anesvi
commented
5 years ago Please download Philosopher version 1.5.1
From: May2020 [mailto:notifications@github.com] Sent: Tuesday, September 10, 2019 12:13 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Nesvilab/FragPipe] Cannot read file: open .meta\meta.bin: The system cannot find the path specified. (#135)
External Email - Use Caution Describe the problem
· I'm submitting a:
* [ X] problem running the software
* [ ] bug report
* [ ] feature request
* [ ] question· My MSFragger use case:
* [ X] Closed search (standard small precursor mass tolerance)
* [ ] Open search (large precursor mass tolerance)put your general problem description here
System info
System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_201, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 10.1 MSFragger version 2.1 Philosopher version 1.5.0 (build 1565983386)
You can find that printed on the Config tab.
- OS and version: your response here
- Java version: your response here
Describe your experiment
Hela test run
Genral proteomics experiment description
e.g. "TMT, Human, full cell lysate with Trypsin" , "AP-MS pulldowns, mouse, liver tissue" all setting are below ...
Input data files
e.g. "fractionated HeLa, 5 samples, 3 bio replicates, 2 technical replicates" or "ten 3 hour LC gradients, full cell lysate, fruit fly" or or at least "5 mzml files 1.5Gb each"
Sequence database
human uniprot
your response here, preferably a link or at least name, organism etc. Size of the either in proteins or in megabytes
Attach fragger.params file
You can find it in the output directory you specified for analysis.
Run log output
System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_201, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 10.1 MSFragger version 2.1 Philosopher version 1.5.0 (build 1565983386)
LCMS files: Experiment/Group: Hela200ngC1.mzXML
- Y:\RawData\Hela\Column60\Hela200ngC1.mzXML Experiment/Group: Hela200ngC2.mzXML
- Y:\RawData\Hela\Column60\Hela200ngC2.mzXML
23 commands to execute: Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init MsFragger [Work dir: E:\FragPipeResult\HELAtest\trial02] C:\Program Files\Python37\python C:\Users\huangm\AppData\Local\Temp\fragpipe\msfragger_pep_split.py 5 "java -jar -Dfile.encoding=UTF-8 -Xmx28G" E:\software\MSFragger-2.1.jar E:\FragPipeResult\HELAtest\trial02\fragger.params Y:\RawData\Hela\Column60\Hela200ngC1.mzXML Y:\RawData\Hela\Column60\Hela200ngC2.mzXML MsFragger java -cp E:\software\FragPipe 10.1\FragPipe-10.1.jar umich.msfragger.util.FileMove Y:\RawData\Hela\Column60\Hela200ngC1.pepXML E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML\Hela200ngC1.pepXML MsFragger java -cp E:\software\FragPipe 10.1\FragPipe-10.1.jar umich.msfragger.util.FileMove Y:\RawData\Hela\Column60\Hela200ngC2.pepXML E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML\Hela200ngC2.pepXML ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev PeptideProphet [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\Database\uniprot-human-filtered-reviewed_yes.fasta Hela200ngC2.pepXML PeptideProphet [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\Database\uniprot-human-filtered-reviewed_yes.fasta Hela200ngC1.pepXML ProteinProphet [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML\interact-Hela200ngC2.pep.xml E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML\interact-Hela200ngC1.pep.xml ReportFilter [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML --protxml E:\FragPipeResult\HELAtest\trial02\combined.prot.xml ReportFilter [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML --protxml E:\FragPipeResult\HELAtest\trial02\combined.prot.xml ReportReport [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe report ReportReport [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: E:\FragPipeResult\HELAtest\trial02] java -cp "C:\Users\huangm\AppData\Local\Temp\fragpipe\batmass-io-1.16.1.jar;C:\Users\huangm\AppData\Local\Temp\fragpipe\commons-math3-3.6.1.jar;C:\Users\huangm\AppData\Local\Temp\fragpipe\ptmshepherd-0.2.2.jar" edu.umich.andykong.ptmshepherd.PTMShepherd E:\FragPipeResult\HELAtest\trial02\shepherd.config Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean
#FragPipe (10.1) runtime properties
#Tue Sep 10 10:54:22 CDT 2019
override_charge=false
ui.name.report.check.genspeclib=false
calibrate_mass=Off
search_enzyme_butnotafter=P
max_variable_mods_per_mod=3
delta_mass_exclude_ranges=(-1.5,3.5)
output_report_topN=1
misc.fragger.remove-precursor-range-hi=1.5
misc.slice-db=5
output_format=TSV_AND_PEPXML
ui.name.downstream.check.run-pep-proph=true
histo_smoothbins=3
peakpicking_width=0.002
ui.name.report.check.dontuseprotprophfile=false
misc.fragger.precursor-charge-hi=4
ui.name.report.check.multiexp=false
misc.fragger.digest-mass-lo=200
min_fragments_modelling=3
ui.name.report.check.printdecoys=false
allowed_missed_cleavage=1
search_enzyme_cutafter=KR
precursor_mass_lower=-10
misc.fragger.clear-mz-hi=0
peakpicking_promRatio=0.3
misc.fragger.remove-precursor-range-lo=-1.5
fragment_mass_units=ABS
num_enzyme_termini=ENZYMATIC
ui.name.report.text.filter=--sequential --razor --mapmods --prot 0.01
ui.name.report.check.labelfree=false
min_matched_fragments=4
max_fragment_charge=2
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
intensity_transform=None
add_topN_complementary=0
num_threads=0
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
precursor_mass_units=PPM
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
precursor_true_units=PPM
ui.name.downstream.check.combine-pepxml=false
localize_delta_mass=false
ui.name.downstream.check.run-crystalc=false
max_variable_mods_combinations=5000
ui.name.downstream.check.run-prot-proph=true
search_enzyme_name=Trypsin
clip_nTerm_M=false
ui.name.report.run-shepherd=true
ion_series_definitions=
ui.name.downstream.text.prot-proph-cmd=--maxppmdiff 2000000
fragment_ion_series=b,y
ui.name.report.text.labelfree=--ptw 0.4 --tol 10 --isolated
precursor_true_tolerance=10
precursor_mass_upper=10
report_alternative_proteins=false
isotope_error=-1/0/1/2
misc.fragger.digest-mass-hi=5000
fragment_mass_tolerance=0.1
minimum_ratio=0.01
Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML]
E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean
INFO[10:54:23] Executing Workspace v1.5.0
INFO[10:54:24] Removing workspace
FATA[10:54:24] Cannot read file: open .meta\meta.bin: The system cannot find the path specified.
