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sebastian-gregoricchio / snakeATAC

Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
GNU General Public License v3.0
2 stars 0 forks source link

So hard to install #2

Closed chaofan520 closed 2 days ago

chaofan520 commented 3 days ago 
conda env create -f snakeATAC_conda_env_stable.yaml                                                          
anaconda/linux-64                                             No change
bioconda/linux-64                                             No change
anaconda/noarch                                               No change
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
bioconda/noarch                                               No change
conda-forge/noarch                                  19.0MB @  86.8kB/s 3m:37.6s
conda-forge/linux-64                                44.7MB @  26.4kB/s 28m:10.3s
Collect all metadata (repodata.json): done
Solving environment: done                                                                                                      

==> WARNING: A newer version of conda exists. <==                                                                              
    current version: 23.1.0                                                                                                    
    latest version: 24.7.1                                                                                                     

Please update conda by running

    $ conda update -n base -c conda-forge conda

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: | 

    Installed package of scikit-learn can be accelerated using scikit-learn-intelex.
    More details are available here: https://intel.github.io/scikit-learn-intelex

    For example:

        $ conda install scikit-learn-intelex
        $ python -m sklearnex my_application.py

                                                                                                                             done
ERROR conda.core.link:_execute(745): An error occurred while installing package 'bioconda::bioconductor-copyhelper-1.30.0-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:

Does anyone konw how to fix it?

chaofan520 commented 3 days ago 
post-link script failed for package bioconda::bioconductor-copyhelper-1.30.0-r42hdfd78af_0
location of failed script: /data/chaofan/software/miniconda/envs/ATAC/bin/.bioconductor-copyhelper-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: ++ dirname -- /data/chaofan/software/miniconda/envs/ATAC/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages
+ json=/data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."copyhelper-1.30.0".fn' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"CopyhelpeR_1.30.0.tar.gz"'
+ IFS=
+ read -r value
++ yq '."copyhelper-1.30.0".urls[]' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."copyhelper-1.30.0".md5' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"2be26e5fb90270541b426a5b2baf1824"'
+ STAGING=/data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0
+ mkdir -p /data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0
+ TARBALL='/data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0/"CopyhelpeR_1.30.0.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz
++ echo '"2be26e5fb90270541b426a5b2baf1824"'
++ tr -d '"'
+ MD5=2be26e5fb90270541b426a5b2baf1824
+ curl -L https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   410  100   410    0     0    200      0  0:00:02  0:00:02 --:--:--   200
 17 42.6M   17 7549k    0     0  49713      0  0:14:59  0:02:35  0:12:24 71654
curl: (18) transfer closed with 36997413 bytes remaining to read

return code: 18

kwargs:
{}

Traceback (most recent call last):
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1124, in __call__
    return func(*args, **kwargs)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda_env/cli/main.py", line 78, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/notices/core.py", line 109, in wrapper
    return func(*args, **kwargs)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 154, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda_env/installers/conda.py", line 58, in install
    unlink_link_transaction.execute()
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/core/link.py", line 286, in execute
    self._execute(
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/core/link.py", line 761, in _execute
    raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-copyhelper-1.30.0-r42hdfd78af_0
location of failed script: /data/chaofan/software/miniconda/envs/ATAC/bin/.bioconductor-copyhelper-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: ++ dirname -- /data/chaofan/software/miniconda/envs/ATAC/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages
+ json=/data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."copyhelper-1.30.0".fn' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"CopyhelpeR_1.30.0.tar.gz"'
+ IFS=
+ read -r value
++ yq '."copyhelper-1.30.0".urls[]' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."copyhelper-1.30.0".md5' /data/chaofan/software/miniconda/envs/ATAC/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"2be26e5fb90270541b426a5b2baf1824"'
+ STAGING=/data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0
+ mkdir -p /data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0
+ TARBALL='/data/chaofan/software/miniconda/envs/ATAC/share/copyhelper-1.30.0/"CopyhelpeR_1.30.0.tar.gz"'
+ SUCCESS=0
+ for URL in ${URLS[@]}
++ echo '"https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz
++ echo '"2be26e5fb90270541b426a5b2baf1824"'
++ tr -d '"'
+ MD5=2be26e5fb90270541b426a5b2baf1824
+ curl -L https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   410  100   410    0     0    200      0  0:00:02  0:00:02 --:--:--   200
 17 42.6M   17 7549k    0     0  49713      0  0:14:59  0:02:35  0:12:24 71654
curl: (18) transfer closed with 36997413 bytes remaining to read

return code: 18

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/chaofan/software/miniconda/bin/conda-env", line 7, in <module>
    sys.exit(main())
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda_env/cli/main.py", line 89, in main
    return conda_exception_handler(do_call, args, parser)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1424, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1127, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1156, in handle_exception
    return self.handle_application_exception(exc_val, exc_tb)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1170, in handle_application_exception
    self._print_conda_exception(exc_val, exc_tb)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1174, in _print_conda_exception
    print_conda_exception(exc_val, exc_tb)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1101, in print_conda_exception
    stderrlog.error("\n%r\n", exc_val)
  File "/data/chaofan/software/miniconda/lib/python3.9/logging/__init__.py", line 1475, in error
    self._log(ERROR, msg, args, **kwargs)
  File "/data/chaofan/software/miniconda/lib/python3.9/logging/__init__.py", line 1589, in _log
    self.handle(record)
  File "/data/chaofan/software/miniconda/lib/python3.9/logging/__init__.py", line 1598, in handle
    if (not self.disabled) and self.filter(record):
  File "/data/chaofan/software/miniconda/lib/python3.9/logging/__init__.py", line 806, in filter
    result = f.filter(record)
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/gateways/logging.py", line 48, in filter
    record.msg = record.msg % new_args
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/__init__.py", line 107, in __repr__
    errs.append(e.__repr__())
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/__init__.py", line 62, in __repr__
    return f"{self.__class__.__name__}: {self}"
  File "/data/chaofan/software/miniconda/lib/python3.9/site-packages/conda/__init__.py", line 66, in __str__
    return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 1887
sebastian-gregoricchio commented 3 days ago

Thank you for your message.

Recently I made a bioconda recipe to install it. Did you try with it?

Have a look in the documentation: https://github.com/sebastian-gregoricchio/snakeATAC/wiki/02.-Installation-an-dependencies#221-installation-via-condamamba-recommended

chaofan520 commented 3 days ago

Thank you for your reply! I'll try.

chaofan520 commented 3 days ago

OHHH

mamba install -c bioconda -c anaconda -c conda-forge -c defaults -n snakeATAC snakeatac_env
Not a conda environment: /data/chaofan/software/miniconda/envs/mamba/envs/snakeATAC

EnvironmentLocationNotFound: Not a conda environment: /data/chaofan/software/miniconda/envs/mamba/envs/snakeATAC
sebastian-gregoricchio commented 3 days ago

Did you create a conda environment with that name? conda env create -n snakeATAC

Otherwise, what is the output of conda env list?

The full steps would be:

conda create -n snakeATAC

conda activate mamba

mamba install -c bioconda -c anaconda -c conda-forge -c defaults -n snakeATAC snakeatac_env

conda activate snakeATAC
chaofan520 commented 2 days ago

image

I replace the name of snakeATAC.

chaofan520 commented 2 days ago 
conda create -n mamba conda-forge::mamba
conda activate mamba
mamba install -c bioconda -c anaconda -c conda-forge -c defaults snakeatac_env

It works. Thank you! @sebastian-gregoricchio

chaofan520 commented 2 days ago 
snakemake \
> -s /data/chaofan/software/snakeATAC/workflow/snakeATAC_analyses.snakefile \
> --configfile /data/chaofan/pipelines/04.ATAC_seq/snakeATAC_analyses_config.yaml \
> --cores 12 -n
Traceback (most recent call last):

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/snakemake/cli.py", line 1976, in args_to_api
    config_settings=ConfigSettings(
                    ^^^^^^^^^^^^^^^

  File "<string>", line 6, in __init__

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/snakemake/settings/types.py", line 333, in __post_init__
    self.overwrite_config = self._get_overwrite_config()
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/snakemake/settings/types.py", line 341, in _get_overwrite_config
    update_config(overwrite_config, load_configfile(f))
                                    ^^^^^^^^^^^^^^^^^^

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/snakemake/common/configfile.py", line 38, in load_configfile
    config = _load_configfile(configpath)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/snakemake/common/configfile.py", line 23, in _load_configfile
    import yte

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/yte/__init__.py", line 3, in <module>
    import plac

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/plac.py", line 29, in <module>
    from plac_ext import (Interpreter, import_main, ReadlineInput,

  File "/data/chaofan/software/miniconda/envs/mamba/lib/python3.12/site-packages/plac_ext.py", line 806, in <module>
    import asyncore

ModuleNotFoundError: No module named 'asyncore'
chaofan520 commented 2 days ago 
pip install pyasyncore
pip install pyasynchat