SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
i installed secnicplus as follows tutorial and i never change any package version.
but when i run snakemake --cores 20, the error is occured
2024-10-28 10:54:17,839 SCENIC+ INFO Reading multiome MuData.
/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
2024-10-28 10:54:54,931 SCENIC+ INFO Reading search space
2024-10-28 10:54:56,999 R2G INFO Calculating region to gene importances, using GBM method
Running using 20 cores: 0%| | 20/22610 [00:04<1:18:10, 4.82it/s]joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker
r = call_item()
^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 291, in call
return self.fn(*self.args, self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in call
return [func(*args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in
return [func(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 140, in _score_regions_to_single_gene
from arboreto import core as arboreto_core
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/arboreto/core.py", line 12, in
from dask.dataframe import from_delayed
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/init.py", line 100, in
from dask.dataframe import backends, dispatch, rolling
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/backends.py", line 15, in
from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/core.py", line 36, in
from dask.dataframe import methods
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/methods.py", line 34, in
from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/utils.py", line 20, in
from dask.dataframe import ( # noqa: F401 register pandas extension types
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/_dtypes.py", line 9, in
from dask.dataframe.extensions import make_array_nonempty, make_scalar
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/extensions.py", line 8, in
from dask.dataframe.accessor import (
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 126, in
class DatetimeAccessor(Accessor):
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 81, in init_subclass__
_bind_property(cls, pd_cls, attr, min_version)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 35, in _bind_property
setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 987, in wrapper
method.doc__ = _derived_from(
^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 940, in _derived_from
method_args = get_named_args(method)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 701, in get_named_args
s = inspect.signature(func)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 3263, in signature
return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 3011, in from_callable
return _signature_from_callable(obj, sigcls=cls,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 2599, in _signature_from_callable
call = _descriptor_get(call, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 2432, in _descriptor_get
return get(descriptor, obj, type(obj))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/node06/anaconda3/envs/scenicplus/bin/scenicplus", line 8, in
sys.exit(main())
^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1137, in main
args.func(args)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 330, in TF_to_gene
infer_region_to_gene(
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/commands.py", line 739, in infer_region_to_gene
adj = calculate_regions_to_genes_relationships(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 261, in calculate_regions_to_genes_relationships
region_to_gene_importances = _score_regions_to_genes(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 219, in _score_regions_to_genes
joblib.Parallel(
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1952, in call
return output if self.return_generator else list(output)
^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1595, in _get_outputs
yield from self._retrieve()
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1699, in _retrieve
self._raise_error_fast()
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast
error_job.get_result(self.timeout)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 736, in get_result
return self._return_or_raise()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 754, in _return_or_raise
raise self._result
TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object
[Mon Oct 28 10:55:16 2024]
Error in rule region_to_gene:
jobid: 10
input: ACC_GEX.h5mu, search_space.tsv
output: region_to_gene_adj.tsv
shell:
scenicplus grn_inference region_to_gene --multiome_mudata_fname ACC_GEX.h5mu --search_space_fname search_space.tsv --temp_dir /HDD_4TB/jungsook/scenic/cd14/tmp --out_region_to_gene_adjacencies region_to_gene_adj.tsv --importance_scoring_method GBM --correlation_scoring_method SR --n_cpu 20
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-10-28T104929.895977.snakemake.log
WorkflowError:
At least one job did not complete successfully.
i installed secnicplus as follows tutorial and i never change any package version. but when i run snakemake --cores 20, the error is occured
2024-10-28 10:54:17,839 SCENIC+ INFO Reading multiome MuData. /home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( 2024-10-28 10:54:54,931 SCENIC+ INFO Reading search space 2024-10-28 10:54:56,999 R2G INFO Calculating region to gene importances, using GBM method Running using 20 cores: 0%| | 20/22610 [00:04<1:18:10, 4.82it/s]joblib.externals.loky.process_executor._RemoteTraceback: """ Traceback (most recent call last): File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker r = call_item() ^^^^^^^^^^^ File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 291, in call return self.fn(*self.args, self.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in call return [func(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^ File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in
return [func( args, kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 140, in _score_regions_to_single_gene
from arboreto import core as arboreto_core
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/arboreto/core.py", line 12, in
from dask.dataframe import from_delayed
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/init.py", line 100, in
from dask.dataframe import backends, dispatch, rolling
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/backends.py", line 15, in
from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/core.py", line 36, in
from dask.dataframe import methods
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/methods.py", line 34, in
from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/utils.py", line 20, in
from dask.dataframe import ( # noqa: F401 register pandas extension types
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/_dtypes.py", line 9, in
from dask.dataframe.extensions import make_array_nonempty, make_scalar
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/extensions.py", line 8, in
from dask.dataframe.accessor import (
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 126, in
class DatetimeAccessor(Accessor):
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 81, in init_subclass__
_bind_property(cls, pd_cls, attr, min_version)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 35, in _bind_property
setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 987, in wrapper
method.doc__ = _derived_from(
^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 940, in _derived_from
method_args = get_named_args(method)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 701, in get_named_args
s = inspect.signature(func)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 3263, in signature
return Signature.from_callable(obj, follow_wrapped=follow_wrapped,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 3011, in from_callable
return _signature_from_callable(obj, sigcls=cls,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 2599, in _signature_from_callable
call = _descriptor_get(call, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/inspect.py", line 2432, in _descriptor_get
return get(descriptor, obj, type(obj))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/node06/anaconda3/envs/scenicplus/bin/scenicplus", line 8, in
sys.exit(main())
^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1137, in main
args.func(args)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 330, in TF_to_gene
infer_region_to_gene(
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/commands.py", line 739, in infer_region_to_gene
adj = calculate_regions_to_genes_relationships(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 261, in calculate_regions_to_genes_relationships
region_to_gene_importances = _score_regions_to_genes(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 219, in _score_regions_to_genes
joblib.Parallel(
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1952, in call
return output if self.return_generator else list(output)
^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1595, in _get_outputs
yield from self._retrieve()
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1699, in _retrieve
self._raise_error_fast()
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast
error_job.get_result(self.timeout)
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 736, in get_result
return self._return_or_raise()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/node06/anaconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 754, in _return_or_raise
raise self._result
TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object
[Mon Oct 28 10:55:16 2024]
Error in rule region_to_gene:
jobid: 10
input: ACC_GEX.h5mu, search_space.tsv
output: region_to_gene_adj.tsv
shell:
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-10-28T104929.895977.snakemake.log WorkflowError: At least one job did not complete successfully.