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Both DEMO datasets Fails with: ImportError: cannot import name 'LineagePair' from 'sourmash.lca' #237

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JoshuaTCooper opened this issue Jul 3, 2023 · 1 comment · May be fixed by #239
Open

Both DEMO datasets Fails with: ImportError: cannot import name 'LineagePair' from 'sourmash.lca' #237

JoshuaTCooper opened this issue Jul 3, 2023 · 1 comment · May be fixed by #239

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@JoshuaTCooper
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Trying again to run the Demo from the instructions, but this time, there is something broken with respect to LineagePair from sourmash.lca.

I also don't know why in the output it says == This is sourmash version 4.8.2. ==, however when I do sourmash --version it outputs 4.4.3? (In case that is an issue with versioning).

(base) cooperjo@nkusa1:charcoal$git clone https://github.com/dib-lab/charcoal
(base) cooperjo@nkusa1:charcoal$cd ./charcoal/
(base) cooperjo@nkusa1:charcoal$mamba env create -f environment.yml -n charcoal
bioconda/noarch                                      4.3MB @   2.9MB/s  1.5s
bioconda/linux-64                                    5.0MB @   2.4MB/s  2.1s
pkgs/main/linux-64                                   5.9MB @   2.2MB/s  2.8s
pkgs/main/noarch                                   850.6kB @ 231.4kB/s  1.6s
pkgs/r/noarch                                        1.3MB @ 338.1kB/s  2.4s
pkgs/r/linux-64                                      1.4MB @ 343.9kB/s  1.4s
conda-forge/noarch                                  13.2MB @   2.4MB/s  6.3s
conda-forge/linux-64                                32.8MB @   2.8MB/s 13.8s

Looking for: ["python[version='>=3.8,<3.10']", 'snakemake-minimal=6.5.1', 'screed', "click[version='>=7,<8']", 'pip', 'mamba', 'sourmash=4.4.3']

Transaction

Prefix: /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal

Updating specs:

 - python[version='>=3.8,<3.10']
 - snakemake-minimal=6.5.1
 - screed
 - click[version='>=7,<8']
 - pip
 - mamba
 - sourmash=4.4.3

