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(bactopia) ht@prp:~$ bactopia download --build_all --keep_file
2023-01-21 07:13:30:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details.
2023-01-21 07:13:30:root:INFO - Found /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/linux/assembly_qc.yml (3 of 6), begin build to /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x
External command failed with exit code 1!
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.
The default QUAST package does not include:
GRIDSS (needed for structural variants detection)
SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)
BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!
To be able to use those, please run
quast-download-gridss
quast-download-silva
quast-download-busco
done
Rolling back transaction: ...working... done
Standard error:
ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'.
LinkError: post-link script failed for package bioconda::checkm-genome-1.2.2-pyhdfd78af_1
location of failed script: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/bin/.checkm-genome-post-link.sh
==> script messages <==
ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.
Hi, I find a bug as follows:
(bactopia) ht@prp:~$ bactopia download --build_all --keep_file
2023-01-21 07:13:30:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details.
2023-01-21 07:13:30:root:INFO - Found /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/linux/assembly_qc.yml (3 of 6), begin build to /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x
External command failed with exit code 1!
Command:
bash -c 'mamba env create -f /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/linux/assembly_qc.yml --prefix /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x --force'
Standard output:
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
Transaction
Prefix: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x
Updating specs:
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────
Summary:
Install: 207 packages
Total download: 0 B
────────────────────────────────────────────────────────────────────────────────────────────────────────
Looking for: ['_libgcc_mutex=0.1', '_openmp_mutex=4.5', 'alsa-lib=1.2.8', 'bedtools=2.30.0', 'blast=2.13.0', 'brotli=1.0.9', 'brotli-bin=1.0.9', 'bwa=0.7.17', 'bzip2=1.0.8', 'c-ares=1.18.1', 'ca-certificates=2022.9.24', 'cairo=1.16.0', 'certifi=2022.9.24', 'checkm-genome=1.2.2', 'circos=0.69.8', 'contourpy=1.0.6', 'coreutils=9.1', 'curl=7.86.0', 'cycler=0.11.0', 'dendropy=4.5.2', 'entrez-direct=16.2', 'expat=2.5.0', 'font-ttf-dejavu-sans-mono=2.37', 'font-ttf-inconsolata=3.000', 'font-ttf-source-code-pro=2.038', 'font-ttf-ubuntu=0.83', 'fontconfig=2.14.1', 'fonts-conda-ecosystem=1', 'fonts-conda-forge=1', 'fonttools=4.38.0', 'freetype=2.12.1', 'gettext=0.21.1', 'giflib=5.2.1', 'glimmerhmm=3.0.4', 'graphite2=1.3.13', 'harfbuzz=5.3.0', 'hmmer=3.3.2', 'icu=70.1', 'joblib=1.2.0', 'jpeg=9e', 'k8=0.2.5', 'keyutils=1.6.1', 'kiwisolver=1.4.4', 'krb5=1.19.3', 'lcms2=2.14', 'ld_impl_linux-64=2.39', 'lerc=4.0.0', 'libblas=3.9.0', 'libbrotlicommon=1.0.9', 'libbrotlidec=1.0.9', 'libbrotlienc=1.0.9', 'libcblas=3.9.0', 'libcups=2.3.3', 'libcurl=7.86.0', 'libdeflate=1.13', 'libedit=3.1.20191231', 'libev=4.33', 'libffi=3.4.2', 'libgcc-ng=12.2.0', 'libgd=2.3.3', 'libgfortran-ng=12.2.0', 'libgfortran5=12.2.0', 'libglib=2.74.1', 'libgomp=12.2.0', 'libiconv=1.17', 'libidn2=2.3.4', 'liblapack=3.9.0', 'libnghttp2=1.47.0', 'libnsl=2.0.0', 'libopenblas=0.3.21', 'libpng=1.6.38', 