71250d609029a99f76dda0869838ba9fff9fbbd7 hiram Wed Jul 1 10:53:01 2020 -0700 chainNet droSim2 vs. droSec1 per user request refs #134764 diff --git src/hg/makeDb/doc/droSim2/initialBuild.txt src/hg/makeDb/doc/droSim2/initialBuild.txt index 4a64d98..120dc4e 100644 --- src/hg/makeDb/doc/droSim2/initialBuild.txt +++ src/hg/makeDb/doc/droSim2/initialBuild.txt @@ -1,564 +1,633 @@ # for emacs: -*- mode: sh; -*- # This file describes browser build for the droSim2 # Organism name: Drosophila simulans # Must find the photograph first, can not continue until finding # the photograph. ######################################################################### # Initial steps, find photograph (DONE - 2016-11-01 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/droSim2 cd ~/kent/src/hg/makeDb/doc/droSim2 sed -e 's/gorGor5/droSim2/g; s/GorGor5/DroSim2/g; s/TBD/TBD/g;' ../gorGor5/initialBuild.txt > initialBuild.txt mkdir -p /hive/data/genomes/droSim2/refseq cd /hive/data/genomes/droSim2/refseq rsync -a -P -L \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Drosophila_simulans/all_assembly_versions/GCF_000754195.2_ASM75419v2/ ./ # obtain photo from wikimedia commons mkdir /hive/data/genomes/droSim2/photograph cd /hive/data/genomes/droSim2/photograph wget --timestamping \ https://upload.wikimedia.org/wikipedia/commons/0/03/Drosophila_simulans-female.jpg cd /hive/data/genomes/droSim2 printf "photoCreditURL https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg photoCreditName Wikimedia Commons/Dr. Andrew Weeks\n" > photoReference.txt # this information is from the top of # refseq/*_assembly_report.txt # (aka: refseq/GCF_000754195.2_ASM75419v2_assembly_report.txt) # Assembly name: ASM75419v2 # Organism name: Drosophila simulans (flies) # Infraspecific name: strain=w501 # Taxid: 7240 # BioSample: SAMN01086904 # BioProject: PRJNA297806 # Submitter: Princeton University # Date: 2014-9-19 # Assembly type: haploid # Release type: # Assembly level: Chromosome # Genome representation: full # WGS project: JPYS01 # Assembly method: Velvet v. 1.1.04 # Expected final version: No # Genome coverage: 75.0x # Sequencing technology: Illumina; Sanger # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000754195.2 # RefSeq assembly accession: GCF_000754195.2 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000754205.2 GCF_000754205.1 Primary Assembly ## GCA_000754215.1 GCF_000045355.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2016-11-01) cd /hive/data/genomes/droSim2 /cluster/home/hiram/kent/src/hg/utils/automation/prepConfig.pl \ droSim2 insect drosophila ./refseq/*_assembly_report.txt # change commonName "Flies" to "D. simulans" # verify it looks sane cat droSim2.config.ra # config parameters for makeGenomeDb.pl: db droSim2 clade insect genomeCladePriority 70 scientificName Drosophila simulans commonName D. simulans assemblyDate Sep. 2014 assemblyLabel Princeton University assemblyShortLabel ASM75419v2 orderKey 6684 # mitochondrial sequence included in refseq release # mitoAcc NC_005781.1 mitoAcc none fastaFiles /hive/data/genomes/droSim2/ucsc/*.fa.gz agpFiles /hive/data/genomes/droSim2/ucsc/*.agp # qualFiles none dbDbSpeciesDir drosophila photoCreditURL https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg photoCreditName Wikimedia Commons/Dr. Andrew Weeks ncbiGenomeId 200 ncbiAssemblyId 800241 ncbiAssemblyName ASM75419v2 ncbiBioProject 297806 ncbiBioSample SAMN01086904 genBankAccessionID GCF_000754195.2 taxId 7240 ############################################################################# # setup UCSC named files (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/ucsc cd /hive/data/genomes/droSim2/ucsc # measure what is in the genbank release: faSize ../refseq/G*2_genomic.fna.gz # 124963774 bases (378345 N's 124585429 real 98768053 upper 25817376 lower) # in 7619 sequences in 1 files # Total size: mean 16401.6 sd 603260.6 min 200 (NW_015503630.1) # max 27160941 (NT_479536.1) median 320 # %20.66 masked total, %20.72 masked real # check for duplicate sequences, twoBitDup should be silent output: faToTwoBit -noMask ../refseq/*2_genomic.fna.gz refseq.2bit twoBitDup refseq.2bit # no output is a good result, otherwise, would have to eliminate duplicates ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/*2_genomic.fna.gz \ ../refseq/*_assembly_structure/Primary_Assembly # real 0m43.539s ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # real 0m57.496s (two steps above) export mitoAcc=`grep "^# mitoAcc" ../droSim2.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" zcat ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa gzip chrM.fa faToTwoBit *.fa.gz test.2bit twoBitDup test.2bit cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # no longer need the 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2016-11-01 - Hiram) # verify sequence and AGP are OK: cd /hive/data/genomes/droSim2 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ droSim2.config.ra) > makeGenomeDb.log # real 1m43.905s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2016-11-02 - Hiram) mkdir /hive/data/genomes/droSim2/bed/cpgIslandsUnmasked cd /hive/data/genomes/droSim2/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/droSim2/droSim2.