Open lifeifeifeifei opened 3 years ago
Hi, I need to update database for manual install. Could you use the command: instead for now?
virsorter setup -d db -j 4
Hi, I need to update database for manual install. Could you use the command: instead for now?
virsorter setup -d db -j 4
When I first tried to update the database, I used this command, but an error was reported, so I used the second one.
Now I use this command virsorter setup -d db -j 4
, it report error as before.
[2021-10-12 01:53 INFO] VirSorter 2.2.3
[2021-10-12 01:53 INFO] /Software/anaconda3/envs/vs2/bin/virsorter setup -d db -j 4
[2021-10-12 01:53 INFO] Setting up VirSorter2 database; this might take ~10 mins and only needs to be done once.
[2021-10-12 01:53 INFO] saving /Software/VirSorter2/db as DBDIR to config file /
CreateCondaEnvironmentException:
Could not create conda environment from /Software/VirSorter2/virsorter/rules/../envs/vs2.yaml:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda/exceptions.py", line
return func(*args, **kwargs)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main.py", lin
exit_code = getattr(module, func_name)(args, parser)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main_create.p
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/mamba_env.py", line 4
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 123,
index = get_index(
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 104,
is_downloaded = dlist.download(True)
RuntimeError: Multi-download failed.
`$ /Software/anaconda3/envs/vs2/bin/mamba create --quiet --file /Software/VirSor
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_BACKUP_ADDR2LINE=/Software/anaconda3/bin/x86_64-conda-linux-gnu-
addr2line
CONDA_BACKUP_AR=/Software/anaconda3/bin/x86_64-conda-linux-gnu-ar
CONDA_BACKUP_AS=/Software/anaconda3/bin/x86_64-conda-linux-gnu-as
CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu
CONDA_BACKUP_CC=/Software/anaconda3/bin/x86_64-conda-linux-gnu-cc
CONDA_BACKUP_CC_FOR_BUILD=/Software/anaconda3/bin/x86_64-conda-linux-gnu-cc
CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_CMAKE_PREFIX_PATH=/Software/anaconda3:/Software/anaconda
3/x86_64-conda-linux-gnu/sysroot/usr
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/Software/anaconda3/x86_64-conda-linux-gnu/sysroot
CONDA_BACKUP_CPP=/Software/anaconda3/bin/x86_64-conda-linux-gnu-cpp
CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem
/Software/anaconda3/include
CONDA_BACKUP_CXX=/Software/anaconda3/bin/x86_64-conda-linux-gnu-c++
CONDA_BACKUP_CXXFILT=/Software/anaconda3/bin/x86_64-conda-linux-gnu-c++filt
CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_CXX_FOR_BUILD=/Software/anaconda3/bin/x86_64-conda-linux-gnu-c++
CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem
/Software/anaconda3/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-
all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments
-ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_ELFEDIT=/Software/anaconda3/bin/x86_64-conda-linux-gnu-elfedit
CONDA_BACKUP_F77=/Software/anaconda3/bin/x86_64-conda-linux-gnu-
gfortran
CONDA_BACKUP_F90=/Software/anaconda3/bin/x86_64-conda-linux-gnu-
gfortran
CONDA_BACKUP_F95=/Software/anaconda3/bin/x86_64-conda-linux-gnu-f95
CONDA_BACKUP_FC=/Software/anaconda3/bin/x86_64-conda-linux-gnu-
gfortran
CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-
protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/Software/anaconda3/include
CONDA_BACKUP_GCC=/Software/anaconda3/bin/x86_64-conda-linux-gnu-gcc
CONDA_BACKUP_GCC_AR=/Software/anaconda3/bin/x86_64-conda-linux-gnu-gcc-ar
CONDA_BACKUP_GCC_NM=/Software/anaconda3/bin/x86_64-conda-linux-gnu-gcc-nm
CONDA_BACKUP_GCC_RANLIB=/Software/anaconda3/bin/x86_64-conda-linux-gnu-gcc-
ranlib
CONDA_BACKUP_GFORTRAN=/Software/anaconda3/bin/x86_64-conda-linux-gnu-
gfortran
CONDA_BACKUP_GPROF=/Software/anaconda3/bin/x86_64-conda-linux-gnu-gprof
CONDA_BACKUP_GXX=/Software/anaconda3/bin/x86_64-conda-linux-gnu-g++
CONDA_BACKUP_HOST=x86_64-conda-linux-gnu
CONDA_BACKUP_LD=/Software/anaconda3/bin/x86_64-conda-linux-gnu-ld
CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,
