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metadata not defined in forest_local.py

Open sipesk opened this issue 9 months ago • 7 comments

Hello,

Phylofisher is great and was running smoothly until i brought the sgt_construct_out.tar.gz to my local machine.

I downloaded forest_local.py and now get an error with the metadata args. I've checked the .tar.gz to make sure than the metadata.tsv are there and contain text

$ python3 forest_local.py -i sgt_constructor_out_Apr.24.2024-local.tar.gz -t 10

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/Cellar/[email protected]/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/local/Cellar/[email protected]/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/Users/au706677/Documents/AU/DeepPurple/Cryobio/Leftovers/EUKBINS/phylofisher/forest_local.py", line 197, in suspicious_clades
    groups.add(metadata[org]['Higher Taxonomy'])
NameError: name 'metadata' is not defined
"""

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

Traceback (most recent call last):
  File "/Users/au706677/Documents/AU/DeepPurple/Cryobio/Leftovers/EUKBINS/phylofisher/forest_local.py", line 684, in <module>
    suspicious = parallel_susp_clades(trees)
  File "/Users/au706677/Documents/AU/DeepPurple/Cryobio/Leftovers/EUKBINS/phylofisher/forest_local.py", line 503, in parallel_susp_clades
    suspicious = list(pool.map(suspicious_clades, trees))
  File "/usr/local/Cellar/[email protected]/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/local/Cellar/[email protected]/3.10.14/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
NameError: name 'metadata' is not defined

sipesk avatar Apr 29 '24 11:04 sipesk