diff --git a/ingest/nextstrain_env.yaml b/ingest/nextstrain_env.yaml
deleted file mode 100644
index 4b898a8..0000000
--- a/ingest/nextstrain_env.yaml
+++ /dev/null
@@ -1,551 +0,0 @@
-name: nextstrain_env
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - abseil-cpp=20210324.2=he49afe7_0
-  - aioeasywebdav=2.4.0=py38h50d1736_1001
-  - aiohttp=3.8.3=py38hef030d1_1
-  - aiosignal=1.3.1=pyhd8ed1ab_0
-  - alabaster=0.7.13=pyhd8ed1ab_0
-  - altair=4.2.2=pyhd8ed1ab_0
-  - amply=0.1.5=pyhd8ed1ab_0
-  - anyio=3.6.2=pyhd8ed1ab_0
-  - appdirs=1.4.4=pyh9f0ad1d_0
-  - appnope=0.1.3=pyhd8ed1ab_0
-  - argcomplete=2.0.0=pyhd8ed1ab_0
-  - argon2-cffi=21.3.0=pyhd8ed1ab_0
-  - argon2-cffi-bindings=21.2.0=py38hef030d1_3
-  - arrow-cpp=6.0.1=py38h03f22f6_4_cpu
-  - asttokens=2.2.1=pyhd8ed1ab_0
-  - async-timeout=4.0.2=pyhd8ed1ab_0
-  - atomicwrites=1.4.1=pyhd8ed1ab_0
-  - attmap=0.13.2=pyhd8ed1ab_0
-  - attrs=22.2.0=pyh71513ae_0
-  - auspice=2.39.0=hb19a6fa_0
-  - aws-c-auth=0.6.8=h8f5e388_1
-  - aws-c-cal=0.5.12=hda7428a_7
-  - aws-c-common=0.6.17=h0d85af4_0
-  - aws-c-compression=0.2.14=h8451fdb_7
-  - aws-c-event-stream=0.2.7=ha663dc4_32
-  - aws-c-http=0.6.10=heb655c9_3
-  - aws-c-io=0.10.14=h3cf48f6_1
-  - aws-c-mqtt=0.7.10=h6d234a2_0
-  - aws-c-s3=0.1.29=h73af6b9_0
-  - aws-c-sdkutils=0.1.1=h8451fdb_4
-  - aws-checksums=0.1.12=h8451fdb_6
-  - aws-crt-cpp=0.17.10=haa61d5f_5
-  - aws-sdk-cpp=1.9.160=h075ee0a_0
-  - awscli=1.27.65=py38h50d1736_0
-  - babel=2.11.0=pyhd8ed1ab_0
-  - backcall=0.2.0=pyh9f0ad1d_0
-  - backports=1.0=pyhd8ed1ab_3
-  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
-  - backports.zoneinfo=0.2.1=py38hef030d1_7
-  - backrefs=5.2=pyhd8ed1ab_2
-  - bcbio-gff=0.6.9=pyh5e36f6f_0
-  - bcrypt=3.2.2=py38hef030d1_1
-  - beautifulsoup4=4.11.2=pyha770c72_0
-  - black=23.1.0=py38h50d1736_0
-  - blast=2.12.0=h0370960_3
-  - bleach=6.0.0=pyhd8ed1ab_0
-  - blinker=1.5=pyhd8ed1ab_0
-  - boltons=23.0.0=pyhd8ed1ab_0
-  - boost-cpp=1.74.0=h8b082ac_8
-  - boto3=1.26.65=pyhd8ed1ab_0
-  - botocore=1.29.65=pyhd8ed1ab_0
-  - bracex=2.2.1=pyhd8ed1ab_0
-  - brotli=1.0.9=hb7f2c08_8
-  - brotli-bin=1.0.9=hb7f2c08_8
-  - brotlipy=0.7.0=py38hef030d1_1005
-  - bullet-python=2.2.0=py38h50d1736_6
-  - bx-python=0.9.0=py38h27f87a4_0
-  - bzip2=1.0.8=h0d85af4_4
-  - c-ares=1.18.1=h0d85af4_0
-  - ca-certificates=2022.12.7=h033912b_0
-  - cachetools=5.3.0=pyhd8ed1ab_0
-  - cattrs=22.2.0=pyhd8ed1ab_0
-  - certifi=2022.12.7=pyhd8ed1ab_0
-  - cffi=1.15.1=py38hb368cf1_3
