLDDSTICYEKDGQIGLYRPREGTAIVFQAATYYTEQGKKNTAKIKHHEVFEGYSNVYAVAKERLSLRYGWNLSSIHNQIAKTMTEWNHRVQQNYEWGFKRSDCLAQGLLAAQHMLKKPICGVNVCTGGLGWSTGQPSPVVFDLVMVKKGLIAAEKACSLGGSGGGIIILDYDYALDEQLLKQLLGSQYAQFTQDCGGVHVKNVFINPVTKQNTIESLVEQVRAGDDVQDLELVNCEVGLSSFLEKVRTSHPCYSKSFIVVRSREILGVLHRRLEERAESSRSPGPSSLRARRGPPSLVRAGRVHGSRRNPADGAKGPGPSQPPSREM .......:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS .68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL ......:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:... Total: 84730 Computing degenerate peptides for 7907 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 9455 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9455 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9455 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9455 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 9455 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 4687 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=1.49733e-06, db_size=95676307 Computing MU for 9455 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Process 'ProteinProphet' finished, exit code: 0 INFO[10:38:59] Done PhilosopherDbAnnotate [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas --prefix rev_ INFO[10:39:00] Executing Database v4.0.0 INFO[10:39:00] Annotating the database Process 'PhilosopherDbAnnotate' finished, exit code: 0 INFO[10:39:03] Done PhilosopherFilter [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev_ --pepxml F:\TEST --protxml F:\TEST\combined.prot.xml INFO[10:39:03] Executing Filter v4.0.0 INFO[10:39:03] Processing peptide identification files INFO[10:39:12] 1+ Charge profile decoy=0 target=0 INFO[10:39:12] 2+ Charge profile decoy=1058 target=51220 INFO[10:39:12] 3+ Charge profile decoy=828 target=41650 INFO[10:39:12] 4+ Charge profile decoy=341 target=12952 INFO[10:39:12] 5+ Charge profile decoy=102 target=2056 INFO[10:39:12] 6+ Charge profile decoy=0 target=0 INFO[10:39:13] Database search results ions=38333 peptides=30187 psms=110207 INFO[10:39:13] Converged to 1.00 % FDR with 105136 PSMs decoy=1060 threshold=0.3119 total=106196 INFO[10:39:14] Converged to 1.00 % FDR with 25463 Peptides decoy=257 threshold=0.8067 total=25720 INFO[10:39:15] Converged to 1.00 % FDR with 33432 Ions decoy=337 threshold=0.7488 total=33769 INFO[10:39:16] Protein inference results decoy=145 target=4542 INFO[10:39:17] Converged to 1.03 % FDR with 2906 Proteins decoy=30 threshold=0.9759 total=2936 INFO[10:39:19] 2D FDR estimation: Protein mirror image decoy=2906 target=2906 INFO[10:39:19] Second filtering results ions=34739 peptides=26631 psms=106335 INFO[10:39:19] Converged to 0.40 % FDR with 105902 PSMs decoy=433 threshold=0.0501 total=106335 INFO[10:39:19] Converged to 1.00 % FDR with 26030 Peptides decoy=262 threshold=0.1433 total=26292 INFO[10:39:19] Converged to 1.00 % FDR with 34273 Ions decoy=345 threshold=0.066 total=34618 INFO[10:39:26] Post processing identifications INFO[10:39:29] Assigning protein identifications to layers INFO[10:39:30] Processing protein inference INFO[10:39:39] Synchronizing PSMs and proteins INFO[10:39:40] Saving Process 'PhilosopherFilter' finished, exit code: 0 INFO[10:39:47] Done PhilosopherReport [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe report INFO[10:39:47] Executing Report v4.0.0 INFO[10:39:53] Creating reports INFO[10:39:55] Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:39:55] Executing Workspace v4.0.0 INFO[10:39:55] Removing workspace INFO[10:39:55] Done Process 'WorkspaceClean' finished, exit code: 0 SpecLibGen [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\anaconda3\python.exe -u C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas F:\TEST F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_2_2646_uncalibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_calibrated.mgf;F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645_uncalibrated.mgf F:\TEST True unused use_easypqp iRT 16 "--rt_lowess_fraction 0.01" Traceback (most recent call last): File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 428, in <module> raise RuntimeError('missing spectra files') RuntimeError: missing spectra files Using (un)calibrated.mgfs. Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping Please cite: (Regular searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020) (Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. bioRxiv. DOI: 10.1101/2020.07.08.192583 (2020) (Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods DOI: 10.1101/2020.05.18.10266 (2020) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19: 1575 (2020) (PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020) (DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015) ==================================================================================DONE============================================================ ~~~~~~~~~~~~~~~~~~~~ Cancelling 0 remaining tasks 10:39:57 ERROR: Error writing log to file java.nio.channels.ClosedByInterruptException: null at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202) at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:216) at java.nio.channels.Channels.writeFullyImpl(Channels.java:78) at java.nio.channels.Channels.writeFully(Channels.java:101) at java.nio.channels.Channels.access$000(Channels.java:61) at java.nio.channels.Channels$1.write(Channels.java:174) at java.nio.file.Files.write(Files.java:3297) at com.dmtavt.fragpipe.tabs.TabRun.saveLogToFile(TabRun.java:354) at com.dmtavt.fragpipe.tabs.TabRun.on(TabRun.java:308) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.greenrobot.eventbus.EventBus.invokeSubscriber(EventBus.java:510) at org.greenrobot.eventbus.EventBus.postToSubscription(EventBus.java:447) at org.greenrobot.eventbus.EventBus.postSingleEventForEventType(EventBus.java:414) at org.greenrobot.eventbus.EventBus.postSingleEvent(EventBus.java:387) at org.greenrobot.eventbus.EventBus.post(EventBus.java:268) at com.dmtavt.fragpipe.api.Bus.post(Bus.java:51) at com.dmtavt.fragpipe.FragpipeRun.lambda$run$6(FragpipeRun.java:283) at java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1640) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK Version info: FragPipe version 14.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421) LCMS files: Experiment/Group: - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d 14 commands to execute: WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx21G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML F:\TEST\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML PeptideProphet: Workspace init [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas ..\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML PeptideProphet: Delete temp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete F:\TEST\fragpipe-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pepXML-temp Rewrite pepxml [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.pep.xml F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645.d ProteinProphet [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined F:\TEST\interact-201124kw_GiorgioCellFrac_Chrom_1_Slot1-34_1_2645

