amingson
commented
5 months ago 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 \ $tfs
- 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. @jit 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
jesusch10
Thanks a lot urget help needed
Describe the bug A clear and concise description of what the bug is.
Steps to reproduce the behavior
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/hg38refseq-r8010kb_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 \ $tfs
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. @jit 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
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.