User:Lindenb/Notebook/UMR915/20100609

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Contents

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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