Nesvilab/FragPipe

Fragpipe v22.0 error with DIA-PASEF file

Closed this issue · 14 comments

hcadre commented

Dear All,

Thank you very much first and foremost for your continuing work on this marvelous piece of software!

I took the chance to test drive the new FragPipe version v22.0 with a single phospho-enriched sample measured by DIA-PASEF using diaTracer for spectrum deconvolution and and DIA-NN for quantification. During the quantification step, however, Fragpipe stops and throws an error message:

image

Can you see any obvious mistake that I made? Log file attached.

Thank you for looking into that issue!

log_2024-06-03_11-20-31.txt

fcyu commented

Could you verify if Python and EasyPQP have been well configured in the "config" tab of FragPipe?

Thanks,

Fengchao

hcadre commented
fcyu commented

Hi Hannes,

Then, could you double check if the "Spec Lib" tab was enabled/checked?

Thanks,

Fengchao

hcadre commented

Hi Fengchao,
"Spec Lib" tab was checked / enabled.
image
I guess it is not essential to also tick "Generate spectral library from search results"
Best,
Hannes

fcyu commented

Hi Hannes,

Is the problem resolved after you enabled the spec lib generation?

Thanks,

Fengchao

hcadre commented
fcyu commented

Hi Hannes,

Can you go to #1606 and upload your log file there?

Thanks.

Fengchao

fcyu commented

I think it is because the Pandas package is too old. Could run the following command to upgrade it

pip uninstall pandas
pip install pandas>=1.5.0

Best,

Fengchao

hcadre commented

Re-installed Pandas package. Now version 2.2.2 is available:

image

Still the same error, no matter whether DIA_Speclib_Quant_diaPASEF or DIA_Speclib_Quant_Phospho_diaPASEF workflow is loaded:

image

log file is attached:

log_2024-06-19_14-23-40.txt

Best,

Hannes

fcyu commented

Thanks for the testing. I will let @guoci take a look. Maybe pandas version 2.2.2 is too new?

Thanks,

Fengchao

fcyu commented

@guoci , any idea about this one?

Thanks,

Fengchao

guoci commented

@hcadre I think you might have installed on to a different python.
Can you show the full output of pip show pandas? There should be a Location: field after the License: field, like this:

$ pip show pandas
Name: pandas
Version: 2.0.3
Summary: Powerful data structures for data analysis, time series, and statistics
Home-page: 
Author: 
Author-email: The Pandas Development Team <pandas-dev@python.org>
License: BSD 3-Clause License

Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team
All rights reserved.

Copyright (c) 2011-2023, Open source contributors.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
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  this list of conditions and the following disclaimer in the documentation
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Location: /home/ci/anaconda3/lib/python3.11/site-packages
Requires: numpy, numpy, python-dateutil, pytz, tzdata
Required-by: altair, bokeh, datasets, datashader, holoviews, hvplot, panel, seaborn, statsmodels, streamlit, xarray

That location should start with:
D:\MSFragger\Anaconda\

fcyu commented

No response.