User Tools

Site Tools


spades-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
spades-software [2015/02/14 23:55]
aorth
spades-software [2017/12/25 23:48]
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 3.5.0+  * Version: 3.11.1
   * Added: September, 2014   * Added: September, 2014
-  * Updated: ​February2015 +  * Updated: ​December2017 
-  * Link: http://bioinf.spbau.ru/spades+  * Link: http://cab.spbu.ru/software/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>​ 
 + 
 +After loading the module, consult the built-in help: 
 +<​code>​$ spades.py --help</​code>​
  
 === Example batch job === === Example batch job ===
Line 18: Line 21:
 <​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/3.5.0+module load spades/3.6.1
  
 readonly DATADIR=~/​data/​bfusca readonly DATADIR=~/​data/​bfusca
Line 29: Line 32:
 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
Line 41: Line 44:
 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  http://cab.spbu.ru/files/release3.11.1/SPAdes-3.11.1.tar.gz 
-$ wget http://spades.bioinf.spbau.ru/​release3.5.0/SPAdes-3.5.0.tar.gz +$ tar xf SPAdes-3.11.1.tar.gz 
-$ tar xf SPAdes-3.5.0.tar.gz +$ cd SPAdes-3.11.1 
-$ cd SPAdes-3.5.+$ sudo mkdir /​export/​apps/​spades/​3.11.1 
-$ scl enable devtoolset-2 bash +$ sudo chown aorth /​export/​apps/​spades/​3.11.
-$ sudo mkdir -p /​export/​apps/​spades/​3.5.0 +$ sudo yum install cmake 
-$ sudo chown aorth:aorth /​export/​apps/​spades/​3.5.0 +$ PREFIX=/​export/​apps/​spades/​3.11../​spades_compile.sh 
-$ PREFIX=/​export/​apps/​spades/​3.5../​spades_compile.sh +$ sudo chown -R root:root /​export/​apps/​spades/​3.11.1</​code>​
-$ 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.txt · Last modified: 2019/10/04 15:58 by aorth