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Bioinformatics - SOAPdenovo-Trans
Instructions on how to run (and, if needed, install a customized version of) SOAPdenovo-Trans
SOAPdenovo-Trans is a de novo transcriptome assembler designed specifically for RNA-Seq.
Please refer to the CCAST User Guide and the the article Running Bioinformatics Software on HPC Clusters for general information about using CCAST resources and running bioinformatics software on CCAST's HPC clusters.1. Running SOAPdenovo-Trans on Thunder
Example: Assemble reads into full-length transcript sets
Location: /gpfs1/projects/ccastest/training/examples/SOAPdenovo-Trans_example
File list
· soapdenovo-trans.pbs: job submission script
· config.txt: the configuration file directs SOAP to performance function
· example_reads (directory): sequences to be assembled in fasta format
Steps
· Copy example directory to your SCRATCH directory
o “cp -r /gpfs1/projects/ccastest/training/examples/SOAPdenovo-Trans_example $SCRATCH”
· Go to the copied directory
o “cd $SCRATCH/SOAPdenovo-Trans_example”
· Edit the job submission script as needed, then submit the job
o “qsub soapdenovo-trans_job.pbs”
2. Install Customized SOAPdenovo-Trans on Thunder
Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.
Summary
(a) Require 64-bit Linux systems
(b) For animal transcriptomes like mouse, about 30-35GB memory would be required.
(c) This installation will create dynamically linked libraries – as statically linked libraries has been found to cause a number of errors with this program.
(d) Denote number of threads with “-p $NCPUS.” Not multi-node.
Details
In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME” is your username on Thunder.
(a) Install SOAPdenovo-Trans from source
· Go to the SOFTWARE directory:
o "cd /gpfs1/home/USERNAME/SOFTWARE"
· Clone SOAPdenovo-Trans:
o "git clone https://github.com/aquaskyline/SOAPdenovo-Trans.git"
· Go to SOAPdenovo-Trans directory:
o "cd SOAPdenovo-Trans"
· Remove the "-static" flag:
o "sed -i '/CFLAGS=/s/-static//g' src/Makefile"
· Make:
o "sh make.sh"
(b) Test
One must write a config file before invoking one of the two commands "SOAPdenovo-Trans-127mer" and "SOAPdenovo-Trans-31mer"
· Go to the scratch directory:
o "cd /gpfs1/scratch/USERNAME"
· Make and go into test directory:
o "mkdir SOAPdenovo-Trans_example"
o "cd SOAPdenovo-Trans_example"
· Download data file and unzip: (Only use some of them, as same as the one used in fastqc test)
o "wget http://de.cyverse.org/dl/d/C4416643-CA5C-4CDD-9FB0-86520AB61059/example_reads.tar.gz"
o "tar -zxvf example_reads.tar.gz"
· Write config file:
cat > config.txt <<CONFIG
max_rd_len=301
[LIB]
avg_ins=300
reverse_seq=0
asm_flags=3
q1=/gpfs1/scratch/USERNAME/SOAPdenovo-Trans_example/example_reads/EGL245_S19_L001_R1_001.fastq
q2=/gpfs1/scratch/USERNAME/SOAPdenovo-Trans_example/example_reads/EGL245_S19_L001_R2_001.fastq
q1=/gpfs1/scratch/USERNAME/SOAPdenovo-Trans_example/example_reads/EGL290_S65_L001_R1_001.fastq
q2=/gpfs1/scratch/USERNAME/SOAPdenovo-Trans_example/example_reads/EGL290_S65_L001_R2_001.fastq
CONFIG
· Write and submit the test job:
o "qsub soapdenovo-trans_job.pbs”
--------------- soapdenovo-trans_job.pbs -----------------
#!/bin/bash
#PBS -q default
#PBS -N SOAPdenovo-Trans_test
#PBS -l select=1:mem=15gb:ncpus=4
#PBS -l walltime=1:00:00
## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”
#PBS -W group_list=x-ccast-prj
cd $PBS_O_WORKDIR
# Add your SOAPdenovo-Trans binaries to path
export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/SOAPdenovo-Trans
SOAPdenovo-Trans-127mer all -s config.txt -o assembly -p $NCPUS
exit 0