No such command 'init'.

animesh commented 3 years ago

init commands fails

atlas init
Usage: atlas [OPTIONS] COMMAND [ARGS]...
Try 'atlas -h' for help.

Error: No such command 'init'.

SilasK commented 3 years ago

Very strange. Do you really have metagenome-atlas. atlas might refer to another tool.

Try to run just. atlas

I get:

atlas
Usage: atlas [OPTIONS] COMMAND [ARGS]...

  ATLAS - workflows for assembly, annotation, and genomic binning of
  metagenomic and metatranscriptomic data.

  For updates and reporting issues, see: https://github.com/metagenome-
  atlas/atlas

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  download  download reference files (need ~50GB)
  init      prepare configuration file and sample table for atlas run
  run       run atlas main workflow

and which atlas

animesh commented 3 years ago

Help invocation emits:

(py36) animeshs@DMED7596:/mnt/z/ayu$ atlas -h
Usage: atlas [OPTIONS] COMMAND [ARGS]...

  ATLAS - workflows for assembly, annotation, and genomic binning of
  metagenomic and metatranscriptomic data.

  For updates and reporting issues, see: https://github.com/metagenome-
  atlas/atlas

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  assemble      assembly workflow
  bin-genomes   bins contigs using different binners to genomes
  download      download reference files
  gff2tsv       writes version of Prokka TSV with contig as new first column
  make-config   prepopulate a configuration file with samples and defaults
  merge-tables  merge genepredictions TSV, Counts, and Taxonomy
  munge-blast   adds contig ID to prokka annotated ORFs
  qc            quality control workflow (without assembly)
  refseq        enables tree based LCA and LCA star methods

I tried qc and it seems to be working?

(py36) animeshs@DMED7596:/mnt/z/ayu$ atlas make-config sample reads
[2021-01-08 15:16 INFO] Found 19 samples under /mnt/z/ayu/reads
[2021-01-08 15:16 INFO] Configuration file written to /mnt/z/ayu/sample

(py36) animeshs@DMED7596:/mnt/z/ayu$ atlas qc sample
[2021-01-08 15:17 INFO] Executing: snakemake --snakefile /home/animeshs/.local/lib/python3.6/site-packages/atlas/Snakefile --directory /mnt/z/ayu --printshellcmds --jobs 24 --rerun-incomplete --configfile '/mnt/z/ayu/sample' --nolock --use-conda  --config workflow=qc --
You have 19 in 19 groups
localrules directive specifies rules that are not present in the Snakefile:
        initialize_checkm
        finalize_QC

Building DAG of jobs...
Creating conda environment /home/animeshs/.local/lib/python3.6/site-packages/atlas/envs/required_packages.yaml...
Downloading and installing remote packages.
Environment for ../../../home/animeshs/.local/lib/python3.6/site-packages/atlas/envs/required_packages.yaml created (location: .snakemake/conda/3d7da0b3)
...

SilasK commented 3 years ago

Seems you got metagenomes V1.

Look up the docs 'getting started' for how to configure conda channels before installing atlas. I aso recommend to use mamba .

You are working on a linux, aren't you?

animesh commented 3 years ago

Are you referring to https://metagenome-atlas.readthedocs.io/en/latest/usage/getting_started.html# @SilasK ? I tried to follow it through again and looks like channels were already there:

(py36) animeshs@DMED7596:~$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
(py36) animeshs@DMED7596:~$ conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top
(py36) animeshs@DMED7596:~$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top

I tried the git clone using the fork (yes i am using Ubuntu 20.04) without much difference...

So i went for update and looks like there was nothing to be updated?


(py36) animeshs@DMED7596:~$ mamba install metagenome-atlas --update-all
conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
bioconda/linux-64        Using cache
bioconda/noarch          Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
Transaction

  Prefix: /home/animeshs/anaconda3/envs/py36

  All requested packages already installed

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.7.6) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['metagenome-atlas']

and following atlas command gave back the same -h:


(py36) animeshs@DMED7596:~$ atlas -h
Usage: atlas [OPTIONS] COMMAND [ARGS]...

  ATLAS - workflows for assembly, annotation, and genomic binning of
  metagenomic and metatranscriptomic data.

