Comments (7)
Just a quick note on the FAQs
Can I assemble more than one genome at a time?
If you would like to assemble more than one genome using Dragonflye, I would recommend you do this with [Bactopia](https://bactopia.github.io/). Bactopia will allow you to process a single genome or thousands, and it also includes many other bacterial genome analyses. If you don't want to use Bactopia, I suggest you see the next question!"
You could also include a note in the above statement about the bacass Nextflow pipeline (https://github.com/nf-core/bacass), which uses Dragonflye (or other select assemblers) to assemble more than one genome.
Thanks once again for your excellent pipeline.
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I see from this section (https://github.com/rpetit3/dragonflye/blob/main/bin/dragonflye#L416) that the current version of dragonflye has the correct Polypolish sub-command. So, I edited that section of the dragonflye script. Everything now works correctly. I guess the dragonflye version from nfcore (https://github.com/nf-core/modules/blob/master/modules/nf-core/dragonflye/environment.yml) needs to be updated accordingly.
from dragonflye.
Hi @ayoraind
Thank you for letting me know about this, and I'm glad you found a solution.
I'm curious what error v1.2.0 was giving you on the install. I wonder if I need to make a fix on the recipe on bioconda
Thanks again!
Robert
from dragonflye.
Hi @rpetit3,
I am not entirely sure what to infer from the error message on dragonflye v1.2.0 installation trial. I show you the exact error message below:
Failed to create Conda environment command: conda env create --prefix /MIGE/01_DATA/07_TOOLS_AND_SOFTWARE/nextflow_pipelines/genome_assembly/bacass_local/work/conda/dragonflye-d3b17908bb97f659610e7f564f13c8d5 --file /MIGE/01_DATA/07_TOOLS_AND_SOFTWARE/nextflow_pipelines/genome_assembly/bacass_local/conda_environments/dragonflye.yml status : 143 message: Retrieving notices: ...working... done Collecting package metadata (repodata.json): ...working... WARNING conda.models.version:get_matcher(544): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1 WARNING conda.models.version:get_matcher(544): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0 WARNING conda.models.version:get_matcher(544): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0 WARNING conda.models.version:get_matcher(544): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0 done Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <== current version: 22.11.1 latest version: 24.3.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=24.3.0
Downloading and Extracting Packages
pyyaml-6.0.1 | 167 KB | | 0%
On the other hand, I was able to conda install the previous version (dragonflye v1.1.2) without any issue.
from dragonflye.
Hi @ayoraind
Looks like it might be a conda issue. I'm able to solve the environment using conda version 24.3.0, but not on version 23.7.3.
I think its related to conda 24 using libmamba, so in your case if its possible to upgrade or use mamba I think you'll be able to use v1.2.0.
Cheers,
Robert
from dragonflye.
Hi @rpetit3,
Many thanks. I updated my conda version as you suggested and re-ran dragonflye (v1.2.0). Everything works perfectly.
from dragonflye.
Ok I added mention of bacass is the alternatives.
Going to go ahead and close this, feel free to reopen
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