search

MrOlm / drep

Rapid comparison and dereplication of genomes
264 stars 38 forks source link

Something worng while running evaluate module #41

Closed Zhong17 closed 5 years ago

Zhong17 commented 6 years ago

I run the module respectively， command: dRep evaluate work_dir -e a , and get the error like this:

will compare winners will provide warnings about clusters 2 warnings generated: saved to /stor9000/apps/users/NWSUAF/2013130172/Jingrx/drep/log/warnings.txt will produce Widb (winner information db) Traceback (most recent call last): File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/indexes/bas return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Bin Id'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/bin/dRep", line 33, in controller.parseArguments(args) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/controller.py", li self.evaluate_operation(vars(args)) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/controller.py", li drep.d_evaluate.d_evaluate_wrapper(kwargs['work_directory'],kwargs) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/d_evaluate.py", li Widb = evaluate_winners(wd, **kwargs) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/d_evaluate.py", li d = Chdb[Chdb['Bin Id'] == row['genome']] File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/frame.py", return self._getitem_column(key) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/frame.py", return self._get_item_cache(key) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/generic.py" values = self._data.get(item) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/internals.p loc = self.items.get_loc(item) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/indexes/bas return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Bin Id' I wonder what's wrong with the Bin id?

Zhong17 commented 6 years ago

by the way, the data_table fail to get Widb.csc, but Wmdb.csv and Wndb.csv instead, Is anyone know what's Wmdb file and Wndb.csv file?

MrOlm commented 6 years ago

Hi Zhong17,

Are you providing Chdb.csv yourself, or was it generated from dRep running checkM at an earlier step?

Widb.csv contains information about the winning genomes (it's really just a subset of Chdb.csv), whereas Wmdb and Wndb contain information about genome similarities that are close to the thresholds chosen.

-Matt

Zhong17 commented 6 years ago

Hi Matt, thanks for replying, the Chdb.csv were added by me at the earlier step (choose step), I run the module respectively.

Zhong17 commented 6 years ago

the Chdb.csv were generated from checkM and add in the data_table, after running cluster step, and then run the choose step.

MrOlm commented 6 years ago

I see. So this is a slightly complicated situation with dRep. Could you send me the very top of your Chdb.csv file? It would be helpful to know what column names you have.

Best, -Matt