#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -o runtrinity.out
#PBS -q debug
#PBS -N runtrinity
# define where the input data is stored
DATADIR=~nigra/trinity/data
# turn on accounting
ja
# turn on echo
set -x
# set up the module command
source /usr/share/modules/init/bash
# load the trinity module
# Here we use version r2012-05-18
# Be careful to load the specific version you want
module load trinity/r2012-05-18
# move to your scratch directory
cd $SCRATCH
# copy the input data here
cp $DATADIR/reads.*.fq.gz .
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
## ##
## redirect trinity output to a file in $SCRATCH ##
## ##
## IMPORTANT NOTE ##
## So that you can see the ##
## entire trinity command line on your screen ##
## we've broken it up here into multiple lines. ##
## When you submit a job, BE SURE that ##
## your trinity command is all on one line. ##
#######################################################
Trinity.pl --seqType fq --kmer_method jellyfish --max_memory 8G --left reads.left.fq.gz
--right reads.right.fq.gz --SS_lib_type RF --group_pairs_distance 501
--path_reinforcement_distance 76 --min_contig_length 201 --CPU 12 --bflyCPU 12
--bflyGCThreads 12 --bfly_opts "-V10 --stderr" > trinity.output
#############################
#### Done. ###############
#############################
cp -r trinity_out_dir $DATADIR
cp trinity.output $DATADIR
# get some job statistics
ja -o | gawk '$3 > 10.0 {print}'
ja -set
Trinity job script
Resources for Users
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
- Set or change your PSC password
Connect to PSC systems:
PSC Policies
Technical questions:
Call the PSC hotline: 412-268-6350 / 800-221-1641 or mail to remarks@psc.edu.
