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MrOlm / drep

Rapid comparison and dereplication of genomes
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How could i get strain_heterogeneity? #40

Closed Zhong17 closed 5 years ago

Zhong17 commented 6 years ago

when I run choose muddle of dRep, according the guid of Advanced use, and get the error: Loading work directory 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.choose_operation(vars(args)) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/controller.py", li drep.d_choose.d_choose_wrapper(kwargs['work_directory'],kwargs) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/d_choose.py", line Gdb = drep.d_filter._get_run_genomeInfo(wd, bdb, **kwargs) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/d_filter.py", line Idb = chdb_to_genomeInfo(Chdb) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/drep/d_filter.py", line Gdb = Gdb[['genome', 'completeness', 'contamination', 'strain_heterogeneity']] File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/frame.py", return self._getitem_array(key) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/frame.py", indexer = self.loc._convert_to_indexer(key, axis=1) File "/stor9000/apps/users/NWSUAF/2013130172/software/miniconda_dRep/lib/python3.6/site-packages/pandas/core/indexing.py .format(mask=objarr[mask])) KeyError: "['strain_heterogeneity'] not in index" I have no idea that how could I find strain_heterogeneity information?

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?

-Matt