  For updates and reporting issues, see: https://github.com/metagenome-
  atlas/atlas

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  assemble      assembly workflow
  bin-genomes   bins contigs using different binners to genomes
  download      download reference files
  gff2tsv       writes version of Prokka TSV with contig as new first column
  make-config   prepopulate a configuration file with samples and defaults
  merge-tables  merge genepredictions TSV, Counts, and Taxonomy
  munge-blast   adds contig ID to prokka annotated ORFs
  qc            quality control workflow (without assembly)
  refseq        enables tree based LCA and LCA star methods

jmtsuji commented 3 years ago

@animesh What happens if you specify the desired ATLAS version in the mamba install command?

i.e., mamba install -c bioconda -c conda-forge metagenome-atlas=2.4.5

Also, what happens if you specify the python version in the same command?

i.e., mamba install -c bioconda -c conda-forge metagenome-atlas=2.4.5 python=3.6

Perhaps these commands might give further clues about what is going on.

2021年1月10日(日) 22:53 Ani notifications@github.com:

Are you referring to https://metagenome-atlas.readthedocs.io/en/latest/usage/getting_started.html# @SilasK https://github.com/SilasK ? I tried to follow it through again and looks like channels were already there:

(py36) animeshs@DMED7596:~$ conda config --add channels defaults Warning: 'defaults' already in 'channels' list, moving to the top (py36) animeshs@DMED7596:~$ conda config --add channels bioconda Warning: 'bioconda' already in 'channels' list, moving to the top (py36) animeshs@DMED7596:~$ conda config --add channels conda-forge Warning: 'conda-forge' already in 'channels' list, moving to the top

I tried the git clone using the fork (yes i am using Ubuntu 20.04) without much difference...

So i went for update and looks like there was nothing to be updated?

(py36) animeshs@DMED7596:~$ mamba install metagenome-atlas --update-all conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/linux-64 [====================] (00m:00s) No change pkgs/r/linux-64 [====================] (00m:00s) No change pkgs/main/noarch [====================] (00m:00s) No change pkgs/r/noarch [====================] (00m:00s) No change Transaction

Prefix: /home/animeshs/anaconda3/envs/py36

All requested packages already installed
              __    __    __    __
             /  \  /  \  /  \  /  \
            /    \/    \/    \/    \
███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / _/ _/ _/ \ o _, / _/ ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
    mamba (0.7.6) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████

Looking for: ['metagenome-atlas']

and following atlas command gave back the same -h:

(py36) animeshs@DMED7596:~$ atlas -h Usage: atlas [OPTIONS] COMMAND [ARGS]...

ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

For updates and reporting issues, see: https://github.com/metagenome- atlas/atlas

Options: --version Show the version and exit. -h, --help Show this message and exit.

Commands: assemble assembly workflow bin-genomes bins contigs using different binners to genomes download download reference files gff2tsv writes version of Prokka TSV with contig as new first column make-config prepopulate a configuration file with samples and defaults merge-tables merge genepredictions TSV, Counts, and Taxonomy munge-blast adds contig ID to prokka annotated ORFs qc quality control workflow (without assembly) refseq enables tree based LCA and LCA star methods

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/metagenome-atlas/atlas/issues/355#issuecomment-757479945, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEOYTNBGZTPFRLRLG3Y3BZ3SZGWMXANCNFSM4V2PMJLQ .

animesh commented 3 years ago

@jmtsuji status-quo seems to persist:

(py36) animeshs@DMED7596:/mnt/z/ayu$ mamba install -c bioconda -c conda-forge metagenome-atlas=2.4.5 python=3.6
bioconda/linux-64        Using cache
bioconda/noarch          Using cache
conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
Transaction

  Prefix: /home/animeshs/anaconda3/envs/py36

  All requested packages already installed

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.7.6) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['metagenome-atlas=2.4.5', 'python=3.6']
(py36) animeshs@DMED7596:/mnt/z/ayu$ /home/animeshs/anaconda3/envs/py36/bin/atlas
Usage: atlas [OPTIONS] COMMAND [ARGS]...

