spades-software
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spades-software [2015/06/09 16:38] – aorth | spades-software [2022/02/21 17:48] – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: 3.5.0 | + | * Version: 3.15 (3.15.4) |
* Added: September, 2014 | * Added: September, 2014 | ||
- | * Updated: February, | + | * Updated: February, |
- | * Link: http://bioinf.spbau.ru/spades | + | * Link: https://github.com/ablab/spades |
===== Usage ===== | ===== Usage ===== | ||
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See versions of spades which are available: | See versions of spades which are available: | ||
< | < | ||
+ | |||
+ | Load one version into your environment and run it: | ||
+ | < | ||
+ | $ spades.py --help | ||
+ | $ spades.py --test</ | ||
=== Example batch job === | === Example batch job === | ||
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< | < | ||
#SBATCH -p highmem | #SBATCH -p highmem | ||
- | #SBATCH -n 6 | + | #SBATCH -n 8 |
#SBATCH -J spades | #SBATCH -J spades | ||
- | module load spades/3.5.0 | + | module load spades/3.13.0 |
readonly DATADIR=~/ | readonly DATADIR=~/ | ||
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mkdir -p ${OUTDIR} | mkdir -p ${OUTDIR} | ||
- | # run spades with 6 CPUs on mammoth (because 10/16 are already allocated) | + | # 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) | # run spades with 384 GB of RAM (default is 250, but it ran out of memory before) | ||
- | spades.py -k 27 -1 ${DATADIR}/ | + | spades.py -k 27 -1 ${DATADIR}/ |
echo | echo | ||
- | echo " | + | echo " |
echo | echo | ||
echo " | echo " | ||
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Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ cd /tmp | + | $ wget https:// |
- | $ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz | + | $ tar xf SPAdes-3.15.4.tar.gz |
- | $ tar xf SPAdes-3.5.0.tar.gz | + | $ cd SPAdes-3.15.4 |
- | $ cd SPAdes-3.5.0 | + | $ sudo chown aorth / |
- | $ scl enable devtoolset-2 bash | + | $ sudo mkdir -p / |
- | $ sudo mkdir -p / | + | $ scl enable devtoolset-7 bash |
- | $ sudo chown aorth: | + | $ module load python/3.9 |
- | $ PREFIX=/ | + | $ sed -i ' |
- | $ sudo chown -R root:root / | + | $ PREFIX=/ |
- | + | $ sudo chown -R root:root / | |
- | ===== Running ===== | + | |
- | After loading the module, consult the built-in help: | + | |
- | < | + | Note: if you get the error '' |
spades-software.txt · Last modified: 2022/09/20 07:38 by aorth