Natalia Quinones-Olvera

Mash sketching failing silently with conda installation

1

**TL;DR; I think there's a problem with `mash`/`gsl` in the `conda` installation. This causes `mob_init` to fail (silently) in the "Sketching complete plasmid database" step.** When trying to run `mob_typer`,...

Creating empty files when there's no data

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Hello, First of all, fantastic software! I've been trying it out and it's super cool. I have a suggestion regarding the output files. As you mention in the README: _files...

I am using Unicycler to assemble linear phage genomes. They are being marked as _incomplete_ so I can't use the `--start_genes` option, I believe because it does it through [rotate_completed_replicons](https://github.com/rrwick/Unicycler/blob/f3e35b2977eb50003fed6f08881107f70ba312a9/unicycler/unicycler.py#L918)?...

Bacterial library contains archaeal genomes

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The bacterial genome collection, downloaded from [the Zenodo's ProPhyle source data](https://zenodo.org/record/1054426/files/bacteria.tar.gz), contains some archaeal genomes. For example, accession: `NC_002578`. A way to detect this and filter it out is: 1....

Simplification fails in my installation (vpype read -s <svg_file>)

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**Problem:** The following command fails in my installation: `vpype read -s scale_test.svg` I get the following error: ``` Traceback (most recent call last): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/nquinones/miniforge3/envs/vsketch/lib/python3.12/site-packages/vpype/io.py", line 343, in _process_path...