Spectral Library Generation Script did not initialise correctly??

[ChengkangLi]

Describe the problem

• I'm submitting a:

  • [ ] problem running the software
  • [ ] bug report
  • [ ] feature request
  • [x] question

• My MSFragger use case:

  • [ ] Closed search (standard small precursor mass tolerance)
  • [ ] Open search (large precursor mass tolerance)

  FragPipe stop me once i press run button, it is my first time to start a search following the instruction from "https://msfragger.nesvilab.org/tutorial_fragpipe.html". but there is an error message, as shown as the issue title. can anyone help me out.

System info

You can find that printed on the Config tab.

• OS and version: your response here
• Java version: your response here

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Describe your experiment

Genral proteomics experiment description

e.g. "TMT, Human, full cell lysate with Trypsin" , "AP-MS pulldowns, mouse, liver tissue"

...

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

your response here, preferably a link or at least name, organism etc.
Size of the either in proteins or in megabytes

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Attach fragger.params file

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

Run log output

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

[fcyu]

Can you send us your log? It's should be in the folder of your results and the file name looks like "log-fragpipe-run-at_yyyy-mm-dd_hh-mm-ss.log".

Thanks,

Fengchao

[chhh]

@ChengkangLi if it's your first time setting up a search I'd suggest turning off spectral library generation. And while you're just trying to set up your first search, uncheck what's not needed for the search itself:

• Uncheck "Generate Spectral Library from search results" on Report tab
• Uncheck "Label-free Quant" on Report tab
• Uncheck "Run PTM-Shepherd" on Report tab
• Uncheck "Run Crystal-C" on Downstream tab

This will leave you with running MSFragger for the search itself, PeptideProphet and ProteinProphet for PSM validation and protein validation (Downstream tab) and "Create report" on Report tab which runs several tools from Philosopher package. Try that first, once that works and you get the search results you want you can move on to generating spectral library.

[ChengkangLi]

Thank you for both of your answers. @fcyu There is no log file generated, unfortunately, so it stop from the very beginning. @chhh I found an missing modules from the cofiguration page, the msproteomicstools, and i was then trying to get it from pip. however, error message popped out once again at this stage, while PyMSNumpress was trying to be installed. and here i attached the message, in case, i might help.

any suggestion? Thank you in advanced, Chengkang

[guoci]

@ChengkangLi what is the command?

[ChengkangLi]

@guoci pip install msproteomicstools. and most of the related "files" were installed successfully, but not from this one.

[guoci]

@ChengkangLi can you use Anaconda Python3 and try again? https://www.anaconda.com/distribution/#download-section

[fcyu]

No response,

[ChengkangLi]

@fcyu @guoci sorry for the late reply, I have not have time to really try it. but I will give it a try some time in the future. Thank you very much.

[BR-metal]

When I installed Python 3.0.1 and added it's location on the config tab the error about the spectral library generation was resolved.