search

biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

OverflowError: cannot convert float infinity to integer #26

Closed Estel-Kitsune closed 6 years ago

Estel-Kitsune commented 8 years ago

Hi,

I'm using SICER in one of my projects, and I wanted to give epic a try. I'm using epic 0.0.6 (conda install). I downloaded the test.bed and control.bed files.

epic --treatment test.bed --control control.bed

And I'm getting the following error message:

Merging ChIP and Input data. (File: helper_functions, Log level: INFO, Time: Mon, 18 Jul 2016 17:07:42 ) 2290813547.42effective_genome_length (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 200 window size (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 0 total chip count (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 0.0average_window_readcount (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 1island_enriched_threshold (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 4.0gap_contribution (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) 1.0boundary_contribution (File: compute_background_probabilites, Log level: DEBUG, Time: Mon, 18 Jul 2016 17:07:42 ) Traceback (most recent call last): File "/home/estelle/miniconda2/bin/epic", line 4, in import('pkg_resources').run_script('bioepic==0.0.6', 'epic') File "/home/estelle/miniconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script File "/home/estelle/miniconda2/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1491, in run_script File "/home/estelle/miniconda2/lib/python2.7/site-packages/bioepic-0.0.6-py2.7.egg/EGG-INFO/scripts/epic", line 130, in

File "/pica/h1/estelle/miniconda2/lib/python2.7/site-packages/bioepic-0.0.6-py2.7.egg/epic/run/run_epic.py", line 38, in run_epic File "/pica/h1/estelle/miniconda2/lib/python2.7/site-packages/bioepic-0.0.6-py2.7.egg/epic/statistics/compute_background_probabilites.py", line 59, in compute_background_probabilities File "/pica/h1/estelle/miniconda2/lib/python2.7/site-packages/bioepic-0.0.6-py2.7.egg/epic/statistics/compute_score_threshold.py", line 24, in compute_score_threshold OverflowError: cannot convert float infinity to integer

/Estelle

endrebak commented 8 years ago

Thanks for trying epic and reporting issues.

Try the latest version please. Epic is not stable yet and each upgrade fixes bugs :)

pip install -U bioepic

endrebak commented 8 years ago

It claims that there were no reads in the treatment file. See if that persists after upgrading, or if the file is empty.

Estel-Kitsune commented 8 years ago

There was a problem with the BED files (not on your repo, it was my mistake). I've updated to version 0.1.1. and it seems to work fine with the example dataset. Thanks! I'm closing this issue. PS: When you have time, could you document the commands that are needed to run epic after cloning the git repository?

endrebak commented 8 years ago

Will do. Reopening as a reminder 👍