A bug in install of bactopia：assembly_qc-2.2.x and checkm_data_2015_01_16.tar.gz

[plasminogene]

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:

• _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

Package Version Build Channel Size
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Install:
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• _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
• _openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
• alsa-lib 1.2.8 h166bdaf_0 conda-forge/linux-64 Cached
• bedtools 2.30.0 h468198e_3 bioconda/linux-64 Cached
• blast 2.13.0 hf3cf87c_0 bioconda/linux-64 Cached
• brotli 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• brotli-bin 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• bwa 0.7.17 h7132678_9 bioconda/linux-64 Cached
• bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 Cached
• c-ares 1.18.1 h7f98852_0 conda-forge/linux-64 Cached
• ca-certificates 2022.9.24 ha878542_0 conda-forge/linux-64 Cached
• cairo 1.16.0 ha61ee94_1014 conda-forge/linux-64 Cached
• certifi 2022.9.24 pyhd8ed1ab_0 conda-forge/noarch Cached
• checkm-genome 1.2.2 pyhdfd78af_1 bioconda/noarch Cached
• circos 0.69.8 hdfd78af_1 bioconda/noarch Cached
• contourpy 1.0.6 py310hbf28c38_0 conda-forge/linux-64 Cached
• coreutils 9.1 h166bdaf_0 conda-forge/linux-64 Cached
• curl 7.86.0 h7bff187_1 conda-forge/linux-64 Cached
• cycler 0.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached
• dendropy 4.5.2 pyh3252c3a_0 bioconda/noarch Cached
• entrez-direct 16.2 he881be0_1 bioconda/linux-64 Cached
• expat 2.5.0 h27087fc_0 conda-forge/linux-64 Cached
• font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge/noarch Cached
• font-ttf-inconsolata 3.000 h77eed37_0 conda-forge/noarch Cached
• font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge/noarch Cached
• font-ttf-ubuntu 0.83 hab24e00_0 conda-forge/noarch Cached
• fontconfig 2.14.1 hc2a2eb6_0 conda-forge/linux-64 Cached
• fonts-conda-ecosystem 1 0 conda-forge/noarch Cached
• fonts-conda-forge 1 0 conda-forge/noarch Cached
• fonttools 4.38.0 py310h5764c6d_1 conda-forge/linux-64 Cached
• freetype 2.12.1 hca18f0e_0 conda-forge/linux-64 Cached
• gettext 0.21.1 h27087fc_0 conda-forge/linux-64 Cached
• giflib 5.2.1 h36c2ea0_2 conda-forge/linux-64 Cached
• glimmerhmm 3.0.4 pl5321h87f3376_5 bioconda/linux-64 Cached
• graphite2 1.3.13 h58526e2_1001 conda-forge/linux-64 Cached
• harfbuzz 5.3.0 h418a68e_0 conda-forge/linux-64 Cached
• hmmer 3.3.2 h87f3376_2 bioconda/linux-64 Cached
• icu 70.1 h27087fc_0 conda-forge/linux-64 Cached
• joblib 1.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
• jpeg 9e h166bdaf_2 conda-forge/linux-64 Cached
• k8 0.2.5 hd03093a_2 bioconda/linux-64 Cached
• keyutils 1.6.1 h166bdaf_0 conda-forge/linux-64 Cached
• kiwisolver 1.4.4 py310hbf28c38_1 conda-forge/linux-64 Cached
• krb5 1.19.3 h3790be6_0 conda-forge/linux-64 Cached
• lcms2 2.14 h6ed2654_0 conda-forge/linux-64 Cached
• ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge/linux-64 Cached
• lerc 4.0.0 h27087fc_0 conda-forge/linux-64 Cached
• libblas 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libbrotlicommon 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libbrotlidec 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libbrotlienc 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libcblas 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libcups 2.3.3 h3e49a29_2 conda-forge/linux-64 Cached
• libcurl 7.86.0 h7bff187_1 conda-forge/linux-64 Cached
• libdeflate 1.13 h166bdaf_0 conda-forge/linux-64 Cached
• libedit 3.1.20191231 he28a2e2_2 conda-forge/linux-64 Cached
• libev 4.33 h516909a_1 conda-forge/linux-64 Cached
• libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
• libgcc-ng 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
• libgd 2.3.3 h18fbbfe_3 conda-forge/linux-64 Cached
• libgfortran-ng 12.2.0 h69a702a_19 conda-forge/linux-64 Cached
• libgfortran5 12.2.0 h337968e_19 conda-forge/linux-64 Cached
• libglib 2.74.1 h606061b_1 conda-forge/linux-64 Cached
• libgomp 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
