Open rmormando opened 1 year ago
okay I uninstalled kitsune and then redid the installation using pip install kitsune
and after running kitsune kopt -h
I get this error message:
Traceback (most recent call last):
File "/opt/homebrew/bin/kitsune", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/kitsune/kitsune.py", line 70, in main
module = importlib.import_module("kitsune.modules.{}".format(cmd))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/opt/homebrew/lib/python3.11/site-packages/kitsune/modules/kopt.py", line 23, in <module>
from kitsune.modules import kitsunejf as jf
File "/opt/homebrew/lib/python3.11/site-packages/kitsune/modules/kitsunejf.py", line 152, in <module>
distance.kulsinski,
^^^^^^^^^^^^^^^^^^
AttributeError: module 'scipy.spatial.distance' has no attribute 'kulsinski'
I get the normal help message as above when I do kitsune --help
but I don't know why this isn't working...
This error is due to the update of SciPy 1.11.0. The kulsinski function was removed. For a quick fix, Please create a Python environment and install SciPy version 11.10.1 or an earlier version then install Kitsune via pip again.
We will update the new version of Kitsune soon.
I was able to make a python environment with scipy == 1.10.1 and kitsune and I am able to get a help message when I run the command kitsune kopt --help
however when I run the kopt
command I get a new error message:
Computing Cumulative Relative Entropy (CRE)
0%| | 0/6 [00:01<?, ?it/s]
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kitsunejf.py", line 236, in __init__
datadict[dat[0]] = int(dat[1])
^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: 'terminating'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kopt.py", line 331, in par_cre
_, a0 = count_kmers_partial(genome, kmin=kmer, kmax=kmer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kopt.py", line 167, in count_kmers
datadict[kmer] = jf.Kmercount(
^^^^^^^^^^^^^
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kitsunejf.py", line 239, in __init__
raise JellyFishError("Bloom filter file is truncated.")
kitsune.modules.kitsunejf.JellyFishError: Bloom filter file is truncated.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/rimo/kitsune_env/bin/kitsune", line 8, in <module>
sys.exit(main())
^^^^^^
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/kitsune.py", line 71, in main
module.run(sys.argv)
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kopt.py", line 669, in run
optimal_kmer_size(
File "/Users/rimo/kitsune_env/lib/python3.11/site-packages/kitsune/modules/kopt.py", line 587, in optimal_kmer_size
cre_results.append(job.get())
^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 774, in get
raise self._value
kitsune.modules.kitsunejf.JellyFishError: Bloom filter file is truncated.
This is the command I run:
kitsune kopt --filenames ./American/american_paths.txt --k-min 10 --k-max 30 --canonical --closely-related --threads 8 --nproc 2 --output ./American/kitsune_out.txt
Any idea what this might mean/how to fix this error?
Hello I just installed kitsune on my mac from the GitHub source. When I use the help command:
python3 kitsune.py --help
it outputs the normal message:However when I do
python3 kitsune.py kopt --help
I get this message:This happens when I try to use the
kopt
command with parameters set and I don't understand what's wrong or how to fix it.