--disable-new-dtags -Wl,--gc-sections
-Wl,-rpath,/Software/anaconda3/lib -Wl,-rpath-
link,/Software/anaconda3/lib
-L/Software/anaconda3/lib
CONDA_BACKUP_LD_GOLD=/Software/anaconda3/bin/x86_64-conda-linux-gnu-ld.gold
CONDA_BACKUP_NM=/Software/anaconda3/bin/x86_64-conda-linux-gnu-nm
CONDA_BACKUP_OBJCOPY=/Software/anaconda3/bin/x86_64-conda-linux-gnu-objcopy
CONDA_BACKUP_OBJDUMP=/Software/anaconda3/bin/x86_64-conda-linux-gnu-objdump
CONDA_BACKUP_RANLIB=/Software/anaconda3/bin/x86_64-conda-linux-gnu-ranlib
CONDA_BACKUP_READELF=/Software/anaconda3/bin/x86_64-conda-linux-gnu-readelf
CONDA_BACKUP_SIZE=/Software/anaconda3/bin/x86_64-conda-linux-gnu-size
CONDA_BACKUP_STRINGS=/Software/anaconda3/bin/x86_64-conda-linux-gnu-strings
CONDA_BACKUP_STRIP=/Software/anaconda3/bin/x86_64-conda-linux-gnu-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_linux_gnu
CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu
CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu
CONDA_DEFAULT_ENV=vs2
CONDA_EXE=/Software/anaconda3/bin/conda
CONDA_PERL5LIB=/Software/anaconda3/lib/site_perl/5.26.2:/Software/anaconda3/lib/perl5/site_perl/5.22.0:/Sof
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perl-extutils-makemaker-7.36-pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-file-path-2.16-pl526_0/lib/site_perl
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perl-xml-sax-expat-0.51-pl526_3/lib/site_perl/5.26.2:/
Software/anaconda3/pkgs/perl-mime-base64-3.15-pl526_1/lib/site_perl/5.
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Software/anaconda3/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.2
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perl-http-message-6.18-pl526_0/lib/site_perl/5.26.2:/S
oftware/anaconda3/pkgs/perl-compress-raw-zlib-2.087-pl526hc9558a2_0/li
b/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-moo-2
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b/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-file-
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erl-sub-identify-0.14-pl526h14c3975_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-getopt-long-2.50-pl526_1/lib/site_p
erl/5.26.2:/Software/anaconda3/pkgs/perl-json-xs-2.34-
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gs/perl-html-tagset-3.20-pl526_3/lib/site_perl/5.26.2:
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lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
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perl-www-robotrules-6.02-pl526_3/lib/site_perl/5.26.2:
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gs/perl-mro-compat-0.13-pl526_0/lib/site_perl/5.26.2:/
Software/anaconda3/pkgs/perl-html-parser-3.72-pl526h6bb024c_5/lib/site
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gs/perl-encode-locale-1.05-pl526_6/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-apache-test-1.40-pl526_1/lib/site_perl
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erl-mozilla-ca-20180117-pl526_1/lib/site_perl/5.26.2:/
Software/anaconda3/pkgs/perl-params-util-1.07-pl526h6bb024c_4/lib/site
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CONDA_PREFIX=/Software/anaconda3/envs/vs2
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CONDA_PROMPT_MODIFIER=(vs2)
CONDA_PYTHON_EXE=/Software/anaconda3/bin/python
CONDA_ROOT=/Software/anaconda3/envs/vs2
CONDA_SHLVL=2
CURL_CA_BUNDLE=<not set>
PATH=/Software/anaconda3/envs/vs2/bin:/Soft
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vContact2/bin:/Software/vpf-tools:/Sof
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e/bbmap:/Software/sratools/sratoolkit.2.9.6-ubuntu64/b
in:/Software:/Software/anaconda3/envs/
vs2/bin:/Software/orfm-0.7.1_Linux_x86_64:/Software/anaconda3/envs/vContact2/bin:/Software/v
pf-tools:/Software/Augustus/augustus/bin:/Software/Augustus/augustus/scripts:/Software/anaco
nda3/envs/icu-58/lib:/Software/anaconda3/pkgs/icu-58.2
-he6710b0_3/lib:/Software/anaconda3/envs/icu-58:/Software/anaconda3/envs/snakemake/bin:/Soft
ware/anaconda3/lib:/Software/anaconda3/envs/vs2/bin:/Software/anaconda3:/Software/SPAdes-3.1
