# for emacs: -*- mode: sh; -*- # Armadillo May 2005 Broad Assembly # # DOWNLOAD SEQUENCE ssh kkstore01 mkdir /cluster/store9/dasNov1 cd /cluster/data ln -s /cluster/store9/dasNov1 dasNov1 cd /cluster/data/dasNov1 mkdir jkStuff bed mkdir broad cd broad # ftp'ed with password from Broad # -rw-rw-r-- 1 braney protein 69920541 May 20 07:52 assembly.agp # -rw-rw-r-- 1 braney protein 745077193 May 20 08:15 assembly.bases.gz # -rw-rw-r-- 1 braney protein 1222132418 May 20 09:08 assembly.quals.gz # -rw-rw-r-- 1 braney protein 423586027 May 20 09:52 unplaced.fasta.gz # -rw-rw-r-- 1 braney protein 1294098192 May 20 10:38 unplaced.qual.gz gunzip assembly.bases.gz faSize assembly.bases # 2146362222 bases (0 N's 2146362222 real 2146362222 upper 0 lower) in 848432 sequences in 1 files # Total size: mean 2529.8 sd 1972.8 min 61 (contig_80213) max 194887 (contig_17) median 2053 # N count: mean 0.0 sd 0.0 # U count: mean 2529.8 sd 1972.8 # L count: mean 0.0 sd 0.0 ssh kolossus cd /cluster/data/dasNov1/broad /cluster/bin/x86_64/agpAllToFaFile assembly.agp assembly.bases ../dasNov1.fa cd .. faSize dasNov1.fa # 3856777364 bases (1710415142 N's 2146362222 real 2146362222 upper 0 lower) in 304391 sequences in 1 files # Total size: mean 12670.5 sd 24184.9 min 1000 (scaffold_304389) max 974481 (scaffold_0) median 4960 # N count: mean 5619.1 sd 15102.0 # U count: mean 7051.3 sd 10915.0 # L count: mean 0.0 sd 0.0 /cluster/bin/scripts/agpToLift < assembly.agp > ../jkStuff/assembly.lft # PARTITION SCAFFOLDS FOR REPEATMASKER RUN # glom the tiny scaffolds up into ~50k collections ssh kkstore01 cd /cluster/data/dasNov1 mkdir chunks50k zcat broad/assembly.bases.gz | faSplit about stdin 50000 chunks50k/chunk_ cd chunks50k for i in 0 1 2 3 4 5 6 7 8 9; do mkdir $i; mv *$i.fa $i; done # RUN REPEAT MASKER # make the run directory, output directory, and job list ssh kkstore01 cd /cluster/data/dasNov1 cat << '_EOF_' > jkStuff/RMArmadillo #!/bin/csh -fe cd $1 /bin/mkdir -p /tmp/dasNov1/$2 /bin/cp $3 /tmp/dasNov1/$2/ pushd /tmp/dasNov1/$2 /cluster/bluearc/RepeatMasker/RepeatMasker -s -species eutheria $2 popd /bin/cp /tmp/dasNov1/$2/$2.out ./ /bin/rm -fr /tmp/dasNov1/$2/* /bin/rmdir --ignore-fail-on-non-empty /tmp/dasNov1/$2 /bin/rmdir --ignore-fail-on-non-empty /tmp/dasNov1 '_EOF_' # << this line makes emacs coloring happy chmod +x jkStuff/RMArmadillo # mkdir RMRun RMOut # for i in chunks800k/*.fa # do # d="/cluster/data/dasNov1" # c=`basename $i` # echo "../jkStuff/RMArmadillo $d/RMOut $c { check in line+ $d/$i} {check out line+ $d/RMOut/$c.out}" # done > RMRun/RMJobs mkdir RMRun1 RMOut1 cd RMOut1 mkdir 0 1 2 3 4 5 6 7 8 9 cd ../chunks50k for i in */*.fa do e=`dirname $i` d="/cluster/data/dasNov1" c=`basename $i` echo "../jkStuff/RMArmadillo $d/RMOut1/$e $c {check in line+ $d/chunks50k/$i} {check out line+ $d/RMOut1/$e/$c.out}" done > ../RMRun1/RMJobs # do the run ssh kk9 cd /cluster/data/dasNov1/RMRun para create RMJobs para try, check, push, check,... # Completed: 41361 of 41361 jobs # CPU time in finished jobs: 52130147s 868835.79m 14480.60h 603.36d 1.653 y # IO & Wait Time: 224553s 3742.55m 62.38h 2.60d 0.007 y # Average job time: 1266s 21.10m 0.35h 0.01d # Longest finished job: 6884s 114.73m 1.91h 0.08d # Submission to last job: 150113s 2501.88m 41.70h 1.74d # Lift up the split-scaffold .out's to scaffold .out's ssh kkstore01 cd /cluster/data/dasNov1/RMOut1 for i in 0 1 2 3 4 5 6 7 8 9; do echo $i; liftUp -nohead $i.out ../jkStuff/assembly.lft warn $i/*.fa.out>/dev/null; done head -3 0.out > dasNov1.out for i in 0 1 2 3 4 5 6 7 8 9; do tail +4 $i.out; done >> dasNov1.out # Load the .out files into the database with: ssh hgwdev hgLoadOut dasNov1 /cluster/data/dasNov1/RMOut1/dasNov1.out # Loading up table dasNov1_rmsk # note: 24 records dropped due to repStart > repEnd hgsql dasNov1 -e 'rename table dasNov1_rmsk to rmsk' # Fix up the indices too: hgsql dasNov1 -e 'drop index bin on rmsk; \ drop index genoStart on rmsk; \ drop index genoEnd on rmsk; \ create index bin on rmsk (genoName(16), bin); \ create index genoStart on rmsk (genoName(16), genoStart); \ create index genoEnd on rmsk (genoName(16), genoEnd);' # EXTRACTING GAP INFO FROM BLOCKS OF NS (DONE 11/5/04 angie) ssh kkstore01 mkdir /cluster/data/dasNov1/bed/fakeAgp cd /cluster/data/dasNov1/bed/fakeAgp faGapSizes ../../downloads/scaffolds.fasta \ -niceSizes=5,10,20,25,30,40,50,100,250,500,1000,10000,100000 # Wow, all block of N's seem to be exactly 100bp long. # hgFakeAgp's default -minContigGap of 25 will be fine. hgFakeAgp ../../downloads/scaffolds.fasta fake.agp ssh hgwdev hgLoadGap -unsplit dasNov1 /cluster/data/dasNov1/bed/fakeAgp/fake.agp # SIMPLE REPEATS (TRF) ssh kkstore01 mkdir /cluster/data/dasNov1/bed/simpleRepeat cd /cluster/data/dasNov1/bed/simpleRepeat nice trfBig -trf=/cluster/bin/i386/trf ../../dasNov1.fa /dev/null -bedAt=simpleRepeat.bed -tempDir=/tmp \ | egrep -v '^(Removed|Tandem|Copyright|Loading|Allocating|Initializing|Computing|Scanning|Freeing)' > trf.log & # check on this with tail -f trf.log # Load this into the database as so ssh hgwdev hgLoadBed dasNov1 simpleRepeat /cluster/data/dasNov1/bed/simpleRepeat/simpleRepeat.bed \ -sqlTable=$HOME/kent/src/hg/lib/simpleRepeat.sql # FILTER SIMPLE REPEATS (TRF) INTO MASK # make a filtered version of the trf output: # keep trf's with period <= 12: ssh kkstore01 cd /cluster/data/dasNov1/bed/simpleRepeat awk '{if ($5 <= 12) print;}' simpleRepeat.bed > trfMask.bed # MASK FA USING REPEATMASKER AND FILTERED TRF FILES ssh kolossus cd /cluster/data/dasNov1 nice /cluster/bin/x86_64/maskOutFa -soft dasNov1.fa bed/simpleRepeat/trfMask.bed dasNov1.simple.fa nice /cluster/bin/x86_64/maskOutFa -softAdd dasNov1.simple.fa RMOut1/dasNov1.out dasNov1.masked.fa # WARNING: negative rEnd: -104 scaffold_8757:558-754 L1M4 # WARNING: negative rEnd: -511 scaffold_34788:4357-4433 L1MCc # WARNING: negative rEnd: -154 scaffold_34788:5061-5302 L1MCc # WARNING: negative rEnd: -383 scaffold_119083:539-652 L1M4b # WARNING: negative rEnd: -99 scaffold_181954:1627-2036 L1MCc # WARNING: negative rEnd: -1033 scaffold_269:42483-42807 L1MEc # WARNING: negative rEnd: -15 scaffold_18137:4036-4256 L1M4 # WARNING: negative rEnd: -301 scaffold_79493:4217-4508 L1MCc # WARNING: negative rEnd: -542 scaffold_1800:103399-103624 L1M4b # WARNING: negative rEnd: -594 scaffold_10038:2784-3058 L1MCc # WARNING: negative rEnd: -916 scaffold_58908:40949-41369 L1MEc # WARNING: negative rEnd: -247 scaffold_58908:41562-41685 L1MEc # WARNING: negative rEnd: -99 scaffold_287090:3-415 L1MCc # WARNING: negative rEnd: -162 scaffold_25:281259-281527 L1MCc # WARNING: negative rEnd: -99 scaffold_45825:10398-10807 L1MCc # WARNING: negative rEnd: -34 scaffold_47500:8156-8385 L1M4b # WARNING: negative rEnd: -99 scaffold_67:113583-113881 L1MCc mv dasNov1.fa dasNov1.unmasked.fa # Now clean up the unmasked split scaffolds to avoid confusion later. rm -r chunks500k scaffoldsSplit.fa jkStuff/scaffoldsSplit.lft # CREATING DATABASE # Create the database. ssh hgwdev # Make sure there is at least 5 gig free for the database df -h /var/lib/mysql Filesystem Size Used Avail Use% Mounted on # /dev/sdc1 1.8T 915G 746G 56% /var/lib/mysql