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_302_409_-
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_83_418_+
2_749_1246_-
/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 — Reply to this email directly, view it on GitHub <#71 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AM624NC2RPSN6S4XKEBMV6TZVVMTDAVCNFSM6AAAAABNZTYVJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZXGQ3TKMRXGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[WW-web-ctrl]

May I ask how you solved the first conda problem
Thank you in advance

[ofleitas]

Hello

If my memory serves me correctly, it was by following these instructions :

https://stackoverflow.com/questions/68261254/conda-error-sysconfigdata-x86-64-conda-linux-gnu

hope it help