error? - Githubissues

hivtrace -i test.fas -a resolve -r HXB2_prrt -t .015 -m 500 -g .05 -c Traceback (most recent call last): File "/Users/opt/miniconda3/bin/hivtrace", line 8, in sys.exit(main()) File "/Users/opt/miniconda3/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 793, in main results = hivtrace( File "/Users/opt/miniconda3/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 585, in hivtrace raise subprocess.CalledProcessError( subprocess.CalledProcessError: <exception str() failed>

Dear @liamxg,

Do you have all dependencies installed?

Best, Steven

@stevenweaver how to check all of them?

Hello @stevenweaver we are getting the same error after installing everything as indicated with pip3

Do you have any suggestion?

@stevenweaver need your help.

Dear @liamxg and @AAMCgenomics,

Could ya'll please provide which version of Python you are using? There is an issue with Python 3.10 and above that I'm actively trying to resolve at the moment.

Best, Steven

Could you show the contents of pip freeze?

I've also updated hivtrace to be compatible with Python 3.10 and above with 0.7.0.

sure, here you go: pip freeze anyio==3.7.0 appnope==0.1.3 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 arrow==1.2.3 asttokens==2.2.1 attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work backcall==0.2.0 baltic==0.2.2 bcbio-gff @ file:///opt/conda/conda-bld/bcbio-gff_1678732237644/work beautifulsoup4==4.12.2 bio==1.5.9 bioext==0.20.6 biopython @ file:///Users/runner/miniforge3/conda-bld/biopython_1676639327409/work biothings-client==0.3.0 bleach==6.0.0 boltons @ file:///home/conda/feedstock_root/build_artifacts/boltons_1677499911949/work brotlipy @ file:///Users/runner/miniforge3/conda-bld/brotlipy_1666764741656/work bx-python @ file:///opt/mambaforge/envs/bioconda/conda-bld/bx-python_1690503254316/work Cartopy==0.22.0 certifi==2023.7.22 cffi @ file:///Users/runner/miniforge3/conda-bld/cffi_1671179477998/work charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1678108872112/work click==8.1.4 click-plugins==1.1.1 cligj==0.7.2 clusters==66.0.2 colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work comm==0.1.3 conda @ file:///Users/runner/miniforge3/conda-bld/conda_1694556161885/work conda-content-trust @ file:///home/conda/feedstock_root/build_artifacts/conda-content-trust_1621370699668/work conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1669907009957/work conda_package_streaming @ file:///home/conda/feedstock_root/build_artifacts/conda-package-streaming_1685101166527/work contourpy @ file:///Users/runner/miniforge3/conda-bld/contourpy_1686734082710/work convert==0.1.2 cryptography @ file:///Users/runner/miniforge3/conda-bld/cryptography-split_1681508838526/work cutadapt @ file:///opt/mambaforge/envs/bioconda/conda-bld/cutadapt_1684428436186/work cvxopt==0.0.0 cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work Cython==0.29.36 debugpy==1.6.7 decorator==5.1.1 defusedxml==0.7.1 DendroPy==4.6.1 discreteMarkovChain==0.22 distlib==0.3.6 dnaio @ file:///opt/mambaforge/envs/bioconda/conda-bld/dnaio_1694228626325/work docx==0.2.4 ete3==3.1.3 exceptiongroup==1.1.2 executing==1.2.0 fakemp==0.9.1 fastjsonschema==2.17.1 filelock==3.12.2 Fiona==1.9.4.post1 flutile==1.0.1 fonttools==4.40.0 fqdn==1.5.1 geographiclib==2.0 geopandas==0.13.2 geopy==2.3.0 gprofiler-official==1.0.0 helpers==0.2.0 hivclustering==1.6.7 hivtrace==0.6.3 hppy==0.9.9 hyphy-python==0.1.11 idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1663625384323/work importlib==1.0.4 importlib-metadata==6.7.0 importlib-resources==5.12.0 ipykernel==6.24.0 ipython==8.14.0 ipython-genutils==0.2.0 isal @ file:///Users/runner/miniforge3/conda-bld/python-isal_1690179250909/work isodate @ file:///home/conda/feedstock_root/build_artifacts/isodate_1639582763789/work isoduration==20.11.0 jedi==0.18.2 Jinja2==3.1.2 joblib==1.3.1 jsonpatch @ file:///home/conda/feedstock_root/build_artifacts/jsonpatch_1632759296524/work jsonpointer==2.0 jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema_1614815863336/work jupyter-events==0.6.3 jupyter_client==8.3.0 jupyter_core==5.3.1 jupyter_server==2.7.0 jupyter_server_terminals==0.4.4 jupyterlab-pygments==0.2.2 jupyterlab-widgets==3.0.7 kaleido==0.2.1 kiwisolver @ file:///Users/runner/miniforge3/conda-bld/kiwisolver_1666805987080/work libmambapy @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/libmambapy lxml==4.9.3 mamba @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/mamba MarkupSafe==2.1.3 matplotlib @ file:///Users/runner/miniforge3/conda-bld/matplotlib-suite_1678135704702/work matplotlib-inline==0.1.6 mistune==3.0.1 munkres==1.1.4 mygene==3.2.2 nbclassic==1.0.0 nbclient==0.8.0 nbconvert==7.6.0 nbformat==5.9.0 nest-asyncio==1.5.6 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work nextstrain-augur @ file:///opt/conda/conda-bld/augur_1690832453867/work notebook==6.5.4 notebook_shim==0.2.3 numpy @ file:///Users/runner/miniforge3/conda-bld/numpy_1691056329545/work octofludb==1.0.1 overrides==7.3.1 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work pandas==1.5.3 pandas-flavor==0.6.0 pandocfilters==1.5.0 parsec==3.15 parso==0.8.3 pdf2image==1.16.3 pexpect==4.8.0 pgraphdb==1.0.1 phylo-treetime @ file:///opt/conda/conda-bld/treetime_1685025734035/work phylopandas==0.8.0 pickleshare==0.7.5 Pillow @ file:///Users/runner/miniforge3/conda-bld/pillow_1688255956759/work platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1690813113769/work plotly==5.15.0 pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1667232663820/work pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1679580333621/work prometheus-client==0.17.0 prompt-toolkit==3.0.38 psutil==5.9.5 ptyprocess==0.7.0 pure-eval==0.2.2 pycosat @ file:///Users/runner/miniforge3/conda-bld/pycosat_1666836599375/work pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work pyfastx @ file:///Users/runner/bioconda/conda-bld/pyfastx_1645701556855/work Pygments==2.15.1 pygtrie==2.5.0 pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1685514481738/work pyparsing==3.0.9 pyproj==3.6.0 pyrsistent @ file:///Users/runner/miniforge3/conda-bld/pyrsistent_1672681525787/work pysam==0.21.0 pyshp==2.3.1 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-json-logger==2.0.7 pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work Pyvolve==1.1.0 PyYAML==6.0 pyzmq==25.1.0 QtPy==2.3.1 rdflib==6.3.2 requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 ruamel-yaml-conda @ file:///Users/runner/miniforge3/conda-bld/ruamel_yaml_1666820002387/work ruamel.yaml @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml_1686994012442/work ruamel.yaml.clib @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml.clib_1670412931817/work scipy==1.10.1 seaborn==0.12.2 Send2Trash==1.8.2 seqmagick==0.8.6 shapely==2.0.1 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work smallBixTools==0.0.34 smof==2.22.2 sniffio==1.3.0 soupsieve==2.4.1 SPARQLWrapper==2.0.0 stack-data==0.6.2 tenacity==8.2.2 termcolor==2.3.0 terminado==0.17.1 tinycss2==1.2.1 toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work tornado==6.3.2 tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1677948868469/work traitlets==5.9.0 treesap==1.0.10 treeswift==1.1.37 typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1688315532570/work tzdata==2023.3 unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1667240005777/work uri-template==1.3.0 urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1686156552494/work virtualenv==20.23.1 wcwidth==0.2.6 webcolors==1.13 webencodings==0.5.1 websocket-client==1.6.1 widgetsnbextension==4.0.7 xarray==2023.8.0 xlrd==2.0.1 xopen @ file:///Users/runner/miniforge3/conda-bld/xopen_1683032209719/work zipp==3.15.0 zstandard==0.19.0