hgsql '' -e 'create database dasNov1' # STORE SEQUENCE AND ASSEMBLY INFORMATION # Translate to 2bit ssh kolossus cd /cluster/data/dasNov1 /cluster/bin/x86_64/faToTwoBit dasNov1.masked.fa dasNov1.2bit # Make chromInfo.tab. mkdir bed/chromInfo twoBitInfo dasNov1.2bit stdout | awk '{printf "%s\t%s\t/gbdb/dasNov1/dasNov1.2bit\n",$1,$2;}' \ | sort > bed/chromInfo/chromInfo.tab # Make symbolic a link from /gbdb/dasNov1 to the 2bit. ssh hgwdev mkdir -p /gbdb/dasNov1 ln -s /cluster/data/dasNov1/dasNov1.2bit /gbdb/dasNov1/ # Load chromInfo table. hgsql dasNov1 < $HOME/kent/src/hg/lib/chromInfo.sql hgsql dasNov1 -e 'load data local infile "/cluster/data/dasNov1/bed/chromInfo/chromInfo.tab" into table chromInfo' # Make chrom.sizes from chromInfo contents and check scaffold count. hgsql dasNov1 -N -e 'select chrom,size from chromInfo' > /cluster/data/dasNov1/chrom.sizes wc -l /cluster/data/dasNov1/chrom.sizes # 304391 /cluster/data/dasNov1/chrom.sizes # CREATING GRP TABLE FOR TRACK GROUPING # Copy all the data from the table "grp" # in an existing database to the new database ssh hgwdev hgsql dasNov1 -e 'create table grp (PRIMARY KEY(NAME)) select * from hg17.grp' # MAKE HGCENTRALTEST ENTRY AND TRACKDB TABLE # Warning: genome and organism fields must correspond # with defaultDb values echo 'INSERT INTO genomeClade (genome,clade,priority) values ("Armadillo", "vertebrate",56);' \ | hgsql -h genome-testdb hgcentraltest echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, \ htmlPath, hgNearOk, hgPbOk, sourceName) values ("dasNov1", "May. 2005", "/gbdb/dasNov1", "Armadillo", \ "", 1, 57, "Armadillo", "Dasypus novemcinctus", "/gbdb/dasNov1/html/description.html", 0, 0, "Broad May 2005");'\ | hgsql -h genome-testdb hgcentraltest echo 'INSERT INTO defaultDb (genome, name) values ("Armadillo", "dasNov1");' \ | hgsql -h genome-testdb hgcentraltest # Make trackDb table so browser knows what tracks to expect: ssh hgwdev cd ~/kent/src/hg/makeDb/trackDb cvs up -d -P # Edit trackDb/makefile to add dasNov1 to the DBS variable. mkdir drosophila/dasNov1 # Create a simple drosophila/dasNov1/description.html file. cvs add drosophila/dasNov1 cvs add drosophila/dasNov1/description.html make update DBS=dasNov1 ZOO_DBS= # go public on genome-test cvs ci makefile cvs ci drosophila/dasNov1 mkdir /gbdb/dasNov1/html # in a clean, updated tree's kent/src/hg/makeDb/trackDb: make alpha # PUT SEQUENCE ON /ISCRATCH FOR BLASTZ (DONE 11/3/04 angie) # First, agglomerate small scaffolds into chunks of ~100k median # (many scaffolds are larger than that) so we don't have too many # files for one dir, but keep a reasonably low job run time: ssh kkstore01 cd /cluster/data/dasNov1 mkdir chunksUnsplit faSplit about scaffolds.fa 100000 chunksUnsplit/chunk_ ssh kkr1u00 mkdir /iscratch/i/dasNov1 cp -pR /cluster/data/dasNov1/chunksUnsplit /iscratch/i/dasNov1/ cp -p /cluster/data/dasNov1/dasNov1.2bit /iscratch/i/dasNov1/ iSync # PRODUCING GENSCAN PREDICTIONS (DONE 11/4/04 angie) ssh kkstore01 # Make hard-masked scaffolds and split up for processing: cd /cluster/data/dasNov1 maskOutFa scaffolds.fa hard scaffolds.fa.masked mkdir chunksUnsplitMasked faSplit about scaffolds.fa.masked 100000 chunksUnsplitMasked/chunk_ mkdir /cluster/data/dasNov1/bed/genscan cd /cluster/data/dasNov1/bed/genscan # Check out hg3rdParty/genscanlinux to get latest genscan: cvs co hg3rdParty/genscanlinux # Make 3 subdirectories for genscan to put their output files in mkdir gtf pep subopt ls -1S ../../chunksUnsplitMasked/chunk*.fa > chunks.list cat << '_EOF_' > gsub #LOOP 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 