Authentication plugin 'mysql_native_password' cannot be loaded

[nick-youngblut]

What happened?

code:

gget.search(["gene_name1", "gene_name2"], species="homo_sapiens")

The error:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[34], line 23
     13     return(results)
     15     # Create a mapping from gene names to Ensembl IDs
     16     #mapping = {gene: data["ensembl_id"] for gene, data in results.items() if data}
     17 
   (...)
     20 
     21     #return converted_genes
---> 23 get_ensembl_index(df["var_id"][:5])

Cell In[34], line 12, in get_ensembl_index(genes, species)
      6 gene_names = [g for g in genes if not g.startswith("ENS")]
      8 #if not gene_names:
      9 #    return {g: g for g in genes}  # If all are already Ensembl IDs, return as is
     10 
     11 # Query Ensembl using gget
---> 12 results = gget.search(gene_names, species=species)
     13 return(results)

File ~/miniforge3/envs/tiledb/lib/python3.12/site-packages/gget/gget_search.py:233, in search(searchwords, species, release, id_type, seqtype, andor, limit, wrap_text, json, save, verbose)
    225         raise RuntimeError(
    226             f"""
    227             The Ensembl server returned the following error: {str(last_exception)}.
   (...)
    230             """
    231         )
    232     else:
--> 233         raise RuntimeError(
    234             f"The Ensembl server returned the following error: {str(last_exception)}"
    235         )
    237 ## Clean up list of searchwords
    238 # If single searchword passed as string, convert to list
    239 if type(searchwords) == str:

RuntimeError: The Ensembl server returned the following error: 2059 (HY000): Authentication plugin 'mysql_native_password' cannot be loaded: /usr/lib/mysql/plugin/mysql_native_password.so: cannot open shared object file: No such file or directory

