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metagenome-atlas / atlas_analyze

Scripts to get the most of the output of metagenome-atlas
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Suggestion for ./setup.sh if problems with mamba #3

Open Sofie8 opened 3 years ago

Sofie8 commented 3 years ago

When running ./setup.sh I got an error with mamba:

InstallError: Error: the following specs depend on 'conda' and can only be installed into the root environment: mamba

Only when I run it in my directory miniconda3/bin; conda install mamba -c conda-forge

It wants to update a lot of things:

Package plan for installation in environment /vsc-hard-mounts/leuven-data/314/vs                                                                                                                 c31426/miniconda3:

The following NEW packages will be INSTALLED:

    _libgcc_mutex:          0.1-conda_forge          conda-forge
    _openmp_mutex:          4.5-1_gnu                conda-forge
    brotlipy:               0.7.0-py36he6145b8_1001  conda-forge
    bzip2:                  1.0.8-h7f98852_4         conda-forge
    c-ares:                 1.17.1-h36c2ea0_0        conda-forge
    ca-certificates:        2020.12.5-ha878542_0     conda-forge
    certifi:                2020.12.5-py36h5fab9bb_1 conda-forge
    chardet:                4.0.0-py36h5fab9bb_1     conda-forge
    conda-package-handling: 1.7.2-py36he6145b8_0     conda-forge
    icu:                    68.1-h58526e2_0          conda-forge
    krb5:                   1.17.2-h926e7f8_0        conda-forge
    ld_impl_linux-64:       2.35.1-hed1e6ac_1        conda-forge
    libarchive:             3.5.1-h3f442fb_1         conda-forge
    libcurl:                7.71.1-hcdd3856_8        conda-forge
    libedit:                3.1.20191231-he28a2e2_2  conda-forge
    libev:                  4.33-h516909a_1          conda-forge
    libgcc-ng:              9.3.0-h2828fa1_18        conda-forge
    libgomp:                9.3.0-h2828fa1_18        conda-forge
    libiconv:               1.16-h516909a_0          conda-forge
    libnghttp2:             1.41.0-h8cfc5f6_2        conda-forge
    libsolv:                0.7.16-h8b12597_0        conda-forge
    libssh2:                1.9.0-hab1572f_5         conda-forge
    libstdcxx-ng:           9.3.0-h6de172a_18        conda-forge
    libxml2:                2.9.10-h72842e0_3        conda-forge
    lz4-c:                  1.9.3-h9c3ff4c_0         conda-forge
    lzo:                    2.10-h516909a_1000       conda-forge
    mamba:                  0.7.8-py36h05d92e0_1     conda-forge
    ncurses:                6.2-h58526e2_4           conda-forge
    pysocks:                1.7.1-py36h5fab9bb_3     conda-forge
    python_abi:             3.6-1_cp36m              conda-forge
    reproc:                 14.2.1-h36c2ea0_0        conda-forge
    reproc-cpp:             14.2.1-h58526e2_0        conda-forge
    tqdm:                   4.56.0-pyhd8ed1ab_0      conda-forge
    urllib3:                1.26.2-pyhd8ed1ab_0      conda-forge
    zstd:                   1.4.8-ha95c52a_1         conda-forge

The following packages will be UPDATED:

    conda:                  4.3.21-py36_0                        --> 4.9.2-py36h                                                                                                                 5fab9bb_0      conda-forge
    conda-env:              2.6.0-0                              --> 2.6.0-1                                                                                                                                    conda-forge
    cryptography:           1.8.1-py36_0                         --> 3.3.1-py36h                                                                                                                 0a59100_1      conda-forge
    openssl:                1.0.2l-0                             --> 1.1.1i-h7f9                                                                                                                 8852_0         conda-forge
    pycosat:                0.6.2-py36_0                         --> 0.6.3-py36h                                                                                                                 8f6f2f9_1006   conda-forge
    python:                 3.6.1-2                              --> 3.6.11-h6f2                                                                                                                 ec95_2_cpython conda-forge
    readline:               6.2-2                                --> 8.0-he28a2e                                                                                                                 2_2            conda-forge
    requests:               2.14.2-py36_0                        --> 2.25.1-pyhd                                                                                                                 3deb0d_0       conda-forge
    setuptools:             27.2.0-py36_0                        --> 49.6.0-py36                                                                                                                 h5fab9bb_3     conda-forge
    sqlite:                 3.13.0-0                             --> 3.34.0-h74c                                                                                                                 db3f_0         conda-forge
    tk:                     8.5.18-0                             --> 8.6.10-hed6                                                                                                                 95b0_1         conda-forge
    xz:                     5.2.2-1                              --> 5.2.5-h5169                                                                                                                 09a_1          conda-forge
    zlib:                   1.2.8-3                              --> 1.2.11-h516                                                                                                                 909a_1010      conda-forge

Proceed ([y]/n)? n

I was not sure about it if it wouldn't interfere with other miniconda envs..

