jcvi
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An error with blast.py and base.py
I have tried to run
python -m jcvi.compara.catalog ortholog G1 G9 --no_strip_names --cpu=35
but an error occured
Traceback (most recent call last):
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 12, in <module>
from jcvi.formats.blast import BlastLine
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/site-packages/jcvi/formats/blast.py", line 12, in <module>
from jcvi.formats.base import LineFile, BaseFile, must_open
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/site-packages/jcvi/formats/base.py", line 14, in <module>
from jcvi.apps.base import (
File "/data/home/wuk/miniconda3/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/base.py", line 14, in <module>
from more_itertools import flatten
ModuleNotFoundError: No module named 'more_itertools'
jcvi and lastal version 1268 were installed through conda.
I installed more_itertools by
pip3 install more_itertools
with an error message
Installing collected packages: more-itertools
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
jcvi 1.2.7 requires cython, which is not installed.
jcvi 1.2.7 requires deap, which is not installed.
jcvi 1.2.7 requires ftpretty, which is not installed.
jcvi 1.2.7 requires graphviz, which is not installed.
jcvi 1.2.7 requires ortools, which is not installed.
jcvi 1.2.7 requires pybedtools, which is not installed.
jcvi 1.2.7 requires scikit-image, which is not installed.
jcvi 1.2.7 requires webcolors, which is not installed.
The problem solved after I have installed all packages above