rpetit3
commented
2 years ago Hmmm, let me see if I can borrow a macbook to replicate this. It's been a while since the conda envs have been built for Mac, so a refresh might be needed.
Closed zephykoh closed 1 year ago
rpetit3
commented
2 years ago Hmmm, let me see if I can borrow a macbook to replicate this. It's been a while since the conda envs have been built for Mac, so a refresh might be needed.
rpetit3
commented
2 years ago Got my hands on a macbook to test on. Will update soon
rpetit3
commented
2 years ago Can you share the contents of your base environment?
Open a new terminal, then conda env export
zephykoh
commented
2 years ago Thank you! Here it is:
name: base channels:
rpetit3
commented
2 years ago Looks good to me. It seems Conda is installing older versions of mamba in the bactopia environment, so lets try this:
conda deactivate
conda install -c conda-forge 'mamba>=0.27'mamba create -n bactopia -c rpetit3 -c conda-forge -c bioconda bactopia 'conda>=22' 'mamba>=0.27'
conda activate bactopia
bactopia download --use_defaults --force_rebuild --max_retry 1I'm also going to have you install my dev build, just had a recent mac specific fix (https://github.com/bactopia/bactopia/commit/ecf05d13a0a4c4a75d52316e414fc17f11e46b33)
Sorry for another update! I'm trying to run Bactopia using SRA samples. I typed in
(bactopia) zephykoh@dynamic-oit-vapornet100-10-8-22-104 ~ % bactopia --accession SRX17858519 --datasets datasets/ \
--species "vibrio cholerae" --coverage 100 --genome_size median --outdir ena-single-sample --force and got back
2022-10-20 16:53:46:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details. 2022-10-20 16:53:46:root:INFO - Found /Users/zephykoh/opt/miniconda3/envs/bactopia/share/bactopia-2.1.x/conda/mac/annotate_genome.yml (1 of 6), begin build to /Users/zephykoh/opt/miniconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs/annotate_genome-2.1.x External command failed with exit code 1!
Command: bash -c 'mamba env create -f /Users/zephykoh/opt/miniconda3/envs/bactopia/share/bactopia-2.1.x/conda/mac/annotate_genome.yml --prefix /Users/zephykoh/opt/miniconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs/annotate_genome-2.1.x --force'
Standard output: conda-forge/osx-64 Using cache conda-forge/noarch Using cache bioconda/osx-64 Using cache bioconda/noarch Using cache
Looking for: ['aragorn=1.2.41', 'barrnap=0.9', 'bedtools=2.30.0', 'blast=2.12.0', 'bzip2=1.0.8', 'c-ares=1.18.1', 'ca-certificates=2022.5.18.1', 'clustalw=2.1', 'coreutils=9.1', 'curl=7.83.1', 'entrez-direct=16.2', 'expat=2.4.8', 'fontconfig=2.14.0', 'freetype=2.10.4', 'gettext=0.19.8.1', 'giflib=5.2.1', 'graphviz=2.42.3', 'hmmer=3.3.2', 'icu=70.1', 'infernal=1.1.4', 'jpeg=9e', 'krb5=1.19.3', 'libcurl=7.83.1', 'libcxx=14.0.4', 'libdb=6.2.32', 'libedit=3.1.20191231', 'libev=4.33', 'libffi=3.4.2', 'libgcc=4.8.5', 'libgd=2.2.5', 'libgfortran=3.0.1', 'libiconv=1.16', 'libidn11=1.34', 'libnghttp2=1.47.0', 'libpng=1.6.37', 'libssh2=1.10.0', 'libtiff=4.1.0', 'libwebp=1.0.2', 'libxml2=2.9.14', 