Thank you @stevenweaver for your fast fix, however, I am getting another error code:

hivtrace -i HIV20_23ALNclean.fasta -a resolve -r HXB2_prrt -t .015 -m 500 -g .05 -c

Traceback (most recent call last): File "/opt/conda/bin/hivtrace", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 793, in main results = hivtrace( File "/opt/conda/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 704, in hivtrace annotate_lanl(LANL_OUTPUT_CLUSTER_JSON, LANL_FASTA) File "/opt/conda/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 252, in annotate_lanl node_ids = set([n["id"] for n in nodes]) File "/opt/conda/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 252, in node_ids = set([n["id"] for n in nodes]) TypeError: string indices must be integers

Dear @stevenweaver, this is the pip freeze output: aiohttp @ file:///home/conda/feedstock_root/build_artifacts/aiohttp_1637087032947/work aiosignal @ file:///home/conda/feedstock_root/build_artifacts/aiosignal_1636093929600/work alembic @ file:///home/conda/feedstock_root/build_artifacts/alembic_1622150326904/work altair==4.1.0 anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1626998561214/work/dist appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1603108395799/work argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1610522573621/work async-generator==1.10 async-timeout @ file:///home/conda/feedstock_root/build_artifacts/async-timeout_1640026696943/work attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1620387926260/work Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1619719576210/work backcall @ file:///home/conda/feedstock_root/build_artifacts/backcall_1592338393461/work backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1618230623929/work beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1601745390275/work bioext==0.21.0 biopython @ file:///home/conda/feedstock_root/build_artifacts/biopython_1636053343550/work bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1628022386512/work blinker==1.4 bokeh @ file:///home/conda/feedstock_root/build_artifacts/bokeh_1625756941579/work Bottleneck @ file:///home/conda/feedstock_root/build_artifacts/bottleneck_1611195604063/work brotlipy==0.7.0 cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work certifi==2021.10.8 certipy==0.1.3 cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1625835307225/work chardet @ file:///home/conda/feedstock_root/build_artifacts/chardet_1610093492116/work charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1626371162869/work click @ file:///home/conda/feedstock_root/build_artifacts/click_1621503702258/work cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1598400192773/work colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1602866480661/work conda==4.10.3 conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1618231390031/work cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1616851485986/work cycler==0.10.0 Cython @ file:///home/conda/feedstock_root/build_artifacts/cython_1626221483532/work cytoolz==0.11.0 dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1627691555247/work debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1627074853231/work decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1621187651333/work defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work dill @ file:///home/conda/feedstock_root/build_artifacts/dill_1623610058511/work distributed @ file:///home/conda/feedstock_root/build_artifacts/distributed_1627703868845/work entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1605121927639/work/dist/entrypoints-0.3-py2.py3-none-any.whl fakemp==0.9.1 frozenlist @ file:///home/conda/feedstock_root/build_artifacts/frozenlist_1636286801527/work fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1626188337504/work gmpy2==2.1.0b5 greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1628272056983/work h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1624405615966/work HeapDict==1.0.1 hivclustering==1.6.8 hivtrace==0.7.0 hppy==0.9.9 hyphy-python==0.1.11 idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1609836280497/work imagecodecs-lite @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs-lite_1636571354112/work imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1594044661732/work importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1627748919761/work ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1626728141143/work/dist/ipykernel-6.0.3-py3-none-any.whl ipympl @ file:///home/conda/feedstock_root/build_artifacts/ipympl_1616486184438/work ipyparallel @ file:///home/conda/feedstock_root/build_artifacts/ipyparallel_1638429161446/work ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1627911646738/work ipython-genutils==0.2.0 ipywidgets @ file:///home/conda/feedstock_root/build_artifacts/ipywidgets_1609995587151/work jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1610146787869/work Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1621419064915/work joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1612898609989/work json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1600692310011/work jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema_1614815863336/work jupyter-client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1615693636836/work jupyter-core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1612125253154/work jupyter-resource-usage==0.6.1 jupyter-server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1627951139499/work jupyter-server-proxy @ file:///home/conda/feedstock_root/build_artifacts/jupyter-server-proxy_1638279709332/work jupyter-telemetry @ file:///home/conda/feedstock_root/build_artifacts/jupyter_telemetry_1605173804246/work jupyterhub @ file:///home/conda/feedstock_root/build_artifacts/jupyterhub-feedstock_1621023455565/work jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1621368934875/work jupyterlab-nvdashboard==0.6.0 jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1601375948261/work jupyterlab-server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server_1628008856752/work jupyterlab-system-monitor==0.8.0 jupyterlab-topbar==0.6.1 jupyterlab-widgets @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_widgets_1609173350931/work kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1610099772044/work lckr-jupyterlab-variableinspector==3.0.9 llvmlite==0.36.0 locket==0.2.0 Mako @ file:///home/conda/feedstock_root/build_artifacts/mako_1610659158978/work