Suggestion for ./setup.sh if problems with mamba

[Sofie8]

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]

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]

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]

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]

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]

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]

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