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[BUG]not shutting down client, client was created externally #522

@asmlgkj

Description

Thanks a lot
urget help needed

Describe the bug
A clear and concise description of what the bug is.

Mote that most errors are due to the input from the user, and therefore should be treated as questions in the Discussions. Please, only report them as bugs if you are quite certain that they are not behaving as expected.

Steps to reproduce the behavior

  • Command run when the error occurred:
  • # R command
    library(Seurat)
    library(SeuratData) 
    getOption('timeout')
    options(timeout=10000)
    #InstallData("pbmc3k")  
    data("pbmc3k")  
    sce <- pbmc3k.final   
    library(Seurat)
    table(Idents(sce))
    p1=DimPlot(sce,label = T) 
    write.csv(t(as.matrix(sce@assays$RNA@counts)), file = "pbmc_3k.all.csv")
    # python command
    import os
    import loompy as lp
    import numpy as np
    import scanpy as sc
    x=sc.read_csv("pbmc_3k.all.csv")
    row_attrs = {"Gene": np.array(x.var_names),}
    col_attrs = {"CellID": np.array(x.obs_names)}
    lp.create("pbmc_3k.loom", x.X.transpose(), row_attrs, col_attrs)
    # shell command
    dir = '/home/lebrown/
    tfs=$dir/hs_hgnc_tfs.txt
    feather=$dir/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather
    tbl=$dir/motifs-v9-nr.hgnc-m0.001-o0.0.tbl 
    # 一定要保证上面的数据库文件完整无误哦 
    input_loom='pbmc_3k.loom'
    ls $tfs  $feather  $tbl  $input_loom
    #2.1 grn
    pyscenic grn \
    --num_workers 4 \
    --output adj.sample.tsv \
    --method grnboost2 \
    $input_loom \
    
  • Error encountered:
  • 2023-12-17 17:33:27,732 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
    /home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/distributed/node.py:182: UserWarning: Port 8787 is already in use.
    Perhaps you already have a cluster running?
    Hosting the HTTP server on port 36777 instead
      warnings.warn(
    site-packages/loompy/bus_file.py:101: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
    preparing dask client
    parsing input
    not shutting down client, client was created externally
    finished
    Traceback (most recent call last):
      File "/home/lebrown/software/miniconda38/envs/py311/bin/pyscenic", line 8, in <module>
        sys.exit(main())
                 ^^^^^^
      File "/home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/pyscenic/cli/pyscenic.py", line 713, in main
        args.func(args)
      File "/home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/pyscenic/cli/pyscenic.py", line 106, in find_adjacencies_command
        network = method(
                  ^^^^^^^
      File "/home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/arboreto/algo.py", line 39, in grnboost2
        return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/arboreto/algo.py", line 115, in diy
        expression_matrix, gene_names, tf_names = _prepare_input(expression_data, gene_names, tf_names)
                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/lebrown/software/miniconda38/envs/py311/lib/python3.11/site-packages/arboreto/algo.py", line 229, in _prepare_input
        raise ValueError('Intersection of gene_names and tf_names is empty.')
    ValueError: Intersection of gene_names and tf_names is empty.