guoci · 2021-10-19T20:39:22Z

@giorgiolivi Can you show me the list of files you have in F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction?
Also, the log is truncated.

giorgiolivi · 2021-10-20T12:06:38Z

Hi Guoci, I've attached again the log, hopefully they are fine now. log_43 = using fragpipe 16 log_34= using fragpipe 14 samples are : 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d Thanks again for your kind help. Regards, Giorgio

On Tue, 19 Oct 2021 at 20:39, guoci ***@***.***> wrote: @giorgiolivi <https://github.com/giorgiolivi> Can you show me the list of files you have in F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction? Also, the log is truncated. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASNT4C6TI4OTEFGO6IXW54LUHXJQJANCNFSM5BWDA3DA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_301, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation Version info: FragPipe version 16.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421) LCMS files: Experiment/Group: - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d 22 commands to execute: CheckCentroid java -Xmx20G -cp "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d 16 WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: F:\TEST] java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d MSFragger move pepxml java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pepXML F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pepXML MSFragger move pin java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin MSFragger move pepxml java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pepXML F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pepXML MSFragger move pin java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Percolator [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Percolator [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin Percolator: Convert to pepxml [Work dir: F:\TEST] java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv interact-201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663 DDA Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: F:\TEST] java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv interact-201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685 DDA Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv ProteinProphet [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.7 --output combined F:\TEST\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev_ --pepxml F:\TEST --protxml F:\TEST\combined.prot.xml --razorbin F:\TEST\.meta\razor.bin PhilosopherReport [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\anaconda3\envs\easypqp\pythonw.exe -u C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas F:\TEST unused F:\TEST True unused use_easypqp noiRT;noIM 16 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.05" delete_intermediate_files F:\TEST\filelist_speclibgen.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [F:\TEST] Cmd: [CheckCentroid], Work dir: [F:\TEST] Cmd: [WorkspaceCleanInit], Work dir: [F:\TEST] Cmd: [MSFragger], Work dir: [F:\TEST] Cmd: [Percolator], Work dir: [F:\TEST] Cmd: [ProteinProphet], Work dir: [F:\TEST] Cmd: [PhilosopherDbAnnotate], Work dir: [F:\TEST] Cmd: [PhilosopherFilter], Work dir: [F:\TEST] Cmd: [PhilosopherReport], Work dir: [F:\TEST] Cmd: [WorkspaceClean], Work dir: [F:\TEST] Cmd: [SpecLibGen], Work dir: [F:\TEST] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v16.0ui state cache AdjustFragIntensity=true BoostComplementaryIon=true CorrThreshold=0 DeltaApex=0.2 ExportPrecursorPeak=true RFmax=500 RPmax=25 RTOverlap=0.3 SE.EstimateBG=true SE.IsoPattern=0.3 SE.MS1PPM=10 SE.MS2PPM=20 SE.MS2SN=1.1 SE.MassDefectFilter=true SE.MassDefectOffset=0.1 SE.NoMissedScan=1 SE.SN=1.1 Table.editor=-18.0106 crystalc.correct_isotope_error=false crystalc.isotope_number=3 crystalc.max-charge=6 crystalc.precursor_isolation_window=0.7 crystalc.precursor_mass=20 crystalc.run-crystalc=false database.db-path=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Desktop\\fasta\\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas database.decoy-tag=rev_ diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fragpipe-config.bin-msfragger=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Downloads\\FragPipe-15.0\\fragpipe\\tools\\MSFragger-3.3\\MSFragger-3.3.jar fragpipe-config.bin-philosopher=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\Downloads\\FragPipe-16.0\\fragpipe\\tools\\philosopher\\philosopher.exe