keeps emacs coloring happy gensub2 chunks.list single gsub jobList ssh kki cd /cluster/data/dasNov1/bed/genscan para create jobList para try, check, push, check, ... #Completed: 463 of 463 jobs #Average job time: 12s 0.21m 0.00h 0.00d #Longest job: 317s 5.28m 0.09h 0.00d #Submission to last job: 445s 7.42m 0.12h 0.01d # If there are crashes, diagnose with "para problems". # If a job crashes due to genscan running out of memory, re-run it # manually with "-window=1200000" instead of "-window=2400000". # Concatenate scaffold-level results: ssh kkstore01 cd /cluster/data/dasNov1/bed/genscan cat gtf/*.gtf > genscan.gtf cat subopt/*.bed > genscanSubopt.bed cat pep/*.pep > genscan.pep # Clean up rm -r /cluster/data/dasNov1/chunksUnsplitMasked # Load into the database as so: ssh hgwdev cd /cluster/data/dasNov1/bed/genscan # Reloaded without -genePredExt 1/6/05: ldHgGene -gtf dasNov1 genscan genscan.gtf hgPepPred dasNov1 generic genscanPep genscan.pep hgLoadBed dasNov1 genscanSubopt genscanSubopt.bed # MAKE DOWNLOADABLE FILES (DONE 11/4/04 angie) # RECREATE BIGZIPS DOWNLOADS AND README FILE (DONE, 2006-05-05, hartera) # ADDED md5sum.txt FILE FOR LIFTOVER DOWNLOADS AND CREATED CORRECT md5sum.txt # FOR vsMm7 AND vsHg18 DOWNLOADS (DONE, 2006-05-23, hartera) ssh kkstore01 mkdir /cluster/data/dasNov1/zips cd /cluster/data/dasNov1 zip -j zips/scaffoldOut.zip RMOut/scaffolds.fa.out zip -j zips/scaffoldFa.zip scaffolds.fa zip -j zips/scaffoldFaMasked.zip scaffolds.fa.masked zip -j zips/scaffoldTrf.zip bed/simpleRepeat/trfMask.bed foreach f (zips/*.zip) echo $f unzip -t $f | tail -1 end ssh hgwdev mkdir /usr/local/apache/htdocs/goldenPath/dasNov1 cd /usr/local/apache/htdocs/goldenPath/dasNov1 mkdir bigZips database # Create README.txt files in bigZips/ and database/ to explain the files. cd bigZips cp -p /cluster/data/dasNov1/zips/*.zip . md5sum *.zip > md5sum.txt # Add more bigZips downloads. Some of the above downloads don't exist # anymore in bigZips in /usr/local/apache/htdocs/goldenPath/... on hgwdev # (2006-05-05, hartera) ssh kkstore04 mkdir /cluster/data/dasNov1/bigZips cd /cluster/data/dasNov1 # soft-masked scaffolds sequences cp -p dasNov1.masked.fa.gz ./bigZips/scaffoldSoftMask.fa.gz # assembly agp cp -p ./broad/assembly.agp.gz ./bigZips/ # Simple Repeats cp -p ./bed/simpleRepeat/trfMask.bed ./bigZips/trf.bed # RepeatMasker output cp -p ./RMOut1/dasNov1.out ./bigZips/rmsk.out # unmasked scaffolds sequences cp -p dasNov1.unmasked.fa.gz ./bigZips/scaffold.fa.gz cd bigZips gzip trf.bed gzip rmsk.out # check integrity of files foreach f (*.gz) echo $f gunzip -t $f | tail -1 end md5sum *.gz > md5sum.txt # link the *.gz and *.txt files to hgwdev:/usr/local/apache/.... ssh hgwdev set gp=/usr/local/apache/htdocs/goldenPath/dasNov1 rm -r $gp/bigZips mkdir -p $gp/bigZips ln -s /cluster/data/dasNov1/bigZips/{*.gz,*.txt} $gp/bigZips # copy over README.txt and edit for bigZips # dasNov1ToMm7.over.chain.gz is in the md5sum.txt in the # vsMm7 directory. It should be in the liftOver directory so move it there # and re-make md5sum.txt for vsMm7 dir. # Add liftOver md5sum.txt (hartera, 2006-05-23) ssh hgwdev set gp=/usr/local/apache/htdocs/goldenPath/dasNov1 # copy over from hgwdevold cd /cluster/data/dasNov1/bed/liftOver scp hgwdevold:$gp/liftOver/dasNov1ToMm7.over.chain.gz . ln -s /cluster/data/dasNov1/bed/liftOver/*.gz $gp/liftOver cd $gp/liftOver # create md5sum.txt md5sum *.gz > md5sum.txt # recreate md5sum.txt for vsMm7 files cd $gp/vsMm7 rm md5sum.txt md5sum *.gz > md5sum.txt # recreate md5sum.txt for vsHg18 files as