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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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error of step3 #204

Open 2061574124 opened 2 weeks ago

2061574124 commented 2 weeks ago

run code just following: virsorter run -w out -i /home/dell/database/H1_assembly.contigs.fa --min-length 1000 -j 16 all [2024-06-20 00:55 INFO] VirSorter 2.2.3 [2024-06-20 00:55 INFO] /home/dell/miniconda3/envs/vs2/bin/virsorter run -w out -i /home/dell/database/H1_assembly.contigs.fa --min-length 1000 -j 16 all [2024-06-20 00:55 INFO] Using /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/template-config.yaml as config template [2024-06-20 00:55 INFO] conig file written to /home/dell/database/out/config.yaml

[2024-06-20 00:55 INFO] Executing: snakemake --snakefile /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/Snakefile --directory /home/dell/database/out --jobs 16 --configfile /home/dell/database/out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /home/dell/database/virsorter/conda_envs --use-conda --quiet all
Job counts: count jobs 1 all 1 check_point_for_reclassify 1 circular_linear_split 1 classify 2 classify_by_group 2 classify_full_and_part_by_group 1 combine_linear_circular 2 combine_linear_circular_by_group 1 extract_feature 1 extract_provirus_seqs 1 finalize 1 gff_feature 2 gff_feature_by_group 2 hmm_features_by_group 1 hmm_sort_to_best_hit_taxon 2 hmm_sort_to_best_hit_taxon_by_group 1 merge_classification 1 merge_full_and_part_classification 2 merge_hmm_gff_features_by_group 2 merge_provirus_call_by_group_by_split 1 merge_provirus_call_from_groups 5 merge_split_hmmtbl 10 merge_split_hmmtbl_by_group 10 merge_split_hmmtbl_by_group_tmp 1 pick_viral_fullseq 1 preprocess 1 split_faa 2 split_faa_by_group 2 split_gff_by_group 61 [2024-06-20 00:55 INFO] # of seqs < 1000 bp and removed: 93518 [2024-06-20 00:55 INFO] # of circular seqs: 60 [2024-06-20 00:55 INFO] # of linear seqs : 30941 [2024-06-20 00:55 INFO] Finish spliting circular contig file with common rbs [2024-06-20 00:55 INFO] Finish spliting linear contig file with common rbs [2024-06-20 00:58 INFO] Step 1 - preprocess finished.

[2024-06-20 03:41 INFO] Step 2 - extract-feature finished. [2024-06-20 03:41 ERROR] S**ee error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-dsDNAphage.log [2024-06-20 03:41 ERROR] See error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-ssDNA.log [Thu Jun 20 03:41:20 2024] [Thu Jun 20 03:41:20 2024] Error in rule classify_by_group: Error in rule classify_by_group: jobid: 56 jobid: 57 output: iter-0/dsDNAphage/all.pdg.clf output: iter-0/ssDNA/all.pdg.clf conda-env: /home/dell/database/virsorter/conda_envs/3bfc9270 conda-env: /home/dell/database/virsorter/conda_envs/3bfc9270 shell:

    Log=/home/dell/database/out/log/iter-0/step3-classify/all-score-dsDNAphage.log
    python /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py iter-0/dsDNAphage/all.pdg.ftr /home/dell/database/virsorter/group/dsDNAphage/model dsDNAphage iter-0/dsDNAphage/all.pdg.clf 2> $Log || { echo "See error details in $Log" | python /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
shell:

    Log=/home/dell/database/out/log/iter-0/step3-classify/all-score-ssDNA.log
    python /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py iter-0/ssDNA/all.pdg.ftr /home/dell/database/virsorter/group/ssDNA/model ssDNA iter-0/ssDNA/all.pdg.clf 2> $Log || { echo "See error details in $Log" | python /home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message**

*** An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting Issues can be raised at: https://github.com/jiarong/VirSorter2/issues

after setup, when performed "virsorter2 run" was exit, i wonder how to fix. THANKS!

2061574124 commented 2 weeks ago

and this is the error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-dsDNAphage.log:

Traceback (most recent call last): File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 77, in main() File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 60, in main model = joblib.load(model_f) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load obj = _unpickle(fobj, filename, mmap_mode) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle obj = unpickler.load() File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1212, in load dispatchkey[0] File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1537, in load_stack_global self.append(self.find_class(module, name)) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1579, in find_class import(module, level=0) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/init.py", line 7, in from ._forest import RandomForestClassifier File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 56, in from ..tree import (DecisionTreeClassifier, DecisionTreeRegressor, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/init.py", line 6, in from ._classes import BaseDecisionTree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 40, in from ._criterion import Criterion File "sklearn/tree/_splitter.pxd", line 34, in init sklearn.tree._criterion File "sklearn/tree/_tree.pxd", line 37, in init sklearn.tree._splitter File "sklearn/neighbors/_quad_tree.pxd", line 55, in init sklearn.tree._tree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/init.py", line 17, in from ._nca import NeighborhoodComponentsAnalysis File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in from ..decomposition import PCA File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/init.py", line 17, in from .dict_learning import dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 4, in from . import _dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/init.py", line 12, in from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 30, in method='lar', copy_X=True, eps=np.finfo(np.float).eps, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

