José Luis Villanueva-Cañas

[bug]

3

**Description** Hi, I am having problems downloading the datasets for the tutorial. I have tried the regular bactopia datasets and also restricting to --ariba card (see below) but both apporaches...

[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...

[question] limit memory kraken2

5

Hi, I am trying to run kraken2 on a machine with 50Gb RAM. ``` bactopia -profile singularity --wf kraken2 \ --bactopia /home/jlvillanueva/Documents/SALMONELLA/bactopia_v3_results \ --kraken2_db /home/jlvillanueva/bactopia/kraken_db/k2_pluspf_20221209.tar.gz \ --include includes.txt --max_cpus 4...

[error] SIGSEGV: Illegal storage access. (Attempt to read from nil?) Segmentation fault (core dumped) (

14

Hi, I am getting an error in the last step of ancestry calling, after succesfully generating all the *.somalier query files and downloading the relevant ancestry-labels-1kg.tsv file and 1kg.somalier/*.somalier files....

manta path error

14

### Description of the bug Manta fails with a path error: ``` error [java.lang.InterruptedException]: java.lang.InterruptedException Jan-16 03:00:07.184 [Actor Thread 16] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (1)' Caused...

somalier (sample control + ancestry)

1

### Description of feature Implement the software somalier to have a quality control to detect sample swaps, as well as some output on the ancestry of the sample, very useful...

error installation

5

I am getting this error while trying to install clodius. `sudo pip install clodius` > Collecting clodius > Downloading https://files.pythonhosted.org/packages/7f/f4/9409fa3e1917cd8de859943de7dd77286391873c7aa0f55bccfdfad86cb2/clodius-0.9.3.tar.gz (90kB) > 100% |████████████████████████████████| 92kB 2.1MB/s > Requirement already satisfied:...

Hi, I am getting an error related with multi-core usage. I am executing cfdnapipe in a slurm cluster in a job with 24 cores available. A fraction of the log...