gget version

0.29.0

Entire conda env:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiobotocore               2.19.0                   pypi_0    pypi
aiohappyeyeballs          2.4.4              pyhd8ed1ab_1    conda-forge
aiohttp                   3.11.11         py312h178313f_0    conda-forge
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.2              pyhd8ed1ab_0    conda-forge
anndata                   0.11.3             pyhd8ed1ab_0    conda-forge
array-api-compat          1.10.0             pyhd8ed1ab_0    conda-forge
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
attrs                     25.1.0             pyh71513ae_0    conda-forge
aws-c-auth                0.8.1                h205f482_0    conda-forge
aws-c-cal                 0.8.1                h1a47875_3    conda-forge
aws-c-common              0.10.6               hb9d3cd8_0    conda-forge
aws-c-compression         0.3.0                h4e1184b_5    conda-forge
aws-c-event-stream        0.5.0               h7959bf6_11    conda-forge
aws-c-http                0.9.2                hefd7a92_4    conda-forge
aws-c-io                  0.15.3               h173a860_6    conda-forge
aws-c-mqtt                0.11.0              h11f4f37_12    conda-forge
aws-c-s3                  0.7.9                he1b24dc_1    conda-forge
aws-c-sdkutils            0.2.2                h4e1184b_0    conda-forge
aws-checksums             0.2.2                h4e1184b_4    conda-forge
aws-crt-cpp               0.29.9               he0e7f3f_2    conda-forge
aws-sdk-cpp               1.11.489             h4d475cb_0    conda-forge
azure-core-cpp            1.14.0               h5cfcd09_0    conda-forge
azure-identity-cpp        1.10.0               h113e628_0    conda-forge
azure-storage-blobs-cpp   12.13.0              h3cf044e_1    conda-forge
azure-storage-common-cpp  12.8.0               h736e048_1    conda-forge
azure-storage-files-datalake-cpp 12.12.0              ha633028_1    conda-forge
beautifulsoup4            4.13.3             pyha770c72_0    conda-forge
botocore                  1.36.3                   pypi_0    pypi
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0           py312h2ec8cdc_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.4               hb9d3cd8_0    conda-forge
ca-certificates           2025.1.31            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.5.1              pyhd8ed1ab_0    conda-forge
capnproto                 1.0.2                h766bdaa_3    conda-forge
cellxgene-census          1.16.2                   pypi_0    pypi
certifi                   2024.12.14         pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312h06ac9bb_0    conda-forge
charset-normalizer        3.4.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.2              pyhd8ed1ab_1    conda-forge
contourpy                 1.3.1           py312h68727a3_0    conda-forge
cryptography              44.0.0          py312hda17c39_1    conda-forge
cycler                    0.12.1             pyhd8ed1ab_1    conda-forge
cyrus-sasl                2.1.27               h54b06d7_7    conda-forge
debugpy                   1.8.12          py312h2ec8cdc_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
fmt                       11.0.2               h434a139_0    conda-forge
fonttools                 4.55.6          py312h178313f_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
frozenlist                1.5.0           py312h178313f_1    conda-forge
fsspec                    2025.2.0                 pypi_0    pypi
geos                      3.13.0               h5888daf_0    conda-forge
gflags                    2.2.2             h5888daf_1005    conda-forge
gget                      0.29.0             pyh29332c3_0    conda-forge
glog                      0.7.1                hbabe93e_0    conda-forge
google-api-core           2.24.0             pyhd8ed1ab_0    conda-forge
google-api-core-grpc      2.24.0               hd8ed1ab_0    conda-forge
google-auth               2.38.0             pyhd8ed1ab_0    conda-forge
google-cloud-secret-manager 2.22.1             pyhd8ed1ab_0    conda-forge
googleapis-common-protos  1.66.0             pyhff2d567_0    conda-forge
googleapis-common-protos-grpc 1.66.0             pyhff2d567_0    conda-forge
grpc-google-iam-v1        0.14.0             pyhd8ed1ab_0    conda-forge
grpcio                    1.67.1          py312hacea422_1    conda-forge
grpcio-status             1.67.1             pyhd8ed1ab_1    conda-forge
h2                        4.1.0              pyhd8ed1ab_1    conda-forge
h5py                      3.12.1          nompi_py312hd203070_103    conda-forge
hdf5                      1.14.4          nompi_h2d575fe_105    conda-forge
hpack                     4.1.0              pyhd8ed1ab_0    conda-forge
hyperframe                6.1.0              pyhd8ed1ab_0    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
importlib-metadata        8.6.1              pyha770c72_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.31.0             pyh707e725_0    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_1    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.4.2              pyhd8ed1ab_1    conda-forge
jupyter_client            8.6.3              pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.8           py312h84d6215_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
legacy-api-wrap           1.4.1              pyhd8ed1ab_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20240722.0      cxx17_hbbce691_4    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libarrow                  19.0.0           h00a82cf_8_cpu    conda-forge
libarrow-acero            19.0.0           hcb10f89_8_cpu    conda-forge
libarrow-dataset          19.0.0           hcb10f89_8_cpu    conda-forge
libarrow-substrait        19.0.0           h08228c5_8_cpu    conda-forge
libblas                   3.9.0           26_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcblas                  3.9.0           26_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   8.11.1               h332b0f4_0    conda-forge
libdeflate                1.23                 h4ddbbb0_0    conda-forge
libedit                   3.1.20240808    pl5321h7949ede_0    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libgoogle-cloud           2.34.0               h2b5623c_0    conda-forge
libgoogle-cloud-storage   2.34.0               h0121fbd_0    conda-forge
libgrpc                   1.67.1               h25350d4_1    conda-forge
libhwloc                  2.11.2          default_h0d58e46_1001    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           26_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
liblzma                   5.6.3                hb9d3cd8_1    conda-forge
libnghttp2                1.64.0               h161d5f1_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libntlm                   1.8                  hb9d3cd8_0    conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libopentelemetry-cpp      1.18.0               hfcad708_1    conda-forge
libopentelemetry-cpp-headers 1.18.0               ha770c72_1    conda-forge
libparquet                19.0.0           h081d1f1_8_cpu    conda-forge
libpng                    1.6.46               h943b412_0    conda-forge
libpq                     17.2                 h3b95a9b_1    conda-forge
libprotobuf               5.28.3               h6128344_1    conda-forge
libre2-11                 2024.07.02           hbbce691_2    conda-forge
libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsqlite                 3.48.0               hee588c1_1    conda-forge
libssh2                   1.11.1               hf672d98_0    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libthrift                 0.21.0               h0e7cc3e_0    conda-forge
libtiff                   4.7.0                hd9ff511_3    conda-forge
libtiledbsoma             1.15.4               h18cd297_0    conda-forge
libutf8proc               2.10.0               h4c51ac1_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.5.0                h851e524_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.13.5               h8d12d68_1    conda-forge
libxslt                   1.1.39               h76b75d6_0    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
llvmlite                  0.43.0          py312h374181b_1    conda-forge
lxml                      5.3.1           py312he28fd5a_0    conda-forge
lz4-c                     1.10.0               h5888daf_1    conda-forge
matplotlib-base           3.10.0          py312hd3ec401_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_1    conda-forge
mizani                    0.13.1             pyhd8ed1ab_0    conda-forge
multidict                 6.1.0           py312h178313f_2    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              9.0.1                h266115a_4    conda-forge
mysql-connector-python    9.0.0           py312h374181b_1    conda-forge
mysql-libs                9.0.1                he0572af_4    conda-forge
natsort                   8.4.0              pyh29332c3_1    conda-forge
ncurses                   6.5                  h2d0b736_2    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_1    conda-forge
networkx                  3.4.2              pyh267e887_2    conda-forge
nlohmann_json             3.11.3               he02047a_1    conda-forge
numba                     0.60.0          py312h83e6fd3_0    conda-forge
numpy                     1.26.4                   pypi_0    pypi
openjpeg                  2.5.3                h5fbd93e_0    conda-forge
openldap                  2.6.9                he970967_0    conda-forge
openssl                   3.4.1                h7b32b05_0    conda-forge
orc                       2.0.3                h12ee42a_2    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
pandas                    2.2.3           py312hf9745cd_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_1    conda-forge
patsy                     1.0.1              pyhd8ed1ab_1    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pickleshare               0.7.5           pyhd8ed1ab_1004    conda-forge
pillow                    11.1.0          py312h80c1187_0    conda-forge
pip                       25.0               pyh8b19718_0    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_1    conda-forge
plotnine                  0.14.5             pyhd8ed1ab_0    conda-forge
prometheus-cpp            1.3.0                ha5d0236_0    conda-forge
prompt-toolkit            3.0.50             pyha770c72_0    conda-forge
propcache                 0.2.1           py312h178313f_1    conda-forge
proto-plus                1.26.0             pyhd8ed1ab_0    conda-forge
protobuf                  5.28.3          py312h2ec8cdc_0    conda-forge
psutil                    6.1.1           py312h66e93f0_0    conda-forge
psycopg2                  2.9.9           py312hfaedaf9_2    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pyarrow                   19.0.0          py312h7900ff3_0    conda-forge
pyarrow-core              19.0.0          py312h01725c0_0_cpu    conda-forge
pyarrow-hotfix            0.6                pyhd8ed1ab_1    conda-forge
pyasn1                    0.6.1              pyhd8ed1ab_2    conda-forge
pyasn1-modules            0.4.1              pyhd8ed1ab_1    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pygments                  2.19.1             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.13             pyhd8ed1ab_1    conda-forge
pyopenssl                 25.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.2.1              pyhd8ed1ab_0    conda-forge
pypika                    0.48.9             pyhd8ed1ab_1    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.12.8          h9e4cc4f_1_cpython    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-dotenv             1.0.1              pyhd8ed1ab_1    conda-forge
python-tzdata             2025.1             pyhd8ed1ab_0    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_1    conda-forge
pyzmq                     26.2.0          py312hbf22597_3    conda-forge
qhull                     2020.2               h434a139_5    conda-forge
re2                       2024.07.02           h9925aae_2    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
rsa                       4.9                pyhd8ed1ab_1    conda-forge
s2n                       1.5.11               h072c03f_0    conda-forge
s3fs                      2025.2.0                 pypi_0    pypi
scanpy                    1.10.4             pyhd8ed1ab_0    conda-forge
scikit-learn              1.6.1           py312h7a48858_0    conda-forge
scipy                     1.15.1          py312h180e4f1_0    conda-forge
seaborn                   0.13.2               hd8ed1ab_3    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_3    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                75.8.0             pyhff2d567_0    conda-forge
shapely                   2.0.6           py312h391bc85_2    conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
snappy                    1.2.1                h8bd8927_1    conda-forge
somacore                  1.0.26             pyh29332c3_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
spdlog                    1.15.0               h10c9db5_0    conda-forge
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
statsmodels               0.14.4          py312hc0a28a1_0    conda-forge
stdlib-list               0.11.0             pyhd8ed1ab_1    conda-forge
tbb                       2022.0.0             hceb3a55_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tiledb                    2.27.0               hcd65521_8    conda-forge
tiledbsoma-py             1.15.4          py312hee7031d_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tornado                   6.4.2           py312h66e93f0_0    conda-forge
tqdm                      4.67.1             pyhd8ed1ab_1    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
typing-extensions         4.12.2               hd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
tzdata                    2025a                h78e105d_0    conda-forge
umap-learn                0.5.7           py312h7900ff3_0    conda-forge
unicodedata2              16.0.0          py312h66e93f0_0    conda-forge
urllib3                   2.3.0              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_1    conda-forge
wrapt                     1.17.2                   pypi_0    pypi
xorg-libxau               1.0.12               hb9d3cd8_0    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
yarl                      1.18.3          py312h178313f_1    conda-forge
zeromq                    4.3.5                h3b0a872_7    conda-forge
zipp                      3.21.0             pyhd8ed1ab_1    conda-forge
zlib                      1.3.1                hb9d3cd8_2    conda-forge
zstandard                 0.23.0          py312hef9b889_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Operating System (OS)