• libiconv 1.17 h166bdaf_0 conda-forge/linux-64 Cached
• libidn2 2.3.4 h166bdaf_0 conda-forge/linux-64 Cached
• liblapack 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libnghttp2 1.47.0 hdcd2b5c_1 conda-forge/linux-64 Cached
• libnsl 2.0.0 h7f98852_0 conda-forge/linux-64 Cached
• libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge/linux-64 Cached
• libpng 1.6.38 h753d276_0 conda-forge/linux-64 Cached
• libsqlite 3.39.4 h753d276_0 conda-forge/linux-64 Cached
• libssh2 1.10.0 haa6b8db_3 conda-forge/linux-64 Cached
• libstdcxx-ng 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
• libtiff 4.4.0 h0e0dad5_3 conda-forge/linux-64 Cached
• libunistring 0.9.10 h7f98852_0 conda-forge/linux-64 Cached
• libuuid 2.32.1 h7f98852_1000 conda-forge/linux-64 Cached
• libwebp 1.2.4 h522a892_0 conda-forge/linux-64 Cached
• libwebp-base 1.2.4 h166bdaf_0 conda-forge/linux-64 Cached
• libxcb 1.13 h7f98852_1004 conda-forge/linux-64 Cached
• libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
• matplotlib-base 3.6.2 py310h8d5ebf3_0 conda-forge/linux-64 Cached
• minimap2 2.24 h7132678_1 bioconda/linux-64 Cached
• munkres 1.1.4 pyh9f0ad1d_0 conda-forge/noarch Cached
• ncurses 6.3 h27087fc_1 conda-forge/linux-64 Cached
• numpy 1.23.4 py310h53a5b5f_1 conda-forge/linux-64 Cached
• openjdk 17.0.3 hafdced1_4 conda-forge/linux-64 Cached
• openjpeg 2.5.0 h7d73246_1 conda-forge/linux-64 Cached
• openssl 1.1.1s h0b41bf4_1 conda-forge/linux-64 Cached
• packaging 21.3 pyhd8ed1ab_0 conda-forge/noarch Cached
• pcre 8.45 h9c3ff4c_0 conda-forge/linux-64 Cached
• pcre2 10.40 hc3806b6_0 conda-forge/linux-64 Cached
• perl 5.32.1 2_h7f98852_perl5 conda-forge/linux-64 Cached
• perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-b-cow 0.007 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-clone 0.46 pl5321hec16e2b_0 bioconda/linux-64 Cached
• perl-common-sense 3.75 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda/linux-64 Cached
• perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-config-general 2.65 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-constant 1.33 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-cpan-meta 2.150010 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-cpan-meta-requirements 2.140 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-cpan-meta-yaml 0.018 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-data-dumper 2.183 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-encode 3.19 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-extutils-config 0.008 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-extutils-helpers 0.026 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-extutils-installpaths 0.012 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-extutils-parsexs 3.44 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-extutils-pl2bat 0.005 pl5321ha770c72_0 conda-forge/linux-64 Cached
• perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-gd 2.76 pl5321h5b5514e_1 bioconda/linux-64 Cached
• perl-getopt-long 2.54 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-io-compress 2.201 pl5321h87f3376_0 bioconda/linux-64 Cached
• perl-io-string 1.08 pl5321hdfd78af_4 bioconda/noarch Cached
• perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-ipc-cmd 1.04 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json 4.10 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json-pp 4.11 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json-xs 2.34 pl5321h9f5acd7_5 bioconda/linux-64 Cached
• perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-list-moreutils-xs 0.430 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-locale-maketext-simple 0.21 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-math-round 0.07 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-module-build-tiny 0.039 pl5321hdfd78af_5 bioconda/noarch Cached
• perl-module-corelist 5.20220620 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-implementation 0.09 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-module-load 0.34 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-load-conditional 0.68 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-module-metadata 1.000037 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-number-format 1.75 pl5321hdfd78af_4 bioconda/noarch Cached
