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using-slurm

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using-slurm [2019/11/11 13:20]
aorth 		using-slurm [2020/10/08 13:06]
jean-baka [Batch jobs]
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 ==== Batch jobs ==== ==== Batch jobs ====
-Request 4 CPUs for a NCBI BLAST+ job in the ''batch'' partition.  Create a file //blast.sbatch//:+We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//:
 <code>#!/usr/bin/env bash <code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
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 blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code> blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code>
  
-Submit the script with ''sbatch'':+We then submit the script with the ''sbatch'' command:
 <code>$ sbatch blast.sbatch  <code>$ sbatch blast.sbatch 
 Submitted batch job 1082</code> Submitted batch job 1082</code>
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 <code>#!/usr/bin/env bash <code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
-#SBATCH -n 4 
 #SBATCH -J blastn #SBATCH -J blastn
 +#SBATCH -n 4
  
 # load the blast module # load the blast module
using-slurm.txt · Last modified: 2020/10/08 13:06 by jean-baka

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