conda install ONT environment fails about vgp-assembly HOT 5 CLOSED

my conda info is this:

active environment : None
shell level : 0
user config file : /home/estolle/.condarc
populated config files : /home/estolle/.condarc
conda version : 4.8.2
conda-build version : 3.18.11
python version : 3.7.6.final.0
virtual packages : __glibc=2.17
base environment : /share/scientific_bin/anaconda3/2020.02 (read only)
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/w-l/linux-64
https://conda.anaconda.org/w-l/noarch
https://conda.anaconda.org/r/linux-64
https://conda.anaconda.org/r/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /share/scientific_bin/anaconda3/2020.02/pkgs
/home/estolle/.conda/pkgs
envs directories : /home/estolle/.conda/envs
/share/scientific_bin/anaconda3/2020.02/envs
platform : linux-64
user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/3.10.0-693.5.2.el7.x86_64 centos/7.4.1708 glibc/2.17
UID:GID : 1018:1018
netrc file : None
offline mode : False

from vgp-assembly.

Hi Eckart, sorry I must have overlooked this message as it wasn't mentioning the mitoVGP pipeline directly. You are referring to this right? Short answer to your second question: no you cannot use the Pacbio pipeline for ONT data, the two data types have to be treated differently and hence they undergo different steps, particularly during polishing. Were you able to solve the issue in the meantime? If not I can look into it. Best, Giulio

from vgp-assembly.

Dear Giulio

Thanks alot. I've tried a similar approach with my ONT assemblies/reads which in principle should work. But It seems the MT is not part of the two assembled genomes I analyzed nor has useful amounts of MT reads. I think I'll leave it at that for the moment.

from vgp-assembly.

Sounds good Eckart. Don't hesitate to contact me if you have any more requests. Best Giulio

from vgp-assembly.

Feel free to reopen if needed.

from vgp-assembly.