• perl-params-check 0.38 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-params-validate 1.31 pl5321hec16e2b_0 bioconda/linux-64 Cached
• perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-pathtools 3.75 pl5321hec16e2b_3 bioconda/linux-64 Cached
• perl-perl-ostype 1.010 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-readonly 2.05 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-regexp-common 2017060201 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-storable 3.15 pl5321hec16e2b_3 bioconda/linux-64 Cached
• perl-svg 2.87 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-test-fatal 0.016 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-text-format 0.62 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-text-parsewords 3.31 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-time-hires 1.9764 pl5321hec16e2b_2 bioconda/linux-64 Cached
• perl-try-tiny 0.31 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-version 0.9924 pl5321hec16e2b_2 bioconda/linux-64 Cached
• perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge/linux-64 Cached
• pigz 2.6 h27826a3_0 conda-forge/linux-64 Cached
• pillow 9.2.0 py310h454ad03_3 conda-forge/linux-64 Cached
• pip 22.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
• pixman 0.40.0 h36c2ea0_0 conda-forge/linux-64 Cached
• pplacer 1.1.alpha19 h9ee0642_2 bioconda/linux-64 Cached
• prodigal 2.6.3 hec16e2b_4 bioconda/linux-64 Cached
• pthread-stubs 0.4 h36c2ea0_1001 conda-forge/linux-64 Cached
• pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge/noarch Cached
• pysam 0.19.1 py310hff46b53_1 bioconda/linux-64 Cached
• python 3.10.6 h582c2e5_0_cpython conda-forge/linux-64 Cached
• python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached
• python_abi 3.10 3_cp310 conda-forge/linux-64 Cached
• quast 5.2.0 py310pl5321hc8f18ef_2 bioconda/linux-64 Cached
• readline 8.1.2 h0f457ee_0 conda-forge/linux-64 Cached
• scipy 1.9.3 py310hdfbd76f_2 conda-forge/linux-64 Cached
• sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
• setuptools 65.5.1 pyhd8ed1ab_0 conda-forge/noarch Cached
• simplejson 3.18.0 py310h5764c6d_0 conda-forge/linux-64 Cached
• six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached
• tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
• tzdata 2022f h191b570_0 conda-forge/noarch Cached
• unicodedata2 15.0.0 py310h5764c6d_0 conda-forge/linux-64 Cached
• wget 1.20.3 ha56f1ee_1 conda-forge/linux-64 Cached
• wheel 0.38.4 pyhd8ed1ab_0 conda-forge/noarch Cached
• xorg-fixesproto 5.0 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-inputproto 2.3.2 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-kbproto 1.0.7 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-libice 1.0.10 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libsm 1.2.3 hd9c2040_1000 conda-forge/linux-64 Cached
• xorg-libx11 1.7.2 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxau 1.0.9 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxext 1.3.4 h7f98852_1 conda-forge/linux-64 Cached
• xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge/linux-64 Cached
• xorg-libxi 1.7.10 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxrender 0.9.10 h7f98852_1003 conda-forge/linux-64 Cached
• xorg-libxtst 1.2.3 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-recordproto 1.14.2 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-renderproto 0.11.1 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-xextproto 7.3.0 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-xproto 7.0.31 h7f98852_1007 conda-forge/linux-64 Cached
• xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
• zlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
• zstd 1.5.2 h3eb15da_6 conda-forge/linux-64 Cached

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:

• 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.

==> 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