'libxslt=1.1.35', 'libzlib=1.2.12', 'llvm-openmp=14.0.4', 'lz4-c=1.9.3', 'minced=0.4.2', 'ncbi-amrfinderplus=3.10.30', 'ncurses=6.3', 'openjdk=11.0.9.1', 'openssl=3.0.3', 'paml=4.9', 'parallel=20220522', 'pcre=8.45', 'perl=5.26.2', 'perl-aceperl=1.92', 'perl-algorithm-diff=1.1903', 'perl-algorithm-munkres=0.08', 'perl-apache-test=1.40', 'perl-app-cpanminus=1.7044', 'perl-appconfig=1.71', 'perl-archive-tar=2.32', 'perl-array-compare=3.0.1', 'perl-autoloader=5.74', 'perl-base=2.23', 'perl-bio-asn1-entrezgene=1.73', 'perl-bio-coordinate=1.007001', 'perl-bio-featureio=1.6.905', 'perl-bio-phylo=0.58', 'perl-bio-samtools=1.43', 'perl-bio-tools-phylo-paml=1.7.3', 'perl-bio-tools-run-alignment-clustalw=1.7.4', 'perl-bioperl=1.7.2', 'perl-bioperl-core=1.007002', 'perl-bioperl-run=1.007002', 'perl-business-isbn=3.004', 'perl-business-isbn-data=20140910.003', 'perl-cache-cache=1.08', 'perl-capture-tiny=0.48', 'perl-carp=1.38', 'perl-cgi=4.44', 'perl-class-data-inheritable=0.08', 'perl-class-inspector=1.34', 'perl-class-load=0.25', 'perl-class-load-xs=0.10', 'perl-class-method-modifiers=2.12', 'perl-clone=0.42', 'perl-common-sense=3.74', 'perl-compress-raw-bzip2=2.087', 'perl-compress-raw-zlib=2.087', 'perl-constant=1.33', 'perl-convert-binary-c=0.78', 'perl-convert-binhex=1.125', 'perl-crypt-rc4=2.02', 'perl-data-dumper=2.173', 'perl-data-optlist=0.110', 'perl-data-stag=0.14', 'perl-date-format=2.30', 'perl-db-file=1.855', 'perl-dbd-sqlite=1.64', 'perl-dbi=1.642', 'perl-devel-globaldestruction=0.14', 'perl-devel-overloadinfo=0.005', 'perl-devel-stacktrace=2.04', 'perl-digest-hmac=1.03', 'perl-digest-md5=2.55', 'perl-digest-perl-md5=1.9', 'perl-digest-sha1=2.13', 'perl-dist-checkconflicts=0.11', 'perl-dynaloader=1.25', 'perl-email-date-format=1.005', 'perl-encode=2.88', 'perl-encode-locale=1.05', 'perl-error=0.17027', 'perl-eval-closure=0.14', 'perl-exception-class=1.44', 'perl-exporter=5.72', 'perl-exporter-tiny=1.002001', 'perl-extutils-makemaker=7.36', 'perl-file-listing=6.04', 'perl-file-path=2.16', 'perl-file-slurp-tiny=0.004', 'perl-file-sort=1.01', 'perl-file-temp=0.2304', 'perl-file-which=1.23', 'perl-font-afm=1.20', 'perl-font-ttf=1.06', 'perl-gd=2.71', 'perl-getopt-long=2.50', 'perl-graph=0.9704', 'perl-graphviz=2.24', 'perl-html-element-extended=1.18', 'perl-html-entities-numbered=0.04', 'perl-html-formatter=2.16', 'perl-html-parser=3.72', 'perl-html-tableextract=2.13', 'perl-html-tagset=3.20', 'perl-html-tidy=1.60', 'perl-html-tree=5.07', 'perl-html-treebuilder-xpath=0.14', 'perl-http-cookies=6.04', 'perl-http-daemon=6.01', 'perl-http-date=6.02', 'perl-http-message=6.18', 'perl-http-negotiate=6.01', 'perl-image-info=1.38', 'perl-image-size=3.300', 'perl-io-compress=2.087', 'perl-io-html=1.001', 'perl-io-sessiondata=1.03', 'perl-io-socket-ssl=2.066', 'perl-io-string=1.08', 'perl-io-stringy=2.111', 'perl-io-tty=1.12', 'perl-io-zlib=1.10', 'perl-ipc-run=20180523.0', 'perl-ipc-sharelite=0.17', 'perl-jcode=2.07', 'perl-json=4.02', 'perl-json-xs=2.34', 'perl-lib=0.63', 'perl-libwww-perl=6.39', 