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No such command 'init'. #355
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Very strange. Do you really have metagenome-atlas. atlas might refer to another tool. Try to run just. I get:
and |
Help invocation emits:
I tried qc and it seems to be working?
|
Seems you got metagenomes V1. Look up the docs 'getting started' for how to configure conda channels before installing atlas. You are working on a linux, aren't you? |
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:
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?
and following atlas command gave back the same -h:
|
@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) ***@***.***:~$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
(py36) ***@***.***:~$ conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top
(py36) ***@***.***:~$ 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) ***@***.***:~$ 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
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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) ***@***.***:~$ 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
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<#355 (comment)>,
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.
|
@jmtsuji status-quo seems to persist:
|
@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) ***@***.***:/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) ***@***.***:/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
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You are receiving this because you were mentioned.
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<#355 (comment)>,
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.
|
Yes @jmtsuji
|
Hey @animesh can you please tell me the output of 'which atlas' |
Sure @SilasK, |
Hmm.. Check the content of the file It should be something like:
And then let's check:
Which should be something like:
(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 |
Looks like init Script atlas.py
|
Ok, No I think you got atlas v2.4.5 correctly installed. |
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:
|
Not that i am aware of installing v1 but python is still magic as
|
I think the snake is eating its own tail. 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. |
Thanks for the tip @SilasK ,
|
yes, so far ... so good! |
init commands fails
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