CAMI-challenge / AMBER

AMBER: Assessment of Metagenome BinnERs
https://cami-challenge.github.io/AMBER/
GNU General Public License v3.0
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Error creating genome binning plots #37

Closed ohickl closed 4 years ago

ohickl commented 4 years ago

Hi, I get the following error when running amber on some binnings of the medium complexity toy data set of cami:

2020-02-07 10:00:58,977 INFO done
2020-02-07 10:00:58,979 INFO Computing metrics for Gold standard - genome binning, CAMI_toy_medium...
2020-02-07 10:01:01,114 INFO done
2020-02-07 10:01:01,118 INFO Computing metrics for CONCOCT - genome binning, CAMI_toy_medium...
2020-02-07 10:01:01,628 INFO done
2020-02-07 10:01:01,628 INFO Computing metrics for MaxBin2 - genome binning, CAMI_toy_medium...
2020-02-07 10:01:02,127 INFO done
2020-02-07 10:01:02,128 INFO Computing metrics for MetaBAT2 - genome binning, CAMI_toy_medium...
2020-02-07 10:01:02,619 INFO done
2020-02-07 10:01:02,619 INFO Computing metrics for MetaWrap - genome binning, CAMI_toy_medium...
2020-02-07 10:01:02,950 INFO done
2020-02-07 10:01:02,950 INFO Computing metrics for MetaWrap_ra - genome binning, CAMI_toy_medium...
2020-02-07 10:01:03,245 INFO done
2020-02-07 10:01:03,245 INFO Computing metrics for MetaWrap_qc - genome binning, CAMI_toy_medium...
2020-02-07 10:01:03,575 INFO done
2020-02-07 10:01:03,575 INFO Computing metrics for DAS_tool - genome binning, CAMI_toy_medium...
2020-02-07 10:01:03,900 INFO done
2020-02-07 10:01:03,902 INFO Saving computed metrics...
2020-02-07 10:01:03,980 INFO done
2020-02-07 10:01:03,981 INFO Creating genome binning plots...
Traceback (most recent call last):
  File "../../tools/AMBER/amber.py", line 412, in <module>
    main()
  File "../../tools/AMBER/amber.py", line 398, in main
    plot_genome_binning(sample_id_to_queries_list, df_summary, pd_bins, args.plot_heatmaps, output_dir)
  File "../../tools/AMBER/amber.py", line 269, in plot_genome_binning
    plots.plot_avg_precision_recall(df_summary_g, output_dir)
  File "/mnt/lscratch/users/ohickl/binning/tools/AMBER/src/plots.py", line 262, in plot_avg_precision_recall
    'Average completeness per genome [%]')
  File "/mnt/lscratch/users/ohickl/binning/tools/AMBER/src/plots.py", line 240, in plot_summary
    plt.tight_layout()
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1352, in tight_layout
    fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/figure.py", line 2307, in tight_layout
    pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/tight_layout.py", line 349, in get_tight_layout_figure
    pad=pad, h_pad=h_pad, w_pad=w_pad)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/tight_layout.py", line 114, in auto_adjust_subplotpars
    tight_bbox_raw = union([ax.get_tightbbox(renderer) for ax in subplots
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/tight_layout.py", line 115, in <listcomp>
    if ax.get_visible()])
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 4198, in get_tightbbox
    bb_xaxis = self.xaxis.get_tightbbox(renderer)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 1145, in get_tightbbox
    ticks_to_draw = self._update_ticks(renderer)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 1028, in _update_ticks
    tick_tups = list(self.iter_ticks())  # iter_ticks calls the locator
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 978, in iter_ticks
    minorTicks = self.get_minor_ticks(len(minorLocs))
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 1415, in get_minor_ticks
    tick = self._get_tick(major=False)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 1792, in _get_tick
    return XTick(self.axes, 0, '', major=major, **tick_kw)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 178, in __init__
    self.gridline = self._get_gridline()
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/axis.py", line 503, in _get_gridline
    **self._grid_kw)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/lines.py", line 391, in __init__
    self.set_linestyle(linestyle)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/lines.py", line 1125, in set_linestyle
    self._us_dashOffset, self._us_dashSeq, self._linewidth)
  File "/home/users/ohickl/anaconda3/envs/amber/lib/python3.7/site-packages/matplotlib/lines.py", line 68, in _scale_dashes
    scaled_offset = offset * lw
TypeError: can't multiply sequence by non-int of type 'float'

Could that be some python2 > python3 problem?

Best

Oskar