 Package                         Version  Build                Channel                    Size
─────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                     0.1  conda_forge          conda-forge/linux-64        3kB
  + _openmp_mutex                     4.5  2_gnu                conda-forge/linux-64       24kB
  + amply                           0.1.6  pyhd8ed1ab_0         conda-forge/noarch         22kB
  + appdirs                         1.4.4  pyh9f0ad1d_0         conda-forge/noarch         13kB
  + attrs                          23.1.0  pyh71513ae_1         conda-forge/noarch         55kB
  + bitstring                       3.1.9  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + boltons                        23.0.0  pyhd8ed1ab_0         conda-forge/noarch        303kB
  + brotli                          1.0.9  h166bdaf_9           conda-forge/linux-64       20kB
  + brotli-bin                      1.0.9  h166bdaf_9           conda-forge/linux-64       20kB
  + brotli-python                   1.0.9  py39h5a03fae_9       conda-forge/linux-64      327kB
  + bzip2                           1.0.8  h7f98852_4           conda-forge/linux-64     Cached
  + c-ares                         1.19.1  hd590300_0           conda-forge/linux-64     Cached
  + ca-certificates              2023.5.7  hbcca054_0           conda-forge/linux-64     Cached
  + cachetools                      4.2.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + certifi                      2023.5.7  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + cffi                           1.15.1  py39he91dace_3       conda-forge/linux-64      235kB
  + charset-normalizer              3.1.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + click                           7.1.2  pyh9f0ad1d_0         conda-forge/noarch         65kB
  + coin-or-cbc                   2.10.10  h9002f0b_0           conda-forge/linux-64      941kB
  + coin-or-cgl                    0.60.7  h516709c_0           conda-forge/linux-64      551kB
  + coin-or-clp                    1.17.8  h1ee7a9c_0           conda-forge/linux-64        1MB
  + coin-or-osi                   0.108.8  ha2443b9_0           conda-forge/linux-64      389kB
  + coin-or-utils                  2.11.9  hee58242_0           conda-forge/linux-64      687kB
  + coincbc                       2.10.10  0_metapackage        conda-forge/noarch         12kB
  + colorama                        0.4.6  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + conda                          23.5.0  py39hf3d152e_1       conda-forge/linux-64        1MB
  + conda-package-handling          2.0.2  pyh38be061_0         conda-forge/noarch        253kB
  + conda-package-streaming         0.8.0  pyhd8ed1ab_0         conda-forge/noarch         19kB
  + configargparse                  1.5.5  pyhd8ed1ab_0         conda-forge/noarch         41kB
  + connection_pool                 0.0.3  pyhd3deb0d_0         conda-forge/noarch          8kB
  + contourpy                       1.1.0  py39h7633fee_0       conda-forge/linux-64      221kB
  + cryptography                   41.0.1  py39hd4f0224_0       conda-forge/linux-64        2MB
  + cycler                         0.11.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + datrie                          0.8.2  py39hb9d737c_6       conda-forge/linux-64      149kB
  + deprecation                     2.1.0  pyh9f0ad1d_0         conda-forge/noarch       Cached
  + docutils                       0.20.1  py39hf3d152e_0       conda-forge/linux-64      704kB
  + filelock                       3.12.2  pyhd8ed1ab_0         conda-forge/noarch         15kB
  + fmt                             9.1.0  h924138e_0           conda-forge/linux-64      190kB
  + fonttools                      4.40.0  py39hd1e30aa_0       conda-forge/linux-64        2MB
  + freetype                       2.12.1  hca18f0e_1           conda-forge/linux-64     Cached
  + gitdb                          4.0.10  pyhd8ed1ab_0         conda-forge/noarch         52kB
  + gitpython                      3.1.31  pyhd8ed1ab_0         conda-forge/noarch        142kB
  + icu                              72.1  hcb278e6_0           conda-forge/linux-64       12MB
  + idna                              3.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + importlib-metadata              6.7.0  pyha770c72_0         conda-forge/noarch         26kB
  + importlib-resources            5.12.0  pyhd8ed1ab_0         conda-forge/noarch          9kB
  + importlib_resources            5.12.0  pyhd8ed1ab_0         conda-forge/noarch         31kB
  + jsonpatch                        1.32  pyhd8ed1ab_0         conda-forge/noarch         15kB
  + jsonpointer                       2.0  py_0                 conda-forge/noarch          9kB
  + jsonschema                     4.17.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyter_core                    5.3.1  py39hf3d152e_0       conda-forge/linux-64       92kB
  + keyutils                        1.6.1  h166bdaf_0           conda-forge/linux-64     Cached
  + kiwisolver                      1.4.4  py39hf939315_1       conda-forge/linux-64       78kB