mamba @ file:///home/conda/feedstock_root/build_artifacts/mamba_1626467930043/work MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1621455668600/work matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1620506038354/work matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1618935594181/work mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1624941317779/work mock @ file:///home/conda/feedstock_root/build_artifacts/mock_1610147502688/work mpmath @ file:///home/conda/feedstock_root/build_artifacts/mpmath_1612895720168/work msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1610121709200/work multidict @ file:///home/conda/feedstock_root/build_artifacts/multidict_1636019096528/work nb-conda @ file:///home/conda/feedstock_root/build_artifacts/nb_conda_1611345543444/work nb-conda-kernels @ file:///home/conda/feedstock_root/build_artifacts/nb_conda_kernels_1636999988300/work nbclassic @ file:///home/conda/feedstock_root/build_artifacts/nbclassic_1621947328608/work nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1614336084111/work nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert_1624472721108/work nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1617383142101/work nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1617163391303/work networkx==2.3 notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1621259862661/work numba @ file:///home/conda/feedstock_root/build_artifacts/numba_1623568543876/work numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1614971350662/work numpy==1.22.4 oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1622563202229/work olefile @ file:///home/conda/feedstock_root/build_artifacts/olefile_1602866521163/work packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1625323647219/work pamela==1.0.0 pandas==1.3.5 pandocfilters==1.4.2 parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1617148930513/work partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1617910651905/work patsy==0.5.1 pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1602535608087/work pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1625677815963/work pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1623218528920/work prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1622586138406/work prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1623977816122/work protobuf==3.17.2 psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1610127095958/work ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl PyAAVF==0.1.0 pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1610094799048/work pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1593275161868/work pycurl==7.43.0.6 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1620245170812/work PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1619620644068/work pynvml==11.4.1 pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1608055815057/work pyparsing==2.4.7 pyrsistent @ file:///home/conda/feedstock_root/build_artifacts/pyrsistent_1610146801554/work pysam==0.17.0 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1610291451001/work python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-editor==1.0.4 python-json-logger @ file:///home/conda/feedstock_root/build_artifacts/python-json-logger_1602545356084/work pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1612179539967/work PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1607290805778/work PyYAML==5.4.1 pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1628232904311/work quasitools==0.7.0 requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1626393743643/work requests-unixsocket==0.2.0 rpy2 @ file:///home/conda/feedstock_root/build_artifacts/rpy2_1622826795397/work ruamel-yaml-conda @ file:///home/conda/feedstock_root/build_artifacts/ruamel_yaml_1611943432947/work ruamel.yaml @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml_1624567370519/work ruamel.yaml.clib @ file:///home/conda/feedstock_root/build_artifacts/ruamel.yaml.clib_1610146844134/work scikit-image==0.18.2 scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1628431996847/work scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1628206395139/work seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1611834504644/work Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1628511208346/work simpervisor @ file:///home/conda/feedstock_root/build_artifacts/simpervisor_1609865618711/work simplegeneric==0.8.1 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1610318319523/work sortedcontainers @ file:///home/conda/feedstock_root/build_artifacts/sortedcontainers_1621217038088/work soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1597680516047/work SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1626924678720/work statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1612273598845/work sympy @ file:///home/conda/feedstock_root/build_artifacts/sympy_1618015358275/work tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1610156075642/work tblib @ file:///home/conda/feedstock_root/build_artifacts/tblib_1616261298899/work terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1623365326093/work testpath @ file:///home/conda/feedstock_root/build_artifacts/testpath_1621261527237/work threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1626092076920/work tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1591280222285/work toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1600973991856/work tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1610094708661/work tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1627689047698/work traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1602771532708/work typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1638334978229/work tzlocal @ file:///home/conda/feedstock_root/build_artifacts/tzlocal_1588939190034/work urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1624634538755/work wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1600965781394/work webencodings==0.5.1 websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1610127648202/work widgetsnbextension @ file:///home/conda/feedstock_root/build_artifacts/widgetsnbextension_1605475529901/work xlrd @ file:///home/conda/feedstock_root/build_artifacts/xlrd_1610224409810/work yarl @ file:///home/conda/feedstock_root/build_artifacts/yarl_1636046810561/work zict==2.0.0 zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1625284368454/work

