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error in filtering? #36

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raw937 opened this issue Aug 16, 2019 · 0 comments
Open

error in filtering? #36

raw937 opened this issue Aug 16, 2019 · 0 comments

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@raw937
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raw937 commented Aug 16, 2019

refinem outliers scaffold_stats.tsv .
[2019-08-16 11:45:03] INFO: RefineM v0.0.25
[2019-08-16 11:45:03] INFO: refinem outliers scaffold_stats.tsv .
[2019-08-16 11:45:03] INFO: Reading scaffold statistics.
[2019-08-16 11:45:03] INFO: Calculating statistics for 1 genomes over 156 scaffolds.
[2019-08-16 11:45:03] INFO: Reading reference distributions.
Finding outliers in 1 of 1 (100.0%) genomes.
[2019-08-16 11:45:05] INFO: Outlier information written to: ./outliers.tsv
Plotting scaffold distribution for 1 of 1 (100.0%) genomes.
Unexpected error: <type 'exceptions.TypeError'>
Traceback (most recent call last):
File "/home/raw937/anaconda2/bin/refinem", line 396, in
parser.parse_options(args)
File "/home/raw937/anaconda2/lib/python2.7/site-packages/refinem/main.py", line 684, in parse_options
self.outliers(options)
File "/home/raw937/anaconda2/lib/python2.7/site-packages/refinem/main.py", line 295, in outliers
plot_dir)
File "/home/raw937/anaconda2/lib/python2.7/site-packages/refinem/outliers.py", line 770, in plot
combined_plots.save_html(os.path.join(output_dir, genome_id + '.combined.html'))
File "/home/raw937/anaconda2/lib/python2.7/site-packages/refinem/plots/combined_plots.py", line 220, in save_html
AbstractPlot.save_html(self, output_html, html_script, html_body)
File "/home/raw937/anaconda2/lib/python2.7/site-packages/biolib/plots/abstract_plot.py", line 107, in save_html
html_str = mpld3.fig_to_html(self.fig, template_type='simple')
File "/home/raw937/anaconda2/lib/python2.7/site-packages/mpld3/_display.py", line 251, in fig_to_html
figure_json=json.dumps(figure_json, cls=NumpyEncoder),
File "/home/raw937/anaconda2/lib/python2.7/json/init.py", line 251, in dumps
sort_keys=sort_keys, **kw).encode(obj)
File "/home/raw937/anaconda2/lib/python2.7/json/encoder.py", line 207, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/home/raw937/anaconda2/lib/python2.7/json/encoder.py", line 270, in iterencode
return _iterencode(o, 0)
File "/home/raw937/anaconda2/lib/python2.7/site-packages/mpld3/_display.py", line 138, in default
return json.JSONEncoder.default(self, obj)
File "/home/raw937/anaconda2/lib/python2.7/json/encoder.py", line 184, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: array([0.5]) is not JSON serializable

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