So I did: conda env create -n analyze -f condaenv.yml and this worked with only 2 warnings:

Warning: 2 possible package resolutions (only showing differing packages):
  - conda-forge::glib-2.66.4-hc4f0c31_1, conda-forge::libglib-2.66.4-h748fe8e_1
  - conda-forge::glib-2.66.4-ha03b18c_1, conda-forge::libglib-2.66.4-hdb14261_1

It can maybe help others having the same issue.

Sofie

SilasK commented 3 years ago

Ok, you cannot install mamba in an conda env, ok. but it makes sense.

I think it should be save to install only mamba in your base env. It also updates conda and some other packages. If realy something break there is a way in conda to go back to an erelier configuration. Anyway all the other conda envs stay the same.

panrenzaishu commented 3 years ago

Ok, you cannot install mamba in an conda env, ok. but it makes sense.

I think it should be save to install only mamba in your base env. It also updates conda and some other packages. If realy something break there is a way in conda to go back to an erelier configuration. Anyway all the other conda envs stay the same.

Hi, SilasK:

Following Sofie8`s idea, i had installed the analyze without mamba installation because there seems to be conflict betwen conada base with mamba.

conda env create -n analyze -f condaenv.yml

However, when run the following comment line

conda activate analyze analyze.py path/to/working_file_of_atlas

then the terminal only shows: bash: analyze.py: command not found...

Any ideas for this?

Meanwhile, i also check the snakefile in the download files and it seems to require input of genomes/annotations/KO.tsv and genomes/annotations/CAZy.tsv. But my current output seems not include those two files in the folder of genomes/annotations. Do i miss any steps to generate these two files?

I am looking forward to your reply. Thanks in advance.

