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spades-software [2014/10/08 09:32] – aorthspades-software [2022/09/20 07:38] (current) – aorth
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-====== spades ======+====== SPAdes ====== 
 +SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
  
 ===== Information ===== ===== Information =====
  
-  * Version: 3.1.1+  * Version: 3.15 (3.15.5)
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/spades+  * Updated: September, 2022 
 +  * Link: https://github.com/ablab/spades
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of spades which are available === +See versions of spades 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/3.15 
 +$ spades.py --help 
 +$ spades.py --test</code>
  
 === Example batch job === === Example batch job ===
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 <code>#!/bin/env bash <code>#!/bin/env bash
 #SBATCH -p highmem #SBATCH -p highmem
-#SBATCH -n 6+#SBATCH -n 8
 #SBATCH -J spades #SBATCH -J spades
  
-module load spades/3.1.1+module load spades/3.13.0
  
 readonly DATADIR=~/data/bfusca readonly DATADIR=~/data/bfusca
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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}/1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 6 -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/v3.15.5/SPAdes-3.15.5-Linux.tar.gz 
-wget http://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1.tar.gz +$ tar xf SPAdes-3.15.5-Linux.tar.gz 
-cd SPAdes-3.1.1 +$ sudo mv /export/apps/spades/3.15 /export/apps/spades/3.15.bak 
-sed -i 's/cmake/cmake28/' spades_compile.sh +$ sed -i '1s/python/python3/' SPAdes-3.15.5-Linux/bin/spades.py 
-scl enable devtoolset-1.1 bash +$ sudo cp -r SPAdes-3.15.5-Linux /export/apps/spades/3.15</code>
-sudo mkdir -p /export/apps/spades/3.1.1 +
-sudo chown aorth:aorth /export/apps/spades/3.1.1 +
-PREFIX=/export/apps/spades/3.1.1 ./spades_compile.sh +
-sudo chown -R root:root /export/apps/spades/3.1.1</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.1412760765.txt.gz · Last modified: 2014/10/08 09:32 by aorth