DIA-NN is an application used to process mass spec proteomics data using high-throughput methods. According to the authors:

DIA-NN - a universal software suite for data-independent acquisition (DIA) proteomics data processing. Conceived at the University of Cambridge, UK, in the laboratory of Kathryn Lilley (Cambridge Centre for Proteomics), DIA-NN opened a new chapter in proteomics, introducing a number of algorithms which enabled reliable, robust and quantitatively accurate large-scale experiments using high-throughput methods. DIA-NN is currently being further developed in the laboratory of Vadim Demichev at the Charité (University Medicine Berlin, Germany).

References:

• Demichev, V., Messner, C.B., Vernardis, S.I. et al. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods 17, 41–44 (2020).
• Please see the full citation list on DIA-NN Github Page

• DiaNN Github Site
• diann Command Line Reference

• Module Name: diann (see the modules page for more information)
• Multithreaded
• You can only use DIA-NN's command-line interface (CLI) on Biowulf. The GUI is not available.

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

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=16G
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 diann

[user@cn3144 ~]$ cd /data/$USER/project # change this path accordingly

[user@cn3144 project]$ diann --threads $SLURM_CPUS_PER_TASK \
  --fasta input.fasta \
  --cfg config_file \
  --out report.tsv \
  --dir output_dir

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

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

#!/bin/bash
set -e
module load diann
diann --threads $SLURM_CPUS_PER_TASK \
  --fasta /data/$USER/project/input.fasta \
  --cfg /data/$USER/project/config_file \
  --out report.tsv \
  --dir /data/$USER/project/output_dir

Make sure to update the paths according to your need. Then submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] diann.sh

Create a swarmfile (e.g. diann.swarm). For example:

diann --threads $SLURM_CPUS_PER_TASK --fasta input1.fasta --cfg config.txt --out report1.tsv --dir outdir
diann --threads $SLURM_CPUS_PER_TASK --fasta input2.fasta --cfg config.txt --out report2.tsv --dir outdir
diann --threads $SLURM_CPUS_PER_TASK --fasta input3.fasta --cfg config.txt --out report3.tsv --dir outdir
diann --threads $SLURM_CPUS_PER_TASK --fasta input4.fasta --cfg config.txt --out report4.tsv --dir outdir

Submit this job using the swarm command.

swarm -f diann.swarm [-g #] [-t #] --module diann