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getzlab / SignatureAnalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
MIT License
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GPU from spectra filte cannot reindex duplicate index #20

Open njbernstein opened 4 years ago

njbernstein commented 4 years ago

err and out. files:

---------------------------------------------------------
---------- S I G N A T U R E  A N A L Y Z E R  ----------
---------------------------------------------------------
   * Creating output dir at test_mutsig_filtered
   * Using cosmic3_exome signatures
   * Saving ARD-NMF outputs to test_mutsig_filtered/nmf_output.h5
(mutsig) nicholas@sci-pvm-nicholas:~/projects/genomics/ukbb/ch/analyses/8_6_2020/mutsig$ cat logs/mutsig_15231552.*
/var/spool/slurm/d/job15231552/slurm_script: 10: /var/spool/slurm/d/job15231552/slurm_script: source: not found
/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/sklearn/ensemble/weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed in a future NumPy release.
  from numpy.core.umath_tests import inner1d
Traceback (most recent call last):
  File "/home/nicholas/miniconda3/envs/mutsig/bin/signatureanalyzer", line 8, in <module>
    sys.exit(main())
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/__main__.py", line 186, in main
    **vars(args)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/signatureanalyzer.py", line 234, in run_spectra
    **nmf_kwargs
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/bnmf.py", line 118, in ardnmf
    markers, signatures = select_markers(X, W, H, cut_norm=cut_norm, cut_diff=cut_diff, verbose=verbose)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/utils.py", line 223, in select_markers
    tmp.loc[:,'mean_on'] = X.loc[np.array(tmp.index), H[H['max_id']==n].index].mean(axis=1)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/indexing.py", line 189, in __setitem__
    self._setitem_with_indexer(indexer, value)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/indexing.py", line 366, in _setitem_with_indexer
    self._setitem_with_indexer(new_indexer, value)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/indexing.py", line 469, in _setitem_with_indexer
    value = self._align_series(indexer, value)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/indexing.py", line 734, in _align_series
    return ser.reindex(new_ix)._values
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/series.py", line 3322, in reindex
    return super(Series, self).reindex(index=index, **kwargs)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/generic.py", line 3685, in reindex
    fill_value, copy).__finalize__(self)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/generic.py", line 3703, in _reindex_axes
    copy=copy, allow_dups=False)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/generic.py", line 3806, in _reindex_with_indexers
    copy=copy)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/internals.py", line 4414, in reindex_indexer
    self.axes[axis]._can_reindex(indexer)
  File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3559, in _can_reindex
    raise ValueError("cannot reindex from a duplicate axis")
ValueError: cannot reindex from a duplicate axis
Closing remaining open files:test_mutsig_filtered_2/nmf_output.h5...done
---------------------------------------------------------
---------- S I G N A T U R E  A N A L Y Z E R  ----------
---------------------------------------------------------
   * Creating output dir at test_mutsig_filtered_2
   * Using cosmic3_exome signatures
   * Saving ARD-NMF outputs to test_mutsig_filtered_2/nmf_output.h5
   * Running ARD-NMF...
    0/9: nit=   39 K=1      del=0.00000000

part of input:

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