No option --perform_taxonomic_assignment

[ciemanek]

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]

Hi @ciemanek,

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

[ciemanek]

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]

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]

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