  + krb5                           1.20.1  h81ceb04_0           conda-forge/linux-64     Cached
  + lcms2                            2.15  haa2dc70_1           conda-forge/linux-64     Cached
  + ld_impl_linux-64                 2.40  h41732ed_0           conda-forge/linux-64     Cached
  + lerc                            4.0.0  h27087fc_0           conda-forge/linux-64     Cached
  + libarchive                      3.6.2  h039dbb9_1           conda-forge/linux-64      844kB
  + libblas                         3.9.0  17_linux64_openblas  conda-forge/linux-64       14kB
  + libbrotlicommon                 1.0.9  h166bdaf_9           conda-forge/linux-64       71kB
  + libbrotlidec                    1.0.9  h166bdaf_9           conda-forge/linux-64       33kB
  + libbrotlienc                    1.0.9  h166bdaf_9           conda-forge/linux-64      265kB
  + libcblas                        3.9.0  17_linux64_openblas  conda-forge/linux-64       14kB
  + libcurl                         8.1.2  h409715c_0           conda-forge/linux-64     Cached
  + libdeflate                       1.18  h0b41bf4_0           conda-forge/linux-64     Cached
  + libedit                  3.1.20191231  he28a2e2_2           conda-forge/linux-64     Cached
  + libev                            4.33  h516909a_1           conda-forge/linux-64     Cached
  + libffi                          3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc-ng                      13.1.0  he5830b7_0           conda-forge/linux-64      776kB
  + libgfortran-ng                 13.1.0  h69a702a_0           conda-forge/linux-64       23kB
  + libgfortran5                   13.1.0  h15d22d2_0           conda-forge/linux-64     Cached
  + libgomp                        13.1.0  he5830b7_0           conda-forge/linux-64      419kB
  + libiconv                         1.17  h166bdaf_0           conda-forge/linux-64     Cached
  + libjpeg-turbo                 2.1.5.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + liblapack                       3.9.0  17_linux64_openblas  conda-forge/linux-64       14kB
  + liblapacke                      3.9.0  17_linux64_openblas  conda-forge/linux-64       14kB
  + libmamba                        1.4.6  h658169a_0           conda-forge/linux-64        2MB
  + libmambapy                      1.4.6  py39h78efd80_0       conda-forge/linux-64      288kB
  + libnghttp2                     1.52.0  h61bc06f_0           conda-forge/linux-64     Cached
  + libnsl                          2.0.0  h7f98852_0           conda-forge/linux-64     Cached
  + libopenblas                    0.3.23  pthreads_h80387f5_0  conda-forge/linux-64     Cached
  + libpng                         1.6.39  h753d276_0           conda-forge/linux-64     Cached
  + libsolv                        0.7.24  hfc55251_1           conda-forge/linux-64      467kB
  + libsqlite                      3.42.0  h2797004_0           conda-forge/linux-64     Cached
  + libssh2                        1.11.0  h0841786_0           conda-forge/linux-64     Cached
  + libstdcxx-ng                   13.1.0  hfd8a6a1_0           conda-forge/linux-64     Cached
  + libtiff                         4.5.1  h8b53f26_0           conda-forge/linux-64      418kB
  + libuuid                        2.38.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + libwebp-base                    1.3.1  hd590300_0           conda-forge/linux-64      400kB
  + libxcb                           1.15  h0b41bf4_0           conda-forge/linux-64     Cached
  + libxml2                        2.11.4  h0d562d8_0           conda-forge/linux-64      704kB
  + libzlib                        1.2.13  hd590300_5           conda-forge/linux-64       62kB
  + lz4-c                           1.9.4  hcb278e6_0           conda-forge/linux-64     Cached
  + lzo                              2.10  h516909a_1000        conda-forge/linux-64     Cached
  + mamba                           1.4.6  py39hc5d2bb1_0       conda-forge/linux-64       51kB
  + matplotlib-base                 3.7.1  py39he190548_0       conda-forge/linux-64        7MB
  + munkres                         1.1.4  pyh9f0ad1d_0         conda-forge/noarch       Cached
  + nbformat                        5.9.0  pyhd8ed1ab_0         conda-forge/noarch        101kB
  + ncurses                           6.4  hcb278e6_0           conda-forge/linux-64      881kB
  + numpy                          1.25.0  py39h6183b62_0       conda-forge/linux-64        7MB
  + openjpeg                        2.5.0  hfec8fc6_2           conda-forge/linux-64     Cached
  + openssl                         3.1.1  hd590300_1           conda-forge/linux-64     Cached
  + packaging                        23.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pillow                         10.0.0  py39haaeba84_0       conda-forge/linux-64       46MB
  + pip                            23.1.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pkgutil-resolve-name           1.3.10  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + platformdirs                    3.8.0  pyhd8ed1ab_0         conda-forge/noarch         19kB
  + pluggy                          1.2.0  pyhd8ed1ab_0         conda-forge/noarch         22kB