-  - cfgv=3.3.1=pyhd8ed1ab_0
-  - charset-normalizer=2.1.1=pyhd8ed1ab_0
-  - cheetah3=3.2.6.post2=py38hef030d1_3
-  - click=8.1.3=unix_pyhd8ed1ab_2
-  - coin-or-cbc=2.10.8=hc8a182d_0
-  - coin-or-cgl=0.60.6=ha3c4b8c_2
-  - coin-or-clp=1.17.7=hf0ee74e_2
-  - coin-or-osi=0.108.7=hfef9e4d_2
-  - coin-or-utils=2.11.6=h7a46149_2
-  - coincbc=2.10.8=0_metapackage
-  - colorama=0.4.4=pyh9f0ad1d_0
-  - coloredlogs=15.0.1=pyhd8ed1ab_3
-  - comm=0.1.2=pyhd8ed1ab_0
-  - commonmark=0.9.1=py_0
-  - conda=23.1.0=py38h50d1736_0
-  - conda-package-handling=2.0.2=pyh38be061_0
-  - conda-package-streaming=0.7.0=pyhd8ed1ab_1
-  - configargparse=1.5.3=pyhd8ed1ab_0
-  - connection_pool=0.0.3=pyhd3deb0d_0
-  - constellations=0.1.10=pyh5e36f6f_0
-  - contourpy=1.0.7=py38h98b9b1b_0
-  - coreutils=9.1=h5eb16cf_0
-  - cryptography=39.0.0=py38ha6c3189_0
-  - csvtk=0.25.0=h527b516_0
-  - curl=7.87.0=haf73cf8_0
-  - cvxopt=1.3.0=py38h6671556_4
-  - cycler=0.11.0=pyhd8ed1ab_0
-  - dataclasses=0.8=pyhc8e2a94_3
-  - datrie=0.8.2=py38hef030d1_6
-  - debugpy=1.6.6=py38h4cd09af_0
-  - decorator=5.1.1=pyhd8ed1ab_0
-  - defusedxml=0.7.1=pyhd8ed1ab_0
-  - dendropy=4.5.2=pyh3252c3a_0
-  - distlib=0.3.6=pyhd8ed1ab_0
-  - docker-py=6.0.0=pyhd8ed1ab_0
-  - docutils=0.16=py38h50d1736_3
-  - dpath=2.1.4=py38h50d1736_0
-  - dropbox=11.36.0=pyhd8ed1ab_0
-  - dsdp=5.8=h6e329d1_1203
-  - entrez-direct=16.2=h193322a_1
-  - entrypoints=0.4=pyhd8ed1ab_0
-  - epiweeks=2.1.4=pyhdfd78af_0
-  - et_xmlfile=1.1.0=pyhd8ed1ab_0
-  - exceptiongroup=1.1.0=pyhd8ed1ab_0
-  - executing=1.2.0=pyhd8ed1ab_0
-  - expat=2.5.0=hf0c8a7f_0
-  - fasteners=0.17.3=pyhd8ed1ab_0
-  - fasttree=2.1.11=hdcdfbac_1
-  - fftw=3.3.10=nompi_h4fa670e_106
-  - filechunkio=1.8=py_2
-  - filelock=3.9.0=pyhd8ed1ab_0
-  - filetype=1.2.0=pyhd8ed1ab_0
-  - firecloud=0.16.30=pyh3252c3a_0
-  - flit-core=3.8.0=pyhd8ed1ab_0
-  - fonttools=4.38.0=py38hef030d1_1
-  - freetype=2.12.1=h3f81eb7_1
-  - frozenlist=1.3.3=py38hef030d1_0
-  - fsspec=2023.1.0=pyhd8ed1ab_0
-  - ftputil=5.0.4=pyhd8ed1ab_0
-  - future=0.18.3=pyhd8ed1ab_0
-  - galaxy-containers=22.1.1=pyhd8ed1ab_0
-  - galaxy-tool-util=22.1.5=pyhd8ed1ab_0
-  - galaxy-util=22.1.1=pyhd8ed1ab_0
-  - geographiclib=1.52=pyhd8ed1ab_0
-  - geopy=2.3.0=pyhd8ed1ab_0
-  - gettext=0.21.1=h8a4c099_0
-  - gflags=2.2.2=hb1e8313_1004
-  - giflib=5.2.1=hbcb3906_2
-  - git=2.39.1=pl5321h00ebd2c_0
-  - gitdb=4.0.10=pyhd8ed1ab_0
-  - gitpython=3.1.30=pyhd8ed1ab_0
-  - glog=0.5.0=h25b26a9_0
