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Reporting error in seaborn violin plot generation when running multisample no groups #83

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chris-cheshire opened this issue Jan 6, 2022 · 0 comments
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  Namespace(bin_frag='*bin500.awk.bed', func=<function gen_png at 0x7f98d967aa60>, log='log.txt', meta='meta_table_ctrl.csv', meta_ctrl='meta_table_ctrl.csv', output='.', raw_frag='*.frag_len.txt', seacr_bed='*bed.*.bed')

Command error:
  2022-01-06 08:54:32,287:reporting:INFO - CUT&RUN Python Reporting
  2022-01-06 08:54:32,288:gen_img:INFO - Generating plots to output folder
  Traceback (most recent call last):
    File "/camp/home/cheshic/.nextflow/assets/nf-core/cutandrun/bin/reporting.py", line 72, in <module>
      parsed_args.func(parsed_args)
    File "/camp/home/cheshic/.nextflow/assets/nf-core/cutandrun/bin/reporting.py", line 42, in gen_png
      report_gen.generate_cutandrun_reports(output_path)
    File "/camp/lab/luscomben/home/users/cheshic/nfcache/.nextflow/assets/nf-core/cutandrun/bin/lib/reports.py", line 63, in generate_cutandrun_reports
      plots, data, mqc_frag_hist = self.generate_reports()
    File "/camp/lab/luscomben/home/users/cheshic/nfcache/.nextflow/assets/nf-core/cutandrun/bin/lib/reports.py", line 317, in generate_reports
      plot7b, data7b = self.peak_widths()
    File "/camp/lab/luscomben/home/users/cheshic/nfcache/.nextflow/assets/nf-core/cutandrun/bin/lib/reports.py", line 544, in peak_widths
      ax = sns.violinplot(data=self.seacr_beds, x="group", y="peak_width", hue="replicate", palette = "viridis")
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/seaborn/_decorators.py", line 46, in inner_f
      return f(**kwargs)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/seaborn/categorical.py", line 2397, in violinplot
      plotter = _ViolinPlotter(x, y, hue, data, order, hue_order,
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/seaborn/categorical.py", line 524, in __init__
      self.estimate_densities(bw, cut, scale, scale_hue, gridsize)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/seaborn/categorical.py", line 639, in estimate_densities
      kde, bw_used = self.fit_kde(kde_data, bw)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/seaborn/categorical.py", line 675, in fit_kde
      kde = stats.gaussian_kde(x, bw)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/scipy/stats/kde.py", line 206, in __init__
      self.set_bandwidth(bw_method=bw_method)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/scipy/stats/kde.py", line 556, in set_bandwidth
      self._compute_covariance()
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/scipy/stats/kde.py", line 565, in _compute_covariance
      self._data_covariance = atleast_2d(cov(self.dataset, rowvar=1,
    File "<__array_function__ internals>", line 5, in cov
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/numpy/lib/function_base.py", line 2469, in cov
      avg, w_sum = average(X, axis=1, weights=w, returned=True)
    File "<__array_function__ internals>", line 5, in average
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/numpy/lib/function_base.py", line 407, in average
      scl = wgt.sum(axis=axis, dtype=result_dtype)
    File "/opt/conda/envs/reporting/lib/python3.8/site-packages/numpy/core/_methods.py", line 47, in _sum
      return umr_sum(a, axis, dtype, out, keepdims, initial, where)
  TypeError: No loop matching the specified signature and casting was found for ufunc add
@chris-cheshire chris-cheshire added the bug Something isn't working label Jan 6, 2022
@chris-cheshire chris-cheshire self-assigned this Jan 6, 2022
@chris-cheshire chris-cheshire added the WIP Work in progress label Jan 6, 2022
@chris-cheshire chris-cheshire mentioned this issue Jan 10, 2022
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