donovan-h-parks / RefineM

A toolbox for improving metagenome-assembled genomes.
GNU General Public License v3.0
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error in filtering? #36

Open raw937 opened 5 years ago

raw937 commented 5 years ago

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