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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Failure of reading data file #67

Closed ykim7263 closed 4 years ago

ykim7263 commented 4 years ago

Hi,

I am trying to analyze the proteomics data from tims tof pro. I have used *.mgf files to run in MS fragger (both with fragpipe and proteome discoverer node) Both of them failed to read the spectrum (I guess) "Failed in checking xxxxxx\Glycosylation\test.mzML" is the error message shown on the software. It would be great if I could get the way to solve it

Thanks

fcyu commented 4 years ago

Can you share the log from FragPipe with us?

Best,

Fengchao

On Tue, 24 Mar 2020 at 2:27 AM, ykim7263 notifications@github.com wrote:

Hi,

I am trying to analyze the proteomics data from tims tof pro. I have used *.mgf files to run in MS fragger (both with fragpipe and proteome discoverer node) Both of them failed to read the spectrum (I guess) "Failed in checking xxxxxx\Glycosylation\test.mzML" is the error message shown on the software. It would be great if I could get the way to solve it

Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/67, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABU27W7TAWA5AE2N2PTD62LRJBHERANCNFSM4LSM6GHQ .

-- Dr. Fengchao Yu University of Michigan

ykim7263 commented 4 years ago

Hi I have attached the log that i extracted Thank you for your effort.

Best, Kim

On Tue, Mar 24, 2020 at 8:40 AM Fengchao notifications@github.com wrote:

Can you share the log from FragPipe with us?

Best,

Fengchao

On Tue, 24 Mar 2020 at 2:27 AM, ykim7263 notifications@github.com wrote:

Hi,

I am trying to analyze the proteomics data from tims tof pro. I have used *.mgf files to run in MS fragger (both with fragpipe and proteome discoverer node) Both of them failed to read the spectrum (I guess) "Failed in checking xxxxxx\Glycosylation\test.mzML" is the error message shown on the software. It would be great if I could get the way to solve it

Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/67, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABU27W7TAWA5AE2N2PTD62LRJBHERANCNFSM4LSM6GHQ

.

-- Dr. Fengchao Yu University of Michigan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/67#issuecomment-603214891, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSQ7M4Q3GKGVXB5BI4WEA3RJCS2LANCNFSM4LSM6GHQ .

System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_241, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 12.2 MSFragger version 2.4 Philosopher version 3.2.3 (build 1583959175)

LCMS files: Experiment/Group:

14 commands to execute: Workspace [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --clean Workspace [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --init MsFragger [Work dir: C:\Users\YKim\Desktop\test] java -jar -Dfile.encoding=UTF-8 -Xmx8G C:\Users\YKim\Downloads\MSFragger-2.4\MSFragger-2.4\MSFragger-2.4.jar C:\Users\YKim\Desktop\test\fragger.params C:\Users\YKim\Desktop\Glycosylation\test.mzML MsFragger java -cp C:\Users\YKim\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\Users\YKim\Desktop\Glycosylation\test.pepXML C:\Users\YKim\Desktop\test\test.pepXML MsFragger java -cp C:\Users\YKim\Downloads\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\Users\YKim\Desktop\Glycosylation\test.tsv C:\Users\YKim\Desktop\test\test.tsv ReportDbAnnotate [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe database --annotate C:\Users\YKim\Downloads\uniprot-reviewed_no+taxonomy_10090.fasta (1)\uniprot-reviewed_no+taxonomy10090.fasta (1) --prefix rev PeptideProphet: Workspace init [Work dir: C:\Users\YKim\Desktop\test\fragpipe-test.pepXML-temp] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --init PeptideProphet [Work dir: C:\Users\YKim\Desktop\test\fragpipe-test.pepXML-temp] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\YKim\Downloads\uniprot-reviewed_no+taxonomy_10090.fasta (1)\uniprot-reviewed_no+taxonomy10090.fasta (1) ..\test.pepXML PeptideProphet: Delete temp java -cp C:\Users\YKim\Downloads\FragPipe.exe umich.msfragger.util.FileDelete C:\Users\YKim\Desktop\test\fragpipe-test.pepXML-temp ProteinProphet [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\YKim\Desktop\test\interact-test.pep.xml ReportFilter [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml C:\Users\YKim\Desktop\test --protxml C:\Users\YKim\Desktop\test\combined.prot.xml Freequant [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\Users\YKim\Desktop\Glycosylation ReportReport [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe report Workspace [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --clean


~~~~~~~~~ fragpipe.config ~~~~~~~~~
#FragPipe (12.2) runtime properties
#Tue Mar 24 10:08:51 EDT 2020
override_charge=false
ui.ionquant.is-plot=false
ui.ionquant.is-run=false
calibrate_mass=On and find optimal parameters
search_enzyme_butnotafter=P
delta_mass_exclude_ranges=(-1.5,3.5)
ui.name.crystalc.max-charge=6
ui.ionquant.im-tol=0.05
output_report_topN=1
misc.fragger.remove-precursor-range-hi=1.5
deisotope=1
ui.name.reoirt.pep-level-summary=false
misc.slice-db=1
ui.ionquant.rt-tol=0.4
output_format=PEP_XML
ui.name.downstream.check.run-pep-proph=true
ui.name.crystalc.run-crystalc=false
histo_smoothbins=2
peakpicking_width=0.002
ui.name.report.check.dontuseprotprophfile=false
misc.fragger.precursor-charge-hi=4
ui.name.report.check.multiexp=false
ui.ionquant.mz-tol=10
ui.run-quantification=true
misc.fragger.digest-mass-lo=500
min_fragments_modelling=2
ui.name.report.check.printdecoys=false
allowed_missed_cleavage=2
max_variable_mods_per_peptide=3
search_enzyme_cutafter=KR
precursor_mass_lower=-150
misc.fragger.clear-mz-hi=0
peakpicking_promRatio=0.3
output_extended=false
misc.fragger.remove-precursor-range-lo=-1.5
fragment_mass_units=PPM
localization_background=4
ui.name.crystalc.precursor_mass=20
num_enzyme_termini=ENZYMATIC
ui.name.report.text.filter=--sequential --razor --prot 0.01
ui.name.crystalc.correct_isotope_error=false
min_matched_fragments=4
ui.freequant.is-run=true
max_fragment_charge=3
ui.name.report.speclibgen.use-spectrast=true
misc.fragger.precursor-charge-lo=1
ui.name.downstream.text.pep-proph-cmd=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
ui.name.downstream.check.separate-protxml=false
varmod_masses=
intensity_transform=None
ui.name.report.generate-report=true
add_topN_complementary=0
num_threads=3
output_max_expect=50
use_topN_peaks=100
remove_precursor_peak=Do not remove
zero_bin_mult_expect=1.00
allow_multiple_variable_mods_on_residue=false
precursor_mass_mode=selected
ui.name.report.check.mzid=false
ui.freequant.rt-tol=0.4
precursor_mass_units=Da
mass_offsets=0
misc.ram=0
digest_min_length=6
zero_bin_accept_expect=0.00
minimum_peaks=15
digest_max_length=50
misc.fragger.clear-mz-lo=0
track_zero_topN=0
ui.freequant.mz-tol=10
precursor_true_units=PPM
ui.name.downstream.check.combine-pepxml=false
localize_delta_mass=true
max_variable_mods_combinations=5000
ui.name.report.speclibgen.run=true
misc.fragger.enzyme-dropdown=trypsin
ui.name.downstream.check.run-prot-proph=true
search_enzyme_name=trypsin
clip_nTerm_M=true
ui.name.report.run-shepherd=false
ui.name.crystalc.precursor_isolation_window=0.7
ion_series_definitions=
ui.name.report.speclibgen.use-easypqp=false
ui.name.downstream.text.prot-proph-cmd=--maxppmdiff 2000000
fragment_ion_series=b,y
ui.ionquant.min-freq=0.50
precursor_true_tolerance=20
ui.name.crystalc.isotope_number=3
report_alternative_proteins=true
precursor_mass_upper=500
isotope_error=0
misc.fragger.digest-mass-hi=5000
fragment_mass_tolerance=20
minimum_ratio=0.01

Workspace [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --clean INFO[10:08:51] Executing Workspace v3.2.3
INFO[10:08:51] Removing workspace