3.0-Linux/bin:/Software/bbmap:/Softwar
e/sratools/sratoolkit.2.9.6-ubuntu64/bin:/Software:/Software/anaconda3/envs/vs2/bin:/Softwar
e/orfm-0.7.1_Linux_x86_64:/Software/anaconda3/envs/vCo
ntact2/bin:/Software/vpf-tools:/Softwa
re/Augustus/augustus/bin:/Software/Augustus/augustus/s
cripts:/Software/anaconda3/envs/icu-58/lib:/Software/anaconda3/pkgs/icu-58.2-he6710b0_3/lib:
/Software/anaconda3/envs/icu-58:/Software/anaconda3/en
vs/snakemake/bin:/Software/anaconda3/lib:/Software/anaconda3/bin:/Software/anaconda3:/Software/SPAdes-3.13.0-Linux/bin:/Software/b
bmap:/Software/sratools/sratoolkit.2.9.6-ubuntu64/bin:
/Software:/Software/anaconda3/envs/vs2
/bin:/Software/orfm-0.7.1_Linux_x86_64:/Software/anaconda3/envs/vContact2/bin:/Software/vpf-
tools:/Software/Augustus/augustus/bin:
/Software/Augustus/augustus/scripts:/Software/anaconda
3/envs/icu-58/lib:/Software/anaconda3/pkgs/icu-58.2-he
6710b0_3/lib:/Software/anaconda3/envs/icu-58:/Software/anaconda3/envs/snakemake/bin:/Softwar
e/anaconda3/lib:/Software/anaconda3/bin:/Software/anaconda3:/Software/SPAdes-3.13.0-Linux/bi
n:/Software/bbmap:/Software/sratools/s
ratoolkit.2.9.6-ubuntu64/bin:/Software:/Software/anaconda3/envs/vs2/bin:/Software/orfm-0.7.1
_Linux_x86_64:/Software/vpf-tools:/Sof
tware/Augustus/augustus/bin:/Software/Augustus/augustu
s/scripts:/Software/anaconda3/envs/icu-58/lib:/Software/anaconda3/pkgs/icu-58.2-he6710b0_3/lib:/Software/anaconda3/envs/icu-58:/Software/anaconda3
/envs/snakemake/bin:/Software/anaconda3/lib:/Software/anaconda3/bin:/Software/anaconda3:/Software/SPAdes-3.13.0-Linux/bin:/Softwar
e/bbmap:/Software/sratools/sratoolkit.2.9.6-ubuntu64/b
in:/Software:/Software/orfm-0.7.1_Linu
x_x86_64:/Software/vpf-tools:/Software
/Augustus/augustus/bin:/Software/Augustus/augustus/scr
ipts:/Software/anaconda3/envs/icu-58/lib:/Software/anaconda3/pkgs/icu-58.2-he6710b0_3/lib:/S
oftware/anaconda3/envs/icu-58:/Software/anaconda3/envs
/snakemake/bin:/Software/anaconda3/lib:/Software/anaconda3/bin:/Software/anaconda3:/Software/SPAdes-3.13.0-Linux/bin:/Software/bbm
ap:/Software/sratools/sratoolkit.2.9.6-ubuntu64/bin:/Software:/.local/bin:/Softwar
e/anaconda3/bin:/Software/anaconda3/condabin:/usr/loca
l/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lo
cal/games:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /Software/anaconda3/envs/vs2
shell level : 2
user config file : /home/gled/.condarc
populated config files : /home/gled/.condarc
conda version : 4.10.3
conda-build version : not installed
python version : 3.8.12.final.0
virtual packages : __linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /Software/anaconda3/envs/vs2 (writable)
conda av data dir : /Software/anaconda3/envs/vs2/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://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/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
https://conda.anaconda.org/r/linux-64
https://conda.anaconda.org/r/noarch
https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/linux-64
https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/noarch
package cache : /Software/anaconda3/envs/vs2/pkgs
/home/gled/.conda/pkgs
envs directories : /Software/anaconda3/envs/vs2/envs
/home/gled/.conda/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.12 Linux/4.15.0-128-generic ubuntu/18.04.5 gl
ibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/snakemake/deployment/conda.py",
[2021-10-12 01:53 ERROR] CreateCondaEnvironmentException:
Could not create conda environment from /Software/VirSorter2/virsorter/rules/../envs/vs2.yaml:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda/exceptions.py", line
return func(*args, **kwargs)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main.py", lin
exit_code = getattr(module, func_name)(args, parser)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main_create.p
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/mamba_env.py", line 4
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 123,
index = get_index(
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 104,
is_downloaded = dlist.download(True)
RuntimeError: Multi-download failed.