Linux

User interface

Python

Are you using a computer with an Apple M1 chip?

Not M1

What is the exact command that was run?

Which output/error did you get?

[lauraluebbert]

Hi Nick, I am unable to reproduce this error on my end. Could you please try uninstalling gget from conda (conda remove -y -c bioconda gget) and reinstall using pip (pip install --upgrade gget)? (The conda installation has been causing some issues lately and I am still working to fix it).

[nick-youngblut]

I created a new conda env via mamba create -c conda-forge -c bioconda -n gget_env gget. Running gget search -s homo_sapiens BRCA1 throws the error:

10:25:54 - INFO - Fetching results from database: homo_sapiens_core_113_38
Traceback (most recent call last):
  File "/home/nickyoungblut/miniforge3/envs/gget/bin/gget", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/home/nickyoungblut/miniforge3/envs/gget/lib/python3.13/site-packages/gget/main.py", line 2967, in main
    gget_results = search(
        sw_clean_final,
    ...<7 lines>...
        verbose=args.quiet,
    )
  File "/home/nickyoungblut/miniforge3/envs/gget/lib/python3.13/site-packages/gget/gget_search.py", line 233, in search
    raise RuntimeError(
        f"The Ensembl server returned the following error: {str(last_exception)}"
    )
RuntimeError: The Ensembl server returned the following error: 2059 (HY000): Authentication plugin 'mysql_native_password' cannot be loaded: /usr/lib/mysql/plugin/mysql_native_password.so: cannot open shared object file: No such file or directory

