User:Lindenb/Notebook/UMR915/20100609
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CPUINFO
How many physical processors are there?
grep "physical id" /proc/cpuinfo | sort | uniq | wc -l 4
How many virtual processors are there?
grep ^processor /proc/cpuinfo | wc -l 16
Are the processors dual-core (or multi-core)?
grep 'cpu cores' /proc/cpuinfo | sort | uniq cpu cores : 4
Starting aligning with bwa
at 9H32 (n thread=15) cf. http://biostar.stackexchange.com/questions/1395/bwa-number-of-threads
FASTQDIR=../Iomega_HDD/fastq
HG18=/GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa
for LANE in ####################################
do
for SAMPLE in ###################################################
do
PREFIX=${LANE}_${SAMPLE}
BASE=${FASTQDIR}/${PREFIX}
if [ -f ${BASE}_1.fastq.gz ]
then
echo "Aligning ${FASTQDIR}/${LANE}_${SAMPLE} :";
bwa aln -t ${THREAD} -l 32 -q 15 ${HG18} ${BASE}_1.fastq.gz > bwa_${PREFIX}_1.sai
bwa aln -t ${THREAD} -l 32 -q 15 ${HG18} ${BASE}_2.fastq.gz > bwa_${PREFIX}_2.sai
bwa sampe ${HG18} bwa_${PREFIX}_1.sai bwa_${PREFIX}_2.sai ${BASE}_1.fastq.gz ${BASE}_2.fastq.gz | gzip --best > bwa_${PREFIX}.sam.gz
fi
done
done
end at jun 12 17:37 (~3.5 days)
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