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qiyunlab / HGTector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
BSD 3-Clause "New" or "Revised" License
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An error occurred downloading the database #134

Open taotaoyuan opened 9 months ago

taotaoyuan commented 9 months ago

Database building started at 2023-12-07 17:48:50.178062. Reading NCBI taxonomy database... done. Total number of TaxIDs: 2545202. Reading RefSeq assembly summary... done. Total number of genomes: 344111. Genome categories: bacteria, archaea, fungi, viral, plant Running Command: rsync --list-only --no-motd rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/ Downloading genome list per RefSeq category... bacteria: 325433 archaea: 1889 fungi: 564 viral: 14992 plant: 175 Done. Traceback (most recent call last): File "/home/lx_sky6/software/miniconda3/envs/neoHGT/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3652, in get_loc return self._engine.get_loc(casted_key) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pandas/_libs/index.pyx", line 147, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 176, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: '# assembly_accession'

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

Traceback (most recent call last): File "/home/lx_sky6/yt/soft/neoHGT/scripts/neoHGT", line 88, in main() File "/home/lx_sky6/yt/soft/neoHGT/scripts/neoHGT", line 27, in main module(args) File "/home/lx_sky6/software/miniconda3/envs/neoHGT/lib/python3.11/site-packages/neoHGT-2.0b3-py3.11.egg/neoHGT/database.py", line 153, in call self.retrieve_categories() File "/home/lx_sky6/software/miniconda3/envs/neoHGT/lib/python3.11/site-packages/neoHGT-2.0b3-py3.11.egg/neoHGT/database.py", line 393, in retrieve_categories self.df = self.df[self.df['# assembly_accession'].isin(asmset)]


  File "/home/lx_sky6/software/miniconda3/envs/neoHGT/lib/python3.11/site-packages/pandas/core/frame.py", line 3761, in __getitem__
    indexer = self.columns.get_loc(key)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/lx_sky6/software/miniconda3/envs/neoHGT/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3654, in get_loc
    raise KeyError(key) from err
KeyError: '# assembly_accession'
Mohsin0911 commented 6 months ago

Am also getting this issue, if you got any solution, please share here