peak finding failed: boolean index did not match indexed array mm10 numpy-1.14.5

[Sol Katzman]

Clipper 0.2.0  (dated Jun 28 2018)

-s mm10  (all options defaults)

Immediately fails with:

ERROR:root:peak finding failed:, ENSMUSG00000023795, boolean index did not match indexed array along dimension 0; dimension is 95 but corresponding boolean dimension is 55

In other forums, I have seen messages to the effect that numpy versions 1.11 and earlier tolerated this mismatch.

Full traceback below.

Any help is appreciated.

Traceback (most recent call last):
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/bin/clipper", line 11, in <module>
    sys.exit(call_main())
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/peakfinder.py", line 687, in call_main
    main(options)
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/peakfinder.py", line 582, in main
    jobs.append(func_star(job))
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/peakfinder.py", line 147, in func_star
    return call_peaks(*varables)
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/call_peak.py", line 930, in call_peaks
    verbose=verbose)
  File "/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/call_peak.py", line 1092, in peaks_from_info
    raise error

[Gabriel Pratt]

Try running in --debug mode

(The code written in 2012 is now showing its age)

Gabriel Pratt

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[Sol Katzman]

That run used --debug

/Sol.

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[Sol Katzman]

[Sol Katzman]

I backed out numpy to version 1.11.1

pip uninstall numpy
pip install -Iv numpy==1.11.1

Now I get thousands (tens of thousands) of Warnings instead of the Error

WARNING:py.warnings:/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/call_peak.py:597: VisibleDeprecationWarning: boolean index
did not match indexed array along dimension 0; dimension is 172 but corresponding boolean dimension is 15
  peak_center = [x + peak_start for x in self.xRange[self.find_local_maxima(spline_values[peak_start:(peak_stop + 1)])]]

WARNING:py.warnings:/public/groups/wet/python_virtualenv_dirs/virtualenv_python2.7/lib/python2.7/site-packages/clipper/src/call_peak.py:597: VisibleDeprecationWarning: boolean index
did not match indexed array along dimension 0; dimension is 206 but corresponding boolean dimension is 6
  peak_center = [x + peak_start for x in self.xRange[self.find_local_maxima(spline_values[peak_start:(peak_stop + 1)])]]

The clipper code should be cleaned up.

/Sol.

On Friday, April 10, 2020 at 1:17:00 PM UTC-7, Sol Katzman wrote:

[Brittany Cain]

Hi Sol,

I am not a creator of this package, but I have also ran into this issue. As you had mentioned, moving back the numpy version turns these errors into warnings. I believe these warnings are benign as I received a very similar output to that posted on ENCODE even with millions of these warnings.

However, I upgraded scikit-learn to 0.17.1 from 0.13 and these warnings went away and I still received the same output bedfile as before. Below is the list of packages in my virtual environment that I use to run CLIPper.

argh==0.26.2

backports.functools-lru-cache==1.6.1

clipper @ git+https://github.com/YeoLab/clipper.git@0f09110d018ee41a5141f477df4ceaca3da850f2

configparser==4.0.2

contextlib2==0.6.0.post1

cycler==0.10.0

Cython==0.29.20

gffutils==0.8.7.1

HTSeq==0.6.1

importlib-metadata==1.7.0

kiwisolver==1.1.0

matplotlib==2.2.2

numpy==1.10.2

pandas==0.17.0

pathlib2==2.3.5

pybedtools==0.8.1

pyfaidx==0.5.9

pyparsing==2.4.7

pysam==0.12.0.1

python-dateutil==2.8.1

pytz==2020.1

scandir==1.10.0

scikit-learn==0.17.1

scipy==0.17.1

simplejson==3.17.0

six==1.15.0

subprocess32==3.5.4

zipp==1.2.0

I hope this helps!

Brittany

[Sol Katzman]

Dear Brittany,

Thanks. I will try that if I have to run Clipper in the future.

I notice that you are still using a downlevel version of numpy (1.10.2)

/Sol.

[Brittany Cain]

Sol,

I am still using numpy 1.10.2. After running into several deprecation issues, I started mostly following the package versions from the eCLIP-seq Processing Pipeline v2.2 (attached). There might be newer versions of numpy that work, but I have not sought them out. 

Brittany