sure, here you go: pip freeze anyio==3.7.0 appnope==0.1.3 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 arrow==1.2.3 asttokens==2.2.1 attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work backcall==0.2.0 baltic==0.2.2 bcbio-gff @ file:///opt/conda/conda-bld/bcbio-gff_1678732237644/work beautifulsoup4==4.12.2 bio==1.5.9 bioext==0.20.6 biopython @ file:///Users/runner/miniforge3/conda-bld/biopython_1676639327409/work biothings-client==0.3.0 bleach==6.0.0 boltons @ file:///home/conda/feedstock_root/build_artifacts/boltons_1677499911949/work brotlipy @ file:///Users/runner/miniforge3/conda-bld/brotlipy_1666764741656/work bx-python @ file:///opt/mambaforge/envs/bioconda/conda-bld/bx-python_1690503254316/work Cartopy==0.22.0 certifi==2023.7.22 cffi @ file:///Users/runner/miniforge3/conda-bld/cffi_1671179477998/work charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1678108872112/work click==8.1.4 click-plugins==1.1.1 cligj==0.7.2 clusters==66.0.2 colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work comm==0.1.3 conda @ file:///Users/runner/miniforge3/conda-bld/conda_1694556161885/work conda-content-trust @ file:///home/conda/feedstock_root/build_artifacts/conda-content-trust_1621370699668/work conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1669907009957/work conda_package_streaming @ file:///home/conda/feedstock_root/build_artifacts/conda-package-streaming_1685101166527/work contourpy @ file:///Users/runner/miniforge3/conda-bld/contourpy_1686734082710/work convert==0.1.2 cryptography @ file:///Users/runner/miniforge3/conda-bld/cryptography-split_1681508838526/work cutadapt @ file:///opt/mambaforge/envs/bioconda/conda-bld/cutadapt_1684428436186/work cvxopt==0.0.0 cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work Cython==0.29.36 debugpy==1.6.7 decorator==5.1.1 defusedxml==0.7.1 DendroPy==4.6.1 discreteMarkovChain==0.22 distlib==0.3.6 dnaio @ file:///opt/mambaforge/envs/bioconda/conda-bld/dnaio_1694228626325/work docx==0.2.4 ete3==3.1.3 exceptiongroup==1.1.2 executing==1.2.0 fakemp==0.9.1 fastjsonschema==2.17.1 filelock==3.12.2 Fiona==1.9.4.post1 flutile==1.0.1 fonttools==4.40.0 fqdn==1.5.1 geographiclib==2.0 geopandas==0.13.2 geopy==2.3.0 gprofiler-official==1.0.0 helpers==0.2.0 hivclustering==1.6.7 hivtrace==0.6.3 hppy==0.9.9 hyphy-python==0.1.11 idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1663625384323/work importlib==1.0.4 importlib-metadata==6.7.0 importlib-resources==5.12.0 ipykernel==6.24.0 ipython==8.14.0 ipython-genutils==0.2.0 isal @ file:///Users/runner/miniforge3/conda-bld/python-isal_1690179250909/work isodate @ file:///home/conda/feedstock_root/build_artifacts/isodate_1639582763789/work isoduration==20.11.0 jedi==0.18.2 Jinja2==3.1.2 joblib==1.3.1 jsonpatch @ file:///home/conda/feedstock_root/build_artifacts/jsonpatch_1632759296524/work jsonpointer==2.0 jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema_1614815863336/work jupyter-events==0.6.3 jupyter_client==8.3.0 jupyter_core==5.3.1 jupyter_server==2.7.0 jupyter_server_terminals==0.4.4 jupyterlab-pygments==0.2.2 jupyterlab-widgets==3.0.7 kaleido==0.2.1 kiwisolver @ file:///Users/runner/miniforge3/conda-bld/kiwisolver_1666805987080/work libmambapy @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/libmambapy lxml==4.9.3 mamba @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/mamba MarkupSafe==2.1.3 matplotlib @ file:///Users/runner/miniforge3/conda-bld/matplotlib-suite_1678135704702/work matplotlib-inline==0.1.6 mistune==3.0.1 munkres==1.1.4 mygene==3.2.2 nbclassic==1.0.0 nbclient==0.8.0 nbconvert==7.6.0 nbformat==5.9.0 nest-asyncio==1.5.6 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work nextstrain-augur @ file:///opt/conda/conda-bld/augur_1690832453867/work notebook==6.5.4 notebook_shim==0.2.3 numpy @ file:///Users/runner/miniforge3/conda-bld/numpy_1691056329545/work octofludb==1.0.1 overrides==7.3.1 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work pandas==1.5.3 pandas-flavor==0.6.0 pandocfilters==1.5.0 parsec==3.15 parso==0.8.3 pdf2image==1.16.3 pexpect==4.8.0 pgraphdb==1.0.1 phylo-treetime @ file:///opt/conda/conda-bld/treetime_1685025734035/work phylopandas==0.8.0 pickleshare==0.7.5 Pillow @ file:///Users/runner/miniforge3/conda-bld/pillow_1688255956759/work platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1690813113769/work plotly==5.15.0 pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1667232663820/work pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1679580333621/work prometheus-client==0.17.0 prompt-toolkit==3.0.38 psutil==5.9.5 ptyprocess==0.7.0 pure-eval==0.2.2 pycosat @ file:///Users/runner/miniforge3/conda-bld/pycosat_1666836599375/work pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work pyfastx @ file:///Users/runner/bioconda/conda-bld/pyfastx_1645701556855/work Pygments==2.15.1 pygtrie==2.5.0 pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1685514481738/work pyparsing==3.0.9 pyproj==3.6.0 pyrsistent @ file:///Users/runner/miniforge3/conda-bld/pyrsistent_1672681525787/work pysam==0.21.0 pyshp==2.3.1 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-json-logger==2.0.7 pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work Pyvolve==1.1.0 PyYAML==6.0 pyzmq==25.1.0 QtPy==2.3.1 rdflib==6.3.2 requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 ruamel-yaml-conda @ file:///Users/runner/miniforge3/conda-bld/ruamel_yaml_1666820002387/work ruamel.yaml @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml_1686994012442/work ruamel.yaml.clib @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml.clib_1670412931817/work scipy==1.10.1 seaborn==0.12.2 Send2Trash==1.8.2 seqmagick==0.8.6 shapely==2.0.1 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work smallBixTools==0.0.34 smof==2.22.2 sniffio==1.3.0 soupsieve==2.4.1 SPARQLWrapper==2.0.0 stack-data==0.6.2 tenacity==8.2.2 termcolor==2.3.0 terminado==0.17.1 tinycss2==1.2.1 toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work tornado==6.3.2 tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1677948868469/work traitlets==5.9.0 treesap==1.0.10 treeswift==1.1.37 typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1688315532570/work tzdata==2023.3 unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1667240005777/work uri-template==1.3.0 urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1686156552494/work virtualenv==20.23.1 wcwidth==0.2.6 webcolors==1.13 webencodings==0.5.1 websocket-client==1.6.1 widgetsnbextension==4.0.7 xarray==2023.8.0 xlrd==2.0.1 xopen @ file:///Users/runner/miniforge3/conda-bld/xopen_1683032209719/work zipp==3.15.0 zstandard==0.19.0