INFO[10:08:51] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\Users\YKim\Desktop\test] C:\Users\YKim\Downloads\MSFragger-20171106\MSFragger-20171106\philosopher.exe workspace --init INFO[10:08:52] Executing Workspace v3.2.3
INFO[10:08:52] Creating workspace
INFO[10:08:52] Done
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: C:\Users\YKim\Desktop\test] java -jar -Dfile.encoding=UTF-8 -Xmx8G C:\Users\YKim\Downloads\MSFragger-2.4\MSFragger-2.4\MSFragger-2.4.jar C:\Users\YKim\Desktop\test\fragger.params C:\Users\YKim\Desktop\Glycosylation\test.mzML MSFragger version MSFragger-2.4 Batmass-IO version 1.17.4 (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_241, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 7 GB memory Unknown parameters: max_variable_mods_per_mod = 3 Checking C:\Users\YKim\Desktop\Glycosylation\test.mzML... Failed in checking C:\Users\YKim\Desktop\Glycosylation\test.mzML java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Extraneous characters " 62721" Process 'MsFragger' finished, exit code: 1

Process returned non-zero exit code, stopping MsFragger java -cp C:\Users\YKim\Downloads\FragPipe.exe umich.msfragger.util.FileMove C:\Users\YKim\Desktop\Glycosylation\test.pepXML C:\Users\YKim\Desktop\test\test.pepXML


Cancelling 11 remaining tasks
Processing interrupted, stopping MsFragger
fcyu commented 4 years ago

Looks like something is wrong with your C:\Users\YKim\Desktop\Glycosylation\test.mzML file. Can you double check that?

Thanks,

Fengchao

ykim7263 commented 4 years ago

Can you be more specific? Are you talking about the location?

If yes, I am pretty sure it is in the correct location If no, please let me know

Best, Kim

On Tue, Mar 24, 2020 at 10:13 AM Fengchao notifications@github.com wrote:

Looks like something is wrong with your C:\Users\YKim\Desktop\Glycosylation\test.mzML file. Can you double check that?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/67#issuecomment-603262719, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSQ7M7BTMCZVL2VU73PHKDRJC5XZANCNFSM4LSM6GHQ .

fcyu commented 4 years ago

Your file test.mzML is broken.

chhh commented 4 years ago

@ykim7263 To be more specific we need to see the file in question. Please share test.mzml file.

ykim7263 commented 4 years ago

Hi As you mentioned my mzml file is broken, So i re converted my **.d file from Tims Tof Pro and proceeded on Fragpipe software. However, It still does not work properly. I want to share my log file on it. Furthermore, I want to share my mzml file but due to this huge size, I cant sent it through email.

Best, Kim

On Wed, Mar 25, 2020 at 1:23 PM Dmitry Avtonomov notifications@github.com wrote:

@ykim7263 https://github.com/ykim7263 To be more specific we need to see the file in question. Please share test.mzml file.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/67#issuecomment-603974698, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMSQ7M4H4ZI6ZOC437KOXSLRJI4ZFANCNFSM4LSM6GHQ .

System info: System OS: Windows 8.1, Architecture: AMD64 Java Info: 1.8.0_241, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 12.2 MSFragger version 20171106 Philosopher version 3.2.3 (build 1583959175)

LCMS files: Experiment/Group:

13 commands to execute: Workspace [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --clean Workspace [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --init MsFragger [Work dir: C:\Users\vwlab\Desktop\Kim\Output] java -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Users\vwlab\Desktop\Kim\MSFragger-20171106\MSFragger-20171106.jar C:\Users\vwlab\Desktop\Kim\Output\fragger.params Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.mzML MsFragger java -cp C:\Users\vwlab\Desktop\Kim\FragPipe.exe umich.msfragger.util.FileMove Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.pepXML C:\Users\vwlab\Desktop\Kim\Output\20191001_D-3_C1_M1_P.pepXML MsFragger java -cp C:\Users\vwlab\Desktop\Kim\FragPipe.exe umich.msfragger.util.FileMove --no-err Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.tsv C:\Users\vwlab\Desktop\Kim\Output\20191001_D-3_C1_M1_P.tsv ReportDbAnnotate [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe database --annotate C:\Users\vwlab\Desktop\Kim\Mouse_DB\uniprot-reviewed_no+taxonomy10090.fasta --prefix rev PeptideProphet: Workspace init [Work dir: C:\Users\vwlab\Desktop\Kim\Output\fragpipe-20191001_D-3_C1_M1_P.pepXML-temp] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --init PeptideProphet [Work dir: C:\Users\vwlab\Desktop\Kim\Output\fragpipe-20191001_D-3_C1_M1P.pepXML-temp] C:\Users\vwlab\Desktop\Kim\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\vwlab\Desktop\Kim\Mouse_DB\uniprot-reviewed_no+taxonomy_10090.fasta ..\20191001_D-3_C1_M1_P.pepXML PeptideProphet: Delete temp java -cp C:\Users\vwlab\Desktop\Kim\FragPipe.exe umich.msfragger.util.FileDelete C:\Users\vwlab\Desktop\Kim\Output\fragpipe-20191001_D-3_C1_M1_P.pepXML-temp ProteinProphet [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\vwlab\Desktop\Kim\Output\interact-20191001_D-3_C1_M1P.pep.xml ReportFilter [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\Users\vwlab\Desktop\Kim\Output --protxml C:\Users\vwlab\Desktop\Kim\Output\combined.prot.xml ReportReport [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe report Workspace [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --clean


