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taxid not found #738

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WJT0925 opened this issue Jan 5, 2024 · 1 comment
Open

taxid not found #738

WJT0925 opened this issue Jan 5, 2024 · 1 comment
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@WJT0925
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WJT0925 commented Jan 5, 2024

if 10239 in ncbi.get_lineage(int(sp)):

File "/home/jingtian/software/miniconda3/envs/py3/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 241, in get_lineage
raise ValueError("%s taxid not found" %taxid)
ValueError: 3060017 taxid not found

@dengzq1234 dengzq1234 self-assigned this Jan 8, 2024
@ChongLC
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ChongLC commented Jun 9, 2024

Hi developer and @WJT0925,

I am also encountering a similar error. Below is the error message:

Traceback (most recent call last):
  File "/home/chong/miniconda3/lib/python3.8/threading.py", line 932, in _bootstrap_inner
    self.run()
  File "/home/chong/miniconda3/lib/python3.8/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "../rs_host_extractor.py", line 111, in worker
    full_lineages = get_full_lineages([taxonomy_id], ncbi)
  File "../rs_host_extractor.py", line 74, in get_full_lineages
    ranks = get_ranks(taxon_id, desired_ranks, ncbi)
  File "../rs_host_extractor.py", line 60, in get_ranks
    lineage = ncbi.get_lineage(taxid)
  File "/home/chong/miniconda3/lib/python3.8/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 241, in get_lineage
    raise ValueError("%s taxid not found" %taxid)
ValueError: 3075052 taxid not found

While checking the NCBI Taxonomy, there is such a taxonomy (see the figure below).
3075052

I hope to hear a solution from you soon! Thank you.

Best regards,
Chong

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