Would it be possible to try without the -c parameter?

sure, here you go: pip freeze anyio==3.7.0 appnope==0.1.3 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 arrow==1.2.3 asttokens==2.2.1 attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1683424013410/work backcall==0.2.0 baltic==0.2.2 bcbio-gff @ file:///opt/conda/conda-bld/bcbio-gff_1678732237644/work beautifulsoup4==4.12.2 bio==1.5.9 bioext==0.20.6 biopython @ file:///Users/runner/miniforge3/conda-bld/biopython_1676639327409/work biothings-client==0.3.0 bleach==6.0.0 boltons @ file:///home/conda/feedstock_root/build_artifacts/boltons_1677499911949/work brotlipy @ file:///Users/runner/miniforge3/conda-bld/brotlipy_1666764741656/work bx-python @ file:///opt/mambaforge/envs/bioconda/conda-bld/bx-python_1690503254316/work Cartopy==0.22.0 certifi==2023.7.22 cffi @ file:///Users/runner/miniforge3/conda-bld/cffi_1671179477998/work charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1678108872112/work click==8.1.4 click-plugins==1.1.1 cligj==0.7.2 clusters==66.0.2 colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work comm==0.1.3 conda @ file:///Users/runner/miniforge3/conda-bld/conda_1694556161885/work conda-content-trust @ file:///home/conda/feedstock_root/build_artifacts/conda-content-trust_1621370699668/work conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1669907009957/work conda_package_streaming @ file:///home/conda/feedstock_root/build_artifacts/conda-package-streaming_1685101166527/work contourpy @ file:///Users/runner/miniforge3/conda-bld/contourpy_1686734082710/work convert==0.1.2 cryptography @ file:///Users/runner/miniforge3/conda-bld/cryptography-split_1681508838526/work cutadapt @ file:///opt/mambaforge/envs/bioconda/conda-bld/cutadapt_1684428436186/work cvxopt==0.0.0 cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work Cython==0.29.36 debugpy==1.6.7 decorator==5.1.1 defusedxml==0.7.1 DendroPy==4.6.1 discreteMarkovChain==0.22 distlib==0.3.6 dnaio @ file:///opt/mambaforge/envs/bioconda/conda-bld/dnaio_1694228626325/work docx==0.2.4 ete3==3.1.3 exceptiongroup==1.1.2 executing==1.2.0 fakemp==0.9.1 fastjsonschema==2.17.1 filelock==3.12.2 Fiona==1.9.4.post1 flutile==1.0.1 fonttools==4.40.0 fqdn==1.5.1 geographiclib==2.0 geopandas==0.13.2 geopy==2.3.0 gprofiler-official==1.0.0 helpers==0.2.0 hivclustering==1.6.7 hivtrace==0.6.3 hppy==0.9.9 hyphy-python==0.1.11 idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1663625384323/work importlib==1.0.4 importlib-metadata==6.7.0 importlib-resources==5.12.0 ipykernel==6.24.0 ipython==8.14.0 ipython-genutils==0.2.0 isal @ file:///Users/runner/miniforge3/conda-bld/python-isal_1690179250909/work isodate @ file:///home/conda/feedstock_root/build_artifacts/isodate_1639582763789/work isoduration==20.11.0 jedi==0.18.2 Jinja2==3.1.2 joblib==1.3.1 jsonpatch @ file:///home/conda/feedstock_root/build_artifacts/jsonpatch_1632759296524/work jsonpointer==2.0 jsonschema @ file:///home/conda/feedstock_root/build_artifacts/jsonschema_1614815863336/work jupyter-events==0.6.3 jupyter_client==8.3.0 jupyter_core==5.3.1 jupyter_server==2.7.0 jupyter_server_terminals==0.4.4 jupyterlab-pygments==0.2.2 jupyterlab-widgets==3.0.7 kaleido==0.2.1 kiwisolver @ file:///Users/runner/miniforge3/conda-bld/kiwisolver_1666805987080/work libmambapy @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/libmambapy lxml==4.9.3 mamba @ file:///Users/runner/miniforge3/conda-bld/mamba-split_1689261353646/work/mamba MarkupSafe==2.1.3 matplotlib @ file:///Users/runner/miniforge3/conda-bld/matplotlib-suite_1678135704702/work matplotlib-inline==0.1.6 mistune==3.0.1 munkres==1.1.4 mygene==3.2.2 nbclassic==1.0.0 