  ATLAS - workflows for assembly, annotation, and genomic binning of
  metagenomic and metatranscriptomic data.

  For updates and reporting issues, see: https://github.com/metagenome-
  atlas/atlas

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  assemble      assembly workflow
  bin-genomes   bins contigs using different binners to genomes
  download      download reference files
  gff2tsv       writes version of Prokka TSV with contig as new first column
  make-config   prepopulate a configuration file with samples and defaults
  merge-tables  merge genepredictions TSV, Counts, and Taxonomy
  munge-blast   adds contig ID to prokka annotated ORFs
  qc            quality control workflow (without assembly)
  refseq        enables tree based LCA and LCA star methods

jmtsuji commented 3 years ago

@animesh Strange -- can you please run mamba list while your ATLAS environment is activated and then post the output of that command in your next reply? That will show the exact package versions in your ATLAS environment.

2021年1月10日(日) 23:25 Ani notifications@github.com:

@jmtsuji https://github.com/jmtsuji status-quo seems to persist:

(py36) animeshs@DMED7596:/mnt/z/ayu$ mamba install -c bioconda -c conda-forge metagenome-atlas=2.4.5 python=3.6 bioconda/linux-64 Using cache bioconda/noarch Using cache conda-forge/linux-64 Using cache conda-forge/noarch Using cache pkgs/main/noarch [====================] (00m:00s) No change pkgs/r/linux-64 [====================] (00m:00s) No change pkgs/main/linux-64 [====================] (00m:00s) No change pkgs/r/noarch [====================] (00m:00s) No change Transaction

Prefix: /home/animeshs/anaconda3/envs/py36

All requested packages already installed
              __    __    __    __
             /  \  /  \  /  \  /  \
            /    \/    \/    \/    \
███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / _/ _/ _/ \ o _, / _/ ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
    mamba (0.7.6) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████

Looking for: ['metagenome-atlas=2.4.5', 'python=3.6'] (py36) animeshs@DMED7596:/mnt/z/ayu$ /home/animeshs/anaconda3/envs/py36/bin/atlas Usage: atlas [OPTIONS] COMMAND [ARGS]...

ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

For updates and reporting issues, see: https://github.com/metagenome- atlas/atlas

Options: --version Show the version and exit. -h, --help Show this message and exit.

Commands: assemble assembly workflow bin-genomes bins contigs using different binners to genomes download download reference files gff2tsv writes version of Prokka TSV with contig as new first column make-config prepopulate a configuration file with samples and defaults merge-tables merge genepredictions TSV, Counts, and Taxonomy munge-blast adds contig ID to prokka annotated ORFs qc quality control workflow (without assembly) refseq enables tree based LCA and LCA star methods

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/metagenome-atlas/atlas/issues/355#issuecomment-757484741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEOYTNFJTKIKD6DAWN2FDRLSZG2E5ANCNFSM4V2PMJLQ .

animesh commented 3 years ago

Yes @jmtsuji mamba list says metagenome-atlas 2.4.5 py_0 bioconda followiing is complete listing:


                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.7.6) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

