ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_linux_gnu'

[ofleitas]

Hello

I am trying to run macrel but I got the follow error:

Sequence Data: seqnum=7183;seqlen=1609;seqhdr="k127_22397 flag=3 multi=7.0047 len=1609"

Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="11|Candidatus_Amoebophilus_asiaticus_5a2|B|35.0|11|0";gc_cont=35.00;transl_table=11;uses_sd=0

1_302409- Traceback (most recent call last): File "/home/ofm/anaconda3/envs/env_macrel/bin/macrel", line 11, in sys.exit(main()) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/macrel/main.py", line 282, in main do_predict(args, tdir) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/macrel/main.py", line 241, in do_predict fs) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/macrel/AMP_predict.py", line 7, in predict model1 = pickle.load(gzip.open(model1, 'rb')) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/init.py", line 82, in from .base import clone File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py", line 17, in from .utils import _IS_32BIT File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/utils/init.py", line 25, in from . import _joblib File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/utils/_joblib.py", line 7, in import joblib File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/joblib/init.py", line 113, in from .memory import Memory, MemorizedResult, register_store_backend File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/joblib/memory.py", line 16, in import pydoc File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/pydoc.py", line 370, in class Doc: File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/pydoc.py", line 402, in Doc def getdocloc(self, object, basedir=sysconfig.get_path('stdlib')): File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/sysconfig.py", line 521, in get_path return get_paths(scheme, vars, expand)[name] File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/sysconfig.py", line 511, in get_paths return _expand_vars(scheme, vars) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/sysconfig.py", line 172, in _expand_vars _extend_dict(vars, get_config_vars()) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/sysconfig.py", line 559, in get_config_vars _init_posix(_CONFIG_VARS) File "/home/ofm/anaconda3/envs/env_macrel/lib/python3.7/sysconfig.py", line 430, in _init_posix _temp = import(name, globals(), locals(), ['build_time_vars'], 0) ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_linux_gnu'

What can I do?

Thanks in advance

[ofleitas]

Hello again

I think that I solved the problem but now I am getting the following error:

Sequence Data: seqnum=7183;seqlen=1258;seqhdr="k127_3767 flag=1 multi=3.0000 len=1258"

Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="48|Xylella_fastidiosa_Temecula1|B|51.8|11|1";gc_cont=51.80;transl_table=11;uses_sd=1

1_83418+ 2_7491246- /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:338: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.22.1 when using version 1.0.2. This might lead to breaking code or invalid results. Use at your own risk. For more info please refer to: https://scikit-learn.org/stable/modules/model_persistence.html#security-maintainability-limitations UserWarning, /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:338: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.22.1 when using version 1.0.2. This might lead to breaking code or invalid results. Use at your own risk. For more info please refer to: https://scikit-learn.org/stable/modules/model_persistence.html#security-maintainability-limitations UserWarning, /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:444: UserWarning: X has feature names, but RandomForestClassifier was fitted without feature names f"X has feature names, but {self.class.name} was fitted without" /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:444: UserWarning: X has feature names, but RandomForestClassifier was fitted without feature names f"X has feature names, but {self.class.name} was fitted without" /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:444: UserWarning: X has feature names, but RandomForestClassifier was fitted without feature names f"X has feature names, but {self.class.name} was fitted without" /home/ofm/anaconda3/envs/env_macrel/lib/python3.7/site-packages/sklearn/base.py:444: UserWarning: X has feature names, but RandomForestClassifier was fitted without feature names f"X has feature names, but {self.class.name} was fitted without"

What can I do? Thank you in advance

[luispedro]

The previous error was some conda issue. These are hard to debug, glad you figured it out.

The warnings that you are getting now can be safely ignored (although we should still fix the code to get rid of them)

[ofleitas]

Ok. Thank you very much. When I get the warnings the prediction output file is empty it only contains the column headers. Does this mean that no AMPs were found?

[luispedro]

Yes, none were found

[ofleitas]

OK. Thank you very much

On Mon, Sep 9, 2024 at 2:34 AM Luis Pedro Coelho @.***> wrote:

Yes, none were found

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