'perl-libxml-perl=0.08', 'perl-list-moreutils=0.428', 'perl-list-moreutils-xs=0.428', 'perl-lwp-mediatypes=6.04', 'perl-lwp-protocol-https=6.07', 'perl-lwp-simple=6.15', 'perl-mailtools=2.21', 'perl-math-cdf=0.1', 'perl-math-derivative=1.01', 'perl-math-random=0.72', 'perl-math-spline=0.02', 'perl-mime-base64=3.15', 'perl-mime-lite=3.030', 'perl-mime-tools=5.508', 'perl-mime-types=2.17', 'perl-mldbm=2.05', 'perl-module-implementation=0.09', 'perl-module-runtime=0.016', 'perl-module-runtime-conflicts=0.003', 'perl-moo=2.003004', 'perl-moose=2.2011', 'perl-mozilla-ca=20180117', 'perl-mro-compat=0.13', 'perl-net-http=6.19', 'perl-net-ssleay=1.74', 'perl-ntlm=1.09', 'perl-ole-storage_lite=0.19', 'perl-package-deprecationmanager=0.17', 'perl-package-stash=0.38', 'perl-package-stash-xs=0.28', 'perl-params-util=1.07', 'perl-parent=0.236', 'perl-parse-recdescent=1.967015', 'perl-pathtools=3.75', 'perl-pdf-api2=2.035', 'perl-pod-escapes=1.07', 'perl-pod-usage=1.69', 'perl-postscript=0.06', 'perl-role-tiny=2.000008', 'perl-scalar-list-utils=1.52', 'perl-set-scalar=1.29', 'perl-soap-lite=1.19', 'perl-socket=2.027', 'perl-sort-naturally=1.03', 'perl-spreadsheet-parseexcel=0.65', 'perl-spreadsheet-writeexcel=2.40', 'perl-statistics-descriptive=3.0702', 'perl-storable=3.15', 'perl-sub-exporter=0.987', 'perl-sub-exporter-progressive=0.001013', 'perl-sub-identify=0.14', 'perl-sub-install=0.928', 'perl-sub-name=0.21', 'perl-sub-quote=2.006003', 'perl-sub-uplevel=0.2800', 'perl-svg=2.84', 'perl-svg-graph=0.02', 'perl-task-weaken=1.06', 'perl-template-toolkit=2.26', 'perl-test=1.26', 'perl-test-deep=1.128', 'perl-test-differences=0.67', 'perl-test-exception=0.43', 'perl-test-harness=3.42', 'perl-test-leaktrace=0.16', 'perl-test-most=0.35', 'perl-test-requiresinternet=0.05', 'perl-test-warn=0.36', 'perl-text-diff=1.45', 'perl-threaded=5.32.1', 'perl-tie-ixhash=1.23', 'perl-time-hires=1.9760', 'perl-time-local=1.28', 'perl-timedate=2.30', 'perl-tree-dag_node=1.31', 'perl-try-tiny=0.30', 'perl-type-tiny=1.004004', 'perl-types-serialiser=1.0', 'perl-unicode-map=0.112', 'perl-uri=1.76', 'perl-www-robotrules=6.02', 'perl-xml-dom=1.46', 'perl-xml-dom-xpath=0.14', 'perl-xml-filter-buffertext=1.01', 'perl-xml-libxml=2.0132', 'perl-xml-libxslt=1.94', 'perl-xml-namespacesupport=1.12', 'perl-xml-parser=2.44_01', 'perl-xml-regexp=0.04', 'perl-xml-sax=1.02', 'perl-xml-sax-base=1.09', 'perl-xml-sax-expat=0.51', 'perl-xml-sax-writer=0.57', 'perl-xml-simple=2.25', 'perl-xml-twig=3.52', 'perl-xml-writer=0.625', 'perl-xml-xpath=1.44', 'perl-xml-xpathengine=0.14', 'perl-xsloader=0.24', 'perl-yaml=1.29', 'pigz=2.6', 'pip=22.1.2', 'prodigal=2.6.3', 'prokka=1.14.6', 'python=3.10.4', 'python_abi=3.10', 'readline=8.1', 'sed=4.7', 'setuptools=62.3.3', 'sqlite=3.38.5', 'tbl2asn-forever=25.7.2f', 'tidyp=1.04', 'tk=8.6.12', 'tzdata=2022a', 'wheel=0.37.1', 'xz=5.2.5', 'zlib=1.2.12', 'zstd=1.4.9']
Encountered problems while solving:
package perl-app-cpanminus-1.7044-pl526_1 is excluded by strict repo priority package perl-compress-raw-bzip2-2.087-pl5321h589c0e0_1 is excluded by strict repo priority package perl-compress-raw-zlib-2.087-pl5321hb280591_1 is excluded by strict repo priority package perl-data-dumper-2.173-pl5321hb4d813b_1 is excluded by strict repo priority package perl-dbi-1.642-pl5321hb4d813b_2 is excluded by strict repo priority package perl-digest-md5-2.55-pl5321hb4d813b_1 is excluded by strict repo priority package perl-encode-2.88-pl5321hb4d813b_2 is excluded by strict repo priority package perl-io-stringy-2.111-pl5321hdfd78af_2 is excluded by strict repo priority package perl-io-tty-1.12-pl5321hb4d813b_2 is excluded by strict repo priority package perl-mime-base64-3.15-pl5321hb4d813b_2 is excluded by strict repo priority package perl-net-ssleay-1.74-1 is excluded by strict repo priority package perl-scalar-list-utils-1.52-pl5321hb4d813b_1 is excluded by strict repo priority package perl-try-tiny-0.30-pl5321hdfd78af_2 is excluded by strict repo priority package perl-algorithm-diff-1.1903-pl5321hdfd78af_3 is excluded by strict repo priority package perl-apache-test-1.40-pl5321hdfd78af_2 is excluded by strict repo priority package perl-business-isbn-3.004-pl5321hdfd78af_1 is excluded by strict repo priority package perl-business-isbn-data-20140910.003-pl5321hdfd78af_1 is excluded by strict repo priority package perl-carp-1.38-pl5321hdfd78af_4 is excluded by strict repo priority package perl-common-sense-3.74-pl5321hdfd78af_3 is excluded by strict repo priority package perl-exporter-tiny-1.002001-pl5321hdfd78af_1 is excluded by strict repo priority package perl-io-socket-ssl-2.066-pl5321hdfd78af_1 is excluded by strict repo priority package perl-svg-2.84-pl5321hdfd78af_1 is excluded by strict repo priority package perl-test-deep-1.128-pl5321hdfd78af_2 is excluded by strict repo priority package perl-test-harness-3.42-pl5321hdfd78af_1 is excluded by strict repo priority package perl-test-warn-0.36-pl5321hdfd78af_2 is excluded by strict repo priority package perl-type-tiny-1.004004-pl5321hdfd78af_1 is excluded by strict repo priority package perl-xml-xpath-1.44-pl5321hdfd78af_1 is excluded by strict repo priority package perl-gd-2.71-pl526h5c9b4e4_0 requires libgd >=2.2.5,<2.3.0a0, but none of the providers can be installed package perl-xsloader-0.24-pl5321hd8ed1ab_0 requires perl >=5.32.1,<6.0a0 _perl5, but none of the providers can be installed nothing provides t_coffee needed by perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5262hdfd78af_3 package perl-graphviz-2.24-pl526h734ff71_0 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed package perl-dbd-sqlite-1.64-pl526h01d97ff_0 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed package perl-capture-tiny-0.48-pl5321h694c41f_0 requires perl >=5.32.1,<5.33.0a0 _perl5, but none of the providers can be installed package perl-xml-namespacesupport-1.12-pl5321hd8ed1ab_0 requires perl >=5.32.1,<6.0a0 *_perl5, but none of the providers can be installed package perl-yaml-1.29-pl526_0 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed