ssh kkstore01 mkdir -p /cluster/store10/borEut13 ln -s /cluster/store10/borEut13 /cluster/data/borEut13 cd /cluster/data/borEut13 ls -d /san/sanvol1/scratch/rico/vers13/car* | sed "s/.*car//" > car.names mkdir jkStuff tcsh cat << '_EOF_' > jkStuff/fullCarToChr.sed s/ borEut.13.1$/chr1/ s/ borEut.13.2$/chr2a/ s/ borEut.13.3$/chr2b/ s/ borEut.13.4$/chr3/ s/ borEut.13.5$/chr4/ s/ borEut.13.6$/chr5/ s/ borEut.13.7$/chr6/ s/ borEut.13.8$/chr7/ s/ borEut.13.9$/chr8/ s/ borEut.13.10$/chr9/ s/ borEut.13.11$/chr10/ s/ borEut.13.12$/chr11/ s/ borEut.13.13$/chr12a/ s/ borEut.13.14$/chr12b/ s/ borEut.13.15$/chr13/ s/ borEut.13.16$/chr14/ s/ borEut.13.17$/chr16a/ s/ borEut.13.18$/chr16b/ s/ borEut.13.19$/chr17/ s/ borEut.13.20$/chr18/ s/ borEut.13.21$/chr19/ s/ borEut.13.22$/chr20/ s/ borEut.13.23$/chrX/ '_EOF_' cat << '_EOF_' > jkStuff/carToChr.sed s/^1$/1fart/ s/^2$/2afart/ s/^3$/2bfart/ s/^4$/3fart/ s/^5$/4fart/ s/^6$/5fart/ s/^7$/6fart/ s/^8$/7fart/ s/^9$/8fart/ s/^10$/9fart/ s/^11$/10fart/ s/^12$/11fart/ s/^13$/12afart/ s/^14$/12bfart/ s/^15$/13fart/ s/^16$/14fart/ s/^17$/16afart/ s/^18$/16bfart/ s/^19$/17fart/ s/^20$/18fart/ s/^21$/19fart/ s/^22$/20fart/ s/^23$/Xfart/ s/fart// '_EOF_' exit sed -f jkStuff/carToChr.sed car.names > chr.names for i in `cat car.names` do f=`echo $i | sed -f jkStuff/carToChr.sed` g=/san/sanvol1/scratch/rico/vers13/final-results/borEut.13.$i.gz echo " mkdir $f ; zcat $g | sed -f jkStuff/fullCarToChr.sed > $f/chr$f.fa " done > zcat.jobs for i in `cat chr.names` do echo "mkdir -p $i/split; " echo "faSplit size $i/chr$i.fa 500000 -minGapSize=100 $i/split/\"$i\"_ -lift=$i/$i.lft" done > split.jobs screen sh -x split.jobs exit cat */*.lft > jkStuff/liftAll.lft mkdir blastDb for i in */split/*.fa do f=`basename $i` ln -s `pwd`/$i blastDb/$f done cd /cluster/data/borEut13/blastDb for i in *.fa do /cluster/bluearc/blast229/formatdb -p F -i $i rm $i done rm -rf /san/sanvol1/scratch/borEut13/blastDb mkdir -p /san/sanvol1/scratch/borEut13/blastDb cp *.nhr /san/sanvol1/scratch/borEut13/blastDb cp *.nin /san/sanvol1/scratch/borEut13/blastDb cp *.nsq /san/sanvol1/scratch/borEut13/blastDb mkdir -p /cluster/data/borEut13/bed/tblastn.hg17KG cd /cluster/data/borEut13/bed/tblastn.hg17KG echo /san/sanvol1/scratch/borEut13/blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst f=/san/sanvol1/scratch/rico/vers13/final-results/correct.12.$i.gz zcat ../../from*/correct.gz |sed 1d | tr -d '\012' | sed "s/./& /g" | tr ' ' '\012' | cat wig.head - | wigEncode stdin correct.wig correct.wib # REPEAT MASKING #- Make the run directory and job list: cd /cluster/data/borEut13 mkdir RMRun for i in `cat chr.names` do for j in $i/split/*.fa do echo "`pwd`/jkStuff/RMCanHg `pwd`/$i/split `basename $j` {check out line+ /cluster/data/borEut13/$j.out}" done done > RMRun/RMJobs tcsh cat << '_EOF_' > jkStuff/RMCanHg #!/bin/csh -fe cd $1 pushd . /bin/mkdir -p /tmp/borEut13/$2 /bin/cp $2 /tmp/borEut13/$2/ cd /tmp/borEut13/$2 /cluster/bluearc/RepeatMasker/RepeatMasker -ali -s $2 popd /bin/cp /tmp/borEut13/$2/$2.out ./ if (-e /tmp/borEut13/$2/$2.align) /bin/cp /tmp/borEut13/$2/$2.align ./ if (-e /tmp/borEut13/$2/$2.tbl) /bin/cp /tmp/borEut13/$2/$2.tbl ./ if (-e /tmp/borEut13/$2/$2.cat) /bin/cp /tmp/borEut13/$2/$2.cat ./ /bin/rm -fr /tmp/borEut13/$2/* /bin/rmdir --ignore-fail-on-non-empty /tmp/borEut13/$2 /bin/rmdir --ignore-fail-on-non-empty /tmp/borEut13 '_EOF_' exit # << this line makes emacs coloring happy #- Do the run ssh pk cd /cluster/data/borEut13/RMRun chmod +x ../jkStuff/RMCanHg para create RMJobs para try, para check, para check, para push, para check,... # Completed: 4221 of 4221 jobs # CPU time in finished jobs: 28038273s 467304.55m 7788.41h 324.52d 0.889 y # IO & Wait Time: 22474s 374.56m 6.24h 0.26d 0.001 y # Average job time: 6648s 110.80m 1.85h 0.08d # Longest finished job: 8035s 133.92m 2.23h 0.09d # Submission to last job: 99864s 1664.40m 27.74h 1.16d ssh kkstore01 cd /cluster/data/borEut13 for i in `cat chr.names`; do echo $i;liftUp $i/$i.fa.out $i/$i.lft warn $i/split/*.fa.out > /dev/null; done head -3 `head -1 chr.names`/*.fa.out > all.out for i in `cat chr.names`; do sed "1,3d" $i/$i.fa.out; done >> all.out #- Load the .out files into the database with: ssh hgwdev cd /cluster/data/borEut13 hgLoadOut -nosplit borEut13 all.out featureBits borEut13 rmsk # 683289559 bases of 2105190218 (32.457%) in intersection # STORE SEQUENCE AND ASSEMBLY INFORMATION # Translate to nib cd /cluster/data/borEut13 mkdir nib for i in `cat chr.names` do faToNib $i/chr$i.fa nib/$i.nib done faToTwoBit */*.fa borEut13.2bit # CREATING DATABASE # Create the database. ssh hgwdev cd /cluster/data/borEut13 echo 'create database borEut13' | hgsql '' mkdir -p /gbdb/borEut13/nib ln -s /cluster/data/borEut13/borEut13.2bit /gbdb/borEut13/ # Make symbolic links from /gbdb/borEut13/nib to the real nibs. mkdir -p /gbdb/borEut13/nib ln -s /cluster/data/borEut13/nib/*.nib /gbdb/borEut13/nib hgsql borEut13 < $HOME/kent/src/hg/lib/chromInfo.sql hgNibSeq -preMadeNib borEut13 /gbdb/borEut13/nib */*.fa echo "select chrom,size from chromInfo" | hgsql -N borEut13 > chrom.sizes # create assembly and gap tracks hgGoldGapGl -noGl -chromLst=chr.names borEut13 /cluster/data/borEut13 . echo "create table grp (PRIMARY KEY(NAME)) select * from hg17.grp" | hgsql borEut13 echo 'insert into blatServers values("borEut13", "blat1", "17778", "1","0"); \ insert into blatServers values("borEut13", "blat1", "17779", "0","1");' \ | hgsql -h genome-testdb hgcentraltest mkdir -p /cluster/data/borEut13/bed/gapRmsk cd /cluster/data/borEut13/bed/gapRmsk simpleGap /cluster/data/borEut13/nib gap.bed repeats.bed echo "drop table gap;" | hgsql borEut13 hgsql borEut13 < ~/kent/src/hg/lib/gap.sql hgLoadBed -oldTable borEut13 gap gap.bed echo "create index chrom on gap (chrom(13), bin) ;" | hgsql borEut13 echo "create index chrom_2 on gap (chrom(13), chromStart);" | hgsql borEut13 echo "create index chrom_3 on gap (chrom(13), chromEnd);" | hgsql borEut13 # MAKE GCPERCENT mkdir -p /cluster/data/borEut13/bed/gcPercent cd /cluster/data/borEut13/bed/gcPercent hgsql borEut13 < ~/kent/src/hg/lib/gcPercent.sql # load gcPercent table hgGcPercent borEut13 ../../nib cd ../.. # Add dbDb and defaultDb entries: echo 'insert into dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, \ htmlPath, hgNearOk) values("borEut13", "Apr. 24. 