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: 3.15 (3.15.4)
- Added: September, 2014
- Updated: February, 2022
Usage
See versions of spades which are available:
$ module avail spades
Load one version into your environment and run it:
$ module load spades/3.15 $ spades.py --help $ spades.py --test
Example batch job
#!/bin/env bash #SBATCH -p highmem #SBATCH -n 8 #SBATCH -J spades module load spades/3.13.0 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 compute07:" echo echo " ${OUTDIR}"
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/ablab/spades/releases/download/v3.15.4/SPAdes-3.15.4.tar.gz $ tar xf SPAdes-3.15.4.tar.gz $ cd SPAdes-3.15.4 $ sudo chown aorth /export/apps/spades/3.15 $ sudo mkdir -p /export/apps/spades/3.15 $ scl enable devtoolset-7 bash $ module load python/3.9 $ sed -i 's/^cmake/cmake3/' spades_compile.sh $ PREFIX=/export/apps/spades/3.15 ./spades_compile.sh -j 4 $ sudo chown -R root:root /export/apps/spades/3.15
Note: if you get the error Exception caught basic_string::_S_construct null not valid
you need to call the spades.py script, not the spades binary!
spades-software.1645465709.txt.gz · Last modified: 2022/02/21 17:48 by aorth