-  - glpk=5.0=h3cb5acd_0
-  - gmp=6.2.1=h2e338ed_0
-  - gofasta=1.2.0=h527b516_0
-  - google-api-core=2.10.0=pyhd8ed1ab_0
-  - google-api-python-client=2.77.0=pyhd8ed1ab_0
-  - google-auth=2.16.0=pyh1a96a4e_1
-  - google-auth-httplib2=0.1.0=pyhd8ed1ab_1
-  - google-cloud-core=2.3.2=pyhd8ed1ab_0
-  - google-cloud-storage=2.7.0=pyh1a96a4e_0
-  - google-crc32c=1.1.2=py38h664dbe5_4
-  - google-resumable-media=2.4.1=pyhd8ed1ab_0
-  - googleapis-common-protos=1.57.0=py38h50d1736_0
-  - graphviz=2.42.3=h98dfb87_0
-  - grpc-cpp=1.42.0=h8a858f2_0
-  - grpcio=1.46.3=py38hf25cc3e_0
-  - gsl=2.7=h93259b0_0
-  - httplib2=0.21.0=pyhd8ed1ab_0
-  - humanfriendly=10.0=py38h50d1736_4
-  - icu=70.1=h96cf925_0
-  - identify=2.5.21=pyhd8ed1ab_0
-  - idna=3.4=pyhd8ed1ab_0
-  - imagesize=1.4.1=pyhd8ed1ab_0
-  - importlib-metadata=4.11.4=py38h50d1736_0
-  - importlib_metadata=4.11.4=hd8ed1ab_0
-  - importlib_resources=5.10.2=pyhd8ed1ab_0
-  - iniconfig=2.0.0=pyhd8ed1ab_0
-  - ipykernel=6.21.1=pyh736e0ef_0
-  - ipython=8.9.0=pyhd1c38e8_0
-  - ipython_genutils=0.2.0=py_1
-  - ipywidgets=8.0.4=pyhd8ed1ab_0
-  - iqtree=2.2.0.3=h135ad0d_1
-  - isa-l=2.30.0=h0d85af4_4
-  - isodate=0.6.1=pyhd8ed1ab_0
-  - isort=5.12.0=pyhd8ed1ab_1
-  - itsdangerous=2.1.2=pyhd8ed1ab_0
-  - jedi=0.18.2=pyhd8ed1ab_0
-  - jinja2=3.1.2=pyhd8ed1ab_1
-  - jmespath=1.0.1=pyhd8ed1ab_0
-  - joblib=1.2.0=pyhd8ed1ab_0
-  - jpeg=9e=hac89ed1_2
-  - js2py=0.74=pyhd8ed1ab_0
-  - json5=0.9.5=pyh9f0ad1d_0
-  - jsonschema=3.2.0=pyhd8ed1ab_3
-  - jupyter_client=8.0.2=pyhd8ed1ab_0
-  - jupyter_core=5.2.0=py38h50d1736_0
-  - jupyter_events=0.6.3=pyhd8ed1ab_0
-  - jupyter_server=2.2.1=pyhd8ed1ab_0
-  - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
-  - jupyterlab=3.5.3=pyhd8ed1ab_0
-  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
-  - jupyterlab_server=2.16.6=pyhd8ed1ab_0
-  - jupyterlab_widgets=3.0.5=pyhd8ed1ab_0
-  - k8=0.2.5=h6151dfb_2
-  - kiwisolver=1.4.4=py38h98b9b1b_1
-  - krb5=1.20.1=h0165f36_0
-  - lark=1.1.5=pyhd8ed1ab_0
-  - lark-parser=0.12.0=pyhd8ed1ab_0
-  - lcms2=2.14=h90f4b2a_0
-  - lerc=4.0.0=hb486fe8_0
-  - libblas=3.9.0=16_osx64_openblas
-  - libbrotlicommon=1.0.9=hb7f2c08_8
-  - libbrotlidec=1.0.9=hb7f2c08_8
-  - libbrotlienc=1.0.9=hb7f2c08_8
-  - libcblas=3.9.0=16_osx64_openblas
-  - libcbor=0.9.0=he49afe7_0
-  - libcrc32c=1.1.2=he49afe7_0
-  - libcurl=7.87.0=haf73cf8_0
-  - libcxx=14.0.6=hce7ea42_0
-  - libdeflate=1.13=h775f41a_0
-  - libedit=3.1.20191231=h0678c8f_2
