User:Lindenb/Notebook/UMR915/20100609

=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)

=Git proxy= git config --global proxyhost:proxyport