2061574124 commented 2 weeks ago

and this is the error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-dsDNAphage.log:

Traceback (most recent call last): File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 77, in main() File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 60, in main model = joblib.load(model_f) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load obj = _unpickle(fobj, filename, mmap_mode) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle obj = unpickler.load() File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1212, in load dispatchkey[0] File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1537, in load_stack_global self.append(self.find_class(module, name)) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1579, in find_class import(module, level=0) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/init.py", line 7, in from ._forest import RandomForestClassifier File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 56, in from ..tree import (DecisionTreeClassifier, DecisionTreeRegressor, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/init.py", line 6, in from ._classes import BaseDecisionTree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 40, in from ._criterion import Criterion File "sklearn/tree/_splitter.pxd", line 34, in init sklearn.tree._criterion File "sklearn/tree/_tree.pxd", line 37, in init sklearn.tree._splitter File "sklearn/neighbors/_quad_tree.pxd", line 55, in init sklearn.tree._tree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/init.py", line 17, in from ._nca import NeighborhoodComponentsAnalysis File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in from ..decomposition import PCA File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/init.py", line 17, in from .dict_learning import dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 4, in from . import _dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/init.py", line 12, in from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 30, in method='lar', copy_X=True, eps=np.finfo(np.float).eps, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

2061574124 commented 2 weeks ago

and this is the error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-ssDNAphage.log:

Traceback (most recent call last): File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 77, in main() File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 60, in main model = joblib.load(model_f) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load obj = _unpickle(fobj, filename, mmap_mode) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle obj = unpickler.load() File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1212, in load dispatchkey[0] File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1537, in load_stack_global self.append(self.find_class(module, name)) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1579, in find_class import(module, level=0) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/init.py", line 7, in from ._forest import RandomForestClassifier File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 56, in from ..tree import (DecisionTreeClassifier, DecisionTreeRegressor, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/init.py", line 6, in from ._classes import BaseDecisionTree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 40, in from ._criterion import Criterion File "sklearn/tree/_splitter.pxd", line 34, in init sklearn.tree._criterion File "sklearn/tree/_tree.pxd", line 37, in init sklearn.tree._splitter File "sklearn/neighbors/_quad_tree.pxd", line 55, in init sklearn.tree._tree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/init.py", line 17, in from ._nca import NeighborhoodComponentsAnalysis File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in from ..decomposition import PCA File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/init.py", line 17, in from .dict_learning import dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 4, in from . import _dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/init.py", line 12, in from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 30, in method='lar', copy_X=True, eps=np.finfo(np.float).eps, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

2061574124 commented 2 weeks ago

and this is the error details in /home/dell/database/out/log/iter-0/step3-classify/all-score-ssDNAphage.log:

Traceback (most recent call last): File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 77, in main() File "/home/dell/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/classify.py", line 60, in main model = joblib.load(model_f) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load obj = _unpickle(fobj, filename, mmap_mode) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle obj = unpickler.load() File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1212, in load dispatchkey[0] File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1537, in load_stack_global self.append(self.find_class(module, name)) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/pickle.py", line 1579, in find_class import(module, level=0) File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/init.py", line 7, in from ._forest import RandomForestClassifier File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/ensemble/_forest.py", line 56, in from ..tree import (DecisionTreeClassifier, DecisionTreeRegressor, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/init.py", line 6, in from ._classes import BaseDecisionTree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 40, in from ._criterion import Criterion File "sklearn/tree/_splitter.pxd", line 34, in init sklearn.tree._criterion File "sklearn/tree/_tree.pxd", line 37, in init sklearn.tree._splitter File "sklearn/neighbors/_quad_tree.pxd", line 55, in init sklearn.tree._tree File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/init.py", line 17, in from ._nca import NeighborhoodComponentsAnalysis File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in from ..decomposition import PCA File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/init.py", line 17, in from .dict_learning import dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 4, in from . import _dict_learning File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/init.py", line 12, in from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 30, in method='lar', copy_X=True, eps=np.finfo(np.float).eps, File "/home/dell/database/virsorter/conda_envs/3bfc9270/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(former_attrs[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

Does this mean that numpy version that Virsorer2 conda environment is incorrect?

jiarong commented 2 weeks ago

This is different from issue #90 where you also commented. The most recent version 2.2.4 should have addressed the numpy.float deprecation issue. Or you can use the container version in installation option 3.

mengyuan-JI commented 1 week ago

Hi, I meet the same error , have you solved it?