spades-software
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Table of Contents
SPAdes
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
Information
- Version: 3.5.0
- Added: September, 2014
- Updated: February, 2015
Usage
See versions of spades which are available:
$ module avail spades
Example batch job
#!/bin/env bash #SBATCH -p highmem #SBATCH -n 8 #SBATCH -J spades module load spades/3.5.0 readonly DATADIR=~/data/bfusca readonly OUTDIR=/var/scratch/aorth-spades-oct8 # create output directory mkdir -p ${OUTDIR} # run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical) # run spades with 384 GB of RAM (default is 250, but it ran out of memory before) spades.py -k 27 -1 ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 8 -m 384 echo echo "Remember to check (and clean!) output directory on mammoth:" echo echo " ${OUTDIR}"
Installation
Notes from the sysadmin during installation:
$ sudo yum install cmake28.x86_64 $ cd /tmp $ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz $ tar xf SPAdes-3.5.0.tar.gz $ cd SPAdes-3.5.0 $ scl enable devtoolset-2 bash $ sudo mkdir -p /export/apps/spades/3.5.0 $ sudo chown aorth:aorth /export/apps/spades/3.5.0 $ PREFIX=/export/apps/spades/3.5.0 ./spades_compile.sh $ sudo chown -R root:root /export/apps/spades/3.5.0
Running
After loading the module, consult the built-in help:
$ spades.py --help
spades-software.1438680440.txt.gz · Last modified: 2015/08/04 09:27 by aorth