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aertslab / scenicplus

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.
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TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object #432

Closed degrainger closed 4 months ago

degrainger commented 4 months ago

Describe the bug I am running the SCENICplus Snakemake pipeline but get the error described below. When I paste the error into ChatGPT it says "due to a compatibility issue between different versions of the libraries being used. Specifically, the error suggests a problem with the dask library, which is a dependency for SCENIC+".

Please could you help me identify where this error stems from? Thank you.

Error output

Assuming unrestricted shared filesystem usage for local execution. Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Job stats: job count

AUCell_direct 1 AUCell_extended 1 all 1 eGRN_direct 1 eGRN_extended 1 region_to_gene 1 scplus_mudata 1 tf_to_gene 1 total 8

Select jobs to execute... Execute 1 jobs...

[Wed Jun 26 20:55:46 2024] localrule region_to_gene: input: ACC_GEX.h5mu, search_space.tsv output: region_to_gene_adj.tsv jobid: 10 reason: Missing output files: region_to_gene_adj.tsv threads: 20 resources: tmpdir=/var/scratch/ostone/1800216

2024-06-26 20:56:49,359 SCENIC+ INFO Reading multiome MuData. /ceph/project/Stone_multiome/ostone/conda_local/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( /ceph/project/Stone_multiome/ostone/conda_local/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( 2024-06-26 20:56:56,896 SCENIC+ INFO Reading search space 2024-06-26 20:56:57,586 R2G INFO Calculating region to gene importances, using GBM method

Running using 20 cores: 0%| | 0/16994 [00:00<?, ?it/s] Running using 20 cores: 0%| | 1/16994 [00:00<37:41, 7.51it/s] Running using 20 cores: 0%| | 12/16994 [00:00<04:59, 56.76it/s] Running using 20 cores: 0%| | 20/16994 [00:02<47:54, 5.91it/s] Running using 20 cores: 0%| | 34/16994 [00:02<22:47, 12.40it/s] Running using 20 cores: 0%| | 34/16994 [00:19<22:47, 12.40it/s]joblib.externals.loky.process_executor._RemoteTraceback: """ Traceback (most recent call last): File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker r = call_item() ^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in call return [func(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in return [func(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/arboreto/core.py", line 12, in from dask.dataframe import from_delayed File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/init.py", line 100, in from dask.dataframe import backends, dispatch, rolling File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/core.py", line 36, in from dask.dataframe import methods File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/extensions.py", line 8, in from dask.dataframe.accessor import ( File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/dataframe/accessor.py", line 126, in class DatetimeAccessor(Accessor): File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 987, in wrapper method.doc__ = _derived_from( ^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 940, in _derived_from method_args = get_named_args(method) ^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/dask/utils.py", line 701, in get_named_args s = inspect.signature(func) ^^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/inspect.py", line 3263, in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/inspect.py", line 3011, in from_callable return _signature_from_callable(obj, sigcls=cls, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/inspect.py", line 2599, in _signature_from_callable call = _descriptor_get(call, obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/bin/scenicplus", line 8, in sys.exit(main()) ^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1137, in main args.func(args) File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 330, in TF_to_gene infer_region_to_gene( File "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/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 "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/scenicplus/enhancer_to_gene.py", line 219, in _score_regions_to_genes joblib.Parallel( File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1952, in call return output if self.return_generator else list(output) ^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1595, in _get_outputs yield from self._retrieve() File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1699, in _retrieve self._raise_error_fast() File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast error_job.get_result(self.timeout) File "/ceph/project/Stone_multiome/ostone/conda_local/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 736, in get_result return self._return_or_raise() ^^^^^^^^^^^^^^^^^^^^^^^ File "/ceph/project/Stone_multiome/ostone/conda_local/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 [Wed Jun 26 20:57:24 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 /ceph/project/Stone_multiome/ostone/SCENICplus/scplus_pipeline/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/2024-06-26T205536.041583.snakemake.log WorkflowError: At least one job did not complete successfully.

Version (please complete the following information): Python: 3.11.9 arboreto 0.1.6 dask 2024.2.1 joblib 1.3.2 scenicplus 1.0a1

MatthewTCManion commented 4 months ago

I ran into this issue and it seems to be an incompatibility between dask 2024.2.1 and Python 3.11.9. I was able to resolve this particular issue by rolling back to Python 3.11.8, but I haven't confirmed that the rest of the pipeline will work after this change.

MatthewTCManion commented 4 months ago

I ran into this issue and it seems to be an incompatibility between dask 2024.2.1 and Python 3.11.9. I was able to resolve this particular issue by rolling back to Python 3.11.8, but I haven't confirmed that the rest of the pipeline will work after this change.

On second thought, I am seeing other people resolved this by updating dask to 2024.5.0, which gives a warning, but it sounds like it works fine after that. #386

degrainger commented 4 months ago

Thanks very much @MatthewTCManion! Rolling back to Python 3.11.8 solved my problem and allowed the pipeline to run to the end 😄