bactopia

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[bug] quast workflow fails

11

**Description** I am having some issues with the QUAST workflow, others like genotyphi or mashtree work without problems. problem -> the QUAST workflow fails **Steps to Reproduce** Steps to reproduce...

egenomics

[bug] (or user error) kraken2 db not found

2

Hi! Probably doing something wrong here, but left bug in title just-in-case :) **The Error** ``` -------------------------------------------------------------------- ERROR ~ Required parameters are missing, please check: --kraken2_db -- Check '.nextflow.log' file...

incoherentian

--reference file not working for snippy tool [bug]

3

**Description** I'm trying to run the snippy tool on my samples. I've downloaded the GenBank reference from NCBI (GCA_000013425.1_ASM1342v1_genomic.fna) and have it in my working directory. The code runs but...

aperreault

Sample IDs vs Experiment accessions

2

Hi! In the bactopia tutorial its stated that if a single Experiment has multiple Run accessions associated with it, bactopia will merge the fastq files from each run into a...

andreaniml

roary module in pangenome failed [bug]

9

**Description** While running pangenome through Docker, received message saying roary module was terminated. **Steps to Reproduce** Steps to reproduce the behavior: ``` bactopia --wf pangenome --use_roary --species "Staphylococcus aureus" --bactopia...

aperreault

Error linking to bactopia results for ariba tool[bug]

4

**Description** I tried running the ariba tool after completing the initial bactopia analysis, but received an error related to linking those results to ariba. Something related to the datasets_cache I'm...

aperreault

[bug] bactopia tool phispy does not find samples

11

Hi Robert, I try to use `phispy` for my data, but it stops with: ``` Found 0 samples to process 518 samples were excluded due to missing files. ``` This...

lfenske-93

error message when installing Bactopia on an HPC cluster

1

Hi bactopia users, I am getting the following error after trying to install Bactopia in our HPC cluster: ERROR ~ Error executing process > 'BACTOPIA:GATHER:GATHER_MODULE (1)' Caused by: Failed to...

fransamsing

[feature] Full AMRFinderPlus search combining results to get maximum information

2

Hi @rpetit3 , **Related To** - [x] Bactopia - [x] Bactopia Tools **Is this related to a problem?** **Is this something you would like to see added?** It might be...

llk578496

**Related To** - [ ] Bactopia - [ ] Bactopia Tools **Is this related to a problem?** A description of what the problem is. Ex. I'm always converting X to...

rpetit3