search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
208 stars 38 forks source link

workspace not found #74

Closed assafkacen closed 6 years ago

assafkacen commented 6 years ago

Describe the problem

Hello I get the error message: " workspace not found" after finishing calculating spectral count. I saw an open issue about the same problem but fail to find the solution.

System info

You can find that printed on the Config tab.

Describe your experiment

Genral proteomics experiment description

non specific digestion ...

Input data files

Sequence database

Attach fragger.params file

You can find it in the output directory you specified for analysis.

Run log output

output log 👍 INFO[18:09:06] Executing Workspace 20180808 INFO[18:09:08] Removing workspace INFO[18:09:08] Done INFO[18:09:08] Executing Workspace 20180808 INFO[18:09:09] Creating workspace INFO[18:09:09] Done INFO[18:09:09] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzML in msms_run_summary tag... processed altogether 190 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1701_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 68 2+, 92 3+, 27 4+, 3 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 55 Decoys, and 135 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:12] Done INFO[18:09:12] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzML in msms_run_summary tag... processed altogether 71 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1702_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 14 2+, 47 3+, 9 4+, 0 5+, 1 6+, and 0 7+ spectra. Initialising statistical models ... Found 27 Decoys, and 44 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:13] Done INFO[18:09:13] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzML in msms_run_summary tag... processed altogether 394 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1704_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 210 2+, 124 3+, 33 4+, 18 5+, 5 6+, and 4 7+ spectra. Initialising statistical models ... Found 94 Decoys, and 300 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:17] Done INFO[18:09:17] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzML in msms_run_summary tag... processed altogether 267 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1703_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 146 2+, 88 3+, 21 4+, 8 5+, 4 6+, and 0 7+ spectra. Initialising statistical models ... Found 58 Decoys, and 209 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:19] Done INFO[18:09:19] Executing ProteinProphet 20180808 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1701_1_010718.pep.xml... ...read in 0 1+, 44 2+, 14 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1702_1_010718.pep.xml... ...read in 0 1+, 0 2+, 2 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1703_1_010718.pep.xml... ...read in 0 1+, 81 2+, 28 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1704_1_010718.pep.xml... ...read in 0 1+, 0 2+, 38 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 187 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........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 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 .........:.........:.........:.........:.........: Total: 87507 Computing degenerate peptides for 164 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 116 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 183 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.25341e-07, db_size=91247603

Finished INFO[18:09:22] Done INFO[18:09:22] Executing Database 20180808 INFO[18:09:22] Processing database INFO[18:09:36] Done INFO[18:09:36] Executing Filter 20180808 INFO[18:09:36] Processing peptide identification files INFO[18:09:36] 1+ Charge profile decoy=0 target=0 INFO[18:09:36] 2+ Charge profile decoy=11 target=142 INFO[18:09:36] 3+ Charge profile decoy=31 target=106 INFO[18:09:36] 4+ Charge profile decoy=0 target=0 INFO[18:09:36] 5+ Charge profile decoy=0 target=0 INFO[18:09:36] 6+ Charge profile decoy=0 target=0 INFO[18:09:36] Database search results ions=262 peptides=252 psms=290 INFO[18:09:36] Converged to 0.00 % FDR with 0 PSMs decoy=0 threshold=10 total=0 INFO[18:09:36] Converged to 0.00 % FDR with 0 Peptides decoy=0 threshold=10 total=0 INFO[18:09:36] Converged to 0.00 % FDR with 0 Ions decoy=0 threshold=10 total=0 INFO[18:09:37] Post processing identifications INFO[18:09:38] Processing Protein Inference INFO[18:09:38] Correcting PSM to Protein mappings INFO[18:09:38] Mapping Ion status to PSMs INFO[18:09:38] Calculating Spectral Counts FATA[18:09:38] workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory INFO[18:09:38] Executing Report 20180808 FATA[18:09:38] cannot restore serialized data structures: invalid argument INFO[18:09:39] Executing Workspace 20180808 INFO[18:09:40] Removing workspace INFO[18:09:40] Done

** copy text from the text console in the gui here **

I am running the philosopher commands from a command line: command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean command :/home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --init command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 proteinprophet --output interact /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-*.pep.xml command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 database --annotate /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta --prefix rev command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 filter --tag rev --sequential --pepxml /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/ command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 report command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean

anesvi commented 6 years ago

Hi, I see you are running an old version of MSFragger. Please try with a new version. Also, I am not sure what version of Philosopher you are running. Felipe (cc’ed) can help with that. Alexey

From: assafkacen [mailto:notifications@github.com] Sent: Saturday, August 18, 2018 11:48 AM To: chhh/FragPipe Cc: Subscribed Subject: [chhh/FragPipe] workspace not found (#74)

Describe the problem

Hello I get the error message: " workspace not found" after finishing calculating spectral count. I saw an open issue about the same problem but fail to find the solution.

· 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

You can find that printed on the Config tab.

Describe your experiment Genral proteomics experiment description

non specific digestion ...

Input data files Sequence database

Attach fragger.params file

You can find it in the output directory you specified for analysis.

