i made a mistake. i have no idea with it. need some help

[liucong2016]

(vRhyme) nohup vRhyme -i /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.fa -g /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.ffn -p /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.faa -r total-fastq/*.fastq -t 40 -o out-23.7.6 --method longest

/software1/envs/vRhyme/bin/vRhyme:16: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources Traceback (most recent call last): File "/software1/envs/vRhyme/bin/vRhyme", line 960, in net_data = machine_stuff.machine_stuff(distances, presets, model_method, pairs_machine, cohen_machine, iterations, cohen_check) File "/software1/envs/vRhyme/bin/machine_stuff.py", line 73, in machine_stuff model_ET = pickle.load(read_model_ET) File "sklearn/tree/_tree.pyx", line 714, in sklearn.tree._tree.Tree.setstate File "sklearn/tree/_tree.pyx", line 1418, in sklearn.tree._tree._check_node_ndarray ValueError: node array from the pickle has an incompatible dtype:

• expected: {'names': ['left_child', 'right_child', 'feature', 'threshold', 'impurity', 'n_node_samples', 'weighted_n_node_samples', 'missing_go_to_left'], 'formats': ['<i8', '<i8', '<i8', '<f8', '<f8', '<i8', '<f8', 'u1'], 'offsets': [0, 8, 16, 24, 32, 40, 48, 56], 'itemsize': 64}
• got : [('left_child', '<i8'), ('right_child', '<i8'), ('feature', '<i8'), ('threshold', '<f8'), ('impurity', '<f8'), ('n_node_samples', '<i8'), ('weighted_n_node_samples', '<f8')]

[KrisKieft]

Hi,

What is your version of sklearn?

[liucong2016]

Name: scikit-learn Version: 1.3.0

[KrisKieft]

It's possible this version has changed significantly since development. I'd suggest installing the version listed in the Readme and see if that helps.

[liucong2016]

It's possible this version has changed significantly since development. I'd suggest installing the version listed in the Readme and see if that helps.

Hi, When I downgrade the version of scikit-learn to 0.24 and run the program again, with the following code, I still encounter an error. (vRhyme) nohup vRhyme -i /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.fa -g /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.ffn -p /home/liu-c/virus-data/tuanjuti-virome/virus-otu-23.4/virus-final.faa -r total-fastq/*.fastq -t 40 -o out-23.7.7 --method longest

/software1/envs/vRhyme/bin/vRhyme:16: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources

there is still somothing wrong.

[KrisKieft]

Did any errors occur or just a warning?

[CarlosNavr]

Hello.

Just wanted to comment that I had the same problem, downgraded scikit-learn and it worked. No errors, just that warning.

[liucong2016]

thanks a lot. i will try it again.

[Tina-MengyingWANG]

Hello. May I ask how you downgraded scikit-learn? I installed vRhyme following the full instruction with 'pip install .'. However when I tried to downgrade scikit-learn using 'conda install scikit-learn=0.23.0', all the packages including 'vRhyme=1.1.0' installed by 'pip install .' in the conda env can not be found.

$ test_vRhyme.py -bash: /media/WMY/2_software/miniconda3/envs/vrhyme_1.1.0/bin/test_vRhyme.py: /media/WMY/2_software/miniconda3/envs/vrhyme_1.1.0/bin/python3.10: bad interpreter: No such file or directory

[CarlosNavr]

Hello there

I simply used pip install scikit-learn==version while in the conda environment.

El 21 set. 2023, a les 16:55, Tina-MengyingWANG @.***> va escriure:

Hello. May I ask how you downgraded scikit-learn? I installed vRhyme following the full instruction with 'pip install .'. However when I tried to downgrade scikit-learn using 'conda install scikit-learn=0.23.0', all the packages including 'vRhyme=1.1.0' installed by 'pip install .' in the conda env can not be found.

$ test_vRhyme.py -bash: /media/WMY/2_software/miniconda3/envs/vrhyme_1.1.0/bin/test_vRhyme.py: /media/WMY/2_software/miniconda3/envs/vrhyme_1.1.0/bin/python3.10: bad interpreter: No such file or directory

— Reply to this email directly, view it on GitHubhttps://github.com/AnantharamanLab/vRhyme/issues/24#issuecomment-1729751716, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUIHVGMJLCUTXYB7BDFEXBTX3RINDANCNFSM6AAAAAA2AV3IUM. You are receiving this because you commented.Message ID: @.***>

[Tina-MengyingWANG]

Thank you so much! I will try it again.

[Sanrrone]

using scikit-learn=0.23.0 didin't work for me, I just downgraded from version 1.3 to 1.2 and works perfectly :D

[AndAvia]

May I ask how you downgraded scikit-learn?

Hello.

Just wanted to comment that I had the same problem, downgraded scikit-learn and it worked. No errors, just that warning.

May I ask what you downgraded scikit-learn version?