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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Installation on WSL fails #3430

Closed pastaxingxin closed 3 years ago

pastaxingxin commented 3 years ago

I ran this command line: python bcbio_nextgen_install.py /mnt/e/bcbio/share/bcbio --tooldir=/mnt/e/bcbio --genomes hg38 --aligners bwa --aligners bowtie2 However, I got some errors during the installation, so I failed to install it. There are parts of errors messages: "

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 882, in exception_converter
    raise e
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 876, in exception_converter
    exit_code = _wrapped_main(*args, **kwargs)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 835, in _wrapped_main
    result = do_call(args, p)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 720, in do_call
    exit_code = create(args, parser)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 624, in create
    return install(args, parser, "create")
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 595, in install
    handle_txn(conda_transaction, prefix, args, newenv)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/mamba/mamba.py", line 148, in handle_txn
    unlink_link_transaction.execute()
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/core/link.py", line 244, in execute
    self.verify()
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/core/link.py", line 231, in verify
    exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/core/link.py", line 591, in _verify
    itervalues(prefix_action_groups)):
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/common/io.py", line 525, in map
    yield func(thing)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/core/link.py", line 411, in _verify_individual_level
    error_result = axn.verify()
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/conda/core/path_actions.py", line 323, in verify
    source_size_in_bytes = getsize(self.source_full_path)
  File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/genericpath.py", line 50, in getsize
    return os.stat(filename).st_size
OSError: [Errno 40] Too many levels of symbolic links: '/mnt/e/bcbio/share/bcbio/anaconda/pkgs/ncurses-6.2-h58526e2_4/share/terminfo/N/NCR260VT300WPP'

$ /mnt/e/bcbio/share/bcbio/anaconda/bin/mamba create -q --no-default-packages -y --name python3 python=3 nomkl

environment variables: CIO_TEST= CONDA_EXE=/home/xingxinpan/anaconda3/bin/conda CONDA_PYTHON_EXE=/home/xingxinpan/anaconda3/bin/python CONDA_ROOT=/mnt/e/bcbio/share/bcbio/anaconda CONDA_SHLVL=0 CURL_CABUNDLE= PATH=/mnt/e/bcbio/share/bcbio/anaconda/bin:/home/xingxinpan/meme/bin:/home/ xingxinpan/meme/libexec/meme-5.1.1:/home/xingxinpan/bin:/home/xingxinp an/.local/bin:/home/xingxinpan/anaconda3/condabin:/usr/local/sbin:/usr /local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/ mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.UbuntuonWindows 2004.2020.812.0_x64__79rhkp1fndgsc:/mnt/c/Program Files/Git/usr/local/bin:/mnt/c/Program Files/Java/jdk-11.0.2/bin:/mnt/c/Program Files/Git/bin:/mnt/c/Program Files (x86)/Graphviz2.38/bin:/mnt/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin:/mnt/c/Program Files/NVIDIA GPU Computing Toolk it/CUDA/v10.1/libnvvp:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Wi ndows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mn t/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/c/Program Files/IDM Computer Solutions/UltraCompare:/mnt/c/Program Files/IDM Computer Solutions/UltraFinder:/mnt/c/Program Files/IDM Computer Solutions/UltraEdit:/mnt/d/Program Files/MATLAB/MATLAB Production Server/R2015a/runtime/win64:/mnt/d/Program Files/MATLAB/MATLAB Production Server/R2015a/bin:/mnt/d/Program Files/MATLAB/MATLAB Production Server/R2015a/polyspace/bin:/mnt/c/Program Files/NVIDIA Corporation/Nsight Compute 2019.4.0:/mnt/c/Program Files/Java/jdk-14.0 .1/bin:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/ Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/Sys tem32/OpenSSH:/mnt/c/Program Files/Git/cmd:/mnt/c/Program Files/Docker /Docker/resources/bin:/mnt/c/ProgramData/DockerDesktop/version-bin:/mn t/c/Users/pasta/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/pasta /AppData/Local/Programs/Microsoft VS Code/bin:/mnt/c/Users/pasta/PyCharm 2019.3.2/bin:/mnt/c/Program Files/ Bandizip:/snap/bin:/mnt/e/bioinformatics/homer/bin:/mnt/e/bioinformati cs/htslib-1.9:/mnt/e/bioinformatics/samtools-1.9:/mnt/e/bioinformatics /bcftools-1.9:/mnt/e/bioinformatics/bam-readcount/bin:/mnt/e/bioinform atics/hisat2-2.1.0:/mnt/e/bioinformatics/stringtie-1.3.4d.Linux_x86_64 :/mnt/e/bioinformatics/stringtie-1.3.4d.Linux_x86_64/gffcompare-0.10.6 .Linux_x86_64:/mnt/e/bioinformatics/stringtie-1.3.4d.Linux_x86_64/gffc ompare-0.10.6.Linux_x86_64/htseq-release_0.11.0/scripts:/mnt/e/bioinfo rmatics/tophat-2.1.1.Linux_x86_64:/mnt/e/bioinformatics/kallisto_linux -v0.44.0:/mnt/e/bioinformatics/FastQC:/mnt/e/bioinformatics/flexbar-3. 4.0-linux:/mnt/e/bioinformatics/regtools/build:/mnt/e/bioinformatics/g atk-4.1.7.0:/mnt/e/bioinformatics/bin:/mnt/e/bioinformatics/snpEff:/mn t/e/bioinformatics/sratoolkit.2.9.6-1-ubuntu64/bin:/mnt/e/bioinformati cs/ucsc:/mnt/e/bioinformatics/bedtools2/bin:/mnt/d/Documents/chipseq- project/data/peakcalls/common/buchong/buchong2/33/44/stereogene- master/src:/mnt/e/bioinformatics/geneSCF-master- source-v1.1-p2:/mnt/g/NRSA-v2/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : None
        shell level : 0
   user config file : /home/xingxinpan/.condarc

