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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicCorrectMatrix Error #406

Closed francicco closed 5 years ago

francicco commented 5 years ago

Hi,

running hicCorrectMatrix diagnostic_plot I get this error?

INFO:hicexplorer.hicCorrectMatrix:Removing 389 zero value bins
INFO:hicmatrix.HiCMatrix:Number of poor regions to remove: 389 {'Scf0000010_pilon_pilon_pilon_pilon_pilon': 15, 'Scf0000011_pilon_pilon_pilon_pilon_pilon': 23, 'Scf0000012_pilon_pilon_pilon_pilon_pilon': 26, 'Scf0000021_pilon_pilon_pilon_pilon_pilon': 10, 'Scf0000024_pilon_pilon_pilon_pilon_pilon': 1, 'Scf0000036_pilon_pilon_pilon_pilon_pilon': 4, 'Scf0000038_pilon_pilon_pilon_pilon_pilon': 1 [..]
INFO:hicexplorer.hicCorrectMatrix:mad threshold -0.13865616547334927
Traceback (most recent call last):
  File "/home/fc464/software/hicexplorer/bin/hicCorrectMatrix", line 7, in <module>
    main()
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/hicexplorer/hicCorrectMatrix.py", line 568, in main
    plot_total_contact_dist(ma, args)
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/hicexplorer/hicCorrectMatrix.py", line 497, in plot_total_contact_dist
    plt.savefig(args.plotName)
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/pyplot.py", line 722, in savefig
    res = fig.savefig(*args, **kwargs)
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2014, in print_figure
    canvas = self._get_output_canvas(format)
  File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1956, in _get_output_canvas
    .format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format 'h5' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)

It looks like something is not installed. Is there anything missing?

Thank you a lot F

joachimwolff commented 5 years ago

Hi,

The error indicates you defined as an output image a h5 matrix. This does not work, please use as output for the plot: eps, pdf, pgf, png, ps, raw, rgba, svg, svg

Best,

Joachim

Francesco Cicconardi notifications@github.com schrieb am Do. 4. Juli 2019 um 23:44:

Hi,

running hicCorrectMatrix diagnostic_plot I get this error?

INFO:hicexplorer.hicCorrectMatrix:Removing 389 zero value bins INFO:hicmatrix.HiCMatrix:Number of poor regions to remove: 389 {'Scf0000010_pilon_pilon_pilon_pilon_pilon': 15, 'Scf0000011_pilon_pilon_pilon_pilon_pilon': 23, 'Scf0000012_pilon_pilon_pilon_pilon_pilon': 26, 'Scf0000021_pilon_pilon_pilon_pilon_pilon': 10, 'Scf0000024_pilon_pilon_pilon_pilon_pilon': 1, 'Scf0000036_pilon_pilon_pilon_pilon_pilon': 4, 'Scf0000038_pilon_pilon_pilon_pilon_pilon': 1 [..] INFO:hicexplorer.hicCorrectMatrix:mad threshold -0.13865616547334927 Traceback (most recent call last): File "/home/fc464/software/hicexplorer/bin/hicCorrectMatrix", line 7, in main() File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/hicexplorer/hicCorrectMatrix.py", line 568, in main plot_total_contact_dist(ma, args) File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/hicexplorer/hicCorrectMatrix.py", line 497, in plot_total_contact_dist plt.savefig(args.plotName) File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/pyplot.py", line 722, in savefig res = fig.savefig(*args, kwargs) File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig self.canvas.print_figure(fname, kwargs) File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2014, in print_figure canvas = self._get_output_canvas(format) File "/home/fc464/software/hicexplorer/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1956, in _get_output_canvas .format(fmt, ", ".join(sorted(self.get_supported_filetypes())))) ValueError: Format 'h5' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)

It looks like something is not installed. Is there anything missing?

Thank you a lot F

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francicco commented 5 years ago

Oh, ok I get it. I was just following the instruction from your tutorial

https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html

I guess you have to fix some minor problems.

Thanks a lot F

joachimwolff commented 5 years ago

Yes you are right, these typos need to be fixed.