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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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CreateCondaEnvironmentException: Could not create conda environment from /VirSorter2/virsorter/rules/../envs/vs2.yaml #88

Open lifeifeifeifei opened 3 years ago

lifeifeifeifei commented 3 years ago

I install the virsorter2 as suggested:

conda create -n vs2 -c conda-forge -c bioconda "python>=3.6" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer==3.3 prodigal screed ruamel.yaml "snakemake>=5.18,<=5.26" click mamba
conda activate vs2
git clone https://github.com/jiarong/VirSorter2.git
cd VirSorter2
pip install -e .

tar -xzf db.tgz
virsorter config --init-source --db-dir=./db

but when I run it on a test dataset, it always report error. 

virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all
[2021-10-11 08:04 INFO] VirSorter 2.2.3
[2021-10-11 08:04 INFO] /Software/anaconda3/envs/vs2/bin/virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all
[2021-10-11 08:04 INFO] Using /Software/VirSorter2/virsorter/template-config.yaml as config template
[2021-10-11 08:04 INFO] conig file written to /test.out/config.yaml

[2021-10-11 08:04 INFO] Executing: snakemake --snakefile /Software/VirSorter2/virsorter/Snakefile --directory /test.out --jobs 4 --configfile /test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /Software/VirSorter2/db/conda_envs --use-conda --quiet all
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 1079, in __call__
    return func(*args, **kwargs)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 141, in execute
    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 42, in mamba_install
    index = load_channels(pool, channel_urls, repos, prepend=False)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 123, in load_channels
    index = get_index(
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 104, in get_index
    is_downloaded = dlist.download(True)
RuntimeError: Multi-download failed.
$ /Software/anaconda3/envs/vs2/bin/mamba create --quiet --file /Software/VirSorter2/db/conda_envs/7cf0ba25.yaml --prefix /Software/VirSorter2/db/conda_envs/7cf0ba25

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
jiarong commented 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