panrenzaishu commented 3 years ago

In the envs of analyze, i run conda list. Following packages are shown:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge aioeasywebdav 2.4.0 py37hc8dfbb8_1001 conda-forge aiohttp 3.7.3 py37h5e8e339_2 conda-forge altair 4.1.0 py_1 conda-forge amply 0.1.4 py_0 conda-forge anyio 2.1.0 py37h89c1867_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 20.1.0 py37h5e8e339_2 conda-forge async-timeout 3.0.1 py_1000 conda-forge async_generator 1.10 py_0 conda-forge atk-1.0 2.36.0 h3371d22_4 conda-forge attmap 0.12.11 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge babel 2.9.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge bcrypt 3.2.0 py37h5e8e339_1 conda-forge bleach 3.3.0 pyh44b312d_0 conda-forge boto3 1.17.14 pyhd8ed1ab_0 conda-forge botocore 1.20.14 pyhd8ed1ab_0 conda-forge brotlipy 0.7.0 py37h5e8e339_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h36c2ea0_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cachecontrol 0.12.6 py_0 conda-forge cachetools 4.2.1 pyhd8ed1ab_0 conda-forge cairo 1.16.0 h7979940_1007 conda-forge certifi 2020.12.5 py37h89c1867_1 conda-forge cffi 1.14.5 py37hc58025e_0 conda-forge chardet 3.0.4 py37he5f6b98_1008 conda-forge coincbc 2.10.5 hcee13e7_1 conda-forge configargparse 1.3 pyhd8ed1ab_0 conda-forge cryptography 3.4.4 py37hf1a17b8_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.22 py37hcd2ae1e_0 conda-forge datrie 0.8.2 py37h8f50634_1 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge docutils 0.16 py37h89c1867_3 conda-forge dropbox 11.2.0 pyhd8ed1ab_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge expat 2.2.10 h9c3ff4c_0 conda-forge fftw 3.3.9 nompi_h74d3f13_100 conda-forge filechunkio 1.8 py_2 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 2.001 hab24e00_0 conda-forge font-ttf-source-code-pro 2.030 hab24e00_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 hba837de_1004 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge ftputil 5.0.0 pyhd8ed1ab_0 conda-forge gdk-pixbuf 2.42.2 h0c95a7a_2 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge ghostscript 9.53.3 h58526e2_2 conda-forge giflib 5.2.1 h36c2ea0_2 conda-forge gitdb 4.0.5 pyhd8ed1ab_1 conda-forge gitpython 3.1.13 pyhd8ed1ab_0 conda-forge glib 2.66.7 h9c3ff4c_0 conda-forge glib-tools 2.66.7 h9c3ff4c_0 conda-forge google-api-core 1.25.1 pyh44b312d_0 conda-forge google-api-python-client 1.12.8 pyhd3deb0d_0 conda-forge google-auth 1.24.0 pyhd3deb0d_0 conda-forge google-auth-httplib2 0.0.4 pyh9f0ad1d_0 conda-forge google-cloud-core 1.5.0 pyhd3deb0d_0 conda-forge google-cloud-storage 1.35.0 pyhd3deb0d_0 conda-forge google-crc32c 1.1.2 py37hab72019_0 conda-forge google-resumable-media 1.2.0 pyhd3deb0d_0 conda-forge googleapis-common-protos 1.52.0 py37h89c1867_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 2.46.1 h93c640b_4 conda-forge grpcio 1.35.0 py37hb27c1af_0 conda-forge gst-plugins-base 1.18.3 h04508c2_0 conda-forge gstreamer 1.18.3 h3560a44_0 conda-forge gtk2 2.24.33 hab0c2f8_0 conda-forge gts 0.7.6 h64030ff_2 conda-forge harfbuzz 2.7.4 h5cf4720_0 conda-forge hdmedians 0.14.1 py37h902c9e0_1 conda-forge httplib2 0.19.0 pyhd8ed1ab_0 conda-forge icu 68.1 h58526e2_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge imagemagick 7.0.11_1 pl5262hb503478_0 conda-forge importlib-metadata 3.4.0 py37h89c1867_0 conda-forge importlib_metadata 3.4.0 hd8ed1ab_0 conda-forge iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge ipykernel 5.5.0 py37h888b3d9_1 conda-forge ipython 7.20.0 py37h888b3d9_2 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jbig 2.1 h516909a_2002 conda-forge jedi 0.18.0 py37h89c1867_2 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge jmespath 0.10.0 pyh9f0ad1d_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsonschema 3.2.0 py_2 conda-forge jupyter-packaging 0.7.12 pyhd8ed1ab_0 conda-forge jupyter_client 6.1.11 pyhd8ed1ab_1 conda-forge jupyter_core 4.7.1 py37h89c1867_0 conda-forge jupyter_server 1.4.1 py37h89c1867_0 conda-forge jupyterlab 3.0.9 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_server 2.3.0 pyhd8ed1ab_0 conda-forge kiwisolver 1.3.1 py37h2527ec5_1 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libclang 11.0.1 default_ha53f305_1 conda-forge libcrc32c 1.1.1 h9c3ff4c_2 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgd 2.3.0 h47910db_1 conda-forge libgfortran-ng 9.3.0 hff62375_18 conda-forge libgfortran5 9.3.0 hff62375_18 conda-forge libglib 2.66.7 h1f3bc88_0 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 8_openblas conda-forge libllvm11 11.0.1 hf817b99_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 13.1 hfd2b0eb_1 conda-forge libprotobuf 3.15.1 h780b84a_0 conda-forge librsvg 2.50.3 hfa39831_1 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libtool 2.4.6 h58526e2_1007 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp 1.2.0 h3452ae3_0 conda-forge libwebp-base 1.2.0 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.10 h72842e0_3 conda-forge lockfile 0.12.2 py_1 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py37h5e8e339_3 conda-forge matplotlib 3.3.4 py37h89c1867_0 conda-forge matplotlib-base 3.3.4 py37h0c9df89_0 conda-forge mistune 0.8.4 py37h5e8e339_1003 conda-forge more-itertools 8.7.0 pyhd8ed1ab_0 conda-forge