-  - libev=4.33=haf1e3a3_1
-  - libevent=2.1.10=h815e4d9_4
-  - libffi=3.4.2=h0d85af4_5
-  - libfido2=1.11.0=h875bebe_0
-  - libgfortran=5.0.0=11_3_0_h97931a8_27
-  - libgfortran5=11.3.0=h082f757_27
-  - libiconv=1.17=hac89ed1_0
-  - libidn2=2.3.4=hb7f2c08_0
-  - liblapack=3.9.0=16_osx64_openblas
-  - liblapacke=3.9.0=16_osx64_openblas
-  - libnghttp2=1.51.0=h0dd9d14_0
-  - libopenblas=0.3.21=openmp_h429af6e_3
-  - libpng=1.6.39=ha978bb4_0
-  - libprotobuf=3.18.3=hbc0c0cd_0
-  - libsodium=1.0.18=hbcb3906_1
-  - libsqlite=3.40.0=ha978bb4_0
-  - libssh2=1.10.0=h7535e13_3
-  - libthrift=0.15.0=hab56fdc_1
-  - libtiff=4.4.0=h5e0c7b4_3
-  - libunistring=0.9.10=h0d85af4_0
-  - libutf8proc=2.8.0=hb7f2c08_0
-  - libuuid=2.32.1=h35c211d_1000
-  - libuv=1.44.2=hac89ed1_0
-  - libwebp=1.2.4=hfa4350a_0
-  - libwebp-base=1.2.4=h775f41a_0
-  - libxcb=1.13=h0d85af4_1004
-  - libxml2=2.10.3=hb9e07b5_0
-  - libxslt=1.1.37=h5d22bc9_0
-  - libzlib=1.2.13=hfd90126_4
-  - llvm-openmp=15.0.7=h61d9ccf_0
-  - logmuse=0.2.6=pyh8c360ce_0
-  - lxml=4.9.2=py38h64add32_0
-  - lz4-c=1.9.3=he49afe7_1
-  - lzo=2.10=haf1e3a3_1000
-  - mafft=7.515=h1e3017b_0
-  - markdown=3.4.1=pyhd8ed1ab_0
-  - markdown-it-py=2.1.0=pyhd8ed1ab_0
-  - markupsafe=2.1.2=py38hef030d1_0
-  - matplotlib-base=3.6.3=py38hcb346ec_0
-  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
-  - mdurl=0.1.0=pyhd8ed1ab_0
-  - metis=5.1.0=h2e338ed_1006
-  - minimap2=2.24=h1f540d2_1
-  - miniwdl=1.9.0=pyhd8ed1ab_0
-  - mistune=2.0.5=pyhd8ed1ab_0
-  - more-itertools=9.1.0=pyhd8ed1ab_0
-  - mpfr=4.1.0=h0f52abe_1
-  - mpi=1.0=openmpi
-  - multidict=6.0.4=py38hef030d1_0
-  - munkres=1.1.4=pyh9f0ad1d_0
-  - mypy=1.0.0=py38hef030d1_0
-  - mypy_extensions=1.0.0=pyha770c72_0
-  - mysql-connector-c=6.1.11=h0f02589_1007
-  - nb_conda_kernels=2.3.1=py38h50d1736_2
-  - nbclassic=0.5.1=pyhd8ed1ab_0
-  - nbclient=0.7.2=pyhd8ed1ab_0
-  - nbconvert=7.2.9=pyhd8ed1ab_0
-  - nbconvert-core=7.2.9=pyhd8ed1ab_0
-  - nbconvert-pandoc=7.2.9=pyhd8ed1ab_0
-  - nbformat=5.7.3=pyhd8ed1ab_0
-  - ncurses=6.3=h96cf925_1
-  - nest-asyncio=1.5.6=pyhd8ed1ab_0
-  - networkx=2.8.8=pyhd8ed1ab_0
-  - nextalign=2.11.0=h527b516_0
-  - nextclade=2.11.0=h527b516_0
-  - nextflow=22.10.6=h4a94de4_0
-  - nextstrain-cli=6.1.0.post1=pyhdfd78af_0
-  - nf-core=2.7.2=pyh7cba7a3_0
-  - nodeenv=1.7.0=pyhd8ed1ab_0
-  - nodejs=18.12.1=h3591b89_0
-  - notebook=6.5.2=pyha770c72_1
-  - notebook-shim=0.2.2=pyhd8ed1ab_0
-  - numpy=1.24.2=py38h5a2dcdf_0