# packages in environment at /home/animeshs/anaconda3/envs/py36:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
aioeasywebdav             2.4.0           py36h9f0ad1d_1001    conda-forge
aiohttp                   2.3.9                    py36_0  
alsa-lib                  1.2.3                h516909a_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
arrow                     0.17.0           py36h9f0ad1d_1    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
backports                 1.0                      py36_1    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
bbmap                     38.87                h1296035_0    bioconda
bcrypt                    3.2.0            py36h8c4c3a4_1    conda-forge
binaryornot               0.4.4                    py36_0    conda-forge
biopython                 1.78             py36h8c4c3a4_1    conda-forge
boto3                     1.16.51            pyhd8ed1ab_0    conda-forge
botocore                  1.19.51            pyhd8ed1ab_0    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           2020.12.8            h06a4308_0  
cachetools                4.2.0              pyhd3eb1b0_0  
cairo                     1.16.0            h7979940_1007    conda-forge
certifi                   2020.12.5        py36h5fab9bb_1    conda-forge
cffi                      1.14.4           py36hc120d54_1    conda-forge
chardet                   4.0.0            py36h5fab9bb_1    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
conda                     4.9.2            py36h5fab9bb_0    conda-forge
conda-package-handling    1.7.2            py36he6145b8_0    conda-forge
configargparse            1.2.3              pyh9f0ad1d_0    conda-forge
cookiecutter              1.7.2              pyh9f0ad1d_0    conda-forge
cryptography              3.3.1            py36h0a59100_0    conda-forge
curl                      7.71.1               he644dc0_8    conda-forge
datrie                    0.8.2            py36h8c4c3a4_1    conda-forge
decorator                 4.4.2                      py_0    conda-forge
docutils                  0.16             py36h9880bd3_2    conda-forge
dropbox                   10.10.0          py36h06a4308_0  
expat                     2.2.10               he6710b0_2  
fftw                      3.3.9                h27cfd23_1  
filechunkio               1.8                      py36_1    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            h736d332_1003    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               he06d7ca_0    conda-forge
fribidi                   1.0.10               h516909a_0    conda-forge
ftputil                   4.0.0                      py_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                h516909a_2    conda-forge
git                       2.30.0          pl5320h014a29a_0    conda-forge
gitdb                     4.0.5                      py_0    conda-forge
gitpython                 3.1.12             pyhd8ed1ab_0    conda-forge
glib                      2.66.4               h709712a_1    conda-forge
google-api-core           1.24.1             pyhd3deb0d_0    conda-forge
google-auth               1.24.0             pyhd3eb1b0_0  
google-cloud-core         1.5.0              pyhd3deb0d_0    conda-forge
google-cloud-storage      1.35.0             pyhd3deb0d_0    conda-forge
google-resumable-media    1.2.0              pyhd3eb1b0_1  
googleapis-common-protos  1.52.0           py36h5fab9bb_1    conda-forge
graphite2                 1.3.14               h23475e2_0  
graphviz                  2.42.3               h0511662_0    conda-forge
grpcio                    1.34.0           py36h8e87921_0    conda-forge
harfbuzz                  2.7.4                h5cf4720_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
imagemagick               7.0.10_28       pl5262hfcab4aa_3    conda-forge
importlib-metadata        3.3.0            py36h5fab9bb_2    conda-forge
importlib_metadata        3.3.0                hd8ed1ab_2    conda-forge
jbig                      2.1               h516909a_2002    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jinja2-time               0.2.0                    py36_1    conda-forge
jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
jsonschema                3.2.0            py36h9f0ad1d_1    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
lcms2                     2.11                 hcbb858e_1    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_7  
libarchive                3.5.1                h3f442fb_1    conda-forge
libblas                   3.9.0                7_openblas    conda-forge
libcblas                  3.9.0                7_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libedit                   3.1.20191231         h14c3975_1  
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgfortran-ng            7.5.0               hae1eefd_17    conda-forge
libgfortran4              7.5.0               hae1eefd_17    conda-forge
libglib                   2.66.4               hf9edacf_1    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                7_openblas    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libprotobuf               3.14.0               h780b84a_0    conda-forge
librsvg                   2.50.2               h115801e_2    conda-forge
libsodium                 1.0.18               h516909a_1    conda-forge
libsolv                   0.7.16               h8b12597_0    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
