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Bioinformatics - Maq
Instructions on how to run (and, if needed, install a customized version of) Maq
Maq builds assembly by mapping short reads to reference sequences.
1. Running Maq on Thunder
Example: Map reads to the reference sequence and assemble reads based on mapping result
Location: /mmfs1/thunder/projects/ccastest/training/examples/Maq_example
File list:
· maq_job.pbs: job submission script
· chr8.fa: a reference sequence in fasta format
· test_reads.fq: a set of sequences in fastq format
Steps:
· Copy the example directory to your SCRATCH directory
o “cp -r /mmfs1/thunder/projects/ccastest/training/examples/Maq_example $SCRATCH”
· Go to the copied directory
o “cd $SCRATCH/Maq_example”
· Edit the job submission script as needed, then submit the job
o “qsub maq_job.pbs”
2. Install Customized Maq 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) bzip2 is required for building; (available via ‘module load bzip2’)
(b) Option “--threads INT”: Number of output compression threads to use in addition to the main thread. Only used when --output-type is b or z. Default: 0.
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
· Go to the SOFTWARE directory:
o "cd /mmfs1/home/USERNAME/SOFTWARE"
· Download Maq, unzip and go to the unzipped directory:
o "wget https://sourceforge.net/projects/maq/files/maq/0.7.1/maq-0.7.1.tar.bz2"
o "tar -xjvf maq-0.7.1.tar.bz2"
o "cd maq-0.7.1"
· The file "stdhash.hh" has an issue. We need change all the declarations "int ret = direct_insert_aux..." to "int ret = this->direct_insert_aux...". Use below command to do so:
o "sed -i -E 's/(int ret = )(direct_insert_aux)/\1this->\2/' stdhash.hh"
· Configure and specify the install location:
o "./configure --prefix=/mmfs1/home/USERNAME/SOFTWARE/maq_install_here"
· Build and install:
o "make && make install"
(b) Test
· Make a test directory and go into it:
o "cd /mmfs1/thunder/scratch/USERNAME "
o "mkdir MAQ_example"
o "cd MAQ_example"
· Download test data to current location: (use the test data of RMAP)
o "wget https://github.com/smithlabcode/rmap/raw/master/test/input/{chr8.fa,test_reads.fq}"
· Write and submit the job
o "qsub maq_job.pbs"
------------------------------------------- file maq_job.pbs -------------------------------------------
#!/bin/bash
#PBS -q default
#PBS -N Maq_Test
#PBS -l select=1:mem=10gb:ncpus=1
#PBS -l walltime=02:00:00
## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”
#PBS -W group_list=x-ccast-prj
cd $PBS_O_WORKDIR
# Set path to your maq binaries
export MY_MAQ=/mmfs1/home/USERNAME/SOFTWARE/maq_install_here/bin
$MY_MAQ/maq.pl easyrun -d outdir chr8.fa test_reads.fq
exit 0