-  - oauth2client=4.1.3=py_0
-  - openjdk=17.0.3=hbc0c0cd_5
-  - openjpeg=2.5.0=h5d0d7b0_1
-  - openmpi=4.1.2=hd3cd54c_0
-  - openpyxl=3.1.0=py38hef030d1_0
-  - openssh=9.1p1=hdbdeef1_1
-  - openssl=1.1.1t=hfd90126_0
-  - orc=1.7.1=hf163092_0
-  - oyaml=1.0=pyhd8ed1ab_0
-  - packaging=23.0=pyhd8ed1ab_0
-  - pandas=1.5.3=py38hec72209_0
-  - pandas-stubs=1.5.3.230203=pyhd8ed1ab_0
-  - pandoc=2.19.2=h694c41f_1
-  - pandocfilters=1.5.0=pyhd8ed1ab_0
-  - pango-designation=1.18=pyhdfd78af_0
-  - pangolearn=2022.03.22=pyh5e36f6f_0
-  - pangolin=3.1.11=pyhdfd78af_2
-  - paramiko=3.0.0=pyhd8ed1ab_0
-  - parquet-cpp=1.5.1=2
-  - parso=0.8.3=pyhd8ed1ab_0
-  - pathspec=0.11.0=pyhd8ed1ab_0
-  - pbzip2=1.1.13=h9d27c22_1
-  - pcre=8.45=he49afe7_0
-  - pcre2=10.40=h1c4e4bc_0
-  - peppy=0.35.4=pyhd8ed1ab_0
-  - perl=5.32.1=2_h0d85af4_perl5
-  - perl-archive-tar=2.40=pl5321hdfd78af_0
-  - perl-carp=1.50=pl5321hd8ed1ab_0
-  - perl-common-sense=3.75=pl5321hdfd78af_0
-  - perl-compress-raw-bzip2=2.201=pl5321h9722bc1_0
-  - perl-compress-raw-zlib=2.202=pl5321h775f41a_0
-  - perl-encode=3.19=pl5321ha5712d3_1
-  - perl-exporter=5.74=pl5321hd8ed1ab_0
-  - perl-exporter-tiny=1.002002=pl5321hdfd78af_0
-  - perl-extutils-makemaker=7.66=pl5321hd8ed1ab_0
-  - perl-io-compress=2.201=pl5321h9722bc1_0
-  - perl-io-zlib=1.14=pl5321hdfd78af_0
-  - perl-json=4.10=pl5321hdfd78af_0
-  - perl-json-xs=2.34=pl5321hcd10b59_5
-  - perl-list-moreutils=0.430=pl5321hdfd78af_0
-  - perl-list-moreutils-xs=0.430=pl5321ha5712d3_1
-  - perl-parent=0.239=pl5321hd8ed1ab_0
-  - perl-pathtools=3.75=pl5321ha5712d3_3
-  - perl-scalar-list-utils=1.63=pl5321h775f41a_0
-  - perl-threaded=5.32.1=hdfd78af_1
-  - perl-types-serialiser=1.01=pl5321hdfd78af_0
-  - pexpect=4.8.0=pyh9f0ad1d_2
-  - pickleshare=0.7.5=py_1003
-  - pigz=2.6=h5dbffcc_0
-  - pillow=9.2.0=py38h85595ef_3
-  - pip=23.0=pyhd8ed1ab_0
-  - piper=0.12.3=pyhdfd78af_0
-  - plac=1.3.5=pyhd8ed1ab_0
-  - platformdirs=3.0.0=pyhd8ed1ab_0
-  - plotly=5.13.0=pyhd8ed1ab_0
-  - pluggy=1.0.0=pyhd8ed1ab_5
-  - ply=3.11=py_1
-  - pooch=1.6.0=pyhd8ed1ab_0
-  - pre-commit=3.1.1=pyha770c72_1
-  - prettytable=3.6.0=pyhd8ed1ab_0
-  - prometheus_client=0.16.0=pyhd8ed1ab_0
-  - prompt-toolkit=3.0.36=pyha770c72_0
-  - prompt_toolkit=3.0.36=hd8ed1ab_0
-  - protobuf=3.18.3=py38h4cd09af_0
-  - psutil=5.9.4=py38hef030d1_0
-  - pthread-stubs=0.4=hc929b4f_1001
-  - ptyprocess=0.7.0=pyhd3deb0d_0
-  - pulp=2.7.0=py38h50d1736_0
-  - pure_eval=0.2.2=pyhd8ed1ab_0
