EukDetect on Biowulf

EukDetect is a python-based workflow application that detects eukaryotes in shotgun metagenomic data using eukaryotic gene markers. According to the authors:

EukDetect is accurate, sensitive, has a broad taxonomic coverage of microbial eukaryotes, and is resilient against bacterial contamination in eukaryotic genomes.

The application can be run using the eukdetect executable or with snakemake that comes bundled with the application. The gene markers are available in /fdb/eukdetect/eukdb. User must create a configuration YAML for the pipeline. A default YAML is available to Biowulf users with certain fields edited based on the installation.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=8G -c4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load eukdetect

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ mkdir fastq

[user@cn3144 ~]$ cp $EUKDETECT_EXAMPLES/*fastq.gz fastq/

[user@cn3144 ~]$ cp $EUKDETECT_SHARE/default_configfile.yml .

[user@cn3144 ~]$ nano default_configfile.yml
# Edit YAML and set output_dir, fq_dir, and samples fields correctly

[user@cn3144 ~]$ eukdetect --mode runall --configfile default_configfile.yml --cores 4
  01/20/2022 16:43:16:  Parsing config file ...
  01/20/2022 16:43:16:  Running: snakemake --snakefile /opt/EukDetect/rules/eukdetect.rules --configfile default_configfile.yml --cores 4
  01/20/2022 16:43:16:  Redirecting snakemake output to snakemake_1642714996.749603.log
  01/20/2022 16:43:46:  Snakemake finished
  01/20/2022 16:43:46:  Snakemake pipeline created all files.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load eukdetect
eukdetect --mode runall --configfile default_configfile.yml --cores $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]