2006", "/gbdb/borEut13/nib", "Boreoeutheria", "", 1, \ 44, "Boreoeutheria", "BoreoEutheria", "/gbdb/borEut13/html/description.html", 0);' \ | hgsql -h genome-testdb hgcentraltest # #echo 'INSERT INTO defaultDb VALUES ("Dog/Human", "borEut13");' | hgsql -h genome-testdb hgcentraltest echo 'update defaultDb set name = "borEut13" where genome = "Dog/Human"' | hgsql -h genome-testdb hgcentraltest # #echo 'insert into genomeClade (genome, clade, priority) values ("BoreoEutheria", "vertebrate",65);' \ # | hgsql -h genome-testdb hgcentraltest # echo 'INSERT INTO defaultDb VALUES ("Dog/Human", "borEut13");' | hgsql -h genome-testdb hgcentraltest # Make trackDb table so browser knows what tracks to expect: cd $HOME/kent/src/hg/makeDb/trackDb mkdir -p ancestor/borEut13 cvs add ancestor/borEut13 cp ancestor/canHg12/trackDb.ra ancestor/borEut13 cvs add ancestor/borEut13/trackDb.ra cvs ci ancestor/borEut13/trackDb.ra # Edit that makefile to add borEut13 in all the right places and do make update # SIMPLE REPEATS (TRF) ssh kkstore01 mkdir -p /cluster/data/borEut13/bed/simpleRepeat cd /cluster/data/borEut13/bed/simpleRepeat mkdir trf tcsh cp /dev/null jobs.csh foreach d (/cluster/data/borEut13/*/split) foreach f ($d/*.fa) set fout = $f:t:r.bed echo $fout echo "/cluster/bin/i386/trfBig -trf=/cluster/bin/i386/trf $f /dev/null -bedAt=trf/$fout -tempDir=/tmp" >> jobs.csh end end exit screen csh -ef jobs.csh # check on this with cd /cluster/data/borEut13/bed/simpleRepeat wc -l jobs.csh ls -1 trf | wc -l endsInLf trf/* # When job is done do: liftUp simpleRepeat.bed /cluster/data/borEut13/jkStuff/liftAll.lft warn trf/*.bed # Load into the database: ssh hgwdev hgLoadBed borEut13 simpleRepeat /cluster/data/borEut13/bed/simpleRepeat/simpleRepeat.bed -sqlTable=$HOME/kent/src/hg/lib/simpleRepeat.sql featureBits borEut13 simpleRepeat # 17364898 bases of 2105190218 (0.825%) in intersection # PROCESS SIMPLE REPEATS INTO MASK # After the simpleRepeats track has been built, make a filtered version # of the trf output: keep trf's with period <= 12: ssh kkstore01 cd /cluster/data/borEut13/bed/simpleRepeat awk '{if ($5 <= 12) print;}' simpleRepeat.bed > simpleRepeat12.bed mkdir trfMask for i in `cat ../../chr.names`; do echo "awk \"{if ($i == \\\$1) print}\" simpleRepeat12.bed > trfMask/$i.bed" done > mask.jobs sh -x mask.jobs # Here's the coverage for the filtered TRF: ssh hgwdev featureBits borEut13 /cluster/data/borEut13/bed/simpleRepeat/simpleRepeat12.bed # 3540823 bases of 1792058299 (0.198%) in intersection # MASK SEQUENCE WITH REPEATMASKER AND SIMPLE REPEAT/TRF ssh kkstore01 cd /cluster/data/borEut13 for i in `cat car.names` do f=$i/chr$i.fa echo maskOutFa -soft $f $i/$i.fa.out $f echo maskOutFa -softAdd $f bed/simpleRepeat/trfMask/$i.bed $f echo maskOutFa $f hard $f.masked done > mask.jobs sh -x mask.jobs #- Rebuild the nib files, using the soft masking in the fa: for i in `cat chr.names`; do faToNib -softMask $i/chr$i.fa nib/chr$i.nib; done for i in `cat chr.names`; do cat $i/chr$i.fa; done | faToTwoBit stdin borEut13.2bit # PUT MASKED SEQUENCE OUT FOR CLUSTER RUNS ssh kkr1u00 # Chrom-level mixed nibs that have been repeat- and trf-masked: mkdir -p /iscratch/i/borEut13/nib cp -p /cluster/data/borEut13/borEut13.2bit /iscratch/i/borEut13 cp -p /cluster/data/borEut13/nib/*.nib /iscratch/i/borEut13/nib # Pseudo-contig fa that have been repeat- and trf-masked: rm -rf /iscratch/i/borEut13/trfFa mkdir /iscratch/i/borEut13/trfFa foreach d (/cluster/data/borEut13/*/chr*_?{,?}) cp $d/$d:t.fa /iscratch/i/borEut13/trfFa end cp -p /cluster/data/borEut13/borEut13.2bit /iscratch/i/borEut13/ iSync # MAKE 10.OOC, 11.OOC FILES FOR BLAT ssh kolossus mkdir /cluster/data/borEut13/bed/ooc mkdir -p /cluster/bluearc/borEut13/ cd /cluster/data/borEut13/bed/ooc ls -1 /cluster/data/borEut13/nib/*.nib > nib.lst blat nib.lst /dev/null /dev/null -tileSize=11 -makeOoc=/cluster/bluearc/borEut13/11.ooc -repMatch=1024 # Wrote 7685 overused 11-mers to /cluster/bluearc/borEut13/11.ooc blat nib.lst /dev/null /dev/null -tileSize=10 -makeOoc=/cluster/bluearc/borEut13/10.ooc -repMatch=843 # Wrote 99129 overused 10-mers to /cluster/bluearc/borEut13/10.ooc ssh kkr1u00 cp -p /cluster/bluearc/borEut13/*.ooc /iscratch/i/borEut13/ iSync > sync.out for i in `cat ../../car.names`; do echo "mafToAxt ../buildMaf/borEut13.$i.maf borEut13. hg17. stdout | axtChain stdin /cluster/data/borEut13/borEut13.2bit /cluster/data/hg17/hg17.2bit stdout | chainToPsl stdin /cluster/data/borEut13/chrom.sizes /cluster/data/hg17/chrom.sizes borEut13.lst hg17.lst $i.psl" ; done > jobs # MAKE Human Proteins track ssh kolossus mkdir -p /cluster/data/borEut13/bed/tblastn.hg17KG cd /cluster/data/borEut13/bed/tblastn.hg17KG mkdir expect.genes cd expect.genes tcsh cat << '_EOF_' > doOne grep human /san/sanvol1/scratch/rico/vers13/car$1/car | sed s/human.