Process 'Workspace' finished, exit code: 1
Process returned non-zero exit code, stopping
Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML]
E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init
Stopping 23/24 processes (1 already finished)
** copy text from the text console in the gui here **
```
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May2020
fcyu
Describe the problem
I'm submitting a:
My MSFragger use case:
put your general problem description here
System info
System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_201, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 10.1 MSFragger version 2.1 Philosopher version 1.5.0 (build 1565983386)
You can find that printed on the Config tab.
Describe your experiment
Hela test run
Genral proteomics experiment description
e.g. "TMT, Human, full cell lysate with Trypsin" , "AP-MS pulldowns, mouse, liver tissue" all setting are below ...
Input data files
e.g. "fractionated HeLa, 5 samples, 3 bio replicates, 2 technical replicates" or "ten 3 hour LC gradients, full cell lysate, fruit fly" or or at least "5 mzml files 1.5Gb each"
Sequence database
human uniprot
your response here, preferably a link or at least name, organism etc.
Size of the either in proteins or in megabytes
Attach fragger.params file
You can find it in the output directory you specified for analysis.
Run log output
System info: System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_201, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 10.1 MSFragger version 2.1 Philosopher version 1.5.0 (build 1565983386)
LCMS files: Experiment/Group: Hela200ngC1.mzXML
23 commands to execute: Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init MsFragger [Work dir: E:\FragPipeResult\HELAtest\trial02] C:\Program Files\Python37\python C:\Users\huangm\AppData\Local\Temp\fragpipe\msfragger_pep_split.py 5 "java -jar -Dfile.encoding=UTF-8 -Xmx28G" E:\software\MSFragger-2.1.jar E:\FragPipeResult\HELAtest\trial02\fragger.params Y:\RawData\Hela\Column60\Hela200ngC1.mzXML Y:\RawData\Hela\Column60\Hela200ngC2.mzXML MsFragger java -cp E:\software\FragPipe 10.1\FragPipe-10.1.jar umich.msfragger.util.FileMove Y:\RawData\Hela\Column60\Hela200ngC1.pepXML E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML\Hela200ngC1.pepXML MsFragger java -cp E:\software\FragPipe 10.1\FragPipe-10.1.jar umich.msfragger.util.FileMove Y:\RawData\Hela\Column60\Hela200ngC2.pepXML E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML\Hela200ngC2.pepXML ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev ReportDbAnnotate [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe database --annotate E:\Database\uniprot-human-filtered-reviewedyes.fasta --prefix rev PeptideProphet [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\Database\uniprot-human-filtered-reviewed_yes.fasta Hela200ngC2.pepXML PeptideProphet [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\Database\uniprot-human-filtered-reviewed_yes.fasta Hela200ngC1.pepXML ProteinProphet [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML\interact-Hela200ngC2.pep.xml E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML\interact-Hela200ngC1.pep.xml ReportFilter [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML --protxml E:\FragPipeResult\HELAtest\trial02\combined.prot.xml ReportFilter [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML --protxml E:\FragPipeResult\HELAtest\trial02\combined.prot.xml ReportReport [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe report ReportReport [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: E:\FragPipeResult\HELAtest\trial02] java -cp "C:\Users\huangm\AppData\Local\Temp\fragpipe\batmass-io-1.16.1.jar;C:\Users\huangm\AppData\Local\Temp\fragpipe\commons-math3-3.6.1.jar;C:\Users\huangm\AppData\Local\Temp\fragpipe\ptmshepherd-0.2.2.jar" edu.umich.andykong.ptmshepherd.PTMShepherd E:\FragPipeResult\HELAtest\trial02\shepherd.config Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC2.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --clean INFO[10:54:23] Executing Workspace v1.5.0
INFO[10:54:24] Removing workspace
FATA[10:54:24] Cannot read file: open .meta\meta.bin: The system cannot find the path specified. Process 'Workspace' finished, exit code: 1
Process returned non-zero exit code, stopping Workspace [Work dir: E:\FragPipeResult\HELAtest\trial02\Hela200ngC1.mzXML] E:\software\FragPipe 10.1\philosopher_v1.5.0_windows_amd64\philosopher.exe workspace --init