[BUG]not shutting down client, client was created externally · Issue #522 · aertslab/pySCENIC

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Already on GitHub? Sign in to your account 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.
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.
You could do this ：

conda list |grep distributed

pip uninstall distributed

pip install distributed==2023.12.1
Best,
Anler
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.
You could do this ： conda list |grep distributed pip uninstall distributed pip install distributed==2023.12.1
Best,
Anler
Same error about port in use; Anler's idea fixed it. Thanks