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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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question for running on philosopher v3.2.3 #120

Closed clin888 closed 4 years ago

clin888 commented 4 years ago

1) GitHub unreachable for the moment, can't check for versions right now.? 2) A meta data folder was found and will not be overwritten 3) The current Workspace is corrupted or was created with an older version. Please remove it and create a new one. (I am not sure this is due to incomplete installation on our IT group or new version of philosopher)

Thank you for help,

sarah-haynes commented 4 years ago

Hi clin888, 1 and 2 are warnings that you don't need to worry about. For 3, did your process crash? Try removing the ".meta" folder and re-running the commands.

clin888 commented 4 years ago

Thanks, I rerun it, no crash but no output either.... Should I ask our IT to reinstall v3.2.3? please help,

Thanks again

sarah-haynes commented 4 years ago

Can you copy & paste the log from executing the commands here?

clin888 commented 4 years ago

clin@gizmoj35:~philosopher_linux/new_test_1$ philosopher pipeline --config philosopher_linux/new_test_1/philosopher_323.yml philosopher_linux/new_test_1 WARN[0000] The current Workspace is corrupted or was created with an older version. Please remove it and create a new one INFO[11:18:31] Executing Pipeline v3.2.3 INFO[11:18:31] Initiating the workspace on philosopher_linux/new_test_1 WARN[11:18:31] GitHub unreachable for the moment, can't check for versions right now. INFO[11:18:31] Creating workspace INFO[11:18:31] Processing database INFO[11:18:34] Done

sarah-haynes commented 4 years ago

Are you running Philosopher pipeline? It looks like you need to select the commands you want to run, only the workspace and database commands are selected in the default config .yml file:

commands:
  workspace: yes                               # manage the experiment workspace for the analysis
  database: yes                                # target-decoy database formatting
  comet: no                                    # peptide spectrum matching with Comet
  msfragger: no                                # peptide spectrum matching with MSFragger
  peptideprophet: no                           # peptide assignment validation
  ptmprophet: no                               # PTM site localization
  proteinprophet: no                           # protein identification validation
  filter: no                                   # statistical filtering, validation and False Discovery Rates assessment
  freequant: no                                # label-free Quantification
  labelquant: no                               # isobaric Labeling-Based Relative Quantification
  bioquant: no                                 # protein report based on Uniprot protein clusters
  report: no                                   # multi-level reporting for both narrow-searches and open-searches
  abacus: no                                   # combined analysis of LC-MS/MS results
  tmtintegrator: no                            # integrates channel abundances from multiple TMT samples

Please see the Philosopher documentation (https://github.com/Nesvilab/philosopher/wiki) for tutorials and more information. Depending on what type of analyses you want to run, you may also consider using FragPipe (http://fragpipe.nesvilab.org/).

Best, Sarah

prvst commented 4 years ago

@clin888 You need to elaborate on your issue and provide us with more information about the issue you are having, otherwise it will be a guessing game. These log messages can be displayed in different moments of the processing.

clin888 commented 4 years ago

Thank Sarah and Prvst. It works now. I

sarah-haynes commented 4 years ago

Glad to hear it!

Best, Sarah