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku droSim2) > do.log 2>&1 # real 2m17.187s cat fb.droSim2.cpgIslandExtUnmasked.txt # 21753930 bases of 124963774 (17.408%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/cytoBand cd /hive/data/genomes/droSim2/bed/cytoBand makeCytoBandIdeo.csh droSim2 ############################################################################# # ucscToINSDC table/track (TBD - 2016-08-05 - Hiram) # there are no other names for contigs in this assembly, there are just # the contig names ######################################################################### # fixup search rule for assembly track/gold table (TBD - 2016-08-05 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/gorilla/droSim2 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" droSim2 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 15997 CYUIv1_1 # 1 LN.1 # implies a search rule of: '[CILNUY0-9]+([v0-9_\.]+)?' # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" droSim2 | wc -l # 15998 hgsql -N -e "select frag from gold;" droSim2 \ | egrep -e '[CILNUY0-9]+([v0-9_\.]+)?' | wc -l # 15998 hgsql -N -e "select frag from gold;" droSim2 \ | egrep -v -e '[CILNUY0-9]+([v0-9_\.]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/droSim2/trackDb.ra searchTable gold shortCircuit 1 termRegex [CILNUY0-9]+([v0-9_\.]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 # verify searches work in the position box ########################################################################## # running repeat masker (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/repeatMasker cd /hive/data/genomes/droSim2/bed/repeatMasker # failed to create a log file, made mistake doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku droSim2 # real 1581m32.299s cat faSize.rmsk.txt # 124963774 bases (378345 N's 124585429 real 111673206 upper 12912223 lower) # in 7619 sequences in 1 files # Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1) # max 27160941 (chr3R) median 320 # %10.33 masked total, %10.36 masked real egrep -i "versi|relea" do.log # RepeatMasker version open-4.0.5 # Search Engine: Crossmatch [ 1.090518 ] # Master RepeatMasker Database: /hive/data/staging/data/RepeatMasker140131/Libraries/RepeatMaskerLib.embl ( Complete Database: 20140131 ) # RepeatMasker version open-4.0.5 # January 31 2015 (open-4-0-5) version of RepeatMasker # CC RELEASE 20140131; time featureBits -countGaps droSim2 rmsk # 12951235 bases of 124963774 (10.364%) in intersection # real 0m3.712s # with high contig count assemblies, faster way to get the same result: time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' droSim2 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 12951235.000000 # real 0m0.852s ########################################################################## # running simple repeat (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/simpleRepeat cd /hive/data/genomes/droSim2/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -trf409=6 -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ droSim2) > do.log 2>&1 # real 6m32.563s cat fb.simpleRepeat # 1545440 bases of 124963774 (1.237%) in intersection # add to window masker result after it is done: cd /hive/data/genomes/droSim2 twoBitMask bed/windowMasker/droSim2.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed droSim2.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa droSim2.2bit stdout | faSize stdin > faSize.droSim2.2bit.txt cat faSize.droSim2.2bit.txt # 124963774 bases (378345 N's 124585429 real 97540956 upper 27044473 lower) # in 7619 sequences in 1 files # Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1) # max 27160941 (chr3R) median 320 # %21.64 masked total, %21.71 masked real rm /gbdb/droSim2/droSim2.2bit ln -s `pwd`/droSim2.2bit /gbdb/droSim2/droSim2.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2016-11-01 - Hiram) ssh hgwdev mkdir /cluster/data/droSim2/bed/microsat cd /cluster/data/droSim2/bed/microsat awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \ ../simpleRepeat/simpleRepeat.bed > microsat.bed hgLoadBed droSim2 microsat microsat.bed # Read 24885 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/windowMasker cd /hive/data/genomes/droSim2/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev droSim2) > do.log 2>&1 # real 5m1.607s # Masking statistics cat faSize.droSim2.cleanWMSdust.txt # 124963774 bases (378345 N's 124585429 real 97623025 upper 26962404 lower) # in 7619 sequences in 1 files # Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1) # max 27160941 (chr3R) median 320 # %21.58 masked total, %21.64 masked real cat fb.droSim2.rmsk.windowmaskerSdust.txt # 6298577 bases of 124963774 (5.040%) in intersection ######################################################################### # run up idKeys files for ncbiRefSeq (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/idKeys cd /hive/data/genomes/droSim2/bed/idKeys doIdKeys.pl -twoBit /hive/data/genomes/droSim2/droSim2.unmasked.2bit \ -buildDir=`pwd` droSim2 cat droSim2.keySignature.txt # 42f0f3041c6956e26676c502529a0331 ########################################################################## # ncbiRefSeq - (TBD - 2016-06-24 - Hiram) ########################################################################## # cpgIslands - (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/cpgIslands cd /hive/data/genomes/droSim2/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku droSim2) > do.log 2>&1 # real 1m3.706s cat fb.droSim2.cpgIslandExt.txt # 13417596 bases of 124963774 (10.737%) in intersection ############################################################################## # genscan - (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/genscan cd /hive/data/genomes/droSim2/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku droSim2) > do.log 2>&1 # real 20m37.096s cat fb.droSim2.genscan.txt # 17689863 bases of 124963774 (14.156%) in intersection cat fb.droSim2.genscanSubopt.txt # 605801 bases of 124963774 (0.485%) in intersection ######################################################################## # Create kluster run files (TBD - 2016-06-24 - Hiram) # numerator is droSim2 gapless bases "real" as reported by: featureBits -noRandom -noHap droSim2 gap # 0 bases of 3080431298 (0.000%) in intersection # denominator is hg19 gapless bases as reported by: # featureBits -noRandom -noHap hg19 gap # 234344806 bases of 2861349177 (8.190%) in intersection # 1024 is threshold used for human -repMatch: calc \( 3080431298 / 2861349177 \) \* 1024 # ( 3080431298 / 2861349177 ) * 1024 = 1102.403605 # ==> use -repMatch=1100 according to size scaled up from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/droSim2 blat droSim2.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/droSim2.11.ooc \ -repMatch=1100 # Wrote 31384 overused 11-mers to jkStuff/droSim2.11.ooc # there are no non-bridged gaps (there no gaps at all) hgsql -e 'select count(*) from gap;' droSim2 # +----------+ # | count(*) | # +----------+ # | 0 | # +----------+ hgsql -e 'select count(*) from gap where bridge="no";' droSim2 # +----------+ # | count(*) | # +----------+ # | 0 | # +----------+ # if there were non-bridged gaps, make up a nonBridged.lft file # check non-bridged gaps to see what the typical size is: # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' droSim2 \ # | sort -k7,7nr | ave -col=7 stdin # most non-bridged gaps have size = 100 # decide on a minimum gap for this break, use either 100 or 5000 will # generate 13387 liftOver rows, but if use 6000, only got 11703 rows. # so use 100 here to get more liftOver row. # gapToLift -verbose=2 -minGap=100 droSim2 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ######################################################################## # GENBANK AUTO UPDATE (TBD - 2016-07-22 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Gorilla gorilla 591 0 88 # Gorilla gorilla gorilla 8 0 0 # Edit src/lib/gbGenome.c to add new species # edit etc/genbank.conf to add droSim2 just after balAcu1 # Gorilla droSim2.serverGenome = /hive/data/genomes/droSim2/droSim2.2bit droSim2.clusterGenome = /hive/data/genomes/droSim2/droSim2.2bit droSim2.ooc = /hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc droSim2.lift = no droSim2.perChromTables = no droSim2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} droSim2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} droSim2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} droSim2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} droSim2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} droSim2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} droSim2.downloadDir = droSim2 # default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native # default yes genbank.est.native # default no genbank.mrna.xeno genbank.est.xeno git commit -m "Added droSim2 - Gorilla refs #17580" etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial droSim2 # real 67m3.917s # logFile: var/build/logs/2016.07.05-12:53:02.droSim2.initalign.log # tail -2 var/build/logs/2016.07.05-12:53:02.droSim2.initalign.log # hgwdev 2016.07.05-13:59:57 droSim2.initalign: Succeeded: droSim2 # hgwdev 2016.07.05-14:00:06 droSim2.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.droSim2 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad droSim2 # real 18m33.387s tail -1 var/dbload/hgwdev/logs/2016.07.21-23:42:20.droSim2.dbload.log # hgwdev 2016.07.22-00:00:53 droSim2.