-  - py=1.11.0=pyh6c4a22f_0
-  - pyarrow=6.0.1=py38h2688f9d_4_cpu
-  - pyasn1=0.4.8=py_0
-  - pyasn1-modules=0.2.7=py_0
-  - pycosat=0.6.4=py38hef030d1_1
-  - pycparser=2.21=pyhd8ed1ab_0
-  - pycryptodome=3.16.0=py38hde038e5_0
-  - pydantic=1.10.6=py38hef030d1_0
-  - pydeck=0.8.0=pyhd8ed1ab_0
-  - pydot=1.4.2=py38h50d1736_3
-  - pyfaidx=0.7.2.1=pyh7cba7a3_1
-  - pyfastx=0.8.4=py38hc0a6b99_1
-  - pygments=2.14.0=pyhd8ed1ab_0
-  - pygtail=0.14.0=pyhd8ed1ab_0
-  - pyjsparser=2.7.1=pyh8c360ce_0
-  - pyjwt=2.6.0=pyhd8ed1ab_0
-  - pympler=1.0.1=pyhd8ed1ab_0
-  - pynacl=1.5.0=py38hef030d1_2
-  - pyopenssl=23.0.0=pyhd8ed1ab_0
-  - pyparsing=3.0.9=pyhd8ed1ab_0
-  - pyrsistent=0.19.3=py38hef030d1_0
-  - pysam=0.20.0=py38h85ed9dd_0
-  - pysftp=0.2.9=py_1
-  - pysocks=1.7.1=pyha2e5f31_6
-  - pytest=7.2.1=pyhd8ed1ab_0
-  - pytest-workflow=2.0.1=pyhd8ed1ab_0
-  - python=3.8.15=hc915b28_0_cpython
-  - python-dateutil=2.8.2=pyhd8ed1ab_0
-  - python-fastjsonschema=2.16.2=pyhd8ed1ab_0
-  - python-irodsclient=1.1.6=pyhd8ed1ab_0
-  - python-isal=1.1.0=py38hef030d1_1
-  - python-json-logger=2.0.4=pyhd8ed1ab_0
-  - python-lzo=1.14=py38h5ea95a3_2
-  - python-tzdata=2022.7=pyhd8ed1ab_0
-  - python_abi=3.8=3_cp38
-  - pytz=2022.7.1=pyhd8ed1ab_0
-  - pytz-deprecation-shim=0.1.0.post0=py38h50d1736_3
-  - pyu2f=0.1.5=pyhd8ed1ab_0
-  - pyvcf3=1.0.3=pyhdfd78af_0
-  - pywin32-on-windows=0.1.0=pyh1179c8e_3
-  - pyzmq=25.0.0=py38h0b711fd_0
-  - questionary=1.10.0=pyhd8ed1ab_1
-  - ratelimiter=1.2.0=pyhd8ed1ab_1003
-  - raxml=8.2.12=ha5712d3_4
-  - re2=2021.11.01=he49afe7_0
-  - readline=8.1.2=h3899abd_0
-  - recommonmark=0.7.1=pyhd8ed1ab_0
-  - refgenconf=0.12.2=pyhdfd78af_0
-  - refgenie=0.12.1=pyhdfd78af_0
-  - regex=2022.10.31=py38hef030d1_0
-  - repoze.lru=0.7=py_0
-  - requests=2.28.2=pyhd8ed1ab_0
-  - requests-cache=1.0.0=pyhd8ed1ab_0
-  - reretry=0.11.8=pyhd8ed1ab_0
-  - retry=0.9.2=py_0
-  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
-  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
-  - rich=13.3.1=pyhd8ed1ab_1
-  - rich-click=1.6.1=pyhd8ed1ab_0
-  - routes=2.5.1=pyhd8ed1ab_0
-  - rsa=4.7.2=pyh44b312d_0
-  - ruamel.yaml=0.17.21=py38hef030d1_3
-  - ruamel.yaml.clib=0.2.7=py38hef030d1_1
-  - s3fs=0.4.2=py_0
-  - s3transfer=0.6.0=pyhd8ed1ab_0
-  - scikit-learn=0.23.1=py38hb7f0800_0
-  - scipy=1.10.0=py38hfb8b963_2
-  - scorpio=0.3.17=pyhdfd78af_0
-  - semver=2.13.0=pyh9f0ad1d_0
-  - send2trash=1.8.0=pyhd8ed1ab_0
-  - seqkit=2.3.1=h527b516_0
