Svnipni

[question] mapping directory

7

Hello Robert! I'm having a lot of fun with this pipeline. Right now I'm trying to have bactopia output the mapping files (.bam) too. Thusfar, I hadn't really needed it...

[question] use of max_genome_size?

4

I've had great usage of this pipeline on my isolates. But one isolate sample seems to always return a 11Mbp genome on assembly where a typical P.protegens genome size of...

[question] Error creating Conda environment?

5

Big grats on release V3! I wanted to give it a whirl right away. Installation worked fine but a test run gave me ``` 2023-09-13 11:03:01 ERROR 2023-09-13 11:03:01:root:ERROR -...

[bug] Roary error: .aln.gz Unknown sequence type?

4

**Roary pangenome ends with command exit status: 2** Trying to run roary pangenome wf on bactopia output, but exits at CLONALFRAMEML:IQTREE ``` Error executing process > 'BACTOPIATOOLS:PANGENOME:CLONALFRAMEML:IQTREE (start-tree)' Caused by:...

[feature] genome-guided transcriptomics

1

Hi, Since bactopia has such a comprehensive toolset (both as part of a workflow, or separate modules and tools), I wondered if a transcriptome workflow would could be added if...

[bug] Process `BACTOPIA:DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (1)

3

Hey, I just set up bactopia on a new machine running Ubuntu 25.04 with mamba. Running a basic E.coli assembly `bactopia --r1 sample1_1.fastq.gz --r2 sample1_2.fastq.gz --sample ABAR1 --species "Escherichia coli"...