// | sed "s/-/ /" | tr ' :' '\t\t' | overlapSelect -selectFmt=bed stdin /cluster/data/hg17/bed/blat.hg17KG/hg17KG.psl stdout > $1.psl '_EOF_' exit chmod +x doOne for i in `cat ../../../car.names`; do echo ./doOne $i; done > jobs sh -x jobs for i in *.psl; do f=`basename $i .psl`; pslxToFa $i $f.fa; awk "{print \$10}" $i > $f.lst; done sort -u *.lst > allInCars.lst awk "{print \$10}" /cluster/data/hg17/bed/blat.hg17KG/hg17KG.psl | sort -u > allInHg17.lst diff allInCars.lst allInHg17.lst | grep ">" | sed "s/..//" > missingInCars.lst cd .. mkdir queries for i in `cat ../../chr.names`; do grep b/"$i"_ query.lst > queries/$i.lst; done rm -rf /san/sanvol1/scratch/borEut13/bed/tblastn.hg17KG/blastOut mkdir -p /san/sanvol1/scratch/borEut13/bed/tblastn.hg17KG/blastOut ln -s /san/sanvol1/scratch/borEut13/bed/tblastn.hg17KG/blastOut for i in `cat ../../car.names`; do mkdir blastOut/`basename $i .fa`; done tcsh cat << '_EOF_' > blastGsub #LOOP blastSome $(path1) {check in line $(path2)} {check out exists blastOut/$(root2)/q.$(root1).psl } #ENDLOOP '_EOF_' cat << '_EOF_' > blastSome #!/bin/sh BLASTMAT=/iscratch/i/blast/data export BLASTMAT g=`basename $2` f=/tmp/`basename $3`.$g for eVal in 0.01 0.001 0.0001 0.00001 0.000001 1E-09 1E-11 do if /scratch/blast/blastall -M BLOSUM80 -m 0 -F no -e $eVal -p tblastn -d $1 -i $2 -o $f.8 then mv $f.8 $f.1 break; fi done if test -f $f.1 then if /cluster/bin/i386/blastToPsl $f.1 $f.2 then liftUp -nosort -type=".psl" -nohead $f.3 ../../jkStuff/liftAll.lft carry $f.2 liftUp -nosort -type=".psl" -pslQ -nohead $3.tmp /cluster/data/hg17/bed/blat.hg17KG/protein.lft warn $f.3 if pslCheck -prot $3.tmp then mv $3.tmp $3 rm -f $f.1 $f.2 $f.3 $f.4 fi exit 0 fi fi rm -f $f.1 $f.2 $3.tmp $f.8 $f.3 $f.4 exit 1 '_EOF_' exit chmod +x blastSome for i in `cat ../../car.names` do f=`echo $i | sed -f ../../jkStuff/carToChr.sed` echo expect.genes/$i.fa | gensub2 queries/$f.lst stdin blastGsub stdout done > blastSpec // gensub2 query.lst kg.lst blastGsub blastSpec ssh pk cd /cluster/data/borEut13/bed/tblastn.hg17KG para create blastSpec para push # Completed: 3644 of 3644 jobs # CPU time in finished jobs: 1127288s 18788.13m 313.14h 13.05d 0.036 y # IO & Wait Time: 143129s 2385.49m 39.76h 1.66d 0.005 y # Average job time: 349s 5.81m 0.10h 0.00d # Longest running job: 0s 0.00m 0.00h 0.00d # Longest finished job: 1322s 22.03m 0.37h 0.02d # Submission to last job: 4477s 74.62m 1.24h 0.05d ssh kki cd /cluster/data/borEut13/bed/tblastn.hg17KG tcsh cat << '_EOF_' > chainGsub #LOOP chainOne $(path1) #ENDLOOP '_EOF_' cat << '_EOF_' > chainOne (cd $1; cat q.*.psl | simpleChain -prot -outPsl -maxGap=250000 stdin ../c.`basename $1`.psl) '_EOF_' chmod +x chainOne exit for i in `cat ../../car.names` do ls -1dS `pwd`/blastOut/$i done > chain.lst gensub2 chain.lst single chainGsub chainSpec para create chainSpec para push Completed: 30 of 30 jobs # CPU time in finished jobs: 32583s 543.05m 9.05h 0.38d 0.001 y # IO & Wait Time: 268s 4.46m 0.07h 0.00d 0.000 y # Average job time: 1095s 18.25m 0.30h 0.01d # Longest running job: 0s 0.00m 0.00h 0.00d # Longest finished job: 20831s 347.18m 5.79h 0.24d # Submission to last job: 20987s 349.78m 5.83h 0.24d ssh kkstore01 cd /cluster/data/borEut13/bed/tblastn.hg17KG/blastOut for i in `cat /cluster/data/borEut13/car.names` do awk "(\$13 - \$12)/\$11 > 0.6 {print}" c.$i.psl > c60.$i.psl sort -rn c60.$i.psl | pslUniq stdin u.$i.psl awk "((\$1 / \$11) ) > 0.60 { print }" c60.$i.psl > m60.$i.psl echo $i done sort -T /tmp -k 14,14 -k 16,16n -k 17,17n u.*.psl m60* | uniq > /cluster/data/borEut13/bed/tblastn.hg17KG/blastHg17KG.psl cd .. mkdir found.genes for i in `cat ../../car.names`; do pslSomeRecords blastHg17KG.psl expect.genes/$i.lst found.genes/$i.psl; done cd found.genes for i in *.psl; do cut -f 10 $i | sort -u > `basename $i .psl`.lst; done cd .. mkdir missing.genes for i in `cat ../../car.names`; do diff expect.genes/$i.lst found.genes/$i.lst | grep "<" | sed "s/..//" > missing.genes/$i.lst done ssh hgwdev cd /cluster/data/borEut13/bed/tblastn.hg17KG hgLoadPsl borEut13 blastHg17KG.psl # 28212551 bases of 1814471846 (1.555%) in intersection # 27377895 bases of 1792058299 (1.528%) in intersection (in canHg11) # back to kkstore01 rm -rf blastOut # End tblastn # PRODUCING GENSCAN PREDICTIONS ssh hgwdev mkdir /cluster/data/borEut13/bed/genscan cd /cluster/data/borEut13/bed/genscan # Check out hg3rdParty/genscanlinux to get latest genscan: cvs co hg3rdParty/genscanlinux # Run on small cluster (more mem than big cluster). ssh kki cd /cluster/data/borEut13/bed/genscan # Make 3 subdirectories for genscan to put their output files in mkdir gtf pep subopt # Generate a list file, genome.list, of all the hard-masked contigs that # *do not* consist of all-N's (which would cause genscan to blow up) rm -f genome.list touch genome.list foreach f ( `ls -1S /cluster/data/borEut13/*/chr*/chr*_?{,?}.fa.masked` ) egrep '[ACGT]' $f > /dev/null if ($status == 0) echo $f >> genome.list end wc -l genome.list # Create template file, gsub, for gensub2. For example (3-line file): cat << '_EOF_' > gsub #LOOP /cluster/bin/i386/gsBig {check in line+ $(path1)} {check out line gtf/$(root1).gtf} -trans={check out line pep/$(root1).pep} -subopt={check out line subopt/$(root1).bed} -exe=hg3rdParty/genscanlinux/genscan -par=hg3rdParty/genscanlinux/HumanIso.smat -tmp=/tmp -window=2400000 #ENDLOOP '_EOF_' # << this line makes emacs coloring happy gensub2 genome.list single gsub jobList # did one job on kolossus # Convert these to chromosome level files as so: ssh kkstore01 cd /cluster/data/borEut13/bed/genscan liftUp genscan.gtf ../../jkStuff/liftAll.lft warn gtf/*.gtf liftUp genscanSubopt.bed ../../jkStuff/liftAll.lft warn subopt/*.bed cat pep/*.pep > genscan.pep # Load into the database as so: ssh hgwdev cd /cluster/data/borEut13/bed/genscan ldHgGene borEut13 genscan genscan.gtf hgPepPred borEut13 generic genscanPep genscan.pep hgLoadBed borEut13 genscanSubopt genscanSubopt.bed #END GENSCAN # MAKE Human Known Gene mRNAs Mapped by BLATZ track (hg17 # Create working directory and extract known gene mrna from database mkdir -p /cluster/data/borEut13/bed/blatz.hg17KG cd /cluster/data/borEut13/bed/blatz.hg17KG pepPredToFa hg17 knownGeneMrna known.fa # Split known genes into pieces and load on /iscratch/i temp device ssh kkr1u00 cd /iscratch/i/borEut13 mkdir knownRna cd knownRna faSplit sequence /cluster/data/borEut13/bed/blatz.hg17KG/known.fa 580 known cd iSync > sync.out ssh kk cd /cluster/data/borEut13/bed/blatz.hg17KG # Do parasol job to align via blatz mkdir run0 cd run0 mkdir psl # awk '{print $1;}' /cluster/data/borEut13/chrom.sizes > genome.lst ls -1S /iscratch/i/borEut13/trfFa/*.fa > genome.lst for i in `cat genome.lst` ; do f=`basename $i .fa`; mkdir psl/$f ; done for i in /iscratch/i/canHg3/knownRna/*.fa ; do echo $i; done > mrna.lst cat << '_EOF_' > doBlatz #!/bin/sh f=/tmp/`basename $1`.`basename $2` if blatz -rna -minScore=6000 -out=psl $1 $2 $f.1 then if liftUp -nosort -type=".psl" -nohead $f.2 ../../../jkStuff/liftAll.lft carry $f.1 then mv $f.2 $3 rm $f.1 exit 0 fi fi rm $f.1 $f.2 exit 1 '_EOF_' chmod +x doBlatz cat << '_EOF_' > gsub #LOOP doBlatz $(path1) $(path2) {check out line psl/$(root1)/$(root2).psl} #ENDLOOP '_EOF_' # << this line keeps emacs coloring happy gensub2 genome.lst mrna.lst gsub spec para create spec # Then do usual para try/para push/para time # Completed: 1146 of 1146 jobs # CPU time in finished jobs: 108857s 1814.28m 30.24h 1.26d 0.003 y # IO & Wait Time: 819365s 13656.09m 227.60h 9.48d 0.026 y # Average job time: 810s 13.50m 0.22h 0.01d # Longest running job: 0s 0.00m 0.00h 0.00d # Longest finished job: 2985s 49.75m 0.83h 0.03d # Submission to last job: 2997s 49.95m 0.83h 0.03d # Completed: 6303 of 6303 jobs # CPU time in finished jobs: 920417s 15340.29m 255.67h 10.65d 0.029 y # IO & Wait Time: 23131s 385.51m 6.43h 0.27d 0.001 y # Average job time: 150s 2.49m 0.04h 0.00d # Longest job: 1064s 17.73m 0.30h 0.01d # Submission to last job: 1632s 27.20m 0.45h 0.02d # Do sort and near-besting on file server ssh kkstore01 cd /cluster/data/borEut13/bed/blatz.hg17KG/run0 catDir -r psl | pslFilter -minScore=100 -minAli=255 -noHead stdin stdout | sort -k 10 > ../filtered.psl cd .. pslReps filtered.psl nearBest.psl /dev/null -nohead -minAli=0.8 -nearTop=0.01 -minCover=0.8 sort -k 14 nearBest.psl > blatzHg17KG.psl # Clean up rm -r run0/psl # Load into database ssh hgwdev cd /cluster/data/borEut13/bed/blatz.hg17KG hgLoadPsl borEut13 blatzHg17KG.psl #END BLATZ # BLASTZ SWAP FOR hg17 vs borEut13 BLASTZ TO CREATE borEut13 vs hg17 BLASTZ ssh kolossus mkdir -p /cluster/data/borEut13/bed/blastz.hg17 cd /cluster/data/borEut13/bed/blastz.hg17 set aliDir = /cluster/data/hg17/bed/blastz.borEut13 cp $aliDir/S1.len S2.len cp $aliDir/S2.len S1.len mkdir unsorted axtChrom cat $aliDir/axtChrom/chr*.axt \ | axtSwap stdin $aliDir/S1.len $aliDir/S2.len stdout \ | axtSplitByTarget stdin unsorted # Sort the shuffled .axt files. foreach f (unsorted/*.axt) echo sorting $f:t:r axtSort $f axtChrom/$f:t end du -sh $aliDir/axtChrom unsorted axtChrom # 409M /cluster/data/hg17/bed/blastz.borEut13/axtChrom # 409M unsorted # 409M axtChrom rm -r unsorted # CHAIN HUMAN BLASTZ # Run axtChain on little cluster ssh kki cd /cluster/data/borEut13/bed/blastz.hg17 mkdir -p axtChain/run1 cd axtChain/run1 mkdir out chain ls -1S /cluster/data/borEut13/bed/blastz.hg17/axtChrom/*.axt > input.lst cat << '_EOF_' > gsub #LOOP doChain {check in line+ $(path1)} {check out line+ chain/$(root1).chain} {check out exists out/$(root1).out} #ENDLOOP '_EOF_' # << this line makes emacs coloring happy cat << '_EOF_' > doChain #!/bin/csh axtChain $1 \ /iscratch/i/borEut13/nib \ /iscratch/i/gs.18/build35/bothMaskedNibs $2 > $3 '_EOF_' # << this line makes emacs coloring happy chmod a+x doChain gensub2 input.lst single gsub jobList para create jobList para try, check, push, check... # Completed: 1 of 1 jobs # CPU time in finished jobs: 109s 1.81m 0.03h 0.00d 0.000 y # IO & Wait Time: 104s 1.73m 0.03h 0.00d 0.000 y # Average job time: 212s 3.53m 0.06h 0.00d # Longest finished job: 212s 3.53m 0.06h 0.00d # Submission to last job: 212s 3.53m 0.06h 0.00d # now on the cluster server, sort chains ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.hg17/axtChain chainMergeSort run1/chain/*.chain > all.chain chainSplit chain all.chain rm run1/chain/*.chain # take a look at score distr's foreach f (chain/*.chain) grep chain $f | awk '{print $2;}' | sort -nr > /tmp/score.$f:t:r echo $f:t:r textHistogram -binSize=4000 /tmp/score.$f:t:r echo "" end mv all.chain all.chain.unfiltered chainFilter -minScore=50000 all.chain.unfiltered > all.chain rm chain/* chainSplit chain all.chain gzip all.chain.unfiltered # Load chains into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.hg17/axtChain/chain foreach i (*.chain) set c = $i:r hgLoadChain borEut13 ${c}_chainHg17 $i end featureBits borEut13 chainHg17Link # 52252036 bases of 62796757 (83.208%) in intersection # NET HUMAN BLASTZ ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.hg17/axtChain chainPreNet all.chain ../S1.len ../S2.len stdout \ | chainNet stdin -minSpace=1 ../S1.len ../S2.len stdout /dev/null \ | netSyntenic stdin noClass.net # Add classification info using db tables: ssh hgwdev cd /cluster/data/borEut13/bed/blastz.hg17/axtChain netClass noClass.net borEut13 hg17 human.net # Make a 'syntenic' subset: ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.hg17/axtChain rm noClass.net # Make a 'syntenic' subset of these with netFilter -syn human.net > humanSyn.net # Load the nets into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.hg17/axtChain netFilter -minGap=10 human.net | hgLoadNet borEut13 netHg17 stdin netFilter -minGap=10 humanSyn.net | hgLoadNet borEut13 netSyntenyHg17 stdin # Add entries for chainHg17, netHg17, syntenyHg17 to dog/borEut13 trackDb # GENERATE HG17 MAF FOR MULTIZ FROM NET ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.hg17/axtChain netSplit human.net net cd /cluster/data/borEut13/bed/blastz.hg17 mkdir axtNet foreach f (axtChain/net/*) set chr = $f:t:r netToAxt $f axtChain/chain/$chr.chain /cluster/data/borEut13/nib \ /cluster/data/hg17/nib stdout | axtSort stdin axtNet/$chr.axt end mkdir mafNet foreach f (axtNet/chr*.axt) set maf = mafNet/$f:t:r.maf axtToMaf $f /cluster/data/borEut13/chrom.sizes /cluster/data/hg17/chrom.sizes $maf -tPrefix=borEut13. -qPrefix=hg17. end # BLASTZ SWAP FOR canFam1 vs borEut13 BLASTZ TO CREATE borEut13 vs canFam1 BLASTZ ssh kolossus mkdir -p /cluster/data/borEut13/bed/blastz.canFam1 cd /cluster/data/borEut13/bed/blastz.canFam1 set aliDir = /cluster/data/canFam1/bed/blastz.borEut13 cp $aliDir/S1.len S2.len cp $aliDir/S2.len S1.len mkdir unsorted axtChrom cat $aliDir/axtChrom/chr*.axt \ | axtSwap stdin $aliDir/S1.len $aliDir/S2.len stdout \ | axtSplitByTarget stdin unsorted # Sort the shuffled .axt files. foreach f (unsorted/*.axt) echo sorting $f:t:r axtSort $f axtChrom/$f:t end du -sh $aliDir/axtChrom unsorted axtChrom # 207M /cluster/data/canFam1/bed/blastz.borEut13/axtChrom # 207M unsorted # 207M axtChrom rm -rf unsorted # CHAIN DOG BLASTZ # Run axtChain on little cluster ssh kki cd /cluster/data/borEut13/bed/blastz.canFam1 mkdir -p axtChain/run1 cd axtChain/run1 mkdir out chain ls -1S /cluster/data/borEut13/bed/blastz.canFam1/axtChrom/*.axt > input.lst cat << '_EOF_' > gsub #LOOP doChain {check in line+ $(path1)} {check out line+ chain/$(root1).chain} {check out exists out/$(root1).out} #ENDLOOP '_EOF_' # << this line makes emacs coloring happy cat << '_EOF_' > doChain #!/bin/csh axtChain $1 \ /iscratch/i/borEut13/nib \ /iscratch/i/canFam1/nib $2 > $3 '_EOF_' # << this line makes emacs coloring happy chmod a+x doChain gensub2 input.lst single gsub jobList para create jobList para try, check, push, check... # Completed: 1 of 1 jobs # CPU time in finished jobs: 86s 1.44m 0.02h 0.00d 0.000 y # IO & Wait Time: 7s 0.11m 0.00h 0.00d 0.000 y # Average job time: 93s 1.55m 0.03h 0.00d # Longest finished job: 93s 1.55m 0.03h 0.00d # Submission to last job: 93s 1.55m 0.03h 0.00d # now on the cluster server, sort chains ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.canFam1/axtChain chainMergeSort run1/chain/*.chain > all.chain chainSplit chain all.chain rm run1/chain/*.chain # take a look at score distr's foreach f (chain/*.chain) grep chain $f | awk '{print $2;}' | sort -nr > /tmp/score.$f:t:r echo $f:t:r textHistogram -binSize=4000 /tmp/score.$f:t:r echo "" end mv all.chain all.chain.unfiltered chainFilter -minScore=50000 all.chain.unfiltered > all.chain rm chain/* chainSplit chain all.chain gzip all.chain.unfiltered & # Load chains into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.canFam1/axtChain/chain foreach i (*.chain) set c = $i:r hgLoadChain borEut13 ${c}_chainCanFam1 $i end featureBits borEut13 chainCanFam1Link # 51373603 bases of 62796757 (81.809%) in intersection # GENBANK/REFSEQ alignments: - added borEut to: /cluster/data/genbank/etc/genbank.conf src/hg/makeDb/genbank/src/lib/gbGenome.c src/hg/makeDb/genbank/src/align/gbBlat cvs commit the changes cd src/hg/makeDb/genbank jkmake install-server ssh kkstore01 cd /cluster/data/genbank ./bin/gbAlignStep -initial borEut13 & # load into database ssh hgwdev cd /cluster/data/genbank/ ./bin/gbDbLoadStep -initialLoad borEut13 & # BLASTZ EutGli1 ssh kk mkdir /cluster/data/borEut13/bed/blastz.eutGli1 cd /cluster/data/borEut13/bed/blastz.eutGli1 cat << '_EOF_' > DEF export PATH=/usr/bin:/bin:/usr/local/bin:/cluster/bin/penn:/cluster/bin/i386:/cluster/home/angie/schwartzbin ALIGN=blastz-run BLASTZ=blastz # Default BLASTZ_H=2000 BLASTZ_ABRIDGE_REPEATS=1 SEQ1_DIR=/iscratch/i/borEut13/nib SEQ1_RMSK= SEQ1_FLAG= # SEQ1_SMSK=/scratch/hg/gs.18/build35/linSpecRep.notInDog SEQ1_SMSK= SEQ1_IN_CONTIGS=0 SEQ1_CHUNK=1000000 SEQ1_LAP=10000 SEQ2_DIR=/iscratch/i/eutGli1/nib SEQ2_RMSK= SEQ2_FLAG= #SEQ2_SMSK=/scratch/hg/borEut13/linSpecRep.notInHuman SEQ2_SMSK= SEQ2_IN_CONTIGS=0 SEQ2_CHUNK=1000000 SEQ2_LAP=0 BASE=/cluster/data/borEut13/bed/blastz.eutGli1 DEF=$BASE/DEF RAW=$BASE/raw CDBDIR=$BASE SEQ1_LEN=$BASE/S1.len SEQ2_LEN=$BASE/S2.len '_EOF_' # << this line keeps emacs coloring happy /cluster/data/hg17/jkStuff/BlastZ_run0.sh cd run.0 para push # Completed: 4899 of 4899 jobs # CPU time in finished jobs: 918787s 15313.12m 255.22h 10.63d 0.029 y # IO & Wait Time: 21355s 355.91m 5.93h 0.25d 0.001 y # Average job time: 192s 3.20m 0.05h 0.00d # Longest job: 2206s 36.77m 0.61h 0.03d # Submission to last job: 9206s 153.43m 2.56h 0.11d ssh kki cd /cluster/data/borEut13/bed/blastz.eutGli1 /cluster/data/hg17/jkStuff/BlastZ_run1.sh cd run.1 para push # Completed: 71 of 71 jobs # CPU time in finished jobs: 1139s 18.99m 0.32h 0.01d 0.000 y # IO & Wait Time: 797s 13.28m 0.22h 0.01d 0.000 y # Average job time: 27s 0.45m 0.01h 0.00d # Longest job: 75s 1.25m 0.02h 0.00d # Submission to last job: 282s 4.70m 0.08h 0.00d ssh kk cd /cluster/data/borEut13/bed/blastz.eutGli1 /cluster/data/hg17/jkStuff/BlastZ_run2.sh cd run.2 para push # Completed: 1 of 1 jobs # CPU time in finished jobs: 362s 6.04m 0.10h 0.00d 0.000 y # IO & Wait Time: 1464s 24.39m 0.41h 0.02d 0.000 y # Average job time: 1826s 30.43m 0.51h 0.02d # Longest job: 1826s 30.43m 0.51h 0.02d # Submission to last job: 1826s 30.43m 0.51h 0.02d # END BLASTZ eutGli1 # CHAIN EutGli1 BLASTZ # Run axtChain on little cluster ssh kki cd /cluster/data/borEut13/bed/blastz.eutGli1 mkdir -p axtChain/run1 cd axtChain/run1 mkdir out chain ls -1S /cluster/data/borEut13/bed/blastz.eutGli1/axtChrom/*.axt > input.lst cat << '_EOF_' > gsub #LOOP doChain {check in line+ $(path1)} {check out line+ chain/$(root1).chain} {check out exists out/$(root1).out} #ENDLOOP '_EOF_' # << this line makes emacs coloring happy cat << '_EOF_' > doChain #!/bin/csh /cluster/bin/x86_64/axtChain $1 \ /iscratch/i/borEut13/nib \ /iscratch/i/eutGli1/nib $2 > $3 '_EOF_' # << this line makes emacs coloring happy chmod a+x doChain gensub2 input.lst single gsub jobList para create jobList para try, check, push, check... # Completed: 1 of 1 jobs # CPU time in finished jobs: 197s 3.28m 0.05h 0.00d 0.000 y # IO & Wait Time: 88s 1.47m 0.02h 0.00d 0.000 y # Average job time: 285s 4.75m 0.08h 0.00d # Longest job: 285s 4.75m 0.08h 0.00d # Submission to last job: 285s 4.75m 0.08h 0.00d # now on the cluster server, sort chains ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain chainMergeSort run1/chain/*.chain > all.chain chainSplit chain all.chain rm run1/chain/*.chain # take a look at score distr's foreach f (chain/*.chain) grep chain $f | awk '{print $2;}' | sort -nr > /tmp/score.$f:t:r echo $f:t:r textHistogram -binSize=4000 /tmp/score.$f:t:r echo "" end mv all.chain all.chain.unfiltered chainFilter -minScore=50000 all.chain.unfiltered > all.chain rm chain/* chainSplit chain all.chain gzip all.chain.unfiltered & # Load chains into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain/chain foreach i (*.chain) set c = $i:r hgLoadChain borEut13 ${c}_chainEutGli1 $i end featureBits borEut13 chainEutGli1Link # 66936604 bases of 70435997 (95.032%) in intersection # NET eutGli1 BLASTZ ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain chainPreNet all.chain ../S1.len ../S2.len stdout \ | chainNet stdin -minSpace=1 ../S1.len ../S2.len stdout /dev/null \ | netSyntenic stdin noClass.net # Add classification info using db tables: ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain netClass -noAr noClass.net borEut13 eutGli1 eutGli1.net # Make a 'syntenic' subset: ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain rm noClass.net # Make a 'syntenic' subset of these with netFilter -syn eutGli1.net > eutGli1Syn.net # Load the nets into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain netFilter -minGap=10 eutGli1.net | hgLoadNet borEut13 netEutGli1 stdin netFilter -minGap=10 eutGli1Syn.net | hgLoadNet borEut13 netSyntenyEutGli1 stdin # Add entries for chainHg17, netHg17, syntenyHg17 to dog/borEut13 trackDb # GENERATE EutGli1 MAF FOR MULTIZ FROM NET ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutGli1/axtChain netSplit eutGli1.net net cd /cluster/data/borEut13/bed/blastz.eutGli1 mkdir axtNet foreach f (axtChain/net/*) set chr = $f:t:r netToAxt $f axtChain/chain/$chr.chain /cluster/data/borEut13/nib \ /cluster/data/eutGli1/nib stdout | axtSort stdin axtNet/$chr.axt end mkdir mafNet foreach f (axtNet/chr*.axt) set maf = mafNet/$f:t:r.maf axtToMaf $f /cluster/data/borEut13/chrom.sizes /cluster/data/eutGli1/chrom.sizes $maf -tPrefix=borEut13. -qPrefix=eutGli1. end # BLASTZ EutPri1 ssh kk mkdir /cluster/data/borEut13/bed/blastz.eutPri1 cd /cluster/data/borEut13/bed/blastz.eutPri1 cat << '_EOF_' > DEF export PATH=/usr/bin:/bin:/usr/local/bin:/cluster/bin/penn:/cluster/bin/i386:/cluster/home/angie/schwartzbin ALIGN=blastz-run BLASTZ=blastz # Default BLASTZ_H=2000 BLASTZ_ABRIDGE_REPEATS=1 SEQ1_DIR=/iscratch/i/borEut13/nib SEQ1_RMSK= SEQ1_FLAG= # SEQ1_SMSK=/scratch/hg/gs.18/build35/linSpecRep.notInDog SEQ1_SMSK= SEQ1_IN_CONTIGS=0 SEQ1_CHUNK=1000000 SEQ1_LAP=10000 SEQ2_DIR=/iscratch/i/eutPri1/nib SEQ2_RMSK= SEQ2_FLAG= #SEQ2_SMSK=/scratch/hg/borEut13/linSpecRep.notInHuman SEQ2_SMSK= SEQ2_IN_CONTIGS=0 SEQ2_CHUNK=1000000 SEQ2_LAP=0 BASE=/cluster/data/borEut13/bed/blastz.eutPri1 DEF=$BASE/DEF RAW=$BASE/raw CDBDIR=$BASE SEQ1_LEN=$BASE/S1.len SEQ2_LEN=$BASE/S2.len '_EOF_' # << this line keeps emacs coloring happy /cluster/data/hg17/jkStuff/BlastZ_run0.sh cd run.0 para push # Completed: 6319 of 6319 jobs # CPU time in finished jobs: 144839s 2413.98m 40.23h 1.68d 0.005 y # IO & Wait Time: 21882s 364.71m 6.08h 0.25d 0.001 y # Average job time: 26s 0.44m 0.01h 0.00d # Longest job: 2517s 41.95m 0.70h 0.03d # Submission to last job: 3900s 65.00m 1.08h 0.05d ssh kki cd /cluster/data/borEut13/bed/blastz.eutPri1 /cluster/data/hg17/jkStuff/BlastZ_run1.sh cd run.1 para push # Completed: 71 of 71 jobs # CPU time in finished jobs: 72s 1.21m 0.02h 0.00d 0.000 y # IO & Wait Time: 211s 3.51m 0.06h 0.00d 0.000 y # Average job time: 4s 0.07m 0.00h 0.00d # Longest job: 13s 0.22m 0.00h 0.00d # Submission to last job: 52s 0.87m 0.01h 0.00d ssh kk cd /cluster/data/borEut13/bed/blastz.eutPri1 /cluster/data/hg17/jkStuff/BlastZ_run2.sh cd run.2 para push # Completed: 1 of 1 jobs # CPU time in finished jobs: 52s 0.86m 0.01h 0.00d 0.000 y # IO & Wait Time: 26s 0.44m 0.01h 0.00d 0.000 y # Average job time: 78s 1.30m 0.02h 0.00d # Longest job: 78s 1.30m 0.02h 0.00d # Submission to last job: 80s 1.33m 0.02h 0.00d # END BLASTZ eutPri1 # CHAIN EutPri1 BLASTZ # Run axtChain on little cluster ssh kki cd /cluster/data/borEut13/bed/blastz.eutPri1 mkdir -p axtChain/run1 cd axtChain/run1 mkdir out chain ls -1S /cluster/data/borEut13/bed/blastz.eutPri1/axtChrom/*.axt > input.lst cat << '_EOF_' > gsub #LOOP doChain {check in line+ $(path1)} {check out line+ chain/$(root1).chain} {check out exists out/$(root1).out} #ENDLOOP '_EOF_' # << this line makes emacs coloring happy cat << '_EOF_' > doChain #!/bin/csh /cluster/bin/x86_64/axtChain $1 \ /iscratch/i/borEut13/nib \ /iscratch/i/eutPri1/nib $2 > $3 '_EOF_' # << this line makes emacs coloring happy chmod a+x doChain gensub2 input.lst single gsub jobList para create jobList para try, check, push, check... # Completed: 1 of 1 jobs # CPU time in finished jobs: 72s 1.20m 0.02h 0.00d 0.000 y # IO & Wait Time: 7s 0.12m 0.00h 0.00d 0.000 y # Average job time: 79s 1.32m 0.02h 0.00d # Longest job: 79s 1.32m 0.02h 0.00d # Submission to last job: 79s 1.32m 0.02h 0.00d # now on the cluster server, sort chains ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain chainMergeSort run1/chain/*.chain > all.chain chainSplit chain all.chain rm run1/chain/*.chain # take a look at score distr's foreach f (chain/*.chain) grep chain $f | awk '{print $2;}' | sort -nr > /tmp/score.$f:t:r echo $f:t:r textHistogram -binSize=4000 /tmp/score.$f:t:r echo "" end mv all.chain all.chain.unfiltered chainFilter -minScore=50000 all.chain.unfiltered > all.chain rm chain/* chainSplit chain all.chain gzip all.chain.unfiltered & # Load chains into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain/chain foreach i (*.chain) set c = $i:r hgLoadChain borEut13 ${c}_chainEutPri1 $i end featureBits borEut13 chainEutPri1Link # 65181722 bases of 70435997 (92.540%) in intersection # NET eutPri1 BLASTZ ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain chainPreNet all.chain ../S1.len ../S2.len stdout \ | chainNet stdin -minSpace=1 ../S1.len ../S2.len stdout /dev/null \ | netSyntenic stdin noClass.net # Add classification info using db tables: ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain netClass -noAr noClass.net borEut13 eutPri1 eutPri1.net # Make a 'syntenic' subset: ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain rm noClass.net # Make a 'syntenic' subset of these with netFilter -syn eutPri1.net > eutPri1Syn.net # Load the nets into database ssh hgwdev cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain netFilter -minGap=10 eutPri1.net | hgLoadNet borEut13 netEutPri1 stdin netFilter -minGap=10 eutPri1Syn.net | hgLoadNet borEut13 netSyntenyEutPri1 stdin # Add entries for chainHg17, netHg17, syntenyHg17 to dog/borEut13 trackDb # GENERATE EutPri1 MAF FOR MULTIZ FROM NET ssh kkstore01 cd /cluster/data/borEut13/bed/blastz.eutPri1/axtChain netSplit eutPri1.net net cd /cluster/data/borEut13/bed/blastz.eutPri1 mkdir axtNet foreach f (axtChain/net/*) set chr = $f:t:r netToAxt $f axtChain/chain/$chr.chain /cluster/data/borEut13/nib \ /cluster/data/eutPri1/nib stdout | axtSort stdin axtNet/$chr.axt end mkdir mafNet foreach f (axtNet/chr*.axt) set maf = mafNet/$f:t:r.maf axtToMaf $f /cluster/data/borEut13/chrom.sizes /cluster/data/eutPri1/chrom.sizes $maf -tPrefix=borEut13. -qPrefix=eutPri1. end # Load into database ssh hgwdev cd /cluster/data/borEut13/bed/multizDescend /cluster/bin/pen mkdir -p /gbdb/borEut13/multiz4way ln -s /cluster/data/borEut13/bed/multizDescend/multiz4way.maf /gbdb/borEut13/multiz4way hgLoadMaf borEut13 multiz4way for i in eutGli1 eutPri1 hg17 do f="$i"_netBlastz mkdir -p /gbdb/borEut13/multiz4way/$f ln -s /cluster/data/borEut13/bed/blastz.$i/chr15.maf /gbdb/borEut13/multiz4way/$f/$i.maf hgLoadMaf borEut13 $f -pathPrefix=/gbdb/borEut13/multiz4way/$f done # Load the 9-way with ancestors ssh kkilo mkdir -p /cluster/data/borEut13/bed/webbMaf cd /cluster/data/borEut13/bed/webbMaf /cluster/bin/penn/maf_project borEut13.maf borEut13 > borEut13.local.maf mkdir -p /gbdb/borEut13/multiz4way ln -s /cluster/data/borEut13/bed/multizDescend/multiz4way.maf /gbdb/borEut13/multiz4way hgLoadMaf borEut13 multiz4way #load Webb's maf mkdir -p /cluster/data/borEut13/bed/tba14way zcat ../../fromWebb/borEut.maf.gz | sed "s/chimp/panTro1/g" |sed "s/cow/bosTau1/g" |sed "s/primate/eutPri2.chr15/g" | sed "s/euarch/eutGli2.chr15/g" | sed "s/boreo/borEut13.chr15/g" | sed "s/macaca/rheMac1/g" > global.maf time /cluster/bin/penn/maf_project global.maf borEut13 > borEut13.local.maf mkdir -p /gbdb/borEut13/tba14way ln -s /cluster/data/borEut13/bed/webbMaf/borEut13.local.maf /gbdb/borEut13/webbMaf/webbMaf.maf awk "! /^s/ { print} /^s/ {if (\$3 + \$4 > \$6) print \$1, \$2, \$3, \$4,\$5,\$3+\$4, \$7; else print \$0}" borEut13.local.maf > fixed.local.maf /cluster/bin/penn/maf_order borEut13.local.maf borEut13 mmHg3 panHg3 hg17 panTro1 rheMac1 rabbit mm6 rn3 canFam1 bosTau1 armadillo elephant > borEut13.order.maf hgLoadMaf borEut13 webbMaf -pathPrefix=/gbdb/borEut13/webbMaf mkdir /cluster/data/borEut13/bed/tba12way cd /cluster/data/borEut13/bed/tba12way wget "http://www.bx.psu.edu/~webb/borEut.maf.gz" nice bash grep "^s" *local* | sed "s/\..*$//" | sort -u > species.lst time /cluster/bin/penn/maf_order borEut13.local.maf borEut13 eutGli2 eutPri2 hg17 panTro1 rabbit mouse rat canFam1 bosTau1 armadillo elephant > borEut13.order.maf awk "! /^s/ { print} /^s/ {if (\$3 + \$4 > \$6) print \$1, \$2, \$3, \$4,\$5,\$3+\$4, \$7; else print \$0}" borEut13.local.maf > fixed.local.maf mkdir -p /gbdb/borEut13/tba12way ln -s /cluster/data/borEut13/bed/tba12way/borEut13.order.maf /gbdb/borEut13/tba12way/tba12way.maf hgLoadMaf borEut13 tba12way -pathPrefix=/gbdb/borEut13/tba12way cat borEut13.order.maf | hgLoadMafSummary -minSize=10000 -mergeGap=500 -maxSize=50000 borEut13 tba12waySummary stdin # MAKE Mouse Proteins track ssh kkstore01 mkdir -p /cluster/data/borEut13/blastDb cd /cluster/data/borEut13/blastDb awk "{print \$2}" ../*/chr*/*.lft > subChr.lst for i in `cat subChr.lst` do ln -s ../*/chr*/$i.fa echo formatdb -i $i.fa -p F formatdb -i $i.fa -p F done rm *.log *.fa list cd .. for i in `cat chrom.lst`; do cat $i/chr*/*.lft ; done > jkStuff/subChr.lft ssh kkr1u00 rm -rf /iscratch/i/borEut13/blastDb mkdir -p /iscratch/i/borEut13/blastDb cd /cluster/data/borEut13/blastDb for i in nhr nin nsq; do cp *.