jiarong
commented
1 year ago Hi, you do not need to create env with apptainer version.
Closed TKsh6 closed 1 year ago
jiarong
commented
1 year ago Hi, you do not need to create env with apptainer version.
TKsh6
commented
1 year ago sitll have the problem.
(base) [syl@node2 test_forvir]$ /beegfs/home/syl/software/virsorter2/virsorter2.sif run -w test.out1 -i test.fa --min-length 1500 -j 4 all -d /beegfs/home/syl/database_db/vir
[2023-03-30 15:54 INFO] VirSorter 2.2.3
[2023-03-30 15:54 INFO] /usr/local/bin/virsorter run -w test.out1 -i test.fa --min-length 1500 -j 4 all -d /beegfs/home/syl/database_db/vir
[2023-03-30 15:54 INFO] Using /beegfs/home/syl/.virsorter/template-config.yaml as config template
[2023-03-30 15:54 INFO] conig file written to /beegfs/home/syl/software/test_forvir/test.out1/config.yaml
[2023-03-30 15:54 INFO] Executing: snakemake --snakefile /usr/local/lib/python3.9/site-packages/virsorter/Snakefile --directory /beegfs/home/syl/software/test_forvir/test.out1 --jobs 4 --configfile /beegfs/home/syl/software/test_forvir/test.out1/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /beegfs/home/syl/database_db/vir/conda_envs --use-conda --quiet all
CreateCondaEnvironmentException:
Could not create conda environment from /usr/local/lib/python3.9/site-packages/virsorter/rules/../envs/vs2.yaml:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/usr/local/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 141, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/usr/local/lib/python3.9/site-packages/mamba/mamba_env.py", line 42, in mamba_install
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/usr/local/lib/python3.9/site-packages/mamba/utils.py", line 119, in load_channels
index = get_index(
File "/usr/local/lib/python3.9/site-packages/mamba/utils.py", line 78, in get_index
for channel in api.get_channels(all_channels):
RuntimeError: Read-only file system: '/usr/local/pkgs/cache/a549c71d'
`$ /usr/local/bin/mamba create --quiet --file /beegfs/home/syl/database_db/vir/conda_envs/30eccc62.yaml --prefix /beegfs/home/syl/database_db/vir/conda_envs/30eccc62`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/beegfs/home/syl/anaconda3/bin/conda
CONDA_PREFIX=/beegfs/home/syl/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/beegfs/home/syl/anaconda3/bin/python
CONDA_ROOT=/usr/local
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
JAVA_LD_LIBRARY_PATH=/beegfs/home/syl/anaconda3/jre/lib/amd64/server
LD_LIBRARY_PATH=/.singularity.d/libs
MANPATH=/beegfs/home/public/opt/lmod/lmod/share/man::/beegfs/root/openmpi-4.1.
