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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

KeyError: 0 #46

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago 
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 1625, in pandas._libs.hashtable.Int64HashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1632, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 0

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 326, in <module>
    args.handler(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 43, in command_quant
    quant_main(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/quant.py", line 95, in quant_main
    call_kallisto(args, in_files, metadata,sra_id,output_dir,index)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/quant.py", line 17, in call_kallisto
    nominal_length = metadata.df['nominal_length'][0]
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/series.py", line 851, in __getitem__
    return self._get_value(key)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/pandas/core/series.py", line 959, in _get_value
    loc = self.index.get_loc(label)
  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: 0
Hego-CCTB commented 3 years ago

can you post the metadata sheet? Also did this happen with all samples, or just one of them?

kfuku52 commented 3 years ago

Let me investigate. I'll try to fix it.

kfuku52 commented 3 years ago

fixed in https://github.com/kfuku52/amalgkit/commit/568063d493351a4beae27be8a56530823701e1e3. This error should have happened in any single-end RNA-seq data, so you might want to check the previously processed datasets. There might have been more useful data that happened to have dropped because of this bug.