metadata not defined in forest_local.py

sipesk commented 5 months ago

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/python@3.10/3.10.14/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/python@3.10/3.10.14/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/python@3.10/3.10.14/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/python@3.10/3.10.14/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

robert-ervin-jones commented 5 months ago

Hi @sipesk,

Can you try re-running without the -t option? There may be an issue with the parallelization.

Let me know if that works or not.

Thanks for using PhyloFisher!

Best, Robert

sipesk commented 5 months ago

No dice. I tried both python and python3 as well.

(fisher) au706677@d46989 phylofisher % python3 forest_local.py -i sgt_constructor_out_Apr.24.2024-local.tar.gz
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/Cellar/python@3.10/3.10.14/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/python@3.10/3.10.14/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/python@3.10/3.10.14/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/python@3.10/3.10.14/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

Dir contains metadata.tsv and its a non zero content file.

shuiyujinlan commented 5 months ago

Hi, @robert-ervin-jones . I have the same question in my test with the original "metadata.tsv". How to bypass multiprocessing? And my test in remote server produce no result(except for the empty dir "forest_out_M.D.Y" itself).

Local test error info as below:

python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
  File "D:\2024\05\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 "forest_local.py", line 684, in <module>
    suspicious = parallel_susp_clades(trees)
  File "forest_local.py", line 503, in parallel_susp_clades
    suspicious = list(pool.map(suspicious_clades, trees))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 771, in get
    raise self._value
NameError: name 'metadata' is not defined

After I add "metadata = {}" in line 20, the info changed as below:

>python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
  File "D:\2024\05\forest_local.py", line 198, in suspicious_clades
    groups.add(metadata[org]['Higher Taxonomy'])
KeyError: 'Tisolute'
"""

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

Traceback (most recent call last):
  File "forest_local.py", line 671, in <module>
    suspicious = parallel_susp_clades(trees)
  File "forest_local.py", line 504, in parallel_susp_clades
    suspicious = list(pool.map(suspicious_clades, trees))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 771, in get
    raise self._value
KeyError: 'Tisolute'

Then I commented out the function "def parallel_susp_clades(trees)", and changed "suspicious = parallel_susp_clades(trees)" to "suspicious = suspicious_clades(trees)", the error info changed as below:

>python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
Traceback (most recent call last):
  File "forest_local.py", line 672, in <module>
    suspicious = suspicious_clades(trees)
  File "forest_local.py", line 175, in suspicious_clades
    t = Tree(tree)
  File "C:\Program Files\Python38\lib\site-packages\ete3\coretype\tree.py", line 212, in __init__
    read_newick(newick, root_node = self, format=format,
  File "C:\Program Files\Python38\lib\site-packages\ete3\parser\newick.py", line 269, in read_newick
    raise NewickError("'newick' argument must be either a filename or a newick string.")
ete3.parser.newick.NewickError: 'newick' argument must be either a filename or a newick string.
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

shuiyujinlan commented 5 months ago

Hi, @robert-ervin-jones . I have the same question in my test with the original "metadata.tsv". How to bypass multiprocessing? And my test in remote server produce no result(except for the empty dir "forest_out_M.D.Y" itself).

Local test error info as below:

python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
  File "D:\2024\05\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 "forest_local.py", line 684, in <module>
    suspicious = parallel_susp_clades(trees)
  File "forest_local.py", line 503, in parallel_susp_clades
    suspicious = list(pool.map(suspicious_clades, trees))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 771, in get
    raise self._value
NameError: name 'metadata' is not defined

After I add "metadata = {}" in line 20, the info changed as below:

>python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
  File "D:\2024\05\forest_local.py", line 198, in suspicious_clades
    groups.add(metadata[org]['Higher Taxonomy'])
KeyError: 'Tisolute'
"""

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

Traceback (most recent call last):
  File "forest_local.py", line 671, in <module>
    suspicious = parallel_susp_clades(trees)
  File "forest_local.py", line 504, in parallel_susp_clades
    suspicious = list(pool.map(suspicious_clades, trees))
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Program Files\Python38\lib\multiprocessing\pool.py", line 771, in get
    raise self._value
KeyError: 'Tisolute'

Then I commented out the function "def parallel_susp_clades(trees)", and changed "suspicious = parallel_susp_clades(trees)" to "suspicious = suspicious_clades(trees)", the error info changed as below:

>python forest_local.py -i sgt_constructor_out_Apr.28.2024-local.tar.gz
Traceback (most recent call last):
  File "forest_local.py", line 672, in <module>
    suspicious = suspicious_clades(trees)
  File "forest_local.py", line 175, in suspicious_clades
    t = Tree(tree)
  File "C:\Program Files\Python38\lib\site-packages\ete3\coretype\tree.py", line 212, in __init__
    read_newick(newick, root_node = self, format=format,
  File "C:\Program Files\Python38\lib\site-packages\ete3\parser\newick.py", line 269, in read_newick
    raise NewickError("'newick' argument must be either a filename or a newick string.")
ete3.parser.newick.NewickError: 'newick' argument must be either a filename or a newick string.
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

Solved in a silly way: I successfully changed multiprocessing to a simple "for loop", and then the result came out smoothly in 1 min. To achieve this, change:

    if not args.backpropagate:
        suspicious = parallel_susp_clades(trees)

to

    suspicious = []

    if not args.backpropagate:
#        suspicious = parallel_susp_clades(trees)
        for tree in trees:
            suspicious.append(suspicious_clades(tree))
        print(suspicious)

You will see the list of suspicious genes in the corresponding tree in your terminal. Result files are as below:

Hope this helps! @robert-ervin-jones @sipesk

robert-ervin-jones commented 5 months ago

Hi @shuiyujinlan,

Would it be possible for you to open a PR with your proposed code changes?

Best, Robert

maggielawton commented 5 months ago

Had the same issue, and the fix by shuiyujinlan worked for me as well. Thanks!

shuiyujinlan commented 5 months ago

Hi @shuiyujinlan,

Would it be possible for you to open a PR with your proposed code changes?

Best, Robert

Sure. I opened a PR just now. And hope you'll find some clues in my reply and description to fix it more gracefully (e.g. retain the multiprocessing function).

TheBrownLab / PhyloFisher

metadata not defined in forest_local.py #120