Trinity stage 4 job script 

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -q batch
#PBS -N trinity_stage4
#
# Define the directory where the job will run
OUTDIR=$SCRATCH/trinity_stage_exampl
#
# Start the accounting report
ja
#
# Turn on echo so all commands are echoed in standard output
set -x
#
# Setup the module command
source /usr/share/modules/init/bash
#
# Load the needed modules
# Here trinity version r2012-10-05 is used
# Java is also used
module load trinity/r2012-10-05
module load java
#
# Move to the job directory that was created in stage1
cd $OUTDIR
########################################################
##  Run Trinity to Generate Transcriptome Assemblies  ##
##  Run butterfly, generate final Trinity.fasta file  ##
########################################################
Trinity.pl --JM 8G --CPU 16 --bflyCPU 16 --bflyGCThreads 16 \
--seqType fq  --SS_lib_type RF \
--left reads.left.fq.gz --right reads.right.fq.gz \
--output trinity_out_dir >& trinity_stage4_example.log
##################
####   Done.  ####
##################
#
# Get the accounting report
ja -o | gawk '$3 > 10.0 {print}'
ja -set
Last Updated on Thursday, 29 November 2012 14:50  

More on Trinity

Examples

  • Example files which show how to run Trinity in one run (for very small datasets) or in four stages (for larger datasets).

Documentation

More User Information

Passwords

Connect to PSC systems:

PSC Policies

Technical questions:

Call the PSC hotline: 412-268-6350 / 800-221-1641 or mail to remarks@psc.edu.