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add droSim2 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m "Added droSim2 - Gorilla - refs #17580" etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # augustus gene track (DONE - 2016-11-01 - Hiram) mkdir /hive/data/genomes/droSim2/bed/augustus cd /hive/data/genomes/droSim2/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=fly -dbHost=hgwdev \ -workhorse=hgwdev droSim2) > do.log 2>&1 # real 79m54.233s cat fb.droSim2.augustusGene.txt # 22385355 bases of 124963774 (17.913%) in intersection ############################################################################ # construct liftOver to gorGor4 (TBD - 2016-06-24,26 - Hiram) screen -S gorGor4 # manage this longish running job in a screen mkdir /hive/data/genomes/droSim2/bed/blat.gorGor4.2016-06-24 cd /hive/data/genomes/droSim2/bed/blat.gorGor4.2016-06-24 # check it with -debug first to see if it is going to work: time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \ -ooc=/hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc \ -debug -dbHost=hgwdev -workhorse=hgwdev droSim2 gorGor4 # real 0m2.154s # if that is OK, then run it: time (doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \ -ooc=/hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc \ -dbHost=hgwdev -workhorse=hgwdev droSim2 gorGor4) > do.log 2>&1 # real 2412m36.913s # verify this file exists: # /gbdb/droSim2/liftOver/droSim2ToGorGor4.over.chain.gz # and try out the conversion on genome-test from droSim2 to gorGor4 ############################################################################ # BLATSERVERS ENTRY (TBD - 2016-08-05 - Hiram) # After getting a blat server assigned by the Blat Server Gods, ssh hgwdev hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("droSim2", "blat1d", "17868", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("droSim2", "blat1d", "17869", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## default position (TBD - 2016-08-04 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="CYUI01015056v1:3670206-3687174" where name="droSim2";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (TBD - 2016-08-08 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=droSim2 -tableCoverage all.joiner joinerCheck -database=droSim2 -times all.joiner joinerCheck -database=droSim2 -keys all.joiner cd /hive/data/genomes/droSim2 time (makeDownloads.pl droSim2) > downloads.log 2>&1 # real 19m52.657s # now ready for pushQ entry mkdir /hive/data/genomes/droSim2/pushQ cd /hive/data/genomes/droSim2/pushQ time makePushQSql.pl droSim2 > droSim2.pushQ.sql 2> stderr.out # real 11m56.179s # check for errors in stderr.out, some are OK, e.g.: # WARNING: droSim2 does not have ucscToINSDC # WARNING: hgwdev does not have /gbdb/droSim2/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/droSim2/wib/quality.wib # WARNING: hgwdev does not have /gbdb/droSim2/bbi/qualityBw/quality.bw # WARNING: droSim2 does not have seq # WARNING: droSim2 does not have extFile # WARNING: droSim2 does not have estOrientInfo # copy it to hgwbeta scp -p droSim2.pushQ.sql qateam@hgwbeta:/tmp/ ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/droSim2.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly -######################################################################### +########################################################################### +# LASTZ D. schellia droSec1 (DONE 2020-06-30 - Hiram) + mkdir /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30 + cd /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30 + + cat << '_EOF_' > DEF + printf '# D. simulans vs. D. schellia +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +BLASTZ_H=2000 +BLASTZ_Y=3400 +BLASTZ_L=4000 +BLASTZ_K=2200 +BLASTZ_Q=/hive/data/staging/data/blastz/HoxD55.q + +# TARGET - D. simulans +SEQ1_DIR=/hive/data/genomes/droSim2/droSim2.2bit +SEQ1_CHUNK=5000000 +SEQ1_LAP=10000 +SEQ1_LEN=/hive/data/genomes/droSim2/chrom.sizes + +# QUERY - D. schellia +SEQ2_DIR=/hive/data/genomes/droSec1/droSec1.2bit +SEQ2_CHUNK=5000000 +SEQ2_LAP=10000 +SEQ2_LEN=/hive/data/genomes/droSec1/chrom.sizes + +BASE=/hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ + -chainMinScore=3000 -chainLinearGap=loose \ + -syntenicNet -fileServer=hgwdev \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku) > do.log 2>&1 + # real 170m54.091s + + cat fb.droSim2.chainDroSec1Link.txt + # 117906809 bases of 124963774 (94.353%) in intersection + + cat fb.droSim2.chainSynDroSec1Link.txt + # 110785279 bases of 124963774 (88.654%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` droSim2 droSec1) > rbest.log 2>&1 & + # real 3m47.266s + + cat fb.droSim2.chainRBest.DroSec1.txt + # 113514069 bases of 124963774 (90.838%) in intersection + + # running the swap + mkdir /hive/data/genomes/droSec1/bed/blastz.droSim2.swap + cd /hive/data/genomes/droSec1/bed/blastz.droSim2.swap + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30/DEF \ + -swap -chainMinScore=3000 -chainLinearGap=loose \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 & + # real 6m22.506s + + cat fb.droSec1.chainDroSim2Link.txt + # 134191023 bases of 157238575 (85.342%) in intersection + cat fb.droSec1.chainSynDroSim2Link.txt + # 112329362 bases of 157238575 (71.439%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` droSec1 droSim2) > rbest.log 2>&1 & + # real 4m15.291s + + cat fb.droSec1.chainRBest.DroSim2.txt + # 113366730 bases of 157238575 (72.099%) in intersection + +###########################################################################