  + pooch                           1.7.0  pyha770c72_3         conda-forge/noarch         51kB
  + psutil                          5.9.5  py39h72bdee0_0       conda-forge/linux-64      359kB
  + pthread-stubs                     0.4  h36c2ea0_1001        conda-forge/linux-64        6kB
  + pulp                            2.7.0  py39hf3d152e_0       conda-forge/linux-64      140kB
  + pybind11-abi                        4  hd8ed1ab_3           conda-forge/noarch         10kB
  + pycosat                         0.6.4  py39hb9d737c_1       conda-forge/linux-64      110kB
  + pycparser                        2.21  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pyopenssl                      23.2.0  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + pyparsing                       3.1.0  pyhd8ed1ab_0         conda-forge/noarch         89kB
  + pyrsistent                     0.19.3  py39h72bdee0_0       conda-forge/linux-64       99kB
  + pysocks                         1.7.1  pyha2e5f31_6         conda-forge/noarch       Cached
  + python                         3.9.16  h2782a2a_0_cpython   conda-forge/linux-64       24MB
  + python-dateutil                 2.8.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + python-fastjsonschema          2.17.1  pyhd8ed1ab_0         conda-forge/noarch        226kB
  + python_abi                        3.9  3_cp39               conda-forge/linux-64        6kB
  + pyyaml                            6.0  py39hb9d737c_5       conda-forge/linux-64      184kB
  + ratelimiter                     1.2.0  pyhd8ed1ab_1003      conda-forge/noarch         13kB
  + readline                          8.2  h8228510_1           conda-forge/linux-64     Cached
  + reproc                         14.2.4  h0b41bf4_0           conda-forge/linux-64     Cached
  + reproc-cpp                     14.2.4  hcb278e6_0           conda-forge/linux-64     Cached
  + requests                       2.31.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + ruamel.yaml                   0.17.32  py39hd1e30aa_0       conda-forge/linux-64      200kB
  + ruamel.yaml.clib                0.2.7  py39h72bdee0_1       conda-forge/linux-64      143kB
  + scipy                          1.11.1  py39h6183b62_0       conda-forge/linux-64       15MB
  + screed                          1.1.2  pyhd8ed1ab_0         conda-forge/noarch         87kB
  + setuptools                     68.0.0  pyhd8ed1ab_0         conda-forge/noarch        464kB
  + six                            1.16.0  pyh6c4a22f_0         conda-forge/noarch       Cached
  + smart_open                      6.3.0  pyhd8ed1ab_1         conda-forge/noarch         47kB
  + smmap                           3.0.5  pyh44b312d_0         conda-forge/noarch         23kB
  + snakemake-minimal               6.5.1  pyhdfd78af_0         bioconda/noarch           210kB
  + sourmash                        4.4.3  hdfd78af_0           bioconda/noarch             8kB
  + sourmash-minimal                4.4.3  py39h4ef89ea_0       conda-forge/linux-64        9MB
  + stopit                          1.1.2  py_0                 conda-forge/noarch         16kB
  + tabulate                        0.9.0  pyhd8ed1ab_1         conda-forge/noarch         36kB
  + tk                             8.6.12  h27826a3_0           conda-forge/linux-64     Cached
  + toolz                          0.12.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + toposort                         1.10  pyhd8ed1ab_0         conda-forge/noarch         14kB
  + tqdm                           4.65.0  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + traitlets                       5.9.0  pyhd8ed1ab_0         conda-forge/noarch         98kB
  + typing-extensions               4.7.1  hd8ed1ab_0           conda-forge/noarch         10kB
  + typing_extensions               4.7.1  pyha770c72_0         conda-forge/noarch         36kB
  + tzdata                          2023c  h71feb2d_0           conda-forge/noarch        118kB
  + unicodedata2                   15.0.0  py39hb9d737c_0       conda-forge/linux-64      512kB
  + urllib3                         2.0.3  pyhd8ed1ab_1         conda-forge/noarch         98kB
  + wheel                          0.40.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + wrapt                          1.15.0  py39h72bdee0_0       conda-forge/linux-64       53kB
  + xorg-libxau                    1.0.11  hd590300_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                   1.1.3  h7f98852_0           conda-forge/linux-64     Cached
  + xz                              5.2.6  h166bdaf_0           conda-forge/linux-64     Cached
  + yaml                            0.2.5  h7f98852_2           conda-forge/linux-64     Cached
  + yaml-cpp                        0.7.0  h27087fc_2           conda-forge/linux-64     Cached
  + zipp                           3.15.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + zstandard                      0.19.0  py39h6e5214e_2       conda-forge/linux-64      394kB
  + zstd                            1.5.2  h3eb15da_6           conda-forge/linux-64     Cached

