Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, performs de novo reconstruction of transcriptomes from RNA-seq data. If you run this on Artemis, you will achieve best performance if you specify the --workdir option to use local node storage instead of /project, /scratch, or /home. This is because large assemblies generate millions of small files that degrade the performance of Artemis's Lustre filesystem. Node local storage performs much better for this kind of workload.
The way to tell Trinity to write to node local storage is:
export TRINITY_WORKDIR=${TMPDIR}/trinity_workdir--workdir ${TMPDIR}/t
#!/bin/bash
#PBS -P Project
#PBS -l select=1:ncpus=4:mem=16gb
#PBS -l walltime=1:00:00
#PBS -j oe
module load python
module load bowtie2/2.3.3.1
module load samtools/1.8
module load jellyfish/2.2.6
module load salmon/0.11.0
module load trinity/2.6.6
export TRINITY_WORKDIR=${TMPDIR}/trinity_workdir
export OUTDIR=/project/SASTEST/skol2049/trinity/trinity_output
mkdir -p ${TRINITY_WORKDIR}
cd "${PBS_O_WORKDIR}"
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
Trinity --seqType fq --max_memory 4G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--output ${OUTDIR} \
--workdir ${TRINITY_WORKDIR} \
--SS_lib_type RF \
--CPU 4