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statisticalbiotechnology / triqler

The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
Apache License 2.0
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Still getting errors (but different ones)! #3

Closed magnuspalmblad closed 5 years ago

magnuspalmblad commented 5 years ago

Dear Matthew,

I updated triqler and tried it again. I do get the results, but also some warnings that you may be interested in:

[Anaconda3] C:\Users\nmpalmblad\My Documents\Projects\triqler>triqler --fold_cha nge_eval 0.8 iPRG2016.tsv Triqler version 0.1.3 Copyright (c) 2018 Matthew The. All rights reserved. Written by Matthew The (matthew.the@scilifelab.se) in the School of Engineering Sciences in Chemistry, Biotechnology and Health at the Royal Institute of Technology in Stockholm.

Parsing triqler input file Calculating identification PEPs featureClusterIdx: 0 featureClusterIdx: 10000 Dividing intensities by 100000 for increased readability Surviving spectrumIdxs: 12452 Converting to peptide quant rows Calculating peptide-level identification PEPs Writing peptide quant rows to file Fitting hyperparameters params["muDetect"], params["sigmaDetect"] = 1.048101, 0.376366 params["muXIC"], params["sigmaXIC"] = 3.277408, 0.951171 params["muProtein"], params["sigmaProtein"] = 0.066833, 0.239527 params["muFeatureDiff"], params["sigmaFeatureDiff"] = -0.014124, 0.148583 params["shapeInGroupStdevs"], params["scaleInGroupStdevs"] = 1.027202, 0.089210 Calculating protein quants Traceback (most recent call last): File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\runpy.py", lin e 170, in _run_module_as_main "main", mod_spec) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\runpy.py", lin e 85, in _run_code exec(code, run_globals) File "C:\Users\nmpalmblad\AppData\Local\Continuum\Anaconda3\Scripts\triqler.ex e__main__.py", line 9, in File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\ triqler\triqler.py", line 35, in main runTriqler(params, args.in_file, args.out_file) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\ triqler\triqler.py", line 102, in runTriqler diff_exp.doDiffExp(params, peptQuantRows, triqlerOutputFile, getPickedProtei nCalibration, selectComparisonBayesTmp, qvalMethod = qvalMethod) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\ triqler\diff_exp.py", line 17, in doDiffExp proteinOutputRows = proteinQuantificationMethod(peptQuantRows, params, prote inModifier, getEvalFeatures) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\ triqler\triqler.py", line 360, in getPickedProteinCalibration posteriors = processingPool.checkPool(printProgressEvery = 50) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\ triqler\multiprocessing_pool.py", line 19, in checkPool outputs.append(res.get(True)) File "c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\multiprocessin g\pool.py", line 604, in get c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in g reater_equal return (self.a <= x) & (x <= self.b) raise TimeoutError c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in l ess_equal return (self.a <= x) & (x <= self.b) multiprocessing.context.TimeoutError c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in g reater_equal return (self.a <= x) & (x <= self.b) c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in l ess_equal return (self.a <= x) & (x <= self.b) c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in g reater_equal return (self.a <= x) & (x <= self.b) c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in l ess_equal return (self.a <= x) & (x <= self.b) c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in g reater_equal return (self.a <= x) & (x <= self.b) c:\users\nmpalmblad\appdata\local\continuum\anaconda3\lib\site-packages\scipy\st ats_distn_infrastructure.py:876: RuntimeWarning: invalid value encountered in l ess_equal return (self.a <= x) & (x <= self.b)

[Anaconda3] C:\Users\nmpalmblad\My Documents\Projects\triqler>

MatthewThe commented 5 years ago

Dear Magnus,

Thanks for reporting this. It's safe to ignore these warnings but I'll try to find a way to avoid them.