fragpipe-config.bin-python=C\:\\Users\\giorgio.DESKTOP-OR8T69I\\anaconda3\\envs\\easypqp\\pythonw.exe freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.label= ionquant.light= ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=100000 ionquant.medium= ionquant.minexps=1 ionquant.minfreq=0.5 ionquant.minions=1 ionquant.minisotopes=1 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.proteinquant=2 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=3 ionquant.writeindex=0 msfragger.Y_type_masses= msfragger.add_topN_complementary=0 msfragger.allow_multiple_variable_mods_on_residue=true msfragger.allowed_missed_cleavage=2 msfragger.calibrate_mass=2 msfragger.clip_nTerm_M=true msfragger.data_type=0 msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deltamass_allowed_residues=ST msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown=stricttrypsin msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remove_precursor_peak=0 msfragger.report_alternative_proteins=true msfragger.restrict_deltamass_to=all msfragger.run-msfragger=true msfragger.search_enzyme_butnotafter= msfragger.search_enzyme_cutafter=KR msfragger.search_enzyme_name=stricttrypsin msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1 msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,true,1; -18.010600,nE,true,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_topN_peaks=300 msfragger.write_calibrated_mgf=true msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--razor --picked --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.run-report=true phi-report.write-mzid=true protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.7 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.run-ptmprophet=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.diag_ions= ptmshepherd.glyco_mode=false ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.remainder_masses= ptmshepherd.run-shepherd=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-diaumpire=false run-psm-validation=true speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0.05 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=true speclibgen.use-easypqp=true speclibgen.use-spectrast=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=6 tmtintegrator.dont-run-fq-lq=false tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated tmtintegrator.groupby=0 tmtintegrator.labelquant=--tol 20 --level 2 tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false workdir=F\:\\TEST workflow.input.data-type.im-ms=true workflow.input.data-type.regular-ms=false workflow.process-exps-separately=false workflow.ram=0 workflow.threads=16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx20G -cp "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\batmass-io-1.23.4.jar" com.dmtavt.fragpipe.util.CheckCentroid F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d 16 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[10:18:33] Executing Workspace v4.0.0 INFO[10:18:33] Removing workspace WARN[10:18:33] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[10:18:33] Done WorkspaceCleanInit [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[10:18:33] Executing Workspace v4.0.0 INFO[10:18:33] Creating workspace INFO[10:18:33] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: F:\TEST] java -jar -Dfile.encoding=UTF-8 -Xmx20G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d MSFragger version MSFragger-3.3 Batmass-IO version 1.23.4 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_301, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 17 GB memory Checking database... Checking spectral files... F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d: Scans = 41364 F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d: Scans = 41689 ***********************************FIRST SEARCH************************************ Parameters: num_threads = 16 database_name = C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 365738238 fragments to be searched in 1 slices (5.45 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.48 s 001. 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d loading 99%419.8 s | deisotoping 2.8 s [progress: 101259/101259 (100%) - 9905 spectra/s] 10.2s | postprocessing 0.4 s 002. 