conda install ONT environment fails

[estolle]

Hi there

I wanted to try the pipeline on some insect data (Illumina + ONT reads).

I seem to have problems to use your conda yml file for ONT. I am getting this error:

Solving environment: failed ResolvePackageNotFound:

• gcc_impl_linux-64==7.3.0=habb00fd_2

I could not yet solve it. The pacbio install works.

If I change the listed problematic package to gcc_impl_linux-64=7.3.0 or gcc_impl_linux-64 then it comes up with loads! of conflicts.

Any ideas?

I also wonder whether I could use the pacbio pipeline using error-corrected ONT reads (fasta, corrected with ratatosk from ca 80X coverage)?

Thanks, Eckart

[estolle]

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

[gf777]

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

[estolle]

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.

[gf777]

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

[arangrhie]

Feel free to reopen if needed.