-  - setuptools=67.1.0=pyhd8ed1ab_0
-  - six=1.16.0=pyh6c4a22f_0
-  - slacker=0.14.0=py_0
-  - smart_open=6.3.0=pyhd8ed1ab_1
-  - smmap=3.0.5=pyh44b312d_0
-  - smof=2.22.2=pyhdfd78af_0
-  - snakefmt=0.8.1=pyhdfd78af_0
-  - snakemake=7.21.0=hdfd78af_0
-  - snakemake-minimal=7.21.0=pyhdfd78af_0
-  - snappy=1.1.9=h225ccf5_2
-  - sniffio=1.3.0=pyhd8ed1ab_0
-  - snowballstemmer=2.2.0=pyhd8ed1ab_0
-  - sortedcontainers=2.4.0=pyhd8ed1ab_0
-  - soupsieve=2.3.2.post1=pyhd8ed1ab_0
-  - sphinx=5.1.1=pyhd8ed1ab_1
-  - sphinxcontrib-applehelp=1.0.4=pyhd8ed1ab_0
-  - sphinxcontrib-devhelp=1.0.2=py_0
-  - sphinxcontrib-htmlhelp=2.0.1=pyhd8ed1ab_0
-  - sphinxcontrib-jsmath=1.0.1=py_0
-  - sphinxcontrib-qthelp=1.0.3=py_0
-  - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_2
-  - sqlite=3.40.0=h9ae0607_0
-  - stack_data=0.6.2=pyhd8ed1ab_0
-  - stone=3.3.1=pyhd8ed1ab_0
-  - stopit=1.1.2=py_0
-  - streamlit=1.17.0=pyhd8ed1ab_0
-  - suitesparse=5.10.1=h7aff33d_1
-  - tabulate=0.9.0=pyhd8ed1ab_1
-  - tbb=2021.7.0=hb8565cd_1
-  - tenacity=8.1.0=pyhd8ed1ab_0
-  - terminado=0.17.1=pyhd1c38e8_0
-  - threadpoolctl=3.1.0=pyh8a188c0_0
-  - throttler=1.2.1=pyhd8ed1ab_0
-  - tinycss2=1.2.1=pyhd8ed1ab_0
-  - tk=8.6.12=h5dbffcc_0
-  - toml=0.10.2=pyhd8ed1ab_0
-  - tomli=2.0.1=pyhd8ed1ab_0
-  - toolz=0.12.0=pyhd8ed1ab_0
-  - toposort=1.9=pyhd8ed1ab_0
-  - tornado=6.2=py38hef030d1_1
-  - traitlets=5.9.0=pyhd8ed1ab_0
-  - treetime=0.9.4=pyh7cba7a3_0
-  - tsv-utils=2.2.0=h527b516_0
-  - types-pytz=2022.7.1.0=pyhd8ed1ab_0
-  - typing-extensions=4.4.0=hd8ed1ab_0
-  - typing_extensions=4.4.0=pyha770c72_0
-  - tzdata=2022g=h191b570_0
-  - tzlocal=4.2=py38h50d1736_2
-  - ubiquerg=0.6.2=pyhd8ed1ab_0
-  - ucsc-fasomerecords=377=h516baf0_1
-  - ucsc-fatovcf=426=ha55e18d_0
-  - ujson=5.7.0=py38h4cd09af_0
-  - ukkonen=1.0.1=py38h98b9b1b_3
-  - unicodedata2=15.0.0=py38hef030d1_0
-  - unidecode=1.3.6=pyhd8ed1ab_0
-  - uritemplate=4.1.1=pyhd8ed1ab_0
-  - url-normalize=1.4.3=pyhd8ed1ab_0
-  - urllib3=1.26.14=pyhd8ed1ab_0
-  - usher=0.5.6=h289ebe5_0
-  - validators=0.18.2=pyhd3deb0d_0
-  - vcftools=0.1.16=pl5321h6151dfb_7
-  - veracitools=0.1.3=py_0
-  - virtualenv=20.21.0=pyhd8ed1ab_0
-  - watchdog=2.2.1=py38h3ddec92_0
-  - wcmatch=8.3=pyhd8ed1ab_0
-  - wcwidth=0.2.6=pyhd8ed1ab_0
-  - webencodings=0.5.1=py_1
-  - websocket-client=1.5.1=pyhd8ed1ab_0
-  - wget=1.20.3=h52ee1ee_1
-  - wheel=0.38.4=pyhd8ed1ab_0
-  - whoosh=2.7.4=py38h50d1736_7
-  - widgetsnbextension=4.0.5=pyhd8ed1ab_0
-  - wrapt=1.14.1=py38hef030d1_1
-  - xdg=5.1.1=pyhd8ed1ab_0
-  - xopen=1.7.0=py38h50d1736_0
-  - xorg-libxau=1.0.9=h35c211d_0
-  - xorg-libxdmcp=1.1.3=h35c211d_0
-  - xz=5.2.6=h775f41a_0
-  - yacman=0.9.0=pyhd8ed1ab_0
-  - yaml=0.2.5=h0d85af4_2
-  - yarl=1.8.2=py38hef030d1_0
-  - yte=1.5.1=py38h50d1736_1
-  - zeromq=4.3.4=he49afe7_1
-  - zipp=3.12.1=pyhd8ed1ab_0
-  - zipstream-new=1.1.8=pyhd8ed1ab_0
-  - zlib=1.2.13=hfd90126_4
-  - zstandard=0.19.0=py38h7cbeef7_1
-  - zstd=1.5.2=hbc0c0cd_6
-  - pip:
-    - astroid==2.14.1
-    - bio==1.4.0
-    - biopython==1.79
-    - biothings-client==0.2.6
-    - boto==2.49.0
-    - coverage==7.1.0
-    - cram==0.7
-    - deepdiff==6.2.3
-    - dill==0.3.6
-    - envdir==1.0.1
-    - eutils==0.6.0
-    - freezegun==1.2.2
-    - ipdb==0.13.11
-    - lazy-object-proxy==1.9.0
-    - livereload==2.6.3
-    - mccabe==0.7.0
-    - mygene==3.2.2
-    - nextstrain-sphinx-theme==2022.9
-    - ordered-set==4.1.0
-    - orjson==3.8.5
-    - parsec==3.15
-    - pylint==2.16.1
-    - pytest-cov==4.0.0
-    - pytest-mock==3.10.0
-    - pyyaml==6.0
-    - rethinkdb==2.4.9
-    - smot==0.17.4
-    - sphinx-argparse==0.4.0
-    - sphinx-autobuild==2021.3.14
-    - sphinx-copybutton==0.5.1
-    - sphinx-markdown-tables==0.0.17
-    - sphinx-rtd-theme==1.2.0
-    - sphinxcontrib-jquery==2.0.0
-    - tomlkit==0.11.6
-    - tqdm==4.64.1
-    - xlrd==1.2.0
-prefix: /Users/jchang3/miniconda3/envs/nextstrain
diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
index acb6098..d765daf 100644
--- a/ingest/rules/nextclade.smk
+++ b/ingest/rules/nextclade.smk
@@ -22,7 +22,7 @@ rule nextclade_classify:
         nextclade_tsv="data/nextclade_results/nextclade.tsv",
     shell:
         """
-        nextclade run \
+        nextclade3 run \
           --input-dataset {input.dataset} \
           --output-tsv {output.nextclade_tsv} \
           --silent \
diff --git a/nextclade/rules/assemble_nextclade_dataset.smk b/nextclade/rules/assemble_nextclade_dataset.smk
index aa07085..930aa64 100644
--- a/nextclade/rules/assemble_nextclade_dataset.smk
+++ b/nextclade/rules/assemble_nextclade_dataset.smk
@@ -64,8 +64,8 @@ rule test:
         output=directory("test_out"),
     shell:
         """
-        nextclade run \
+        nextclade3 run \
             --input-dataset {input.dataset} \
             --output-all {output.output} \
             {input.sequences}
-        """
\ No newline at end of file
+        """