Bonjour,
J'ai un soucis quand je lance un pipeline snakemake (3DGB) que j'ai directement installé dans mon projet. Lorsque je lance un script.sh me permettant de lancer le workflow d'analyse, j'obtiens cette erreur dans le slurm :
Using profile smk_profile for setting default command line arguments.
Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
Creating conda environment ../envs/workflow.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /shared/ifbstor1/projects/minomics/groyer/HiC_Results/3d-genome-builder/envs/workflow.yml:
Command:
mamba env create --quiet --file "/shared/ifbstor1/projects/minomics/groyer/HiC_Results/3d-genome-builder/3DGB_p_anserina_KMT6_dedup/.snakemake/conda/75cba1bcba50070e3c784192bb9073ec_.yaml" --prefix "/shared/ifbstor1/projects/minomics/groyer/HiC_Results/3d-genome-builder/3DGB_p_anserina_KMT6_dedup/.snakemake/conda/75cba1bcba50070e3c784192bb9073ec_"
Output:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1129, in __call__
return func(*args, **kwargs)
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/conda/notices/core.py", line 72, in wrapper
return_value = func(*args, **kwargs)
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 156, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/mamba/mamba_env.py", line 55, in mamba_install
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/mamba/utils.py", line 129, in load_channels
index = get_index(
File "/shared/ifbstor1/software/miniconda/lib/python3.9/site-packages/mamba/utils.py", line 110, in get_index
is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (28) Timeout was reached [https://repo.anaconda.com/pkgs/r/noarch/repodata.json]
Failed to connect to repo.anaconda.com port 443 after 6974 ms: Couldn't connect to server
`$ /shared/ifbstor1/software/miniconda/bin/mamba create --quiet --file /shared/ifbstor1/projects/minomics/groyer/HiC_Results/3d-genome-builder/3DGB_p_anserina_KMT6_dedup/.snakemake/conda/75cba1bcba50070e3c784192bb9073ec_.yaml --prefix /shared/ifbstor1/projects/minomics/groyer/HiC_Results/3d-genome-builder/3DGB_p_anserina_KMT6_dedup/.snakemake/conda/75cba1bcba50070e3c784192bb9073ec_`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_ROOT=/shared/ifbstor1/software/miniconda
CPATH=/shared/ifbstor1/software/miniconda/envs/snakemake-8.9.0/include
CURL_CA_BUNDLE=<not set>
GOPATH=/opt/go/packages
MANPATH=:
MODULEPATH=/shared/software/modulefiles
PATH=/shared/ifbstor1/software/miniconda/bin:/shared/ifbstor1/software/mini
conda/envs/snakemake-8.9.0/bin:/shared/ifbstor1/software/miniconda/bin
/:/opt/status_bars/status_bars/:/shared/software/slurm-sinteractive:/s
hared/software/sinteractive:/shared/software/modules/4.6.1/bin:/usr/lo
cal/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/go/1.14.4/bin:/opt/go/
packages/bin:/shared/home/groyer/.local/bin:/shared/home/groyer/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
STATUS_BAR_CONF_PATH=/opt/status_bars/etc/conf.sh
active environment : None
user config file : /shared/home/groyer/.condarc
populated config files : /shared/ifbstor1/software/miniconda/.condarc
conda version : 22.9.0
conda-build version : not installed
python version : 3.9.2.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /shared/ifbstor1/software/miniconda (read only)
conda av data dir : /shared/ifbstor1/software/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /shared/ifbstor1/software/miniconda/pkgs
/shared/home/groyer/.conda/pkgs
envs directories : /shared/home/groyer/.conda/envs
/shared/ifbstor1/software/miniconda/envs
platform : linux-64
user-agent : conda/22.9.0 requests/2.28.1 CPython/3.9.2 Linux/5.4.0-163-generic ubuntu/20.04.6 glibc/2.31
UID:GID : 164810:164810
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
srun: error: cpu-node-100: task 0: Exited with exit code 1
Je ne comprends pas d'où provient cette erreur puisque qu'avant tout fonctionnait correctement. Serait il possible de m'indiquer quelle est l'origine et la solution de ce problème ?
Désolé pour ce dérangement.
Je vous remercie par avance.
Cordialement
Goran