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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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KeyError: 'avg_len' #97

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago 
amalgkit integrate \
> --out_dir "./" \
> --fastq_dir ${dir_fastp_sp} \
> --threads ${NSLOTS} \
> --remove_tmp yes
amalgkit integrate: start
checking SeqKit dependency
SeqKit dependency satisfied. Moving on.
Starting integration of fastq-file metadata...
Found 2 file(s) for ID OY_10. Lib-layout: paired
Getting sequence statistics.
Traceback (most recent call last):
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 4554, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 4562, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'avg_len'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 380, in <module>
    args.handler(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 89, in command_integrate
    integrate_main(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/integrate.py", line 136, in integrate_main
    get_fastq_stats(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/integrate.py", line 95, in get_fastq_stats
    tmp_metadata.loc[row,'spot_length']= tmp_stat_df.loc[0,'avg_len']
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 889, in __getitem__
    return self._getitem_tuple(key)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 1060, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 831, in _getitem_lowerdim
    return getattr(section, self.name)[new_key]
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 895, in __getitem__
    return self._getitem_axis(maybe_callable, axis=axis)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 1124, in _getitem_axis
    return self._get_label(key, axis=axis)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexing.py", line 1073, in _get_label
    return self.obj.xs(label, axis=axis)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/generic.py", line 3738, in xs
    loc = index.get_loc(key)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3082, in get_loc
    raise KeyError(key) from err
KeyError: 'avg_len'