this includes files in an # axtNet directory that is not in this directory. cd $gp/vsHg18 rm md5sum.txt md5sum *.gz > md5sum.txt # Check that README.txt is correct for vsMm7 and vsHg18. # SWAP DM1-DROANA1 BLASTZ (DONE 11/4/04 angie) ssh kkstore01 mkdir /cluster/data/dasNov1/bed/blastz.dm1.swap.2004-11-03 ln -s blastz.dm1.swap.2004-11-03 /cluster/data/dasNov1/bed/blastz.dm1 cd /cluster/data/dasNov1/bed/blastz.dm1 set aliDir = /cluster/data/dm1/bed/blastz.dasNov1 cp $aliDir/S1.len S2.len cp $aliDir/S2.len S1.len # With 11k scaffolds, we don't want a directory with one file per # scaffold. So just make one .axt with everything -- not too huge # anyway, given these little insect genomes. cat $aliDir/axtChrom/chr*.axt \ | axtSwap stdin $aliDir/S1.len $aliDir/S2.len stdout \ | axtSort stdin dm1.axt du -sh $aliDir/axtChrom dm1.axt #389M /cluster/data/dm1/bed/blastz.dasNov1/axtChrom #389M dm1.axt # CHAIN MELANOGASTER BLASTZ (DONE 11/4/04 angie) # Run axtChain on kolossus (one big dm1.axt input) ssh kolossus mkdir /cluster/data/dasNov1/bed/blastz.dm1/axtChain cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain axtChain -verbose=0 ../dm1.axt /cluster/data/dasNov1/dasNov1.2bit \ /cluster/data/dm1/nib stdout \ | chainAntiRepeat /cluster/data/dasNov1/dasNov1.2bit \ /cluster/data/dm1/nib stdin stdout \ | chainMergeSort stdin > all.chain # Load chains into database ssh hgwdev cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain hgLoadChain -tIndex dasNov1 chainDm1 all.chain # NET MELANOGASTER BLASTZ (DONE 11/4/04 angie) ssh kkstore01 cd /cluster/data/dasNov1/bed/blastz.dm1/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/dasNov1/bed/blastz.dm1/axtChain netClass -noAr noClass.net dasNov1 dm1 melanogaster.net \ |& g -v "table gap doesn't exist" # Make a 'syntenic' subset: ssh kkstore01 cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain rm noClass.net netFilter -syn melanogaster.net > melanogasterSyn.net # Load the nets into database ssh hgwdev cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain netFilter -minGap=10 melanogaster.net | hgLoadNet dasNov1 netDm1 stdin netFilter -minGap=10 melanogasterSyn.net \ | hgLoadNet dasNov1 netSyntenyDm1 stdin # MAKE AXTNET (DONE 11/4/04 angie) ssh kkstore01 cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain netToAxt melanogaster.net all.chain /cluster/data/dasNov1/dasNov1.2bit \ /cluster/data/dm1/nib stdout \ | axtSort stdin melanogasterNet.axt # MAKE VSDM1 DOWNLOADABLES (DONE 11/4/04 angie) ssh kkstore01 cd /cluster/data/dasNov1/bed/blastz.dm1/axtChain nice gzip *.{chain,net,axt} ssh hgwdev mkdir /usr/local/apache/htdocs/goldenPath/dasNov1/vsDm1 cd /usr/local/apache/htdocs/goldenPath/dasNov1/vsDm1 cp -p /cluster/data/dasNov1/bed/blastz.dm1/axtChain/all.chain.gz \ melanogaster.chain.gz cp -p /cluster/data/dasNov1/bed/blastz.dm1/axtChain/melanogaster.net.gz . cp -p /cluster/data/dasNov1/bed/blastz.dm1/axtChain/melanogasterNet.axt.gz . # Make a README.txt which explains the files & formats. md5sum *.gz */*.gz > md5sum.txt # MAKE 11.OOC FILE FOR BLAT (DONE 11/4/04 angie) # Use -repMatch=100 (based on size -- for human we use 1024, and # fly size is ~4.4% of human judging by gapless dm1 genome size from # featureBits -- we would use 45, but bump that up a bit to be more # conservative). ssh kkr1u00 mkdir /cluster/bluearc/dasNov1 blat /cluster/data/dasNov1/dasNov1.2bit /dev/null /dev/null -tileSize=11 \ -makeOoc=/cluster/bluearc/dasNov1/11.ooc -repMatch=100 #Wrote 9721 overused 11-mers to /cluster/bluearc/dasNov1/11.ooc cp -p /cluster/bluearc/dasNov1/*.ooc /iscratch/i/dasNov1/ iSync # GET GENBANK mRNA AND EST COUNTS (DONE 11/8/04 angie) # Go to the latest GenBank full release dir and get an idea of how # many mRNAs and ESTs there are to align. ssh eieio cd /cluster/data/genbank/data/processed/genbank.144.0/full awk '$4 == "Drosophila" {print $4 " " $5;}' mrna.gbidx | sort | uniq -c # 9 Drosophila ananassae # 1 Drosophila mojavensis # 33 Drosophila virilis # Wow, questionable whether we should have a native mRNA track here. awk '$4 == "Drosophila" {print $4 " " $5;}' est*.gbidx | sort | uniq -c # 382439 Drosophila melanogaster # 4105 Drosophila simulans # 779 Drosophila yakuba # And a native EST track isn't even a possibility for the new flies # at this point! # AUTO UPDATE GENBANK MRNA RUN (DONE 11/16/04 angie) ssh hgwdev # Update genbank config and source in CVS: cd ~/kent/src/hg/makeDb/genbank cvsup . # Edit etc/genbank.conf and add these lines (note scaffold-browser settings): # dasNov1 (D. ananassae) dasNov1.genome = /iscratch/i/dasNov1/dasNov1.2bit dasNov1.mondoTwoBitParts = 1000 dasNov1.lift = no dasNov1.refseq.mrna.native.load = no dasNov1.refseq.mrna.xeno.load = yes dasNov1.refseq.mrna.xeno.pslReps = -minCover=0.15 -minAli=0.75 -nearTop=0.005 dasNov1.genbank.mrna.xeno.load = yes # GenBank has no D. ananassae ESTs at this point... that may change. dasNov1.genbank.est.native.load = no dasNov1.genbank.est.xeno.load = no dasNov1.downloadDir = dasNov1 dasNov1.perChromTables = no cvs ci etc/genbank.conf # Since D. ananassae is a new species for us, edit src/lib/gbGenome.c. # Pick some other browser species, & monkey-see monkey-do. cvs diff src/lib/gbGenome.c make cvs ci src/lib/gbGenome.c # Edit src/align/gbBlat to add /iscratch/i/dasNov1/11.ooc cvs diff src/align/gbBlat make cvs ci src/align/gbBlat # Install to /cluster/data/genbank: make install-server ssh `fileServer /cluster/data/genbank/` cd /cluster/data/genbank # This is an -initial run, (xeno) RefSeq only: nice bin/gbAlignStep -srcDb=refseq -type=mrna -initial dasNov1 & tail -f [its logfile] # Load results: ssh hgwdev cd /cluster/data/genbank nice bin/gbDbLoadStep -verbose=1 -drop -initialLoad dasNov1 featureBits dasNov1 xenoRefGene #16520385 bases of 165766797 (9.966%) in intersection # Clean up: rm -rf work/initial.dasNov1 # This is an -initial run, mRNA only: nice bin/gbAlignStep -srcDb=genbank -type=mrna -initial dasNov1 & tail -f [its logfile] # Load results: ssh hgwdev cd /cluster/data/genbank nice bin/gbDbLoadStep -verbose=1 -drop -initialLoad dasNov1 featureBits dasNov1 all_mrna #19602 bases of 165766797 (0.012%) in intersection featureBits dasNov1 xenoMrna #17295487 bases of 165766797 (10.434%) in intersection # Clean up: rm -rf work/initial.dasNov1 # MAKE GCPERCENT (DONE 11/4/04 angie) ssh hgwdev mkdir /cluster/data/dasNov1/bed/gcPercent cd /cluster/data/dasNov1/bed/gcPercent # create and load gcPercent table hgGcPercent dasNov1 /cluster/data/dasNov1 # MAKE HGCENTRALTEST BLATSERVERS ENTRY (DONE 7-20-05 braney) ssh hgwdev echo 'insert into blatServers values("dasNov1", "blat2", "17780", 1, 0); \ insert into blatServers values("dasNov1", "blat2", "17781", 0, 1);' \ | hgsql -h genome-testdb hgcentraltest # MAKE Drosophila Proteins track (DONE braney 11/17/04) ssh kkstore01 mkdir -p /cluster/data/dasNov1/blastDb cd /cluster/data/dasNov1/blastDb faSplit sequence ../scaffolds.fa 400 x for i in *.fa; do formatdb -i $i -p F 2> /dev/null; done rm *.fa *.log ssh kkr1u00 mkdir -p /iscratch/i/dasNov1/blastDb cp /cluster/data/dasNov1/blastDb/* /iscratch/i/dasNov1/blastDb (iSync) 2>&1 > sync.out mkdir -p /cluster/data/dasNov1/bed/tblastn.dm1FB