nbclient==0.8.0 nbconvert==7.6.0 nbformat==5.9.0 nest-asyncio==1.5.6 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work nextstrain-augur @ file:///opt/conda/conda-bld/augur_1690832453867/work notebook==6.5.4 notebook_shim==0.2.3 numpy @ file:///Users/runner/miniforge3/conda-bld/numpy_1691056329545/work octofludb==1.0.1 overrides==7.3.1 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1681337016113/work pandas==1.5.3 pandas-flavor==0.6.0 pandocfilters==1.5.0 parsec==3.15 parso==0.8.3 pdf2image==1.16.3 pexpect==4.8.0 pgraphdb==1.0.1 phylo-treetime @ file:///opt/conda/conda-bld/treetime_1685025734035/work phylopandas==0.8.0 pickleshare==0.7.5 Pillow @ file:///Users/runner/miniforge3/conda-bld/pillow_1688255956759/work platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1690813113769/work plotly==5.15.0 pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1667232663820/work pooch @ file:///home/conda/feedstock_root/build_artifacts/pooch_1679580333621/work prometheus-client==0.17.0 prompt-toolkit==3.0.38 psutil==5.9.5 ptyprocess==0.7.0 pure-eval==0.2.2 pycosat @ file:///Users/runner/miniforge3/conda-bld/pycosat_1666836599375/work pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work pyfastx @ file:///Users/runner/bioconda/conda-bld/pyfastx_1645701556855/work Pygments==2.15.1 pygtrie==2.5.0 pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1685514481738/work pyparsing==3.0.9 pyproj==3.6.0 pyrsistent @ file:///Users/runner/miniforge3/conda-bld/pyrsistent_1672681525787/work pysam==0.21.0 pyshp==2.3.1 PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-json-logger==2.0.7 pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work Pyvolve==1.1.0 PyYAML==6.0 pyzmq==25.1.0 QtPy==2.3.1 rdflib==6.3.2 requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 ruamel-yaml-conda @ file:///Users/runner/miniforge3/conda-bld/ruamel_yaml_1666820002387/work ruamel.yaml @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml_1686994012442/work ruamel.yaml.clib @ file:///Users/runner/miniforge3/conda-bld/ruamel.yaml.clib_1670412931817/work scipy==1.10.1 seaborn==0.12.2 Send2Trash==1.8.2 seqmagick==0.8.6 shapely==2.0.1 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work smallBixTools==0.0.34 smof==2.22.2 sniffio==1.3.0 soupsieve==2.4.1 SPARQLWrapper==2.0.0 stack-data==0.6.2 tenacity==8.2.2 termcolor==2.3.0 terminado==0.17.1 tinycss2==1.2.1 toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work tornado==6.3.2 tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1677948868469/work traitlets==5.9.0 treesap==1.0.10 treeswift==1.1.37 typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1688315532570/work tzdata==2023.3 unicodedata2 @ file:///Users/runner/miniforge3/conda-bld/unicodedata2_1667240005777/work uri-template==1.3.0 urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1686156552494/work virtualenv==20.23.1 wcwidth==0.2.6 webcolors==1.13 webencodings==0.5.1 websocket-client==1.6.1 widgetsnbextension==4.0.7 xarray==2023.8.0 xlrd==2.0.1 xopen @ file:///Users/runner/miniforge3/conda-bld/xopen_1683032209719/work zipp==3.15.0 zstandard==0.19.0

Would it be possible to update hivtrace to 0.7.0 and try again?

For me works ver. 0.7.0 and without -c option.

Thank you so much for your fast reply, we will use the tool in a workshop and now we are sure will work in our systems.

Thank you again!!!

how to update to version 0.70? @stevenweaver @AAMCgenomics

pip install -U hivtrace should do the trick.

@stevenweaver thanks, need I update python to python 3.10?

@AAMCgenomics can you share your workshop with me, I want to know more, thanks.

any update with -c ?

veg / hivtrace

error? #85