bactopia

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Apple silicon M2

5

Have you tested Bactopia on M2? If so any tricks?

mabouelk

Core Nextflow options runName : curious_booth container : quay.io/bactopia/bactopia:3.0.0 launchDir : /home/shsmu/Data/Temp/Results workDir : /home/shsmu/Data/Temp/Results/work projectDir : /home/shsmu/anaconda3/envs/bactopia/share/bactopia-3.0.0 userName : shsmu profile : standard configFiles : /home/shsmu/anaconda3/envs/bactopia/share/bactopia-3.0.0/nextflow.config Required Parameters bactopia...

yzhzu

[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 -...

Svnipni

[bug] ValueError: invalid literal for int() with base 10: 'null'

3

**Description** Running bactopia summary --bactopia-path bactopia_out/ -o summary In the merged-results folder, the meta.tsv file has a genome_size of 0 for every entry. In the individual meta.tsv files the genome_size...

waoverholt

[question]

1

Hello! Firstable, I would like to say that Bactopia is awesome and the way is constructed is incredible! 1. I am working on MLST analysis, and I would like to...

Kokejuli

[bug] WARN: There's no process matching config selector:

1

**Description** When using the AWS profile to run bactopia via NF Tower/Batch we get warnings that there are no processes that match some of the profile config selectors. output sample...

rwilliams

multiple ont reads for one sample-how to prepare --sample file[question]

7

Hi @rpetit3 I have multiple ont reads for one sample and I have multiple samples to process in one go. Could you please see my input file below and suggest...

kusandeep

summary path not consistant with the tool suggest argument [bug]

1

**Description** A description of the bug you are experiencing. when running summary program bactopia summay --bactopia /path/to/bactopia/results **Steps to Reproduce** a summary of run Steps to reproduce the behavior: ```...

alarawms

[question] Can I run ariba tool with all databases in one go?

1

Hello! I've setup Bactopia 2.2.0 on my institute HPC. In a previous run with Bactopia about a year ago, I was able to provide a path to a pre-configured ariba...

shigdon

[question] Errors running bactopia singularity container in slurm cluster (ComputeCanada)

5

Hello I have been trying to run the bactopia pipeline from the singularity (supported in my cluster) container pulled from `quay.io`. I managed to download the datasets, which worked only...

azmigueldario