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spades-software [2014/10/08 12:32]
aorth
spades-software [2019/02/15 02:57] (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: 3.13.0
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/spades+  ​* Updated: February, 2019 
 +  ​* 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/​3.13.0 
 +$ spades.py --help</​code>​
  
 === Example batch job === === Example batch job ===
Line 16: Line 22:
 <​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/3.6.1
  
 readonly DATADIR=~/​data/​bfusca readonly DATADIR=~/​data/​bfusca
Line 27: Line 33:
 mkdir -p ${OUTDIR} mkdir -p ${OUTDIR}
  
-# run spades with CPUs on mammoth (because 10/16 are already allocated)+# run spades with 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 -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 -m 384
  
 echo echo
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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/​v3.13.0/SPAdes-3.13.0.tar.gz 
-wget http://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1.tar.gz +$ tar xf SPAdes-3.13.0.tar.gz 
-cd SPAdes-3.1.+$ cd SPAdes-3.13.0 
-sed -i '​s/​cmake/​cmake28/'​ spades_compile.sh +sudo mkdir /​export/​apps/​spades/​3.13.0 
-scl enable devtoolset-1.1 bash +sudo chown aorth /​export/​apps/​spades/​3.13.0 
-sudo mkdir -p /​export/​apps/​spades/​3.1.1 +$ sudo yum install centos-release-scl cmake 
-sudo chown aorth:aorth /​export/​apps/​spades/​3.1.1 +$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 
-PREFIX=/​export/​apps/​spades/​3.1../​spades_compile.sh +PREFIX=/​export/​apps/​spades/​3.13../​spades_compile.sh 
-sudo chown -R root:root /​export/​apps/​spades/​3.1.1</​code>​ +sudo chown -R root:root /​export/​apps/​spades/​3.13.0</​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.1412760765.txt.gz · Last modified: 2014/10/08 12:32 by aorth