~~~~~~~~~ fragpipe.config ~~~~~~~~~
#FragPipe (12.2) runtime properties
#Tue Mar 31 10:31:27 EDT 2020
override_charge=false
ui.ionquant.is-plot=false
ui.ionquant.is-run=false
calibrate_mass=On and find optimal parameters
search_enzyme_butnotafter=P
delta_mass_exclude_ranges=(-1.5,3.5)
ui.name.crystalc.max-charge=6
ui.ionquant.im-tol=0.05
output_report_topN=1
misc.fragger.remove-precursor-range-hi=1.5
deisotope=1
ui.name.reoirt.pep-level-summary=false
misc.slice-db=1
ui.ionquant.rt-tol=0.4
output_format=PEP_XML
ui.name.downstream.check.run-pep-proph=true
ui.name.crystalc.run-crystalc=false
histo_smoothbins=2
peakpicking_width=0.002
ui.name.report.check.dontuseprotprophfile=false
misc.fragger.precursor-charge-hi=4
ui.name.report.check.multiexp=false
ui.ionquant.mz-tol=10
ui.run-quantification=false
misc.fragger.digest-mass-lo=500
min_fragments_modelling=2
ui.name.report.check.printdecoys=false
allowed_missed_cleavage=1
max_variable_mods_per_peptide=3
search_enzyme_cutafter=KR
precursor_mass_lower=-150
misc.fragger.clear-mz-hi=0
peakpicking_promRatio=0.3
output_extended=false
misc.fragger.remove-precursor-range-lo=-1.5
fragment_mass_units=PPM
localization_background=4
ui.name.crystalc.precursor_mass=20
num_enzyme_termini=ENZYMATIC
ui.name.report.text.filter=--sequential --razor --mapmods --prot 0.01
ui.name.crystalc.correct_isotope_error=false
min_matched_fragments=4
ui.freequant.is-run=true
max_fragment_charge=2
ui.name.report.speclibgen.use-spectrast=true
misc.fragger.precursor-charge-lo=1
ui.name.downstream.text.pep-proph-cmd=--decoyprobs --ppm --accmass --nonparam --expectscore
ui.name.downstream.check.separate-protxml=false
varmod_masses=
intensity_transform=None
ui.name.report.generate-report=true
add_topN_complementary=0
num_threads=7
output_max_expect=50
use_topN_peaks=100
remove_precursor_peak=Do not remove
zero_bin_mult_expect=1.00
allow_multiple_variable_mods_on_residue=false
precursor_mass_mode=selected
ui.name.report.check.mzid=false
ui.freequant.rt-tol=0.4
precursor_mass_units=Da
mass_offsets=0
misc.ram=0
digest_min_length=7
zero_bin_accept_expect=0.00
minimum_peaks=15
digest_max_length=50
misc.fragger.clear-mz-lo=0
track_zero_topN=0
ui.freequant.mz-tol=10
precursor_true_units=PPM
ui.name.downstream.check.combine-pepxml=false
localize_delta_mass=true
max_variable_mods_combinations=5000
ui.name.report.speclibgen.run=true
misc.fragger.enzyme-dropdown=trypsin
ui.name.downstream.check.run-prot-proph=true
search_enzyme_name=trypsin
clip_nTerm_M=true
ui.name.report.run-shepherd=false
ui.name.crystalc.precursor_isolation_window=0.7
ion_series_definitions=
ui.name.report.speclibgen.use-easypqp=false
ui.name.downstream.text.prot-proph-cmd=--maxppmdiff 2000000
fragment_ion_series=b,y
ui.ionquant.min-freq=0.50
precursor_true_tolerance=20
ui.name.crystalc.isotope_number=3
report_alternative_proteins=true
precursor_mass_upper=500
isotope_error=0
misc.fragger.digest-mass-hi=5000
fragment_mass_tolerance=20
minimum_ratio=0.01