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d loading 99%466.1 s | deisotoping 2.9 s [progress: 112587/112587 (100%) - 14077 spectra/s] 8.0s | postprocessing 0.3 s ***************************FIRST SEARCH DONE IN 15.345 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | 1.84 4.26 | -0.63 4.17 | 0.55 8.11 | -0.12 8.04 002 | 2.27 4.14 | -0.55 4.09 | 0.91 8.03 | -0.01 7.94 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | skip | skip | 62941| 63448| 63807| 63177 -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 63807| 63837| 63643| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 64882 -------|------- -------|------- Rm P. | 1 -------|------- Count | 65242 -------|------- New fragment_mass_tolerance = 30 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.718 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 16 database_name = C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 30.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 1 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_04 = -17.026500 nQnC 1 variable_mod_05 = -18.010600 nE 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021464 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.15 Da. 390768966 fragments to be searched in 1 slices (5.82 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.96 s 001. 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.mzBIN_calibrated 1.2 s [progress: 101259/101259 (100%) - 15089 spectra/s] 6.7s | postprocessing 7.7 s 002. 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.mzBIN_calibrated 1.5 s [progress: 112587/112587 (100%) - 14675 spectra/s] 7.7s | postprocessing 8.6 s ***************************MAIN SEARCH DONE IN 0.651 MIN*************************** *******************************TOTAL TIME 18.714 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pepXML F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pepXML F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar;/C:/Users/giorgio.DESKTOP-OR8T69I/Downloads/FragPipe-16.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll ***@***.***) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Started Wed Oct 20 10:37:19 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 95311 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 81725 positives and 13586 negatives, size ratio=6.01538 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 43999 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 44037 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 43730 training set positives with q<0.01 in that direction. Found 65847 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.047 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 66516 PSMs with q<0.01 Iteration 2: Estimated 66573 PSMs with q<0.01 Iteration 3: Estimated 66561 PSMs with q<0.01 Iteration 4: Estimated 66566 PSMs with q<0.01 Iteration 5: Estimated 66573 PSMs with q<0.01 Iteration 6: Estimated 66573 PSMs with q<0.01 Iteration 7: Estimated 66571 PSMs with q<0.01 Iteration 8: Estimated 66573 PSMs with q<0.01 Iteration 9: Estimated 66572 PSMs with q<0.01 Iteration 10: Estimated 66567 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0096 0.0037 -0.0059 retentiontime 0.0000 0.0000 0.0000 rank -0.2938 -0.2420 -0.2467 abs_ppm -0.2023 -0.1574 -0.1498 isotope_errors -3.1375 -2.7308 -2.8695 log10_evalue 1.4703 1.2222 1.7877 hyperscore 0.8634 0.9026 0.7737 delta_hyperscore -0.4550 -0.3425 -0.8789 matched_ion_num 0.0256 0.0159 0.0403 peptide_length 0.0000 0.0000 0.0000 ntt -0.1719 -0.1612 -0.1315 nmc 0.0000 0.0000 0.0000 charge_1 0.0926 0.0516 0.0704 charge_2 0.0473 0.0551 0.0452 charge_3 -0.1152 -0.1007 -0.0905 charge_4 -0.1427 -0.0855 -0.1263 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7 3.8557 3.1407 3.1517 m0 Found 66502 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 81725 target PSMs and 13586 decoy PSMs. Calculating q values. Final list yields 66508 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 11.36 cpu seconds or 11 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin Percolator version 3.05.0, Build Date May 18 2020 02:35:01 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll ***@***.***) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\percolator-v3-05.exe --only-psms --no-terminate --post-processing-tdc --num-threads 16 --results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv --decoy-results-psms 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin Started Wed Oct 20 10:37:32 2021 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin Features: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7 Found 104334 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 86355 positives and 17979 negatives, size ratio=4.8031 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 5 as initial direction. Could separate 43323 training set positives with q<0.01 in that direction. Split 2: Selected feature 5 as initial direction. Could separate 43395 training set positives with q<0.01 in that direction. Split 3: Selected feature 5 as initial direction. Could separate 43550 training set positives with q<0.01 in that direction. Found 65158 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.118 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 65954 PSMs with q<0.01 Iteration 2: Estimated 66077 PSMs with q<0.01 Iteration 3: Estimated 66116 PSMs with q<0.01 Iteration 4: Estimated 66133 PSMs with q<0.01 Iteration 5: Estimated 66135 PSMs with q<0.01 Iteration 6: Estimated 66135 PSMs with q<0.01 Iteration 7: Estimated 66130 PSMs with q<0.01 Iteration 8: Estimated 66130 PSMs with q<0.01 Iteration 9: Estimated 66129 PSMs with q<0.01 Iteration 10: Estimated 66132 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0563 -0.0376 -0.0619 retentiontime 0.0000 0.0000 0.0000 rank -0.3583 -0.3676 -0.3126 abs_ppm -0.2240 -0.2414 -0.1784 isotope_errors -3.8028 -4.2785 -3.3465 log10_evalue 2.6413 1.8998 1.6316 hyperscore 0.8784 0.7749 0.7595 delta_hyperscore -1.6212 -1.2137 -0.7722 matched_ion_num 0.1885 0.1248 0.1752 peptide_length 0.0000 0.0000 0.0000 ntt -0.1248 -0.1241 -0.1192 nmc 0.0000 0.0000 0.0000 charge_1 0.1474 0.0963 0.1162 charge_2 0.0529 0.0515 0.0636 charge_3 -0.1109 -0.0868 -0.1066 charge_4 -0.2584 -0.1823 -0.2200 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7 3.8124 3.8727 3.3111 m0 Found 66100 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 86355 target PSMs and 17979 decoy PSMs. Calculating q values. Final list yields 66109 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.18 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: F:\TEST] java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pin 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv 201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv interact-201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663 DDA Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: F:\TEST] java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pin 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv 201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv interact-201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685 DDA Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\fragpipe-16.0.jar com.github.chhh.utils.FileDelete F:\TEST\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.7 --output combined F:\TEST\filelist_proteinprophet.txt INFO[10:38:00] Executing ProteinProphet v4.0.0 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in F:\TEST\interact-201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.pep.xml... ...read in 0 1+, 29493 2+, 28041 3+, 7834 4+, 1069 5+, 0 6+, 0 7+ spectra with min prob 0.7 Reading in F:\TEST\interact-201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.pep.xml... ...read in 0 1+, 28472 2+, 27767 3+, 8593 4+, 1451 5+, 0 6+, 0 7+ spectra with min prob 0.7 Initializing 43286 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: ...90%...100% Calculating protein lengths and molecular weights from database C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9BQE4|SELS_HUMAN : U GUGGSSPGRRGPRWSCAGGGEGSLPNYGGGRLPKRDSKRKLVSSTSPGPSDEEQPKKANGKYSKGEQMSDWMEIKQRRKEEELQKLKEKHKEVQANLEEQMKLRAAALAEQRKVVVDPEVAAAARDLQRQRLARLRASLKQFVVYLLICSFVIYWGYTALLSGVTTHLFRLGETELAPRASLSEEQREM .:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5-2|SELN_HUMAN : U PQLLPLGRRLGEKLFQMYTATSPDEFTSSFSFLNSEIEEPKVSTIDLFYNANIHHVVTGNPLCIMMEVPFSYKELHLGALKQHSSNEQNNQLEELEKVLSWTSIFSENLLTLIPSSELVTERLTRGSGUCSQDDLAGWLLISHVLKNEAKARDFAETFPLYSVKKFPYMAVELRRAAEEWSLEQQWKIEEFVFQLPEGSPLHSDIMSGDEDLIVSPVSPGTAELEMQPIYGIDVEMNSSESAGYLWEMDVNLSRHNPVFLRFDRVHTADKSLIIHGTFQAPSFWFPFDPPESLQFEAHIRFMVTYYFDSIATLCAVAGQPAFRTKVFPRPHFMSLLRHIIVEKGKPPPPYFRNNSLYGTFMSLESPIIWWPEGLEQGPPPLFPQFHRTAFVASPSAAATWNRLGSLALRSVGLFGDKSKTMTEPLLPQFRAEITLTEESPDPPLEEEECSAAPTSGTLKEAIPKFEEPSIYMDGDTDLSSFLFLGDTGLTKLALEQRAAAQAEAHRACVRVAAAAAAALLAGLLALSRARRRPPAPPQAAPGPSPPGRQGPRARGM WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NZV5|SELN_HUMAN : UU PQLLPLGRRLGEKLFQMYTATSPDEFTSSFSFLNSEIEEPKVSTIDLFYNANIHHVVTGNPLCIMMEVPFSYKELHLGALKQHSSNEQNNQLEELEKVLSWTSIFSENLLTLIPSSELVTERLTRGSGUCSQDDLAGWLLISHVLKNEAKARDFAETFPLYSVKKFPYMAVELRRAAEEWSLEQQWKIEEFVFQLPEGSPLHSDIMSGDEDLIVSPVSPGTAELEMQPIYGIDVEMNSSESAGYLWEMDVNLSRHNPVFLRFDRVHTADKSLIIHGTFQAPSFWFPFDPPESLQFEAHIRFMVTYYFDSIATLCAVAGQPAFRTKVFPRPHFMSLLRHIIVEKGKPPPPYFRNNSLYGTFMSLESPIIWWPEGLEQGPPPLFPQFHRTAFVASPSAAATWNRLGSLALRSVGLFGDKSKTMTEPLLPQFRAEITLTEESPDPPLEEEECSAAPTSRLLSLCSSUNLWPLQPQLSSHSCWQVGTQTVSCSGTLKEAIPKFEEPSIYMDGDTDLSSFLFLGDTGLTKLALEQRAAAQAEAHRACVRVAAAAAAALLAGLLALSRARRRPPAPPQAAPGPSPPGRQGPRARGM :.