Comments (6)
The link in the instructions is broken so I used the version linked above.
One issue could be that the download_eggnog_data.py
script failed to download the hmm files so I had to manually go and download the files.
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Thanks for the advice, good luck trying to sort it out.
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I have just tried using the eggnog-mapper, however none of the three inputs produced seem to be accepted as such;
$ carve --egg eggnogmappings.emapper.annotations
Traceback (most recent call last):
File "/usr/local/bin/carve", line 343, in <module>
hard=args.hard
File "/usr/local/bin/carve", line 108, in main
annotations = load_eggnog_data(inputfile)
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 37, in load_eggnog_data
data = split_and_expand(data, 'BiGG_gene', ',')
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 5, in split_and_expand
split_col = df[col].str.split(sep).apply(pd.Series, 1).stack()
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 4372, in __getattr__
return object.__getattribute__(self, name)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/accessor.py", line 133, in __get__
accessor_obj = self._accessor(obj)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1895, in __init__
self._validate(data)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1917, in _validate
raise AttributeError("Can only use .str accessor with string "
AttributeError: Can only use .str accessor with string values, which use np.object_ dtype in pandas
$ carve --egg eggnogmappings.emapper.hmm_hits
Traceback (most recent call last):
File "/usr/local/bin/carve", line 343, in <module>
hard=args.hard
File "/usr/local/bin/carve", line 108, in main
annotations = load_eggnog_data(inputfile)
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 37, in load_eggnog_data
data = split_and_expand(data, 'BiGG_gene', ',')
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 5, in split_and_expand
split_col = df[col].str.split(sep).apply(pd.Series, 1).stack()
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 4372, in __getattr__
return object.__getattribute__(self, name)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/accessor.py", line 133, in __get__
accessor_obj = self._accessor(obj)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1895, in __init__
self._validate(data)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1917, in _validate
raise AttributeError("Can only use .str accessor with string "
AttributeError: Can only use .str accessor with string values, which use np.object_ dtype in pandas
$ carve --egg eggnogmappings.emapper.seed_orthologs
Traceback (most recent call last):
File "/usr/local/bin/carve", line 343, in <module>
hard=args.hard
File "/usr/local/bin/carve", line 108, in main
annotations = load_eggnog_data(inputfile)
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 37, in load_eggnog_data
data = split_and_expand(data, 'BiGG_gene', ',')
File "/usr/local/lib/python2.7/dist-packages/carveme/reconstruction/eggnog.py", line 5, in split_and_expand
split_col = df[col].str.split(sep).apply(pd.Series, 1).stack()
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/generic.py", line 4372, in __getattr__
return object.__getattribute__(self, name)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/accessor.py", line 133, in __get__
accessor_obj = self._accessor(obj)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1895, in __init__
self._validate(data)
File "/home/thomashitch/.local/lib/python2.7/site-packages/pandas/core/strings.py", line 1917, in _validate
raise AttributeError("Can only use .str accessor with string "
AttributeError: Can only use .str accessor with string values, which use np.object_ dtype in pandas
Any idea what is going wrong?
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Did you follow these instructions? https://carveme.readthedocs.io/en/latest/advanced.html#eggnog-mapper
from carveme.
Unfortunately eggnog mapper and carveme are not synchronized, so it is possible that the older eggnog version is not working properly. I will try to look into this as soon as possible. In the meantime I would suggest you just use diamond as the default, unless you really must use eggnog. By the way, the file to use is the annotations file.
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The link in the instructions is broken so I used the version linked above.
One issue could be that the
download_eggnog_data.py
script failed to download the hmm files so I had to manually go and download the files.
Sorry @thh32 I am having the same problem, I can download no database (no bact,euk,viruses nor arch). How did u do?
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