libtiff                   4.2.0                hdc55705_0    conda-forge
libtool                   2.4.6             h58526e2_1007    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.1.0                h56121f0_4    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.14                 h7b6447c_0  
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                     0.7.6            py36hb90a75f_0    conda-forge
markupsafe                1.1.1            py36he6145b8_2    conda-forge
metagenome-atlas          2.4.5                      py_0    bioconda
multidict                 5.1.0            py36h8f6f2f9_0    conda-forge
ncurses                   6.2                  he6710b0_1  
networkx                  2.5                        py_0    conda-forge
numpy                     1.19.5           py36h2aa4a07_0    conda-forge
openjdk                   11.0.8               hacce0ff_0    conda-forge
openjpeg                  2.4.0                hf7af979_0    conda-forge
openssl                   1.1.1i               h7f98852_0    conda-forge
pandas                    0.25.3           py36hb3f55d8_0    conda-forge
pango                     1.42.4               h80147aa_5    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
pbzip2                    1.1.13                        0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h36c2ea0_1008    conda-forge
pip                       20.3.3           py36h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h516909a_1008    conda-forge
poyo                      0.5.0                      py_0    conda-forge
prettytable               2.0.0              pyhd8ed1ab_0    conda-forge
protobuf                  3.14.0           py36hc4f0c31_1    conda-forge
psutil                    5.8.0            py36h8f6f2f9_0    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.8                      py_0  
pycosat                   0.6.3           py36h8f6f2f9_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.7.3              pyhd8ed1ab_0    conda-forge
pygraphviz                1.6              py36hf2b72a0_1    conda-forge
pynacl                    1.4.0            py36h8c4c3a4_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyrsistent                0.17.3           py36h8c4c3a4_1    conda-forge
pysftp                    0.2.9                    py36_0    conda-forge
pysocks                   1.7.1            py36h9880bd3_2    conda-forge
python                    3.6.12               hcff3b4d_2  
python-dateutil           2.8.1                      py_0    conda-forge
python-irodsclient        0.8.2                      py_0    conda-forge
python-slugify            4.0.1              pyh9f0ad1d_0    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
pytz                      2020.5             pyhd8ed1ab_0    conda-forge
pyyaml                    5.3.1            py36he6145b8_1    conda-forge
ratelimiter               1.2.0           py36h9f0ad1d_1001    conda-forge
readline                  8.0                  h7b6447c_0  
reproc                    14.2.1               h36c2ea0_0    conda-forge
reproc-cpp                14.2.1               h58526e2_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
rsa                       4.6                pyh9f0ad1d_0    conda-forge
ruamel                    1.0              py36h9f0ad1d_3    conda-forge
ruamel.yaml               0.15.99          py36h516909a_0    conda-forge
ruamel_yaml               0.15.80         py36he6145b8_1003    conda-forge
s3transfer                0.3.3            py36h9f0ad1d_2    conda-forge
setuptools                51.0.0           py36h06a4308_2  
six                       1.15.0             pyh9f0ad1d_0    conda-forge
smmap                     3.0.4              pyh9f0ad1d_0    conda-forge
snakemake                 5.8.2                         0    bioconda
snakemake-minimal         5.8.2                      py_0    bioconda
sqlite                    3.33.0               h62c20be_0  
text-unidecode            1.3                        py_0    conda-forge
tk                        8.6.10               hbc83047_0  
tqdm                      4.55.1             pyhd8ed1ab_0    conda-forge
typing-extensions         3.7.4.3                       0    conda-forge
typing_extensions         3.7.4.3                    py_0    conda-forge
unidecode                 1.1.2              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.2             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.36.2             pyhd3eb1b0_0  
whichcraft                0.6.1                      py_0    conda-forge
wrapt                     1.12.1           py36h8f6f2f9_3    conda-forge
xmlrunner                 1.7.7                      py_0    conda-forge
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_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-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxpm               3.5.13               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h516909a_1003    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-recordproto          1.14.2            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h516909a_0    conda-forge
yarl                      1.5.1            py36h8c4c3a4_0    conda-forge
zipp                      3.4.0                      py_0    conda-forge
zlib                      1.2.11               h7b6447c_3  
zstd                      1.4.8                ha95c52a_1    conda-forge