Summary:
    Install: 162 packages
    Total download: 144MB

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate charcoal
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Retrieving notices: ...working... done
(base) cooperjo@nkusa1:charcoal$conda activate charcoal
(charcoal) cooperjo@nkusa1:charcoal$pip install -e .
Obtaining file:///home/hh.nku.edu/cooperjo/software/charcoal
  Preparing metadata (setup.py) ... done
Collecting snakemake==6.4.1 (from charcoal-bio==0.1.dev336+g90ebdef)
  Using cached snakemake-6.4.1-py3-none-any.whl
Requirement already satisfied: click<8,>=7 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from charcoal-bio==0.1.dev336+g90ebdef) (7.1.2)
Requirement already satisfied: wrapt in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.15.0)
Requirement already satisfied: requests in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (2.31.0)
Requirement already satisfied: ratelimiter in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.2.0)
Requirement already satisfied: pyyaml in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (6.0)
Requirement already satisfied: configargparse in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.5.5)
Requirement already satisfied: appdirs in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.4.4)
Requirement already satisfied: datrie in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (0.8.2)
Requirement already satisfied: jsonschema in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (4.17.3)
Requirement already satisfied: docutils in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (0.20.1)
Requirement already satisfied: gitpython in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.1.31)
Requirement already satisfied: psutil in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (5.9.5)
Requirement already satisfied: nbformat in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (5.9.0)
Requirement already satisfied: toposort in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.10)
Requirement already satisfied: connection-pool>=0.0.3 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (0.0.3)
Requirement already satisfied: pulp>=2.0 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (2.7.0)
Requirement already satisfied: smart-open>=3.0 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (6.3.0)
Requirement already satisfied: filelock in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.12.2)
Requirement already satisfied: stopit in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (1.1.2)
Requirement already satisfied: gitdb<5,>=4.0.1 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from gitpython->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (4.0.10)
Requirement already satisfied: attrs>=17.4.0 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from jsonschema->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (23.1.0)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from jsonschema->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (0.19.3)
Requirement already satisfied: fastjsonschema in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from nbformat->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (2.17.1)
Requirement already satisfied: jupyter-core in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from nbformat->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (5.3.1)
Requirement already satisfied: traitlets>=5.1 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from nbformat->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (5.9.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from requests->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.1.0)
Requirement already satisfied: idna<4,>=2.5 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from requests->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from requests->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (2.0.3)
Requirement already satisfied: certifi>=2017.4.17 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from requests->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (2023.5.7)
Requirement already satisfied: smmap<6,>=3.0.1 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from gitdb<5,>=4.0.1->gitpython->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.0.5)
Requirement already satisfied: platformdirs>=2.5 in /home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages (from jupyter-core->nbformat->snakemake==6.4.1->charcoal-bio==0.1.dev336+g90ebdef) (3.8.0)
Installing collected packages: snakemake, charcoal-bio
  Attempting uninstall: snakemake
    Found existing installation: snakemake 6.5.1
    Uninstalling snakemake-6.5.1:
      Successfully uninstalled snakemake-6.5.1
  Running setup.py develop for charcoal-bio
Successfully installed charcoal-bio-0.1.dev336+g90ebdef snakemake-6.4.1
(charcoal) cooperjo@nkusa1:charcoal$python -m charcoal run demo/demo.conf -j 4
** read 3 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Building DAG of jobs...
Creating conda environment charcoal/conf/env-sourmash.yml...
Downloading and installing remote packages.
Environment for charcoal/conf/env-sourmash.yml created (location: .snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4)
Creating conda environment charcoal/conf/env-reporting.yml...
Downloading and installing remote packages.
Environment for charcoal/conf/env-reporting.yml created (location: .snakemake/conda/e9ba1f6c53a410b3e66d5239b9c07d13)
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       all
        1       combine_genome_summary
        1       combine_hit_list
        6       compare_taxonomy_single_wc
        6       contigs_sig_wc
        6       make_contigs_search_taxonomy_wc
        1       make_index
        6       prefetch_all_matches_wc
        1       set_kernel
        29
Select jobs to execute...

[Mon Jul  3 20:28:02 2023]
rule contigs_sig_wc:
    input: demo/genomes/TARA_ANE_MAG_00014.fa.gz
    output: output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.sig
    jobid: 17
    wildcards: g=TARA_ANE_MAG_00014.fa.gz

Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:02 2023]
rule contigs_sig_wc:
    input: demo/genomes/GCF_000005845-subset.fa.gz
    output: output.demo/stage1/GCF_000005845-subset.fa.gz.sig
    jobid: 5
    wildcards: g=GCF_000005845-subset.fa.gz

Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:03 2023]
rule contigs_sig_wc:
    input: demo/genomes/LoombaR_2017__SID1050_bax__bin.11.fa.gz
    output: output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.sig
    jobid: 9
    wildcards: g=LoombaR_2017__SID1050_bax__bin.11.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** WARNING: the sourmash compute command is DEPRECATED as of 4.0 and
** will be removed in 5.0. Please see the 'sourmash sketch' command instead.