'libsqlite=3.39.4', 'libssh2=1.10.0', 'libstdcxx-ng=12.2.0', 'libtiff=4.4.0', 'libunistring=0.9.10', 'libuuid=2.32.1', 'libwebp=1.2.4', 'libwebp-base=1.2.4', 'libxcb=1.13', 'libzlib=1.2.13', 'matplotlib-base=3.6.2', 'minimap2=2.24', 'munkres=1.1.4', 'ncurses=6.3', 'numpy=1.23.4', 'openjdk=17.0.3', 'openjpeg=2.5.0', 'openssl=1.1.1s', 'packaging=21.3', 'pcre=8.45', 'pcre2=10.40', 'perl=5.32.1', 'perl-archive-tar=2.40', 'perl-b-cow=0.007', 'perl-carp=1.50', 'perl-clone=0.46', 'perl-common-sense=3.75', 'perl-compress-raw-bzip2=2.201', 'perl-compress-raw-zlib=2.202', 'perl-config-general=2.65', 'perl-digest-perl-md5=1.9', 'perl-encode=3.19', 'perl-exporter=5.74', 'perl-exporter-tiny=1.002002', 'perl-extutils-config=0.008', 'perl-extutils-helpers=0.026', 'perl-extutils-installpaths=0.012', 'perl-extutils-makemaker=7.64', 'perl-extutils-pl2bat=0.005', 'perl-font-ttf=1.06', 'perl-gd=2.76', 'perl-io-compress=2.201', 'perl-io-string=1.08', 'perl-io-zlib=1.11', 'perl-json=4.10', 'perl-json-xs=2.34', 'perl-list-moreutils=0.430', 'perl-list-moreutils-xs=0.430', 'perl-math-bezier=0.01', 'perl-math-round=0.07', 'perl-math-vecstat=0.08', 'perl-module-build-tiny=0.039', 'perl-module-implementation=0.09', 'perl-module-runtime=0.016', 'perl-number-format=1.75', 'perl-params-validate=1.31', 'perl-parent=0.238', 'perl-pathtools=3.75', 'perl-readonly=2.05', 'perl-regexp-common=2017060201', 'perl-scalar-list-utils=1.63', 'perl-set-intspan=1.19', 'perl-statistics-basic=1.6611', 'perl-storable=3.15', 'perl-svg=2.87', 'perl-test-fatal=0.016', 'perl-text-format=0.62', 'perl-time-hires=1.9764', 'perl-try-tiny=0.31', 'perl-types-serialiser=1.01', 'perl-xml-parser=2.44_01', 'pigz=2.6', 'pillow=9.2.0', 'pip=22.3.1', 'pixman=0.40.0', 'pplacer=1.1.alpha19', 'prodigal=2.6.3', 'pthread-stubs=0.4', 'pyparsing=3.0.9', 'pysam=0.19.1', 'python=3.10.6', 'python-dateutil=2.8.2', 'python_abi=3.10', 'quast=5.2.0', 'readline=8.1.2', 'scipy=1.9.3', 'sed=4.8', 'setuptools=65.5.1', 'simplejson=3.18.0', 'six=1.16.0', 'tk=8.6.12', 'tzdata=2022f', 'unicodedata2=15.0.0', 'wget=1.20.3', 'wheel=0.38.4', 'xorg-fixesproto=5.0', 'xorg-inputproto=2.3.2', 'xorg-kbproto=1.0.7', 'xorg-libice=1.0.10', 'xorg-libsm=1.2.3', 'xorg-libx11=1.7.2', 'xorg-libxau=1.0.9', 'xorg-libxdmcp=1.1.3', 'xorg-libxext=1.3.4', 'xorg-libxfixes=5.0.3', 'xorg-libxi=1.7.10', 'xorg-libxrender=0.9.10', 'xorg-libxtst=1.2.3', 'xorg-recordproto=1.14.2', 'xorg-renderproto=0.11.1', 'xorg-xextproto=7.3.0', 'xorg-xproto=7.0.31', 'xz=5.2.6', 'zlib=1.2.13', 'zstd=1.5.2']
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.
The default QUAST package does not include:
To be able to use those, please run
quast-download-gridss
quast-download-silva
quast-download-busco
done
Rolling back transaction: ...working... done
Standard error:
ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'.
LinkError: post-link script failed for package bioconda::checkm-genome-1.2.2-pyhdfd78af_1
location of failed script: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/bin/.checkm-genome-post-link.sh
==> script messages <==
ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.
==> script output <==
stdout: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz: FAILED
stderr: --2023-01-21 07:31:28-- https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz
Resolving zenodo.org (zenodo.org)... ::
Connecting to zenodo.org (zenodo.org)|::|:443... failed: Connection refused.
sha256sum: WARNING: 1 computed checksum did NOT match
return code: 1
()
Thanks
Haitao
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