1/share/man
MODULEPATH=/beegfs/home/public/opt/easybuild/modules/bio:/beegfs/home/public/opt/
PATH/bio/:/beegfs/home/public/opt/easybuild/modules/mpi:/beegfs/home/p
ublic/opt/easybuild/modules/all:/beegfs/home/public/opt/modulefiles/Li
nux:/beegfs/home/public/opt/modulefiles/Core:/beegfs/home/public/opt/l
mod/lmod/modulefiles/Core
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
USER_PATH=/beegfs/home/syl/anaconda3/envs/vs2/lib/python3.10/bin:/beegfs/home/sy
l/software/FAPROTAX_1.2.6/collapse_table.py:/beegfs/home/syl/software/
bamdst-master/:/beegfs/home/syl/software/site-
packages/lefse:/beegfs/home/syl/software/site-
packages/lefse-1.1.2.dist-info:/beegfs/home/syl/software/site-
packages/lefsebiom:/beegfs/home/syl/software/python-scripts:/beegfs/ho
me/syl/software:/beegfs/home/syl/software/quast-5.2.0/bin:/beegfs/home
/syl/software/soap/bin:/beegfs/home/syl/software/Trimmomatic-0.39:/bee
gfs/home/syl/software/metabat/:/beegfs/home/syl/software/metabat/:/bee
gfs/home/syl/software/:/beegfs/home/syl/software/ANIcalculator_v1:/bee
gfs/home/syl/software/mummer-4.0.0rc1:/beegfs/home/syl/software/mash-
Linux64v2.3:/beegfs/home/syl/software/mash-
Linux64v2.3:/beegfs/home/syl/software/RefineM-master/bin:/beegfs/home/
syl/database_db/gtdb:/beegfs/home/syl/software/Checkm_data:/beegfs/hom
e/syl/.aspera/connect/bin:/beegfs/home/syl/anaconda3/bin:/beegfs/home/
syl/anaconda3/bin:/beegfs/home/syl/anaconda3/condabin:/usr/local/bin:/
usr/bin:/usr/local/sbin:/usr/sbin:/beegfs/root/openmpi-4.1.1/bin:/beeg
fs/root/software/stubl-master/bin:/beegfs/root/software/pestat:/beegfs
/root/software/GTX.Zip:/opt/ibutils/bin:/usr/local/cuda-11.4/bin:/beeg
fs/home/syl/.local/bin:/beegfs/home/syl/bin:/bin:/usr/bin:/sbin:/usr/s
bin:/usr/local/bin:/usr/local/sbin
active environment : /beegfs/home/syl/anaconda3
active env location : /beegfs/home/syl/anaconda3
shell level : 1
user config file : /beegfs/home/syl/.condarc
populated config files : /beegfs/home/syl/.condarc
conda version : 4.10.3
conda-build version : not installed
python version : 3.9.6.final.0
virtual packages : __linux=3.10.0=0
__glibc=2.28=0
__unix=0=0
__archspec=1=x86_64
base environment : /usr/local (read only)
conda av data dir : /usr/local/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/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 : /usr/local/pkgs
/beegfs/home/syl/.conda/pkgs
envs directories : /beegfs/home/syl/.conda/envs
/usr/local/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.6 Linux/3.10.0-1062.18.1.el7.x86_64 debian/10 glibc/2.28
UID:GID : 1036:1001
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
File "/usr/local/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 350, in create
Try below:
/beegfs/home/syl/software/virsorter2/virsorter2.sif run -w test.out1 -i test.fa --min-length 1500 -j 4 allIt says it doesn't have the db file here.
(base) [syl@node2 test_forvir]$ /beegfs/home/syl/software/virsorter2/virsorter2.sif run -w test.out1 -i test.fa --min-length 1500 -j 4 all
[2023-03-30 16:00 INFO] VirSorter 2.2.3
[2023-03-30 16:00 INFO] /usr/local/bin/virsorter run -w test.out1 -i test.fa --min-length 1500 -j 4 all
[2023-03-30 16:00 INFO] Using /beegfs/home/syl/.virsorter/template-config.yaml as config template
Traceback (most recent call last):
File "/usr/local/bin/virsorter", line 10, in <module>
sys.exit(cli())
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1137, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 763, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/virsorter/virsorter.py", line 356, in run_workflow
make_config(
File "/usr/local/lib/python3.9/site-packages/virsorter/config.py", line 151, in make_config
groups_avail = os.listdir(f'{db_dir}/group')
FileNotFoundError: [Errno 2] No such file or directory: '/beegfs/home/syl/database_db/virsorter2/group'
Aha, you need to delete this file:
rm /beegfs/home/syl/.virsorter/template-config.yamlJust a note for others having the same issue:
With the apptainer version, you do not need to worry about the database. However, if you have run the virsorter setup or virsorter run --db-dir, you need to delete the .virsorter/template-config.yaml file in your user home directory.
TKsh6
commented
1 year ago Thank you for your help, it worked.
jowodo
commented
1 year ago I think this issue is ready to be closed.
Cause I chose option3 for installation, but I met this problem,
So how can I do to solve this?
yours tk