cd /cluster/data/dasNov1/bed/tblastn.dm1FB ls -1S /iscratch/i/dasNov1/blastDb/*.nsq | sed "s/\.nsq//" > bug.lst exit # back to kkstore01 cd /cluster/data/dasNov1/bed/tblastn.dm1FB mkdir fbfa # calculate a reasonable number of jobs calc `wc /cluster/data/dm1/bed/blat.dm1FB/dm1FB.psl | awk "{print \\\$1}"`/\(150000/`wc bug.lst | awk "{print \\\$1}"`\) # 18735/(150000/396) = 49.460400 split -l 49 /cluster/data/dm1/bed/blat.dm1FB/dm1FB.psl fbfa/fb cd fbfa for i in *; do pslxToFa $i $i.fa; rm $i; done cd .. ls -1S fbfa/*.fa > fb.lst mkdir blastOut for i in `cat fb.lst`; do mkdir blastOut/`basename $i .fa`; done 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" -pslQ -nohead $3.tmp /iscratch/i/dm1/protein.lft warn $f.2 mv $3.tmp $3 rm -f $f.1 $f.2 exit 0 fi fi rm -f $f.1 $f.2 $3.tmp exit 1 '_EOF_' chmod +x blastSome gensub2 bug.lst fb.lst blastGsub blastSpec ssh kk cd /cluster/data/dasNov1/bed/tblastn.dm1FB para create blastSpec para try, push # Completed: 151668 of 151668 jobs # CPU time in finished jobs: 2932565s 48876.08m 814.60h 33.94d 0.093 y # IO & Wait Time: 694006s 11566.77m 192.78h 8.03d 0.022 y # Average job time: 24s 0.40m 0.01h 0.00d # Longest job: 2721s 45.35m 0.76h 0.03d # Submission to last job: 73860s 1231.00m 20.52h 0.85d cat << '_EOF_' > chainGsub #LOOP chainSome $(path1) #ENDLOOP '_EOF_' cat << '_EOF_' > chainSome (cd $1; cat q.*.psl | simpleChain -prot -outPsl -maxGap=25000 stdin ../c.`basename $1`.psl) '_EOF_' chmod +x chainSome ls -1dS `pwd`/blastOut/fb?? > chain.lst gensub2 chain.lst single chainGsub chainSpec para create chainSpec # should run this on the mini-cluster or with my shove script # so you can limit the number of jobs starting to 3 or 4 para try, push... # Completed: 383 of 383 jobs # CPU time in finished jobs: 327s 5.44m 0.09h 0.00d 0.000 y # IO & Wait Time: 8218s 136.97m 2.28h 0.10d 0.000 y # Average job time: 22s 0.37m 0.01h 0.00d # Longest job: 54s 0.90m 0.01h 0.00d # Submission to last job: 674s 11.23m 0.19h 0.01d exit # back to kkstore01 cd /cluster/data/dasNov1/bed/tblastn.dm1FB/blastOut for i in fb?? do awk "(\$13 - \$12)/\$11 > 0.6 {print}" c.$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/dasNov1/bed/tblastn.dm1FB/blastDm1FB.psl ssh hgwdev cd /cluster/data/dasNov1/bed/tblastn.dm1FB hgLoadPsl dasNov1 blastDm1FB.psl # End tblastn # SWAP CHAINS FROM DM2, BUILD NETS ETC. (DONE 3/2/05 angie) ssh kkstore01 mkdir /cluster/data/dasNov1/bed/blastz.dm2.swap cd /cluster/data/dasNov1/bed/blastz.dm2.swap doBlastzChainNet.pl -swap /cluster/data/dm2/bed/blastz.dasNov1/DEF \ >& do.log & tail -f do.log # Add {chain,net}Dm2 to trackDb.ra if necessary. # Add /usr/local/apache/htdocs/goldenPath/dasNov1/vsDm2/README.txt # CHAIN AND NET SWAPPED HUMAN BLASTZ (WORKING 12/22/05 kate) # Working in Brian's blastz dir (not doced). # This procedure follows conventions in doBlastzNetChain.pl, # so it can be used to complete the processing ssh kki cd /cluster/data/dasNov1/bed/zb.hg17 ln -s `pwd` /cluster/data/hg17/bed/blastz.dasNov1 mkdir -p axtChain/run/chain ls -1S /cluster/data/dasNov1/bed/zb.hg17/axtChrom/*.axt.gz | \ sed 's/.gz//' > axtChain/run/input.lst cd axtChain/run cat > chain.csh << 'EOF' #!