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$ pycistopic tss gene_annotation_list | grep Human
Traceback (most recent call last):
File "/home/tur/miniconda3/envs/scenicplus/bin/pycistopic", line 8, in<module>sys.exit(main())
^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/pycistopic.py", line 26, in main
args.func(args)
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/subcommand/tss.py", line 479, in run_tss_gene_annotation_list
get_species_gene_annotation_ensembl_biomart_dataset_names(
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/subcommand/tss.py", line 299, in get_species_gene_annotation_ensembl_biomart_dataset_names
biomart_datasets = ga.get_all_gene_annotation_ensembl_biomart_dataset_names(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/gene_annotation.py", line 56, in get_all_gene_annotation_ensembl_biomart_dataset_names
import pybiomart as pbm
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/__init__.py", line 3, in<module>
from .server import Server
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/server.py", line 12, in<module>
from .base import ServerBase
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/base.py", line 15, in<module>
requests_cache.install_cache('.pybiomart')
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/patcher.py", line 41, in install_cache
backend = init_backend(cache_name, backend, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/__init__.py", line 91, in init_backend
return BACKEND_CLASSES[backend](cache_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 61, in __init__
self.responses: SQLiteDict = SQLiteDict(db_path, table_name='responses', **skwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 225, in __init__
self.init_db()
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 230, in init_db
with self.connection(commit=True) as con:
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 252, in connection
self._connection = sqlite3.connect(self.db_path, **self.connection_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: unable to open database file
(scenicplus) [tur@ap2001 qc]$ !mkdir -p outs/qc
!pycistopic tss get_tss \
--output outs/qc/tss.bed \
--name "hsapiens_gene_ensembl" \
--to-chrom-source ucsc \
--ucsc hg38
mkdir scRNA -p outs/qc
mkdir: cannot create directory ‘scRNA’: Disk quota exceeded
mkdir: cannot create directory ‘outs’: Disk quota exceeded
pycistopic tss gene_annotation_list | grep Human tss get_tss \
grep: unrecognized option '--output'
Usage: grep [OPTION]... PATTERNS [FILE]...
Try 'grep --help'for more information.
Traceback (most recent call last):
File "/home/tur/miniconda3/envs/scenicplus/bin/pycistopic", line 8, in<module>sys.exit(main())
^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/pycistopic.py", line 26, in main
args.func(args)
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/subcommand/tss.py", line 479, in run_tss_gene_annotation_list
get_species_gene_annotation_ensembl_biomart_dataset_names(
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cli/subcommand/tss.py", line 299, in get_species_gene_annotation_ensembl_biomart_dataset_names
biomart_datasets = ga.get_all_gene_annotation_ensembl_biomart_dataset_names(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/gene_annotation.py", line 56, in get_all_gene_annotation_ensembl_biomart_dataset_names
import pybiomart as pbm
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/__init__.py", line 3, in<module>
from .server import Server
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/server.py", line 12, in<module>
from .base import ServerBase
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/base.py", line 15, in<module>
requests_cache.install_cache('.pybiomart')
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/patcher.py", line 41, in install_cache
backend = init_backend(cache_name, backend, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/__init__.py", line 91, in init_backend
return BACKEND_CLASSES[backend](cache_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 61, in __init__
self.responses: SQLiteDict = SQLiteDict(db_path, table_name='responses', **skwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 225, in __init__
self.init_db()
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 230, in init_db
with self.connection(commit=True) as con:
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/tur/miniconda3/envs/scenicplus/lib/python3.11/site-packages/requests_cache/backends/sqlite.py", line 252, in connection
self._connection = sqlite3.connect(self.db_path, **self.connection_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: unable to open database file
Do we need to update the command or something else?
Best,
Steven
The text was updated successfully, but these errors were encountered:
Hello,
Thank you for all your help. We didn't go through any problem since last time untill now with the following command:
Here is the error: (scenicplus) [tur@ap2001 qc]
Do we need to update the command or something else?
Best,
Steven
The text was updated successfully, but these errors were encountered: