Differences

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--- spades-software [2014/09/22 16:08] – aorth
+++ spades-software [2022/02/21 17:48] – aorth
@@ Line 1: / Line 1: @@
-====== spades ======
+====== SPAdes ======
+SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
 ===== Information =====
-  * Version: 3.1.1
+  * Version: 3.15 (3.15.4)
   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/spades
+  * Updated: February, 2022
+  * Link: https://github.com/ablab/spades
 ===== 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 ===
+<code>#!/bin/env bash
+#SBATCH -p highmem
+#SBATCH -n 8
+#SBATCH -J spades
+module load spades/3.13.0
+readonly DATADIR=~/data/bfusca
+readonly OUTDIR=/var/scratch/aorth-spades-oct8
+# create output directory
+mkdir -p ${OUTDIR}
+# 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)
+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 "Remember to check (and clean!) output directory on compute07:"
+echo
+echo "  ${OUTDIR}"</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>sudo yum install cmake28.x86_64
+<code>$ cd /tmp
-cd /tmp
+$ wget https://github.com/ablab/spades/releases/download/v3.15.4/SPAdes-3.15.4.tar.gz
-wget http://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1.tar.gz
+$ tar xf SPAdes-3.15.4.tar.gz
-cd SPAdes-3.1.1
+$ cd SPAdes-3.15.4
-sed -i 's/cmake/cmake28/' spades_compile.sh
+$ sudo chown aorth /export/apps/spades/3.15
-scl enable devtoolset-1.1 bash
+$ sudo mkdir -p /export/apps/spades/3.15
-sudo mkdir -p /export/apps/spades/3.1.1
+$ scl enable devtoolset-7 bash
-sudo chown aorth:aorth /export/apps/spades/3.1.1
+$ module load python/3.9
-PREFIX=/export/apps/spades/3.1.1 ./spades_compile.sh
+$ sed -i 's/^cmake/cmake3/' spades_compile.sh
-sudo chown -R root:root /export/apps/spades/3.1.1</code>
+$ PREFIX=/export/apps/spades/3.15 ./spades_compile.sh -j 4
+$ sudo chown -R root:root /export/apps/spades/3.15</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!