msgpack-python 1.0.2 py37h2527ec5_1 conda-forge multidict 5.1.0 py37h5e8e339_1 conda-forge mysql-common 8.0.23 ha770c72_1 conda-forge mysql-libs 8.0.23 h935591d_1 conda-forge natsort 7.1.1 pyhd8ed1ab_0 conda-forge nbclassic 0.2.6 pyhd8ed1ab_0 conda-forge nbclient 0.5.2 pyhd8ed1ab_0 conda-forge nbconvert 6.0.7 py37h89c1867_3 conda-forge nbformat 5.1.2 pyhd8ed1ab_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge networkx 2.5 py_0 conda-forge notebook 6.2.0 py37h89c1867_0 conda-forge nspr 4.29 h9c3ff4c_1 conda-forge nss 3.62 hb5efdd6_0 conda-forge numpy 1.20.1 py37haa41c4c_0 conda-forge oauth2client 4.1.3 py_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.4.0 hf7af979_0 conda-forge openssl 1.1.1j h7f98852_0 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 0.25.3 py37hb3f55d8_0 conda-forge pandoc 2.11.4 h7f98852_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge pango 1.42.4 h69149e4_5 conda-forge paramiko 2.7.2 pyh9f0ad1d_0 conda-forge parso 0.8.1 pyhd8ed1ab_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge peppy 0.31.0 pyh9f0ad1d_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.0 py37h4600e1f_2 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkg-config 0.29.2 h36c2ea0_1008 conda-forge pluggy 0.13.1 py37h89c1867_4 conda-forge ply 3.11 py_1 conda-forge prettytable 2.0.0 pyhd8ed1ab_0 conda-forge prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge prompt-toolkit 3.0.16 pyha770c72_0 conda-forge protobuf 3.15.1 py37hcd2ae1e_0 conda-forge psutil 5.8.0 py37h5e8e339_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pulp 2.3.1 py37hc8dfbb8_0 conda-forge py 1.10.0 pyhd3deb0d_0 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.8.0 pyhd8ed1ab_0 conda-forge pygraphviz 1.7 py37h0b1d2a2_0 conda-forge pynacl 1.4.0 py37h5e8e339_2 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py37h89c1867_7 conda-forge pyqt-impl 5.12.3 py37he336c9b_7 conda-forge pyqt5-sip 4.19.18 py37hcd2ae1e_7 conda-forge pyqtchart 5.12 py37he336c9b_7 conda-forge pyqtwebengine 5.12.1 py37he336c9b_7 conda-forge pyrsistent 0.17.3 py37h5e8e339_2 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 py37h89c1867_3 conda-forge pytest 6.2.2 py37h89c1867_0 conda-forge python 3.7.10 hffdb5ce_100_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-irodsclient 0.8.2 py_0 conda-forge python_abi 3.7 1_cp37m conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py37h5e8e339_0 conda-forge pyzmq 22.0.3 py37h499b945_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge ratelimiter 1.2.0 py_1002 conda-forge readline 8.0 he28a2e2_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge rsa 4.7.1 pyh44b312d_0 conda-forge s3transfer 0.3.4 pyhd8ed1ab_0 conda-forge scikit-bio 0.5.5 py37h3010b51_1000 conda-forge scikit-learn 0.24.1 py37h69acf81_0 conda-forge scipy 1.6.0 py37h14a347d_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py37h89c1867_3 conda-forge simplejson 3.17.2 py37h5e8e339_2 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge slacker 0.14.0 py_0 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge snakemake 5.32.2 0 bioconda snakemake-minimal 5.32.2 py_0 bioconda sniffio 1.2.0 py37h89c1867_1 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge statsmodels 0.12.2 py37h902c9e0_0 conda-forge stone 3.2.1 pyhd8ed1ab_0 conda-forge terminado 0.9.2 py37h89c1867_0 conda-forge testpath 0.4.4 py_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge toolz 0.11.1 py_0 conda-forge toposort 1.6 pyhd8ed1ab_0 conda-forge tornado 6.1 py37h5e8e339_1 conda-forge traitlets 5.0.5 py_0 conda-forge typing-extensions 3.7.4.3 0 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge ubiquerg 0.6.1 pyh9f0ad1d_0 conda-forge uritemplate 3.0.1 py_0 conda-forge urllib3 1.26.3 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge wrapt 1.12.1 py37h5e8e339_3 conda-forge xmlrunner 1.7.7 py_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.12 h516909a_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxt 1.2.1 h7f98852_0 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge yarl 1.5.1 py37h8f50634_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge

So i am not sure what is missing. Or, what should i update?

SilasK commented 3 years ago

Hey @panrenzaishu

The setup is quite basic, I don't export the path to the analyze.py

but it should work if you run /path/to/atlas_analyze/analyze.py

panrenzaishu commented 3 years ago

Hey @panrenzaishu

The setup is quite basic, I don't export the path to the analyze.py

but it should work if you run /path/to/atlas_analyze/analyze.py

Thank you for your prompt reply. I try the following commend line: /path/to/analyze.py /path/to/atlas_working_file

It works for some step but encounters the error in Nbconverter as shown below: [NbConvertApp] ERROR | Notebook JSON is invalid: Additional properties are not allowe d ('id' was unexpected)

The output file "Results" contains the KO.tsv and CAZy.tsv files.

Thank you for your reply.

SilasK commented 3 years ago

Others also had the nbconverter. It is more likely that I integrate the atlas_analyze into atlas rather than solving this nbvonverter issue.

There should be a Code.ipynb with the same content .

Also have a look at the Jupiter and Rmarkdown of the Tutorial for suggestion how to analyst the results