/bin/csh -ef zcat $1 | \ axtChain -verbose=0 -minScore=3000 -linearGap=medium stdin \ /cluster/data/hg17/nib /cluster/data/dasNov1/dasNov1.2bit stdout | \ chainAntiRepeat /cluster/data/hg17/nib /cluster/data/dasNov1/dasNov1.2bit \ stdin $2 'EOF' # << happy emacs cat > gsub << 'EOF' #LOOP chain.csh {check in exists $(path1).gz} {check out line+ chain/$(root1).chain} #ENDLOOP 'EOF' # << happy emacs chmod a+x chain.csh gensub2 input.lst single gsub jobList para create jobList; para try para check para push # wait for completion para time > run.time # finish pipeline cd /cluster/data/dasNov1/bed/zb.hg17 /cluster/bin/scripts/doBlastzChainNet.pl -verbose=2 \ -continue=chainMerge \ -bigClusterHub=pk \ `pwd`/DEF >& blastz.out & ############################################################################ ## BLASTZ swap from mm9 alignments (2007-11-11 - markd) ssh hgwdev mkdir /cluster/data/dasNov1/bed/blastz.mm9.swap cd /cluster/data/dasNov1/bed/blastz.mm9.swap ln -s blastz.mm9.swap ../blastz.mm9 /cluster/bin/scripts/doBlastzChainNet.pl \ -swap /cluster/data/mm9/bed/blastz.dasNov1/DEF >& swap.out& nice +19 featureBits dasNov1 chainMm9Link # 438318232 bases of 2146362222 (20.421%) in intersection ############################################################################ # TRANSMAP vertebrate.2008-05-20 build (2008-05-24 markd) vertebrate-wide transMap alignments were built Tracks are created and loaded by a single Makefile. This is available from: svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2008-05-20 see doc/builds.txt for specific details. ############################################################################ ############################################################################ # TRANSMAP vertebrate.2008-06-07 build (2008-06-30 markd) vertebrate-wide transMap alignments were built Tracks are created and loaded by a single Makefile. This is available from: svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2008-06-30 see doc/builds.txt for specific details. ############################################################################ # dasNov1 - Armadillo - Ensembl Genes version 51 (DONE - 2008-12-03 - hiram) ssh kkr14u07 cd /hive/data/genomes/dasNov1 cat << '_EOF_' > dasNov1.ensGene.ra # required db variable db dasNov1 # do we need to translate geneScaffold coordinates geneScaffolds yes # ignore genes that do not properly convert to a gene pred, and contig # names that are not in the UCSC assembly skipInvalid yes # ignore the three genes that have invalid structures from Ensembl: # 18192: ENSDNOT00000004471 no exonFrame on CDS exon 7 # 35247: ENSDNOT00000007696 no exonFrame on CDS exon 8 # 38952: ENSDNOT00000019234 no exonFrame on CDS exon 0 '_EOF_' # << happy emacs doEnsGeneUpdate.pl -ensVersion=51 dasNov1.ensGene.ra ssh hgwdev cd /hive/data/genomes/dasNov1/bed/ensGene.51 featureBits dasNov1 ensGene # 22658142 bases of 2146362222 (1.056%) in intersection *** All done! (through the 'makeDoc' step) *** Steps were performed in /hive/data/genomes/dasNov1/bed/ensGene.51 ############################################################################ ############################################################################ # TRANSMAP vertebrate.2009-07-01 build (2009-07-21 markd) vertebrate-wide transMap alignments were built Tracks are created and loaded by a single Makefile. This is available from: svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-07-01 see doc/builds.txt for specific details. ############################################################################ ############################################################################ # TRANSMAP vertebrate.2009-09-13 build (2009-09-20 markd) vertebrate-wide transMap alignments were built Tracks are created and loaded by a single Makefile. This is available from: svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13 see doc/builds.txt for specific details. ############################################################################