populated config files : /mnt/e/bcbio/share/bcbio/anaconda/.condarc /home/xingxinpan/.condarc conda version : 4.9.2 conda-build version : 3.21.4 python version : 3.7.6.final.0 virtual packages : glibc=2.27=0 unix=0=0 __archspec=1=x86_64 base environment : /mnt/e/bcbio/share/bcbio/anaconda (writable) 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 : /mnt/e/bcbio/share/bcbio/anaconda/pkgs /home/xingxinpan/.conda/pkgs envs directories : /mnt/e/bcbio/share/bcbio/anaconda/envs /home/xingxinpan/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.22.0 CPython/3.7.6 Linux/4.19.104-microsoft-standard ubuntu/18.04.4 glibc/2.27 UID:GID : 1000:1000 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

Traceback (most recent call last): File "/mnt/e/bcbio/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 228, in install.upgrade_bcbio(kwargs["args"]) File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 91, in upgrade_bcbio upgrade_thirdparty_tools(args, REMOTES) File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 509, in upgrade_thirdparty_tools cbl_conda.install_in(conda_bin, args.tooldir, package_yaml) File "/mnt/e/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/package/conda.py", line 92, in install_in conda_envs = _create_environments(conda_bin, packages) File "/mnt/e/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/package/conda.py", line 273, in _create_environments .format(**locals()), shell=True) File "/mnt/e/bcbio/share/bcbio/anaconda/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/mnt/e/bcbio/share/bcbio/anaconda/bin/mamba create -q --no-default-packages -y --name python3 python=3 nomkl' returned non-zero exit status 1. Traceback (most recent call last): File "bcbio_nextgen_install.py", line 290, in main(parser.parse_args(), sys.argv[1:]) File "bcbio_nextgen_install.py", line 51, in main subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args)) File "/usr/lib/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/mnt/e/bcbio/share/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/mnt/e/bcbio', '--genomes', 'hg38', '--aligners', 'bwa', '--aligners', 'bowtie2', '--data']' returned non-zero exit status 1 " Could anyone give me solutions to this? Thank you in advance.

pastaxingxin commented 3 years ago

I ran this command in WSL.

naumenko-sa commented 3 years ago

Hi @pastaxingxin!

We have not run bcbio on WSL (Windows Subsystem for Linux). We had similar symbolic links issues - check out https://github.com/bcbio/bcbio-nextgen/search?q=symbolic+links&type=issues They are usually system-specific, not related to bcbio or conda.

Sorry, cannot be of much help here. Let us know how it runs on WSL if you overcome this issue!

Sergey