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........50000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........52000 .........:.........:.........:.........:.........:.........:.........:.........:.....WARNING: Found the following zero-mass residues in protein entry sp|P36969-2|GPX4_HUMAN : U MCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF .WARNING: Found the following zero-mass residues in protein entry sp|P36969|GPX4_HUMAN : U MSLGRLCRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF ...:.........53000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........56000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000 .........:.........:.........:.........:.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|Q8IZQ5|SELH_HUMAN : U MAPRGRKRKAEAAVVAVAEKREKLANGGEGMEEATVVIEHCTSURVYGRNAAALSQALRLEAPELPVKVNPTKPRRGSFEVTLLRPDGSSAELWTGIKKGPPRKLKFPEPQEVVEELKKYLS .68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9C0D9|EPT1_HUMAN : U MAGYEYVSPEQLAGFDKYKYSAVDTNPLSLYVMHPFWNTIVKVFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASAPGHKHVPDWVWIVVGILNFVAYTLDGVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILSHWEKYNTGILFLPWGYDISQVTISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGCALCVTLPMSLLNFFRSYKNNTLKLNSVYEAMVPLFSPCLLFILSTAWILWSPSDILELHPRVFYFMVGTAFANSTCQLIVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYVESILLYTLTTAFTLAHIHYGVRVVKQLSSHFQIYPFSLRKPNSDULGMEEKNIGL ......:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .....WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5-2|SELN_HUMAN : U MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV5|SELN_HUMAN : UU MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAAAAVRVCARHAEAQAAARQELALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQTGVQWCSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTKSKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQELGEPWWIIPSELSMFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFRIHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASESSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSWEEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRETVLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSVKPEEIESNLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP ....:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:... Total: 84730 Computing degenerate peptides for 11629 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 14052 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 14052 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 14052 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 14052 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 14052 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 6839 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=6.59889e-06, db_size=95676307 Computing MU for 14052 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Process 'ProteinProphet' finished, exit code: 0 INFO[10:38:52] Done PhilosopherDbAnnotate [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas --prefix rev_ INFO[10:38:53] Executing Database v4.0.0 INFO[10:38:53] Annotating the database INFO[10:38:56] Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe filter --razor --picked --prot 0.01 --tag rev_ --pepxml F:\TEST --protxml F:\TEST\combined.prot.xml --razorbin F:\TEST\.meta\razor.bin INFO[10:38:56] Executing Filter v4.0.0 INFO[10:38:56] Processing peptide identification files INFO[10:39:12] 1+ Charge profile decoy=0 target=0 INFO[10:39:12] 2+ Charge profile decoy=9997 target=69801 INFO[10:39:12] 3+ Charge profile decoy=11326 target=68184 INFO[10:39:12] 4+ Charge profile decoy=7107 target=24179 INFO[10:39:12] 5+ Charge profile decoy=3135 target=5916 INFO[10:39:12] 6+ Charge profile decoy=0 target=0 INFO[10:39:13] Database search results ions=101049 peptides=89574 psms=199645 INFO[10:39:13] Converged to 1.00 % FDR with 132647 PSMs decoy=1339 threshold=0.604346 total=133986 INFO[10:39:15] Converged to 1.00 % FDR with 32077 Peptides decoy=323 threshold=0.876798 total=32400 INFO[10:39:15] Converged to 1.00 % FDR with 41367 Ions decoy=417 threshold=0.846988 total=41784 INFO[10:39:18] Protein inference results decoy=833 target=6006 INFO[10:39:18] Converged to 1.02 % FDR with 3341 Proteins decoy=34 threshold=0.986 