THREADS=3

#t
#for i in  xab xad xae xaf xag xah xbd xby xca xck xcm xcn xco xcq xcr 
#n1
#for i in  xab xac xad xae xag xah xai xbb xcd xcf xch xcn xcs xcw xcz xda xdb xdf xdi
#n0
#for i in xel xeq xes xet xeu xev xew xex xey xez xfa xfb
for i in xfc xfd xfe xff xfg xfh xfi
#for i in xab xac xad xae xaf xai xam xao xap xaq xar xas xat xax xay xaz xba xbb xbc xbf xbg xbh xbi xbj xbk xbl xbm xbn xbo xbp xbq xbr xbv xbw xbx xbz xcb xcd xcf xcg xch xci xcj xck xcl xcm xcn xco xcp xcq xcr xcs xcu xcv xcw xcx xcz xda xdb xdc xdd xdg xdh xdi xdj xdk xdl xdm xdn xdo xdp xds xdt xdu xdv xdw xdx xdy xea xee xef xeg xeh xei xej xek xel xeq xes xet xeu xev xew xex
do
echo $i;
date
sem --id `hostname`  -j $THREADS "cat ../header.txt $i > $i.tmp; cat $i.tmp | java -Xmx500m    -cp "/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-jexl-2.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/commons-logging-1.1.1.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/htsjdk-1.128.jar:/data/results/tools/align/jvarkit/jvarkit/htsjdk-1.128/dist/snappy-java-1.0.3-rc3.jar:/data/results/tools/align/jvarkit/jvarkit/dist-1.128/biostar59647.jar" com.github.lindenb.jvarkit.tools.biostar.Biostar59647  -r ../backbone_wo_insert.fa $i.tmp  ref:9-20 | xmllint --format - |awk -f /data/images/proton/run149/extract_insert1.awk > $i.ins"
done
sem  --id `hostname`  --wait


#xab xac xad xae xaf xai xam xao xap xaq xar xas xat xax xay xaz xba xbb xbc xbf xbg xbh xbi xbj xbk xbl xbm xbn xbo xbp xbq xbr xbv xbw xbx xbz xcb xcd xcf xcg xch xci xcj xck xcl xcm xcn xco xcp xcq xcr xcs xcu xcv xcw xcx xcz xda xdb xdc xdd xdg xdh xdi xdj xdk xdl xdm xdn xdo xdp xds xdt xdu xdv xdw xdx xdy xea xee xef xeg xeh xei xej xek xel xeq xes xet xeu xev xew