No option --perform_taxonomic_assignment

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics

GNU Affero General Public License v3.0

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No option --perform_taxonomic_assignment #73

Open ciemanek opened 5 years ago

ciemanek commented 5 years ago

When I try to run matam_assembly.py from the conda installation MATAM, I get an error that it doesn't recognize an option --perform_taxonomic_assignment. Does conda version not include this option?

loic-couderc commented 5 years ago

Hi @ciemanek,

The conda version does include the --perform_taxonomic_assignment. Could you please join the full error message ?

ciemanek commented 5 years ago

Hi Loïc,

The error is: Error: unrecognized arguments: --perform_taxonomic_assignment

I tried also an installation via GitHub and the option is valid then (it is also displayed in --help). I think for some reason, when I install MATAM via conda, an older version is installed rather than v1.5.3:

loic-couderc commented 5 years ago

Maybe if you provide the version of MATAM package during the installation and perform the installation in a separate environment will resolve your issue. Can you try the following command ?

conda -n matam -c bonsai-team matam=v1.5.3

ciemanek commented 5 years ago

I think installing from GitHub is sufficient for now, but I also tried specifying a version in conda (conda install -c bonsai-team matam=v1.5.3) which gives me an error:

PackagesNotFoundError: The following packages are not available from current channels: matam=v1.5.3 -> coreutils matam=v1.5.3 -> krona matam=v1.5.3 -> rdptools matam=v1.5.3 -> samtools==1.4.1