Run log output

output log 👍 INFO[18:09:06] Executing Workspace 20180808 INFO[18:09:08] Removing workspace INFO[18:09:08] Done INFO[18:09:08] Executing Workspace 20180808 INFO[18:09:09] Creating workspace INFO[18:09:09] Done INFO[18:09:09] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.mzML in msms_run_summary tag... processed altogether 190 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1701_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 68 2+, 92 3+, 27 4+, 3 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 55 Decoys, and 135 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:12] Done INFO[18:09:12] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.mzML in msms_run_summary tag... processed altogether 71 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1702_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 14 2+, 47 3+, 9 4+, 0 5+, 1 6+, and 0 7+ spectra. Initialising statistical models ... Found 27 Decoys, and 44 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:13] Done INFO[18:09:13] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.mzML in msms_run_summary tag... processed altogether 394 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1704_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 210 2+, 124 3+, 33 4+, 18 5+, 5 6+, and 4 7+ spectra. Initialising statistical models ... Found 94 Decoys, and 300 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:17] Done INFO[18:09:17] Executing PeptideProphet 20180808 file 1: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.pepXML Failed to open input file '/home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzXML'. WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzXML in msms_run_summary tag... trying .mzML ... SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.mzML in msms_run_summary tag... processed altogether 267 results INFO: Results written to file: /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1703_1_010718.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution init with X! Tandem trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 146 2+, 88 3+, 21 4+, 8 5+, 4 6+, and 0 7+ spectra. Initialising statistical models ... Found 58 Decoys, and 209 Non-Decoys Iterations: .........10.........20.... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 25 iterations INFO[18:09:19] Done INFO[18:09:19] Executing ProteinProphet 20180808 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1701_1_010718.pep.xml... ...read in 0 1+, 44 2+, 14 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1702_1_010718.pep.xml... ...read in 0 1+, 0 2+, 2 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1703_1_010718.pep.xml... ...read in 0 1+, 81 2+, 28 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-HF2_7696_YMER_1704_1_010718.pep.xml... ...read in 0 1+, 0 2+, 38 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 187 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........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 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........85000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........86000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........87000 .........:.........:.........:.........:.........: Total: 87507 Computing degenerate peptides for 164 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 183 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 116 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 183 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=3.25341e-07, db_size=91247603

Finished INFO[18:09:22] Done INFO[18:09:22] Executing Database 20180808 INFO[18:09:22] Processing database INFO[18:09:36] Done INFO[18:09:36] Executing Filter 20180808 INFO[18:09:36] Processing peptide identification files INFO[18:09:36] 1+ Charge profile decoy=0 target=0 INFO[18:09:36] 2+ Charge profile decoy=11 target=142 INFO[18:09:36] 3+ Charge profile decoy=31 target=106 INFO[18:09:36] 4+ Charge profile decoy=0 target=0 INFO[18:09:36] 5+ Charge profile decoy=0 target=0 INFO[18:09:36] 6+ Charge profile decoy=0 target=0 INFO[18:09:36] Database search results ions=262 peptides=252 psms=290 INFO[18:09:36] Converged to 0.00 % FDR with 0 PSMs decoy=0 threshold=10 total=0 INFO[18:09:36] Converged to 0.00 % FDR with 0 Peptides decoy=0 threshold=10 total=0 INFO[18:09:36] Converged to 0.00 % FDR with 0 Ions decoy=0 threshold=10 total=0 INFO[18:09:37] Post processing identifications INFO[18:09:38] Processing Protein Inference INFO[18:09:38] Correcting PSM to Protein mappings INFO[18:09:38] Mapping Ion status to PSMs INFO[18:09:38] Calculating Spectral Counts FATA[18:09:38] workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory INFO[18:09:38] Executing Report 20180808 FATA[18:09:38] cannot restore serialized data structures: invalid argument INFO[18:09:39] Executing Workspace 20180808 INFO[18:09:40] Removing workspace INFO[18:09:40] Done

copy text from the text console in the gui here

I am running the philosopher commands from a command line: command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean command :/home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --init command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1701_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1702_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1704_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 peptideprophet --decoy rev --enzyme N --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/HF2_7696_YMER_1703_1_010718.pepXML command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 proteinprophet --output interact /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/interact-*.pep.xml command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 database --annotate /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/mutatedSeqsUniprotName.translated.withFusion.fasta --prefix rev command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linuxamd64 filter --tag rev --sequential --pepxml /home/labs/yifatlab/assafk/modification/Galit/Base/MSFragger/combine/ command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 report command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/chhh/FragPipe/issues/74, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AhDGe15qtAjSTbzdskRNrfYpwxrVW54Cks5uSDcXgaJpZM4WCnhQ.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

assafkacen commented 6 years ago

sorry I didn't include it in the initial report:

MSFragger version MSFragger-20180316 MSFTBX version 1.8.2 (c) University of Michigan

System OS: Linux, Architecture: amd64 Java Info: 1.8.0_121, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 50062MB memory

the philosopher version , as far as I know is the latest version.

prvst commented 6 years ago

@assafkacen I don't know why you are having an issue with the workspace, maybe @chhh can take a look into the GUI back end. Nevertheless, it looks t me that your database search failed, or you don't have enough spectra in your files.

chhh commented 6 years ago

@assafkacen Do I understand this correctly, that you're having the problem while running the commands from the command line? And the command sequence is 

philosopher workspace --clean
philosopher workspace --init
philosopher peptideprophet ... 1701_1_010718.pepXML
philosopher peptideprophet ... 1702_1_010718.pepXML
philosopher peptideprophet ... 1703_1_010718.pepXML
philosopher peptideprophet ... 1704_1_010718.pepXML
philosopher proteinprophet --output interact .../interact-*.pep.xml
philosopher database --annotate ...withFusion.fasta --prefix rev_
philosopher filter --tag rev_ --sequential --pepxml .../combine/
philosopher report
philosopher workspace --clean
assafkacen commented 6 years ago

yes, this is the sequence and I do run it from command line. I re-downloaded all the programs and problem disappeared. maybe we should close the "issue"

chhh commented 6 years ago

@assafkacen I guess then the problem likely was an old version of philosopher