Svnipni

Yes, this was still V2. Will try it with V3 on Monday!

I'm still getting a 11Mbp genome from what I expected to be no larger than 6-7Mbps. I ran `bactopia --r1 B_1.fastq.gz --r2 B_2.fastq.gz --sample sample_Pprotegens_v3 --species "Pseudomonas protegens" --genome_size 6000000...

There are two .aln.gz files. core-genome.aln.gz core_gene_alignment.aln.gz both contain a core_gene_alignment.aln of 190b I can try to load/read it when Im back at the office. Edit: the files only show...

Not entirely sure what you mean. These samples are quite different. They're all isolates from freshwater sediments nearby and individual analyses on these samples showed they're different strains/species. I ran...

I think Im having a similar albeit it different issue. Genovi seems to get stuck on my specific .gbk as it worked out of the box for a few of...

I tried to just update mamba and bactopia first. I made a little progress with removing the environment with `--all` and reinstalling. but once everything was installed, `bactopia -profile test,standard`...

I fully reinstalled mamba and setup bactopia from scratch. Seems it's working now and it passes the `bactopia -profile test,standard` run. > what are the contents of your base environment?...

Hi Robert! No, preferably aligned to the assembled genome. Amongst other things, I mean to wrap several samples up to construct a pangenome with anvio. If I understand correctly, it...

Thank you! I tried running snippy before, but it didn't recognize the genbank reference file downloaded from NCBI. ``` echo "ERROR: Reference file (GCA_012767755.2.gb) does not appear to be a...

Cheers! Yes i assumed as much :) ill keep an eye out for an update