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
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+ 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
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+ 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
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+ 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
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).