IonQuant on Biowulf

IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool.


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 --cpus-per-task=8 --mem=16g
salloc.exe: Pending job allocation 4852341
salloc.exe: job 4852341 queued and waiting for resources
salloc.exe: job 4852341 has been allocated resources
salloc.exe: Granted job allocation 4852341
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0852 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn0852 ~]$ module load ionquant
[+] Loading ionquant  1.8.0  on cn0852
[+] Loading java 12.0.1  ...

[user@cn0852 ~]$ java -jar $IONQUANT_JAR -h | head
IonQuant version IonQuant-1.8.0
Batmass-IO version 1.25.5
timsdata library version timsdata-2-7-0
(c) University of Michigan
System OS: Linux, Architecture: amd64
Java Info:, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 2 GB memory
        java -jar IonQuant.jar  --specdir  --psm  --psm ...

Batch job
Most jobs should be run as batch jobs.

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

set -e
module load ionquanti
cd /path/to/data/and/conf

java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --threads=${SLURM_CPUS_PER_TASK} --filelist <files>

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 1>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 2>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 3>
java -Xmx${SLURM_MEM_PER_NODE}m -jar $IONQUANT_JAR --num_threads=${SLURM_CPUS_PER_TASK} --filelist <files 4>

Submit this job using the swarm command.

swarm -f ionquant.swarm [-g #] [-t #] --module ionquant
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module TEMPLATE Loads the TEMPLATE module for each subjob in the swarm