total=3375 INFO[10:39:21] 2D FDR estimation: Protein mirror image decoy=3341 target=3341 INFO[10:39:22] Second filtering results ions=53828 peptides=43539 psms=148493 INFO[10:39:22] Converged to 1.00 % FDR with 135777 PSMs decoy=1370 threshold=0.185692 total=137147 INFO[10:39:22] Converged to 1.00 % FDR with 32567 Peptides decoy=328 threshold=0.516062 total=32895 INFO[10:39:22] Converged to 1.00 % FDR with 42183 Ions decoy=425 threshold=0.45918 total=42608 INFO[10:39:30] Post processing identifications INFO[10:39:34] Assigning protein identifications to layers INFO[10:39:36] Processing protein inference INFO[10:39:46] Synchronizing PSMs and proteins INFO[10:39:47] Saving INFO[10:39:55] Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe report INFO[10:39:55] Executing Report v4.0.0 INFO[10:40:02] Creating reports INFO[10:40:05] Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[10:40:05] Executing Workspace v4.0.0 INFO[10:40:05] Removing workspace INFO[10:40:05] Done Process 'WorkspaceClean' finished, exit code: 0 SpecLibGen [Work dir: F:\TEST] C:\Users\giorgio.DESKTOP-OR8T69I\anaconda3\envs\easypqp\pythonw.exe -u C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py C:\Users\giorgio.DESKTOP-OR8T69I\Desktop\fasta\2021-09-24-decoys-contam-200210kw_HomoSapienReveiwed_hi3_strep_H3K_2.fasta.fas F:\TEST unused F:\TEST True unused use_easypqp noiRT;noIM 16 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.05" delete_intermediate_files F:\TEST\filelist_speclibgen.txt File list provided Traceback (most recent call last): File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 212, in <module> easypqp = get_bin_path('easypqp', 'easypqp') File "C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\speclib\gen_con_spec_lib.py", line 121, in get_bin_path if dist.get('files') is None and sys.platform == "win32": AttributeError: '_PackageInfo' object has no attribute 'get' Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 1 remaining tasks System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK Version info: FragPipe version 14.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421) LCMS files: Experiment/Group: - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d - F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d 19 commands to execute: WorkspaceCleanInit [Work dir: F:\TEST14] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: F:\TEST14] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-16.0\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: F:\TEST14] C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx22G C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-15.0\fragpipe\tools\MSFragger-3.3\MSFragger-3.3.jar F:\TEST14\fragger.params F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-19_1_2663.d F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_RA_1_Slot1-24_1_2685.d MsFragger move pepxml C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\giorgio.DESKTOP-OR8T69I\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\Gio_timsTOF_RawData_NT2_plus_mine_cell_fraction\201129kw_Giorgio_Chromatin_NT2_1_Slot1-

guoci · 2021-10-20T21:35:17Z

Did you see any .mgf files?
Your log is still truncated, can you email me at teog@umich.edu?

fcyu assigned guoci Aug 6, 2021

fcyu added the speclib label Aug 6, 2021

guoci added a commit that referenced this issue Aug 6, 2021

Fix #421

9fcd83f

fcyu closed this as completed Aug 12, 2021

This was referenced Sep 11, 2021

library.tsv not generated #458

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Error in SpecLib generation #459

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GianArauz mentioned this issue Sep 27, 2021

EasyPQP (v0.1.25) in FragPipe (v16.0) TypeError: unsupported operand type(s) for +: 'int' and 'NoneType' #473

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guoci mentioned this issue Oct 1, 2021

easypqp error #480

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Odd Error at end of SpecLibGen #421

Odd Error at end of SpecLibGen #421

DrDee79 commented Aug 6, 2021

guoci commented Aug 6, 2021

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guoci commented Oct 20, 2021

Odd Error at end of SpecLibGen #421

Odd Error at end of SpecLibGen #421

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DrDee79 commented Aug 6, 2021

guoci commented Aug 6, 2021

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giorgiolivi commented Oct 19, 2021 via email

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