setting num_hashes to 0 because --scaled is set
computing signatures for files: demo/genomes/TARA_ANE_MAG_00014.fa.gz
Computing signature for ksizes: [31]
Computing only nucleotide (and not protein) signatures.
Computing a total of 1 signature(s) for each input.
... reading sequences from demo/genomes/TARA_ANE_MAG_00014.fa.gz
calculated 1 signatures for 64 sequences in demo/genomes/TARA_ANE_MAG_00014.fa.gz
saved 1 signature(s) to 'output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.sig'. Note: signature license is CC0.
[Mon Jul  3 20:28:04 2023]
Finished job 17.
1 of 29 steps (3%) done

== This is sourmash version 4.8.2. ==                                                                                                                                                                                                   [370/1934]
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** WARNING: the sourmash compute command is DEPRECATED as of 4.0 and
** will be removed in 5.0. Please see the 'sourmash sketch' command instead.

setting num_hashes to 0 because --scaled is set
computing signatures for files: demo/genomes/GCF_000005845-subset.fa.gz
Computing signature for ksizes: [31]
Computing only nucleotide (and not protein) signatures.
Computing a total of 1 signature(s) for each input.
... reading sequences from demo/genomes/GCF_000005845-subset.fa.gz
calculated 1 signatures for 1 sequences in demo/genomes/GCF_000005845-subset.fa.gz
saved 1 signature(s) to 'output.demo/stage1/GCF_000005845-subset.fa.gz.sig'. Note: signature license is CC0.
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:04 2023]
rule contigs_sig_wc:
    input: demo/genomes/GCA_001593925.1_ASM159392v1_genomic.fna.gz
    output: output.demo/stage1/GCA_001593925.1_ASM159392v1_genomic.fna.gz.sig
    jobid: 25
    wildcards: g=GCA_001593925.1_ASM159392v1_genomic.fna.gz

[Mon Jul  3 20:28:04 2023]
Finished job 5.
2 of 29 steps (7%) done
Select jobs to execute...
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:05 2023]
rule prefetch_all_matches_wc:
    input: output.demo/stage1/GCF_000005845-subset.fa.gz.sig, demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz, demo/TARA_ANE_MAG_00014.fa.gather-matches.sig.gz, demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz, demo/GCA_001
593925.sig.gz
    output: output.demo/stage1/GCF_000005845-subset.fa.gz.matches.csv, output.demo/stage1/GCF_000005845-subset.fa.gz.matches.txt
    jobid: 6
    wildcards: g=GCF_000005845-subset.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** WARNING: the sourmash compute command is DEPRECATED as of 4.0 and
** will be removed in 5.0. Please see the 'sourmash sketch' command instead.

setting num_hashes to 0 because --scaled is set
computing signatures for files: demo/genomes/LoombaR_2017__SID1050_bax__bin.11.fa.gz
Computing signature for ksizes: [31]
Computing only nucleotide (and not protein) signatures.
Computing a total of 1 signature(s) for each input.
... reading sequences from demo/genomes/LoombaR_2017__SID1050_bax__bin.11.fa.gz
calculated 1 signatures for 60 sequences in demo/genomes/LoombaR_2017__SID1050_bax__bin.11.fa.gz
saved 1 signature(s) to 'output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.sig'. Note: signature license is CC0.
[Mon Jul  3 20:28:06 2023]
Finished job 9.
3 of 29 steps (10%) done
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4


[Mon Jul  3 20:28:06 2023]
rule prefetch_all_matches_wc:
    input: output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.sig, demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz, demo/TARA_ANE_MAG_00014.fa.gather-matches.sig.gz, demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz, demo/GCA_001593925.sig.gz
    output: output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.matches.csv, output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.matches.txt
    jobid: 18
    wildcards: g=TARA_ANE_MAG_00014.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** WARNING: the sourmash compute command is DEPRECATED as of 4.0 and
** will be removed in 5.0. Please see the 'sourmash sketch' command instead.

