Problem with TSS

[ReviewBrandLab2024]

Hello,

Thank you for all your help. We didn't go through any problem since last time untill now with the following command:

!mkdir -p /staging/tur/Erythroid_Final/outs/qc
!pycistopic tss get_tss \
    --output /staging/tur/Erythroid_Final/outs/qc/tss.bed \
    --name "hsapiens_gene_ensembl" \
    --to-chrom-source ucsc \
    --ucsc hg38

Here is the error: (scenicplus) [tur@ap2001 qc]

$ 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

[SeppeDeWinter]

Hi @ReviewBrandLab2024

This looks like a lot of errors, can you run

pycistopic tss gene_annotation_list

in a bash (zsh, ... not python) kernel and show the output please?

All the best,

Seppe