CRwiki

Bedtools is a powerful toolset for genome arithmetic.
About: developed in the quinlanlab.org and by many contributors worldwide. Docs: http://bedtools.readthedocs.io/ Code: https://github.com/arq5x/bedtools2

Version: v2.26.0

…

#!/bin/bash -l
#SBATCH --partition=long
#SBATCH --ntasks=1                  # <--- bedtool uses only one core
#SBATCH --mem 2048M
#SBATCH --job-name="bedtools test"

#test filenames
#https://s3.amazonaws.com/bedtools-tutorials/web/exons.bed
#https://s3.amazonaws.com/bedtools-tutorials/web/genome.txt
BEDFILENAME=exons.bed
GENOMEFILENAME=genome.txt

#dir path with test files
TESTFILEDIR="/home/users/${USER}/bedtools_2.26_test"
 
#run cdhit computation and remove output files
cd ${TESTFILEDIR}
bedtools genomecov -i data/${BEDFILENAME} -g data/${GENOMEFILENAME} > bedtools_test_`date +%s`.txt

…

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software

bedtools : instaled from Ubuntu 16.04 repo (version v2aa.25.0)
tutorial

A fairly comprehensive tutorial that demonstrates both the basics, as well as some more advanced examples of how bedtools can help you in your research.
input file

Files for test come form http://quinlanlab.org/tutorials/bedtools/bedtools.html.

exons.bed , 29 MB , 5b03f1f7fcf23d2f614cce812c355db9
wget https://s3.amazonaws.com/bedtools-tutorials/web/exons.bed
genome.txt , 2.0 KB, 92e3dece8c394033de6e75b16085a907 
wget https://s3.amazonaws.com/bedtools-tutorials/web/genome.txt

batch file

#!/bin/bash -l
#SBATCH --partition=long
#SBATCH --ntasks=1
#SBATCH --mem 2048M
#SBATCH --job-name="bedtools test"

#test filenames
#https://s3.amazonaws.com/bedtools-tutorials/web/exons.bed
#https://s3.amazonaws.com/bedtools-tutorials/web/genome.txt
BEDFILENAME=exons.bed
GENOMEFILENAME=genome.txt

#dir path with test files
TESTFILEDIR="/workspace/${USER}/anthill23_bedtools/_test"
 
#run cdhit computation and remove output files
cd ${TESTFILEDIR}
bedtools genomecov -i ${BEDFILENAME} -g ${GENOMEFILENAME} > bedtools_test_`date +%s`.txt

batch results

In this test each node was occupied only by one job. Memory allocated for each job : 2048 MB
node name 	cores used 	result1 [s] 	result2 [s] 	result3 [s] 	average [s]
ant002 	1 	367.37 	367.31 	366.26 	366.98
ant003 	1 	390.00 	392.07 	390.07 	390.71
ant004 	1 	387.16 	387.15 	389.38 	387.90
ant005 	1 	333.25 	318.55 	327.58 	326.46
ant006 	1 	314.59 	313.71 	308.83 	312.38
ant007 	1 	132.79 	132.87 	133.27 	132.98
ant008 	1 	132.85 	132.71 	132.81 	132.79
ant009 	1 	152.61 	152.72 	152.55 	152.63
ant011 	1 	95.08 	98.28 	95.48 	96.28
ant012 	1 	94.73 	95.34 	94.72 	94.93
ant100 	1 	378.86 	368.82 	363.42 	370.37
ant200 	1 	381.79 	359.60 	361.14 	367.51
ant300 	1 	370.69 	360.64 	366.55 	365.96
ant400 	1 	364.51 	365.66 	362.83 	364.33