lifeifeifeifei commented 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

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
                          tware/anaconda3/pkgs/perl-sub-install-0.928-pl526_2/lib/site_perl/5.26
                          .2:/Software/anaconda3/pkgs/perl-text-parsewords-3.30-
                          pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/
                          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
                          /5.26.2:/Software/anaconda3/pkgs/perl-time-local-1.28-
                          pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/
                          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.
                          26.2:/Software/anaconda3/pkgs/perl-socket-2.027-pl526_
                          1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          http-cookies-6.04-pl526_0/lib/site_perl/5.26.2:/Softwa
                          re/anaconda3/pkgs/perl-package-deprecationmanager-0.17-pl526_0/lib/sit
                          e_perl/5.26.2:/Software/anaconda3/pkgs/perl-xml-namesp
                          acesupport-1.12-pl526_0/lib/site_perl/5.26.2:/Software
                          /anaconda3/pkgs/perl-sub-quote-2.006003-pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-moose-2.2011-pl526hf484d3
                          e_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl
                          -yaml-1.29-pl526_0/lib/site_perl/5.26.2:/Software/anac
                          onda3/pkgs/perl-module-implementation-0.09-pl526_2/lib/site_perl/5.26.
                          2:/Software/anaconda3/pkgs/perl-xsloader-0.24-pl526_0/
                          lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          eval-closure-0.14-pl526h6bb024c_4/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-ipc-cmd-1.02-pl526_0/lib/site_perl/5.26
                          .2:/Software/anaconda3/pkgs/perl-test-requiresinternet
                          -0.05-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3
                          /pkgs/perl-io-zlib-1.10-pl526_2/lib/site_perl/5.26.2:/
                          Software/anaconda3/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.2
                          2.0:/Software/anaconda3/pkgs/perl-class-load-xs-0.10-p
                          l526h6bb024c_2/lib/site_perl/5.26.2:/Software/anaconda
                          3/pkgs/perl-list-moreutils-xs-0.428-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-cpan-meta-requirements-2.140-
                          pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/
                          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
                          .003004-pl526_0/lib/site_perl/5.26.2:/Software/anacond
                          a3/pkgs/perl-common-sense-3.74-pl526_2/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-compress-raw-bzip2-2.087-pl526he1b
                          5a44_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/p
                          erl-scalar-list-utils-1.52-pl526h516909a_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-extutils-parsexs-3.35-pl526_0/
                          lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-ver
                          sion-0.9924-pl526_0/lib/site_perl/5.26.2:/Software/ana
                          conda3/pkgs/perl-http-negotiate-6.01-pl526_3/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-constant-1.33-pl526_1/lib/si
                          te_perl/5.26.2:/Software/anaconda3/pkgs/perl-types-ser
                          ialiser-1.0-pl526_2/lib/site_perl/5.26.2:/Software/ana
                          conda3/pkgs/perl-ntlm-1.09-pl526_4/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-data-dumper-2.173-pl526_0/lib/site_per
                          l/5.26.2:/Software/anaconda3/pkgs/perl-class-load-0.25
                          -pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs
                          /perl-xml-sax-base-1.09-pl526_0/lib/site_perl/5.26.2:/
                          Software/anaconda3/pkgs/perl-module-runtime-conflicts-0.003-pl526_0/li
                          b/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-file-
                          listing-6.04-pl526_1/lib/site_perl/5.26.2:/Software/an
                          aconda3/pkgs/perl-xml-simple-2.25-pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-base-2.23-pl526_1/lib/site_perl
                          /5.26.2:/Software/anaconda3/pkgs/perl-xml-parser-2.44_
                          01-pl5262hc3e0081_1002/lib/site_perl/5.26.2:/Software/
                          anaconda3/pkgs/perl-io-compress-2.087-pl526he1b5a44_0/lib/site_perl/5.
                          26.2:/Software/anaconda3/pkgs/perl-business-isbn-3.004
                          -pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs
                          /perl-digest-md5-2.55-pl526_0/lib/site_perl/5.26.2:/So
                          ftware/anaconda3/pkgs/perl-devel-globaldestruction-0.14-pl526_0/lib/si
                          te_perl/5.26.2:/Software/anaconda3/pkgs/perl-exporter-
                          tiny-1.002001-pl526_0/lib/site_perl/5.26.2:/Software/a
                          naconda3/pkgs/perl-class-method-modifiers-2.12-pl526_0/lib/site_perl/5
                          .26.2:/Software/anaconda3/pkgs/perl-file-temp-0.2304-p
                          l526_2/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/p
                          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-
                          pl526h6bb024c_3/lib/site_perl/5.26.2:/Software/anacond
                          a3/pkgs/perl-file-which-1.23-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-dbi-1.642-pl526_0/lib/site_perl/5.26
                          .2:/Software/anaconda3/pkgs/perl-try-tiny-0.30-pl526_1
                          /lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-js
                          on-4.02-pl526_0/lib/site_perl/5.26.2:/Software/anacond
                          a3/pkgs/perl-locale-maketext-simple-0.21-pl526_2/lib/site_perl/5.26.2:
                          /Software/anaconda3/pkgs/perl-uri-1.76-pl526_0/lib/sit
                          e_perl/5.26.2:/Software/anaconda3/pkgs/perl-parent-0.2
                          36-pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pk
                          gs/perl-html-tagset-3.20-pl526_3/lib/site_perl/5.26.2:
                          /Software/anaconda3/pkgs/perl-list-moreutils-0.428-pl526_1/lib/site_pe