The conda env:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
beautifulsoup4            4.13.3             pyha770c72_0    conda-forge
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0           py313h46c70d0_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2025.1.31            hbcca054_0    conda-forge
certifi                   2024.12.14         pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py313hfab6e84_0    conda-forge
charset-normalizer        3.4.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.2              pyhd8ed1ab_1    conda-forge
contourpy                 1.3.1           py313h33d0bda_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
fonttools                 4.56.0          py313h8060acc_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
gget                      0.29.0             pyh29332c3_0    conda-forge
h2                        4.2.0              pyhd8ed1ab_0    conda-forge
hpack                     4.1.0              pyhd8ed1ab_0    conda-forge
hyperframe                6.1.0              pyhd8ed1ab_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
ipython                   8.32.0             pyh907856f_0    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_1    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_1    conda-forge
kiwisolver                1.4.7           py313h33d0bda_0    conda-forge
lcms2                     2.17                 h717163a_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           29_h59b9bed_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcblas                  3.9.0           29_he106b2a_openblas    conda-forge
libdeflate                1.23                 h4ddbbb0_0    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.6                h2dba641_0    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libhwloc                  2.11.2          default_h0d58e46_1001    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           29_h7ac8fdf_openblas    conda-forge
liblzma                   5.6.4                hb9d3cd8_0    conda-forge
libmpdec                  4.0.0                h4bc722e_0    conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libpng                    1.6.46               h943b412_0    conda-forge
libsqlite                 3.48.0               hee588c1_1    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libtiff                   4.7.0                hd9ff511_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.5.0                h851e524_0    conda-forge
libxcb                    1.17.0               h8a09558_0    conda-forge
libxml2                   2.13.5               h0d44e9d_1    conda-forge
libxslt                   1.1.39               h76b75d6_0    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
llvm-openmp               19.1.7               h024ca30_0    conda-forge
lxml                      5.3.1           py313h6eb7059_0    conda-forge
matplotlib-base           3.10.0          py313h129903b_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_1    conda-forge
mkl                       2024.2.2            ha957f24_16    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              9.0.1                h266115a_4    conda-forge
mysql-connector-python    9.0.0           py313h1b76d92_1    conda-forge
mysql-libs                9.0.1                he0572af_4    conda-forge
ncurses                   6.5                  h2d0b736_3    conda-forge
numpy                     2.2.3           py313h17eae1a_0    conda-forge
openjpeg                  2.5.3                h5fbd93e_0    conda-forge
openssl                   3.4.1                h7b32b05_0    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
pandas                    2.2.3           py313ha87cce1_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_1    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pickleshare               0.7.5           pyhd8ed1ab_1004    conda-forge
pillow                    11.1.0          py313h8db990d_0    conda-forge
pip                       25.0.1             pyh145f28c_0    conda-forge
prompt-toolkit            3.0.50             pyha770c72_0    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pygments                  2.19.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.2.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.13.1          ha99a958_105_cp313    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-tzdata             2025.1             pyhd8ed1ab_0    conda-forge
python_abi                3.13                    5_cp313    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
qhull                     2020.2               h434a139_5    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
tbb                       2021.13.0            hceb3a55_1    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.67.1             pyhd8ed1ab_1    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
typing-extensions         4.12.2               hd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
tzdata                    2025a                h78e105d_0    conda-forge
urllib3                   2.3.0              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_1    conda-forge
xorg-libxau               1.0.12               hb9d3cd8_0    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
zstandard                 0.23.0          py313h80202fe_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

[lauraluebbert]

I am not sure what is causing this error; I unfortunately cannot reproduce it:
https://colab.research.google.com/drive/1Iiif8MSW7xFEgUwisyi4rtExodeFKFPj?usp=sharing

I assume it has something to do with one of the mysql packages not being fully installed or missing files in the environment. Could you please try reinstalling mysql-common (sudo apt install --reinstall mysql-common)?

(I also would def recommend using pip when installing gget as bioconda has not been installing the most recent gget versions correctly - I am still working on a fix for this.)