SilasK commented 3 years ago

Hey @animesh can you please tell me the output of 'which atlas' Somehow atlas refers to the old version even if mamaba has instlled the correct one.

animesh commented 3 years ago

Sure @SilasK, which atlas points to /home/animeshs/anaconda3/envs/py36/bin/atlas

SilasK commented 3 years ago

Hmm..

Check the content of the file cat /home/animeshs/anaconda3/envs/py36/bin/atlas

It should be something like:

#!/Users/silas/miniconda3/envs/atlasenv/bin/python3.6
# -*- coding: utf-8 -*-
import re
import sys

from atlas.atlas import cli

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    sys.exit(cli())

And then let's check:

head /home/animeshs/anaconda3/envs/py36/lib/python3.6/site-packages/atlas/__init__.py

Which should be something like:

__version__ = "2.3.0"

from .scripts import utils

(Note to myselve update updated the version in the init script from 2.3 to 2.4.5)

If you don't get this I suggest you to uninstall and re-install atlas with mamba.

If you have this, I don't understand why you get atlas version 1 when typing atlas

animesh commented 3 years ago

Looks like init init.txt shows __version__ = "2.4.4" not 2.4.5, could that be issue? BTW have tried re-installing without change.

Script atlas.py atlas.txt shows:

#!/home/animeshs/anaconda3/envs/py36/bin/python3.6
# -*- coding: utf-8 -*-
import re
import sys

from atlas.atlas import cli

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    sys.exit(cli())

SilasK commented 3 years ago

Ok, No I think you got atlas v2.4.5 correctly installed.

SilasK commented 3 years ago

I understand why you get the atlas v1 when you have v2 installed?

You have never installed atlas v1 consciously, have you?

Can you try this?

run python in the py36 env, then:


>> from atlas import atlas
>> atlas.__file__ # sould get  /home/animeshs/anaconda3/envs/py36/lib/python3.6/site-packages/atlas/atlas.py
>> atlas.__version__ # should be 2.4.4 
atlas.cli()

animesh commented 3 years ago

Not that i am aware of installing v1 but python is still magic as atlas.__version__ '2.0.0' to me so i am not sure... anithing is possible! I tried to go through your commands and below is what i get:

(py36) animeshs@DMED7596:/mnt/z/ayu$ python
Python 3.6.12 |Anaconda, Inc.| (default, Sep  8 2020, 23:10:56)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from atlas import atlas
>>> atlas.__file__
'/home/animeshs/.local/lib/python3.6/site-packages/atlas/atlas.py'
>>>atlas.__version__
'2.0.0'
>>> atlas.cli()
... kicks out
 download      download reference files
  gff2tsv       writes version of Prokka TSV with contig as new first column
  make-config   prepopulate a configuration file with samples and defaults
  merge-tables  merge genepredictions TSV, Counts, and Taxonomy
  munge-blast   adds contig ID to prokka annotated ORFs
  qc            quality control workflow (without assembly)
  refseq        enables tree based LCA and LCA star methods
(py36) animeshs@DMED7596:/mnt/z/ayu$

SilasK commented 3 years ago

I think the snake is eating its own tail. Ok It seems that there is a atlas v2.00 installed in "/home/animeshs/.local/lib/python3.6/site-packages" And the atlas v2.4 in your environment py36: /home/animeshs/anaconda3/envs/py36/lib/python3.6/site-packages/atlas

The first path takes priority over the second and that's why you get the version 2.00 instead of 2.4.

You should remove 'metagenome-atlas' from the .local/lib . But maybe even better would be to remove the .local/lib path completely from your python paths. Because it can more harm, e.g. if you have python packages installed in the local and the environment-specific directory.

The local seems not to be handled by anaconda and might belong to your machines python. Did you load the machine python module?

I fear I can tell you exactly how to fix the python path problem but you are surely not the first one on the internet.

animesh commented 3 years ago

Thanks for the tip @SilasK , rm -rf /home/animeshs/.local/lib/python3.6/site-packages/atlas/ seems to have magically invoked atlas init but to run all, had to specify --cores argument though?


[2021-01-11 14:15 INFO] Executing: snakemake --snakefile /home/animeshs/anaconda3/envs/py36/lib/python3.6/site-packages/atlas/Snakefile --directory /mnt/z/ayu  --rerun-incomplete --configfile '/mnt/z/ayu/config.yaml' --nolock   --use-conda --conda-prefix /mnt/z/ayu/databases/conda_envs   all  --cores 12
Building DAG of jobs...
Creating conda environment /home/animeshs/anaconda3/envs/py36/lib/python3.6/site-packages/atlas/rules/../envs/DASTool.yaml...
Downloading and installing remote packages.

```so far ... so good?

SilasK commented 3 years ago

yes, so far ... so good! I just fear that there are other packages in the. .local/lib/python3.6 which are loaded in priority.

metagenome-atlas / atlas

No such command 'init'. #355