                          rl/5.26.2:/Software/anaconda3/pkgs/perl-pathtools-3.75
                          -pl526h14c3975_1/lib/site_perl/5.26.2:/Software/anacon
                          da3/pkgs/perl-devel-overloadinfo-0.005-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-xml-sax-1.02-pl526_0/lib/s
                          ite_perl/5.26.2:/Software/anaconda3/pkgs/perl-storable
                          -3.15-pl526h14c3975_0/lib/site_perl/5.26.2:/Software/a
                          naconda3/pkgs/perl-sub-exporter-progressive-0.001013-pl526_0/lib/site_
                          perl/5.26.2:/Software/anaconda3/pkgs/perl-net-ssleay-1
                          .88-pl526h90d6eec_0/lib/site_perl/5.26.2:/Software/ana
                          conda3/pkgs/perl-extutils-manifest-1.72-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-archive-tar-2.32-pl526_0/
                          lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          json-pp-4.04-pl526_0/lib/site_perl/5.26.2:/Software/an
                          aconda3/pkgs/perl-io-socket-ssl-2.066-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-role-tiny-2.000008-pl526_0/
                          lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          dist-checkconflicts-0.11-pl526_2/lib/site_perl/5.26.2:
                          /Software/anaconda3/pkgs/perl-app-cpanminus-1.7044-pl526_1/lib/site_pe
                          rl/5.26.2:/Software/anaconda3/pkgs/perl-net-http-6.19-
                          pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/
                          perl-www-robotrules-6.02-pl526_3/lib/site_perl/5.26.2:
                          /Software/anaconda3/pkgs/perl-encode-2.88-pl526_1/lib/site_perl/5.26.2
                          :/Software/anaconda3/pkgs/perl-sub-exporter-0.987-pl52
                          6_2/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl
                          -http-date-6.02-pl526_3/lib/site_perl/5.26.2:/Software
                          /anaconda3/pkgs/perl-lwp-protocol-https-6.07-pl526_4/lib/site_perl/5.2
                          6.2:/Software/anaconda3/pkgs/perl-module-metadata-1.00
                          0036-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/
                          pkgs/perl-module-build-0.4224-pl526_3/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-text-abbrev-1.02-pl526_0/lib/site_p
                          erl/5.26.2:/Software/anaconda3/pkgs/perl-carp-1.38-pl5
                          26_3/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/per
                          l-perl-ostype-1.010-pl526_1/lib/site_perl/5.26.2:/Soft
                          ware/anaconda3/pkgs/perl-module-load-conditional-0.68-pl526_2/lib/site
                          _perl/5.26.2:/Software/anaconda3/pkgs/perl-package-sta
                          sh-0.38-pl526hf484d3e_1/lib/site_perl/5.26.2:/Software
                          /anaconda3/pkgs/perl-data-optlist-0.110-pl526_2/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-module-runtime-0.016-pl52
                          6_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl
                          -libwww-perl-6.39-pl526_0/lib/site_perl/5.26.2:/Softwa
                          re/anaconda3/pkgs/augustus-3.4.0-pl5262h5a9fe7b_2/lib/site_perl/5.26.2
                          :/Software/anaconda3/pkgs/perl-http-daemon-6.01-pl526_
                          1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          devel-stacktrace-2.04-pl526_0/lib/site_perl/5.26.2:/So
                          ftware/anaconda3/pkgs/perl-module-corelist-5.20190524-pl526_0/lib/site
                          _perl/5.26.2:/Software/anaconda3/pkgs/perl-sub-name-0.
                          21-pl526_1/lib/site_perl/5.26.2:/Software/anaconda3/pk
                          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
                          _perl/5.26.2:/Software/anaconda3/pkgs/perl-extutils-cb
                          uilder-0.280230-pl526_1/lib/site_perl/5.26.2:/Software
                          /anaconda3/pkgs/perl-business-isbn-data-20140910.003-pl526_0/lib/site_
                          perl/5.26.2:/Software/anaconda3/pkgs/perl-io-html-1.00
                          1-pl526_2/lib/site_perl/5.26.2:/Software/anaconda3/pkg
                          s/perl-cpan-meta-yaml-0.018-pl526_0/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-package-stash-xs-0.28-pl526hf484d3e_1
                          /lib/site_perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          lwp-mediatypes-6.04-pl526_0/lib/site_perl/5.26.2:/Soft
                          ware/anaconda3/pkgs/perl-parallel-forkmanager-2.02-pl526_0/lib/site_pe
                          rl/5.26.2:/Software/anaconda3/pkgs/perl-digest-hmac-1.
                          03-pl526_3/lib/site_perl/5.26.2:/Software/anaconda3/pk
                          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
                          /5.26.2:/Software/anaconda3/pkgs/perl-html-tree-5.07-p
                          l526_1/lib/site_perl/5.26.2:/Software/anaconda3/pkgs/p
                          erl-mozilla-ca-20180117-pl526_1/lib/site_perl/5.26.2:/
                          Software/anaconda3/pkgs/perl-params-util-1.07-pl526h6bb024c_4/lib/site
                          _perl/5.26.2:/Software/anaconda3/pkgs/perl-
                          exporter-5.72-pl526_1/lib/site_perl/5.26.2
             CONDA_PREFIX=/Software/anaconda3/envs/vs2
           CONDA_PREFIX_1=/Software/anaconda3
    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
                          ware/orfm-0.7.1_Linux_x86_64:/Software/anaconda3/envs/
                          vContact2/bin:/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/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.
lifeifeifeifei commented 3 years ago

Could someone help me solve this problem? A little anxious.

jiarong commented 3 years ago

Sorry for the late reply. It looks like failing to install the required packages. Does the server have internet connection?

gubingyu commented 2 years ago

I have the same question now,I really hope it can be resolved. Thank you

gubingyu commented 2 years ago

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

lianzhh commented 2 years ago

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.

jiarong commented 2 years ago

The conda installation might have issue with certain OS with specific setting. I recommend the singularity version.