Workspace [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --clean INFO[10:31:33] Executing Workspace v3.2.3
INFO[10:31:33] Removing workspace
INFO[10:31:33] Done
Process 'Workspace' finished, exit code: 0

Workspace [Work dir: C:\Users\vwlab\Desktop\Kim\Output] C:\Users\vwlab\Desktop\Kim\philosopher.exe workspace --init INFO[10:31:41] Executing Workspace v3.2.3
INFO[10:31:41] Creating workspace
INFO[10:31:41] Done
Process 'Workspace' finished, exit code: 0

MsFragger [Work dir: C:\Users\vwlab\Desktop\Kim\Output] java -jar -Dfile.encoding=UTF-8 -Xmx6G C:\Users\vwlab\Desktop\Kim\MSFragger-20171106\MSFragger-20171106.jar C:\Users\vwlab\Desktop\Kim\Output\fragger.params Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.mzML MSFragger version MSFragger-20171106 (c) University of Michigan

Unknown parmameters: calibrate_mass = 2 decoyprefix = rev deisotope = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y intensity_transform = 0 localize_delta_mass = 1 mass_offsets = 0 max_variable_mods_per_peptide = 3 precursor_mass_mode = selected remove_precursor_peak = 0 remove_precursor_range = -1.50,1.50 report_alternative_proteins = 1 Peptide index read in 356ms Selected fragment tolerance 0.02 Da and maximum fragment slice size of 3507.94MB 349381116 fragments to be searched in 1 slices (2.60GB total) Operating on slice 1 of 1: 12716ms 20191001_D-3_C1_M1_P.mzML umich.ms.fileio.exceptions.FileParsingException: java.util.concurrent.TimeoutException at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.buildIndex(AbstractXMLBasedDataSource.java:832) at umich.ms.fileio.filetypes.mzml.MZMLIndexParser.parse(MZMLIndexParser.java:109) at umich.ms.fileio.filetypes.mzml.MZMLFile.parseIndex(MZMLFile.java:65) at umich.ms.fileio.filetypes.mzml.MZMLFile.fetchIndex(MZMLFile.java:54) at umich.ms.fileio.filetypes.mzml.MZMLFile.fetchIndex(MZMLFile.java:31) at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parse(AbstractXMLBasedDataSource.java:114) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:763) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:747) at o.b(Unknown Source) at n.d(Unknown Source) at n.a(Unknown Source) at MSFragger.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58) Caused by: java.util.concurrent.TimeoutException at java.util.concurrent.FutureTask.get(Unknown Source) at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.buildIndex(AbstractXMLBasedDataSource.java:817) ... 16 more Error parsing: 20191001_D-3_C1_M1_P.mzML597170ms Process 'MsFragger' finished, exit code: 0

MsFragger java -cp C:\Users\vwlab\Desktop\Kim\FragPipe.exe umich.msfragger.util.FileMove Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.pepXML C:\Users\vwlab\Desktop\Kim\Output\20191001_D-3_C1_M1_P.pepXML File does not exist: Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.pepXMLProcess 'MsFragger' finished, exit code: 1

Process returned non-zero exit code, stopping MsFragger java -cp C:\Users\vwlab\Desktop\Kim\FragPipe.exe umich.msfragger.util.FileMove --no-err Z:\Group member data folders\Kim\TimsTOF\20191001\20191001_D-3_C1_M1_P.tsv C:\Users\vwlab\Desktop\Kim\Output\20191001_D-3_C1_M1_P.tsv


Cancelling 9 remaining tasks
Processing interrupted, stopping MsFragger
sarah-haynes commented 4 years ago

Hi Kim, have you tried analyzing the .d file directly? FragPipe has the ability to do that, just make sure that your MSFragger .jar file hasn't been moved (so it should be in the same directory as the 'ext' folder which is used for raw spectral file reading).

fcyu commented 4 years ago

No feedback.