setting num_hashes to 0 because --scaled is set
computing signatures for files: demo/genomes/GCA_001593925.1_ASM159392v1_genomic.fna.gz
Computing signature for ksizes: [31]
Computing only nucleotide (and not protein) signatures.
Computing a total of 1 signature(s) for each input.
... reading sequences from demo/genomes/GCA_001593925.1_ASM159392v1_genomic.fna.gz
calculated 1 signatures for 124 sequences in demo/genomes/GCA_001593925.1_ASM159392v1_genomic.fna.gz
saved 1 signature(s) to 'output.demo/stage1/GCA_001593925.1_ASM159392v1_genomic.fna.gz.sig'. Note: signature license is CC0.
[Mon Jul  3 20:28:06 2023]
Finished job 25.
4 of 29 steps (14%) done
Select jobs to execute...
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:07 2023]
rule contigs_sig_wc:
    input: demo/genomes/TARA_PON_MAG_00084.fa.gz
    output: output.demo/stage1/TARA_PON_MAG_00084.fa.gz.sig
    jobid: 21
    wildcards: g=TARA_PON_MAG_00084.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: demo/genomes/GCF_000005845-sub... (k=31, DNA)
query sketch has scaled=1000; will be dynamically downsampled as needed.
--
loaded 64 total signatures from 4 locations.
after selecting signatures compatible with search, 64 remain.
--
total of 0 matching signatures.
saved 0 matches to CSV file 'output.demo/stage1/GCF_000005845-subset.fa.gz.matches.csv'
of 28 distinct query hashes, 0 were found in matches above threshold.
a total of 28 query hashes remain unmatched.
final scaled value (max across query and all matches) is 1000
[Mon Jul  3 20:28:07 2023]
Finished job 6.
5 of 29 steps (17%) done
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:07 2023]
rule prefetch_all_matches_wc:
    input: output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.sig, demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz, demo/TARA_ANE_MAG_00014.fa.gather-matches.sig.gz, demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz, demo/GCA_001593925.sig.gz
    output: output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.matches.csv, output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.matches.txt
    jobid: 10
    wildcards: g=LoombaR_2017__SID1050_bax__bin.11.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: demo/genomes/TARA_ANE_MAG_0001... (k=31, DNA)
query sketch has scaled=1000; will be dynamically downsampled as needed.
--
loaded 64 total signatures from 4 locations.
after selecting signatures compatible with search, 64 remain.
--
total of 1 matching signatures.
saved 1 matches to CSV file 'output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.matches.csv'
of 918 distinct query hashes, 60 were found in matches above threshold.
a total of 858 query hashes remain unmatched.
final scaled value (max across query and all matches) is 1000
[Mon Jul  3 20:28:08 2023]
Finished job 18.
6 of 29 steps (21%) done
Select jobs to execute...
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

** WARNING: the sourmash compute command is DEPRECATED as of 4.0 and
** will be removed in 5.0. Please see the 'sourmash sketch' command instead.

setting num_hashes to 0 because --scaled is set
computing signatures for files: demo/genomes/TARA_PON_MAG_00084.fa.gz
Computing signature for ksizes: [31]
Computing only nucleotide (and not protein) signatures.
Computing a total of 1 signature(s) for each input.
... reading sequences from demo/genomes/TARA_PON_MAG_00084.fa.gz

[Mon Jul  3 20:28:08 2023]
rule make_contigs_search_taxonomy_wc:
    input: demo/genomes/GCF_000005845-subset.fa.gz, output.demo/stage1/GCF_000005845-subset.fa.gz.sig, output.demo/stage1/GCF_000005845-subset.fa.gz.matches.csv, demo/demo-lineages.csv, demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz, demo/TARA_ANE_MAG
_00014.fa.gather-matches.sig.gz, demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz, demo/GCA_001593925.sig.gz
    output: output.demo/stage1/GCF_000005845-subset.fa.gz.contigs-tax.json
    jobid: 4
    wildcards: g=GCF_000005845-subset.fa.gz

calculated 1 signatures for 676 sequences in demo/genomes/TARA_PON_MAG_00084.fa.gz
saved 1 signature(s) to 'output.demo/stage1/TARA_PON_MAG_00084.fa.gz.sig'. Note: signature license is CC0.
[Mon Jul  3 20:28:08 2023]
Finished job 21.
7 of 29 steps (24%) done
Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4

[Mon Jul  3 20:28:09 2023]
rule make_contigs_search_taxonomy_wc:
    input: demo/genomes/TARA_ANE_MAG_00014.fa.gz, output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.sig, output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.matches.csv, demo/demo-lineages.csv, demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz, demo/TARA_ANE_MAG_00014
.fa.gather-matches.sig.gz, demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz, demo/GCA_001593925.sig.gz
    output: output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.contigs-tax.json
    jobid: 16
    wildcards: g=TARA_ANE_MAG_00014.fa.gz