`$ /Software/anaconda3/envs/vs2/bin/mamba create --quiet --file /Software/VirSor
environment variables:
An unexpected error has occurred. Conda has prepared the above report.
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/snakemake/deployment/conda.py",
[2021-10-12 01:53 INFO] First attempt failed; trying the second time.
CreateCondaEnvironmentException:
Could not create conda environment from /Software/VirSorter2/virsorter/rules/../envs/vs2.yaml:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda/exceptions.py", line
return func(*args, **kwargs)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main.py", lin
exit_code = getattr(module, func_name)(args, parser)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main_create.p
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/mamba_env.py", line 4
index = load_channels(pool, channel_urls, repos, prepend=False)
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 123,
index = get_index(
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 104,
is_downloaded = dlist.download(True)
RuntimeError: Multi-download failed.
`$ /Software/anaconda3/envs/vs2/bin/mamba create --quiet --file /Software/VirSor
environment variables:
An unexpected error has occurred. Conda has prepared the above report.
File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create
[2021-10-12 01:53 CRITICAL] Command 'snakemake --snakefile /Software/VirSorter2/virsorter/rules/setup-retry.smk --directory /Software/VirSorter2/db --quiet --config Skip_deps_install=False --jobs 4 --rerun-incomplete --latency-wait 600 --nolock --use-conda --conda-prefix /Software/VirSorter2/db/conda_envs --conda-frontend mamba ' returned non-zero exit status 1.
Could someone help me solve this problem? A little anxious.
Sorry for the late reply. It looks like failing to install the required packages. Does the server have internet connection?
I have the same question now,I really hope it can be resolved. Thank you
I use this command virsorter setup -d db -j 4, it report error . I have tried many methods, but still can not solve, hope to get help, thank you The error : [2021-11-17 18:04 INFO] VirSorter 2.2.3 [2021-11-17 18:04 INFO] /home/zhanyuanchao/miniconda3/envs/vs2/bin/virsorter setup -d db -j 4 [2021-11-17 18:04 INFO] Setting up VirSorter2 database; this might take ~10 mins and only needs to be done once. [2021-11-17 18:04 INFO] saving /home/zhanyuanchao/software/Virsorter2/db as DBDIR to config file /home/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/template-config.yaml
CreateCondaEnvironmentException: Could not create conda environment from /home/miniconda3/envs/vs2/lib/python3.8/site-packages/virsorter/rules/../envs/vs2.yaml: ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it ERROR Path already locked by the same PID WARNING LockFile creation for path '/home/miniconda3/envs/vs2/pkgs/cache' failed, continuing without it Exceeded max retries, giving up LockError: LOCKERROR: It looks like conda is already doing something. The lock ['/home/miniconda3/envs/vs2/pkgs/cache.pid3095.conda_lock'] was found. Wait for it to finish before continuing. If you are sure that conda is not running, remove it and try again. You can also use: $ conda clean --lock
It might be you can't install packages through mamba!You can try to change “--conda-frontend mamba" to “--conda-frontend conda". Though it is slow, but it did works.
The conda installation might have issue with certain OS with specific setting. I recommend the singularity version.
I install the virsorter2 as suggested:
but when I run it on a test dataset, it always report error.