$i /iscratch/i/borEut13/blastDb ; echo $i; done cd iSync > sync.out mkdir -p /cluster/data/borEut13/bed/tblastn.mm6KG cd /cluster/data/borEut13/bed/tblastn.mm6KG echo /iscratch/i/borEut13/blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst # back to kkstore01 exit cd /cluster/data/borEut13/bed/tblastn.mm6KG rm -rf /cluster/bluearc/borEut13/bed/tblastn.mm6KG/kgfa mkdir -p /cluster/bluearc/borEut13/bed/tblastn.mm6KG/kgfa split -l 70 /cluster/data/mm6/bed/blat.mm6KG/mm6KG.psl /cluster/bluearc/borEut13/bed/tblastn.mm6KG/kgfa/kg ln -s /cluster/bluearc/borEut13/bed/tblastn.mm6KG/kgfa kgfa cd kgfa for i in *; do pslxToFa $i $i.fa; rm $i; done cd .. ls -1S kgfa/*.fa > kg.lst rm -rf /cluster/bluearc/borEut13/bed/tblastn.mm6KG/blastOut mkdir -p /cluster/bluearc/borEut13/bed/tblastn.mm6KG/blastOut ln -s /cluster/bluearc/borEut13/bed/tblastn.mm6KG/blastOut for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done tcsh cat << '_EOF_' > blastGsub #LOOP blastSome $(path1) {check in line $(path2)} {check out exists blastOut/$(root2)/q.$(root1).psl } #ENDLOOP '_EOF_' cat << '_EOF_' > blastSome #!/bin/sh BLASTMAT=/iscratch/i/blast/data export BLASTMAT g=`basename $2` f=/tmp/`basename $3`.$g for eVal in 0.01 0.001 0.0001 0.00001 0.000001 1E-09 1E-11 do if /scratch/blast/blastall -M BLOSUM80 -m 0 -F no -e $eVal -p tblastn -d $1 -i $2 -o $f.8 then mv $f.8 $f.1 break; fi done if test -f $f.1 then if /cluster/bin/i386/blastToPsl $f.1 $f.2 then liftUp -nosort -type=".psl" -nohead $f.3 ../../jkStuff/subChr.lft carry $f.2 liftUp -nosort -type=".psl" -nohead $f.4 ../../jkStuff/liftAll.lft carry $f.3 liftUp -nosort -type=".psl" -pslQ -nohead $3.tmp /cluster/data/mm6/bed/blat.mm6KG/protein.lft warn $f.4 if pslCheck -prot $3.tmp then mv $3.tmp $3 rm -f $f.1 $f.2 $f.3 $f.4 fi exit 0 fi fi rm -f $f.1 $f.2 $3.tmp $f.8 $f.3 $f.4 exit 1 '_EOF_' chmod +x blastSome gensub2 query.lst kg.lst blastGsub blastSpec ssh kk cd /cluster/data/borEut13/bed/tblastn.mm6KG para create blastSpec para push # Completed: 37620 of 37620 jobs # CPU time in finished jobs: 1022938s 17048.96m 284.15h 11.84d 0.032 y # IO & Wait Time: 275126s 4585.44m 76.42h 3.18d 0.009 y # Average job time: 35s 0.58m 0.01h 0.00d # Longest finished job: 111s 1.85m 0.03h 0.00d # Submission to last job: 1684s 28.07m 0.47h 0.02d cat << '_EOF_' > chainGsub #LOOP chainSome $(path1) #ENDLOOP '_EOF_' ssh kki cd /cluster/data/borEut13/bed/tblastn.mm6KG tcsh cat << '_EOF_' > chainOne (cd $1; cat q."$2"* | simpleChain -prot -outPsl -maxGap=200000 stdin ../c.`basename $1`.$2.psl) '_EOF_' chmod +x chainOne for j in blastOut/kg??; do for i in `cat ../../chrom.lst`; do echo chainOne $j chr"$i"; done ; done > chainSpec para create chainSpec para push # Completed: 285 of 285 jobs # CPU time in finished jobs: 239s 3.98m 0.07h 0.00d 0.000 y # IO & Wait Time: 731s 12.19m 0.20h 0.01d 0.000 y # Average job time: 3s 0.06m 0.00h 0.00d # Longest running job: 0s 0.00m 0.00h 0.00d # Longest finished job: 14s 0.23m 0.00h 0.00d # Submission to last job: 85s 1.42m 0.02h 0.00d exit # back to kkstore01 cd /cluster/data/borEut13/bed/tblastn.mm6KG/blastOut for i in kg?? do cat c.$i.*.psl | awk "(\$13 - \$12)/\$11 > 0.6 {print}" > c60.$i.psl sort -rn c60.$i.psl | pslUniq stdin u.$i.psl awk "((\$1 / \$11) ) > 0.90 { print }" c60.$i.psl > m60.$i.psl echo $i done sort -u -T /tmp -k 14,14 -k 17,17n -k 17,17n u.*.psl m60* > /cluster/data/borEut13/bed/tblastn.mm6KG/blastMm6KG.psl cd .. ssh hgwdev cd /cluster/data/borEut13/bed/tblastn.mm6KG hgLoadPsl borEut13 blastHg17KG.psl # 1425966 bases of 64944656 (2.196%) # 1368835 bases of 62796757 (2.180%) in borEut2 # back to kkstore01 rm -rf blastOut # End tblastn ########################################################################## # EVOFOLD - RNA secondary structure predictions lifted from hg17 # Jakob Skou Pedersen, Aug 5, 2005 ssh -C hgwdev mkdir -p /cluster/data/borEut13/bed/evofold cd /cluster/data/borEut13/bed/evofold # concatenating chain files cat /cluster/data/borEut13/bed/chains.hg17/hg17/*chain > hg17ToCanHg10.over.chain # lifting evofolds from hg17 to borEut13 echo "select chrom, chromStart, chromEnd, name, score, strand, size, secStr, conf from evofold;" | hgsql hg17 | sed -e 1d > foldsHg17.bed liftOver -minMatch=1.0 foldsHg17.bed hg17ToCanHg10.over.chain tmp.bed unmapped.bed grep "#" unmapped.bed | wc -l # remove elements which are wrong size after lifting awk '$3-$2 == $7' tmp.bed > foldsCanHg10.bed # clean up rm foldsHg17.bed unmapped.bed tmp.bed hgLoadBed -notItemRgb -sqlTable=/cluster/home/jsp/prog/kent/src/hg/lib/evofold.sql borEut13 evofold foldsCanHg10.bed ########################################################################## # RFAMSEEDFOLDS - Rfam seed secondary structure annotation lifted from hg17 # Jakob Skou Pedersen, Aug 5, 2005 # lifting rfamSeed from hg17 to borEut13 echo "select chrom, chromStart, chromEnd, name, score, strand, size, secStr, conf from RfamSeedFolds;" | hgsql hg17 | sed -e 1d > foldsHg17.bed liftOver -minMatch=1.0 foldsHg17.bed hg17ToCanHg10.over.chain tmp.bed unmapped.bed grep "#" unmapped.bed | wc -l # remove elements which are of wrong size after lifting awk '$3-$2 == $7' tmp.bed > foldsCanHg10.bed # clean up rm foldsHg17.bed unmapped.bed tmp.bed hgLoadBed -noBin -notItemRgb -sqlTable=/cluster/home/jsp/prog/kent/src/hg/lib/RfamSeedFolds.sql borEut13 RfamSeedFolds foldsCanHg10.bed