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spades-software [2015/08/04 09:27] – aorthspades-software [2025/05/30 07:39] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.5.0+  * Version: 4.2.0
   * Added: September, 2014   * Added: September, 2014
-  * Updated: February, 2015 +  * Updated: May, 2025 
-  * Link: http://bioinf.spbau.ru/spades+  * Link: https://github.com/ablab/spades
  
 ===== Usage ===== ===== Usage =====
  
-See versions of spades which are available:+See versions which are available:
 <code>$ module avail spades</code> <code>$ module avail spades</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load spades/4.2.0
 +$ spades.py --help
 +$ spades.py --test</code>
  
 === Example batch job === === Example batch job ===
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 #SBATCH -J spades #SBATCH -J spades
  
-module load spades/3.5.0+module load spades/3.15
  
 readonly DATADIR=~/data/bfusca readonly DATADIR=~/data/bfusca
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 mkdir -p ${OUTDIR} mkdir -p ${OUTDIR}
  
-# run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical)+# run spades with 8 CPU threads
 # 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}/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 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
-echo "Remember to check (and clean!) output directory on mammoth:"+echo "Remember to check (and clean!) output directory on compute07:"
 echo echo
 echo "  ${OUTDIR}"</code> echo "  ${OUTDIR}"</code>
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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ sudo yum install cmake28.x86_64 +<code>$ cd /tmp 
-$ cd /tmp +$ wget https://github.com/ablab/spades/releases/download/v4.2.0/SPAdes-4.2.0-Linux.tar.gz 
-$ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz +$ tar xf SPAdes-4.2.0-Linux.tar.gz 
-$ tar xf SPAdes-3.5.0.tar.gz +$ sudo cp -r SPAdes-4.2.0-Linux /export/apps/spades/4.2.0</code>
-$ 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</code> +
- +
-===== Running ===== +
-After loading the module, consult the built-in help:+
  
-<code>$ spades.py --help</code>+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.1438680440.txt.gz · Last modified: by aorth