== This is sourmash version 4.8.2. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: demo/genomes/LoombaR_2017__SID... (k=31, DNA)
query sketch has scaled=1000; will be dynamically downsampled as needed.
--
loaded 64 total signatures from 4 locations.
after selecting signatures compatible with search, 64 remain.
--
total of 18 matching signatures.
saved 18 matches to CSV file 'output.demo/stage1/LoombaR_2017__SID1050_bax__bin.11.fa.gz.matches.csv'
of 2723 distinct query hashes, 2081 were found in matches above threshold.
a total of 642 query hashes remain unmatched.
final scaled value (max across query and all matches) is 1000
[Mon Jul  3 20:28:10 2023]
Finished job 10.
8 of 29 steps (28%) done
Traceback (most recent call last):
  File "/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/contigs_search_taxonomy.py", line 16, in <module>
    from .lineage_db import LineageDB
  File "/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/lineage_db.py", line 19, in <module>
    from sourmash.lca import LineagePair
ImportError: cannot import name 'LineagePair' from 'sourmash.lca' (/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/site-packages/sourmash/lca/__init__.py)
[Mon Jul  3 20:28:10 2023]
Error in rule make_contigs_search_taxonomy_wc:
    jobid: 4
    output: output.demo/stage1/GCF_000005845-subset.fa.gz.contigs-tax.json
    conda-env: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4
    shell:

        python -m charcoal.contigs_search_taxonomy             --genome demo/genomes/GCF_000005845-subset.fa.gz --lineages-csv demo/demo-lineages.csv             --genome-sig output.demo/stage1/GCF_000005845-subset.fa.gz.sig             --matches-csv output.demo/stage1/G
CF_000005845-subset.fa.gz.matches.csv             --databases demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz demo/TARA_ANE_MAG_00014.fa.gather-matches.sig.gz demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz demo/GCA_001593925.sig.gz             --json
-out output.demo/stage1/GCF_000005845-subset.fa.gz.contigs-tax.json             --match-rank genus

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Activating conda environment: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4
Traceback (most recent call last):
  File "/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/contigs_search_taxonomy.py", line 16, in <module>
    from .lineage_db import LineageDB
  File "/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/lineage_db.py", line 19, in <module>
    from sourmash.lca import LineagePair
ImportError: cannot import name 'LineagePair' from 'sourmash.lca' (/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/lib/python3.9/site-packages/sourmash/lca/__init__.py)
[Mon Jul  3 20:28:11 2023]
Error in rule make_contigs_search_taxonomy_wc:
    jobid: 16
    output: output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.contigs-tax.json
    conda-env: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4
    shell:

        python -m charcoal.contigs_search_taxonomy             --genome demo/genomes/TARA_ANE_MAG_00014.fa.gz --lineages-csv demo/demo-lineages.csv             --genome-sig output.demo/stage1/TARA_ANE_MAG_00014.fa.gz.sig             --matches-csv output.demo/stage1/TARA_
ANE_MAG_00014.fa.gz.matches.csv             --databases demo/LoombaR_2017__SID1050_bax__bin.11.fa.gz.gather-matches.sig.gz demo/TARA_ANE_MAG_00014.fa.gather-matches.sig.gz demo/TARA_PON_MAG_00084.fa.gather-matches.sig.gz demo/GCA_001593925.sig.gz             --json-out $
utput.demo/stage1/TARA_ANE_MAG_00014.fa.gz.contigs-tax.json             --match-rank genus

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/log/2023-07-03T202526.110570.snakemake.log
Error in snakemake invocation: Command '['snakemake', '-s', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/defaults.conf', '/home/hh.nku.edu
/cooperjo/software/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1.
(charcoal) cooperjo@nkusa1:charcoal$which sourmash
/home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/bin/sourmash
(charcoal) cooperjo@nkusa1:charcoal$sourmash --version
sourmash 4.4.3
This was referenced Oct 28, 2023
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ctb commented Oct 29, 2023

Fixed in #239

Sorry it's taken me so long!

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MRG: update sourmash and snakemake dependencies dib-lab/charcoal
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@ctb @JoshuaTCooper