Closed pastaxingxin closed 3 years ago
I ran this command in WSL.
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
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 <<<<<<<<<<<<<<<<<<<<<<
$ /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=
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.