File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/ae9de377c1ca0b9efc9e172e20e551/.command.err
Size
13.6 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

View in new tab 
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-wzj4rdqu because there was an issue with the default path (/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (9) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
Traceback (most recent call last):
  File "/usr/local/bin/call_cnv.py", line 2215, in <module>
    main()
  File "/usr/local/bin/call_cnv.py", line 2117, in main
    ss_result, ss_probes, ss_clones, ss_metrics = call_cnv_single_sample(
                                                  ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/call_cnv.py", line 1668, in call_cnv_single_sample
    result_df, clone_summary, metrics = run_germline_decomp(
                                        ^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/clonal_decomp.py", line 1750, in run_germline_decomp
    fit_result = fit_diploid_logr(df, dipLogR_range=germ_dipLogR_range,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/clonal_decomp.py", line 373, in fit_diploid_logr
    fold_cost_curves[fi] = future.result()
                           ^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/clonal_decomp.py", line 361, in _cv_fold
    return _compute_cost_curve(
           ^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/clonal_decomp.py", line 233, in _compute_cost_curve
    chunk_d = max(1, int(5e8 / (S * C * 8)))
                         ~~~~^~~~~~~~~~~~~
ZeroDivisionError: float division by zero