e0811dac684e59711b3aa4d635bc378d57e0c473 hiram Thu Nov 28 10:31:35 2019 -0800 build finished handed off to Regeneron refs #21579 diff --git src/hg/makeDb/doc/regenRn1/initialBuild.txt src/hg/makeDb/doc/regenRn1/initialBuild.txt index d10a4db..1f7c4d1 100644 --- src/hg/makeDb/doc/regenRn1/initialBuild.txt +++ src/hg/makeDb/doc/regenRn1/initialBuild.txt @@ -170,70 +170,68 @@ time (doIdKeys.pl \ -twoBit=/hive/data/genomes/regenRn1/regenRn1.unmasked.2bit \ -buildDir=`pwd` regenRn1) > do.log 2>&1 & # real 0m47.105s cat regenRn1.keySignature.txt # 7850e2d5dabb6134fdc9d7083f1a3a54 ############################################################################# # gapOverlap (DONE - 2019-09-08 - Hiram) mkdir /hive/data/genomes/regenRn1/bed/gapOverlap cd /hive/data/genomes/regenRn1/bed/gapOverlap time (doGapOverlap.pl \ -twoBit=/hive/data/genomes/regenRn1/regenRn1.unmasked.2bit regenRn1 ) \ > do.log 2>&1 & -XXX - running - Sun Sep 8 17:26:16 PDT 2019 - # real 1m51.246s + # real 1m49.029s # there are 7 items found: wc -l bed.tab # 7 bed.tab cat fb.regenRn1.gapOverlap.txt # 5912 bases of 2762428432 (0.000%) in intersection ############################################################################# # tandemDups (DONE - 2019-09-08 - Hiram) mkdir /hive/data/genomes/regenRn1/bed/tandemDups cd /hive/data/genomes/regenRn1/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit=/hive/data/genomes/regenRn1/regenRn1.unmasked.2bit regenRn1) \ > do.log 2>&1 & -XXX - running - Sun Sep 8 17:26:47 PDT 2019 - # real 369m58.055s + # real 371m3.411s cat fb.regenRn1.tandemDups.txt - # 86298981 bases of 2762428432 (3.124%) in intersection + # 75673026 bases of 2395213054 (3.159%) in intersection bigBedInfo regenRn1.tandemDups.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 13 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 -# itemCount: 1,039,087 -# primaryDataSize: 27,356,255 -# primaryIndexSize: 178,160 +# itemCount: 899,735 +# primaryDataSize: 23,487,472 +# primaryIndexSize: 63,376 # zoomLevels: 9 -# chromCount: 3504 -# basesCovered: 1,365,621,612 -# meanDepth (of bases covered): 6.439341 +# chromCount: 22 +# basesCovered: 1,254,230,011 +# meanDepth (of bases covered): 6.233185 # minDepth: 1.000000 -# maxDepth: 307.000000 -# std of depth: 12.663540 +# maxDepth: 253.000000 +# std of depth: 11.790108 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (TBD - 2019-09-08 - Hiram) # construct idKeys for the refseq sequence mkdir /hive/data/genomes/regenRn1/refseq/idKeys cd /hive/data/genomes/regenRn1/refseq/idKeys faToTwoBit ../GCF_000002315.5_GRCg6a_genomic.fna.gz regenRn1.refSeq.2bit time (doIdKeys.pl -buildDir=`pwd` \ -twoBit=`pwd`/regenRn1.refSeq.2bit refseqRegenRn1) > do.log 2>&1 & # real 0m48.786s cat refseqRegenRn1.keySignature.txt # 7850e2d5dabb6134fdc9d7083f1a3a54 @@ -295,34 +293,36 @@ | sed -e 's/INSDC/RefSeq/g;' \ | hgLoadSqlTab regenRn1 ucscToRefSeq stdin ucscToRefSeq.bed # should be quiet for all OK checkTableCoords regenRn1 # should cover %100 entirely: featureBits -countGaps regenRn1 ucscToINSDC # 1065365425 bases of 1065365425 (100.000%) in intersection featureBits -countGaps regenRn1 ucscToRefSeq # 1065365425 bases of 1065365425 (100.000%) in intersection ######################################################################### # add chromAlias table (TBD - 2019-09-08 - Hiram) + # did not run this up, there aren't any names to alias mkdir /hive/data/genomes/regenRn1/bed/chromAlias cd /hive/data/genomes/regenRn1/bed/chromAlias ln -s ../../ucsc/ucsc.regeneron.name.translate regen.tab + ~/kent/src/hg/utils/automation/chromAlias.pl regen.tab \ > regenRn1.chromAlias.tab join regen.tab <(sort -k1,1 ../../chrom.sizes) \ | awk '{printf "%s\t0\t%d\t%s\n", $1, $3, $2}' > regen.alias.bed wc -l * # 6846 regen.alias.bed # 6846 regen.tab # 6846 regenRn1.chromAlias.tab hgLoadSqlTab regenRn1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ regenRn1.chromAlias.tab # display the Regeneron AGP file as a track: @@ -492,55 +492,53 @@ mkdir /hive/data/genomes/regenRn1/bed/cpgIslands cd /hive/data/genomes/regenRn1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku regenRn1) > do.log 2>&1 # real 3m12.993s cat fb.regenRn1.cpgIslandExt.txt # 9240105 bases of 2282482188 (0.405%) in intersection ############################################################################## # genscan - (DONE - 2019-09-09 - Hiram) mkdir /hive/data/genomes/regenRn1/bed/genscan cd /hive/data/genomes/regenRn1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku regenRn1) > do.log 2>&1 -XXX - running - Mon Sep 9 07:20:08 PDT 2019 - # real 126m0.077s + # real 113m30.148s cat fb.regenRn1.genscan.txt - # 54712419 bases of 2534810853 (2.158%) in intersection + # 48448954 bases of 2282482188 (2.123%) in intersection cat fb.regenRn1.genscanSubopt.txt - # 56830306 bases of 2534810853 (2.242%) in intersection + # 51171443 bases of 2282482188 (2.242%) in intersection ######################################################################### -# Create kluster run files (TBD - 2019-06-29 - Hiram) +# Create kluster run files (DONE - 2019-09-11 - Hiram) # numerator is regenRn1 gapless bases "real" as reported by: featureBits -noRandom -noHap regenRn1 gap # 112730866 bases of 2282482188 (4.939%) 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 \( 2282482188 / 2861349177 \) \* 1024 # ( 2282482188 / 2861349177 ) * 1024 = 816.839056 -XXX - # ==> use -repMatch=350 according to size scaled down from 1024 for human. + # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/regenRn1 blat regenRn1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/regenRn1.11.ooc \ -repMatch=800 # Wrote 30001 overused 11-mers to jkStuff/regenRn1.11.ooc # regenRn0 was repMatch 900 and: # Wrote 29409 overused 11-mers to jkStuff/regenRn1.11.ooc # rn6 was repMatch 1000 and: # Wrote 27021 overused 11-mers to jkStuff/rn6.11.ooc # rn5 at repMatch 950 and: # Wrote 34513 overused 11-mers to jkStuff/rn5.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ @@ -554,163 +552,165 @@ ### kent source version 387 ### # chrom count: 23 # found 23482 gaps of size >= 100 # bed output requested to jkStuff/nonBridged.bed # no gaps on chrom: chr11, size: 83994014 # no gaps on chrom: chr2, size: 236134952 # no gaps on chrom: chr8, size: 119798696 # no gaps on chrom: chrM, size: 2246 wc -l jkStuff/nonBri* # 23505 jkStuff/nonBridged.bed # 23505 jkStuff/nonBridged.lift ######################################################################## -# lastz/chain/net swap human/hg38 (TBD - 2019-09-08 - Hiram) +# lastz/chain/net swap human/hg38 (DONE - 2019-09-12 - Hiram) + # original alignment - cd /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-08 + cd /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12 cat fb.hg38.chainRegenRn1Link.txt - # 154079940 bases of 3095998939 (4.977%) in intersection + # 863041482 bases of 3095998939 (27.876%) in intersection cat fb.hg38.chainSynRegenRn1Link.txt - # 95877644 bases of 3095998939 (3.097%) in intersection + # 809332351 bases of 3095998939 (26.141%) in intersection cat fb.hg38.chainRBest.RegenRn1.txt - # 106665747 bases of 3095998939 (3.445%) in intersection + # 792532873 bases of 3095998939 (25.599%) in intersection # and for the swap: mkdir /hive/data/genomes/regenRn1/bed/blastz.hg38.swap cd /hive/data/genomes/regenRn1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-08/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12/DEF \ + -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 - # real 9m45.514s + # real 63m47.773s cat fb.regenRn1.chainHg38Link.txt - # 120955955 bases of 1055588482 (11.459%) in intersection - + # 827167139 bases of 2282482188 (36.240%) in intersection cat fb.regenRn1.chainSynHg38Link.txt - # 92597630 bases of 1055588482 (8.772%) in intersection + # 788025130 bases of 2282482188 (34.525%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenRn1 hg38) > rbest.log 2>&1 & - # real 139m24.408s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 hg38) > rbest.log 2>&1 + # real 300m50.570s cat fb.regenRn1.chainRBest.Hg38.txt - # 106294585 bases of 1055588482 (10.070%) in intersection + # 793987134 bases of 2282482188 (34.786%) in intersection ######################################################################### -# lastz/chain/net swap mouse/mm10 (TBD - 2019-09-08 - Hiram) +# lastz/chain/net swap mouse/mm10 (DONE - 2019-11-26 - Hiram) # original alignment - cd /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-08 + cd /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-12 + cat fb.mm10.chainRegenRn1Link.txt - # 101151132 bases of 2652783500 (3.813%) in intersection + # 1699005386 bases of 2652783500 (64.046%) in intersection cat fb.mm10.chainSynRegenRn1Link.txt - # 70707720 bases of 2652783500 (2.665%) in intersection + # 1591231371 bases of 2652783500 (59.983%) in intersection cat fb.mm10.chainRBest.RegenRn1.txt - # 79649474 bases of 2652783500 (3.002%) in intersection + # 1565180527 bases of 2652783500 (59.001%) in intersection - # and for the swap: mkdir /hive/data/genomes/regenRn1/bed/blastz.mm10.swap cd /hive/data/genomes/regenRn1/bed/blastz.mm10.swap - time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-08/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-12/DEF \ + -swap -syntenicNet -noDbNameCheck \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ - -syntenicNet) > swap.log 2>&1 - # real 6m41.043s + -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 + # real 94m19.060s cat fb.regenRn1.chainMm10Link.txt - # 88539346 bases of 1055588482 (8.388%) in intersection + # 1634389849 bases of 2282482188 (71.606%) in intersection + cat fb.regenRn1.chainSynMm10Link.txt + # 1564752158 bases of 2282482188 (68.555%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenRn1 mm10) > rbest.log 2>&1 & - # real 94m11.007s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 mm10) > rbest.log 2>&1 + # real 488m25.471s cat fb.regenRn1.chainRBest.Mm10.txt - # 79474812 bases of 1055588482 (7.529%) in intersection + # 1565313924 bases of 2282482188 (68.579%) in intersection -######################################################################### -# GENBANK AUTO UPDATE (TBD - 2019-06-29 - Hiram) +############################################################################## +# GENBANK AUTO UPDATE (DONE - 2019-09-11 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt - # Rattus norvegicus 130197 1103594 17642 + # Rattus norvegicus 130204 1103594 17712 # edit etc/genbank.conf to add regenRn1 just before galGal5 # regenRn1 (Regeneron rat assembly) regenRn1.serverGenome = /hive/data/genomes/regenRn1/regenRn1.2bit regenRn1.ooc = /hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc regenRn1.lift = /hive/data/genomes/regenRn1/jkStuff/nonBridged.lift regenRn1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} regenRn1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} regenRn1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} regenRn1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} regenRn1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} regenRn1.downloadDir = regenRn1 regenRn1.refseq.mrna.xeno.load = yes regenRn1.refseq.mrna.xeno.loadDesc = yes regenRn1.genbank.mrna.xeno.load = yes regenRn1.perChromTables = no regenRn1.mgc = yes # regenRn1.upstreamGeneTbl = ensGene # regenRn1.upstreamMaf = multiz13way /hive/data/genomes/regenRn1/bed/multiz13way/species.list.txt # verify the files specified exist before checking in the file: grep ^regenRn1 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og -# -rw-rw-r-- 1 247657 Jun 29 17:16 /hive/data/genomes/regenRn1/jkStuff/nonBridged.lift -# -rw-rw-r-- 1 117644 Jun 29 17:13 /hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc -# -rw-rw-r-- 1 720490674 Jun 29 16:59 /hive/data/genomes/regenRn1/regenRn1.2bit +# -rw-rw-r-- 1 840371 Sep 9 07:27 /hive/data/genomes/regenRn1/jkStuff/nonBridged.lift +# -rw-rw-r-- 1 120012 Sep 11 08:54 /hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc +# -rw-rw-r-- 1 625487112 Sep 9 07:14 /hive/data/genomes/regenRn1/regenRn1.2bit git commit -m "Added regenRn1 - Regeneron rat refs #21579" etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add regenRn1 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs - git commit -m "Added regenRn1 - Regeneron rat refs #21579" etc/hgwdev.dbs + git commit -m "Added regenRn1 - Regeneron rat refs #21579" etc/hgwdev.dbs etc/align.dbs git push make etc-update # wait a few days for genbank magic to take place, the tracks will # appear ############################################################################# -# augustus gene track (TBD - 2019-06-29 - Hiram) +# augustus gene track (DONE - 2019-09-11 - Hiram) mkdir /hive/data/genomes/regenRn1/bed/augustus cd /hive/data/genomes/regenRn1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev regenRn1) > do.log 2>&1 - # real 194m56.414s + # real 144m4.269s cat fb.regenRn1.augustusGene.txt - # 48867584 bases of 2534810853 (1.928%) in intersection + # 43428122 bases of 2282482188 (1.903%) in intersection ######################################################################### # ncbiRefSeq (TBD - 2019-09-08 - Hiram) + # There are no source files for this mkdir /hive/data/genomes/regenRn1/bed/ncbiRefSeq cd /hive/data/genomes/regenRn1/bed/ncbiRefSeq # running step wise just to be careful time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.5_GRCg6a regenRn1) > download.log 2>&1 # real 1m19.029s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ @@ -756,149 +756,134 @@ mkdir /hive/data/genomes/regenRn1/bed/blat.rn6.2019-09-09 cd /hive/data/genomes/regenRn1/bed/blat.rn6.2019-09-09 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc \ regenRn1 rn6 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc \ regenRn1 rn6) > doLiftOverToRn6.log 2>&1 # real 171m37.650s # see if the liftOver menus function in the browser from regenRn1 to rn6 # would like to see this as a track: - time (chainToPsl regenRn1ToRn6.over.chain.gz ../../chrom.sizes \ - /hive/data/genomes/rn6/chrom.sizes ../../regenRn1.2bit \ - /hive/data/genomes/rn6/rn6.2bit regenRn1ToRn6.psl) > chainToPsl.log 2>&1 -XXX - running - Tue Sep 10 13:49:46 PDT 2019 + hgLoadChain regenRn1 chainRn6 regenRn1ToRn6.over.chain.gz + + # Loading 127292 chains into regenRn1.chainRn6 + # real 0m9.461s + + chainSort regenRn1ToRn6.over.chain.gz stdout \ + | chainPreNet stdin \ + /hive/data/genomes/regenRn1/chrom.sizes \ + /hive/data/genomes/rn6/chrom.sizes stdout \ + | chainNet stdin -minSpace=1 /hive/data/genomes/regenRn1/chrom.sizes \ + /hive/data/genomes/rn6/chrom.sizes stdout /dev/null \ + | netSyntenic stdin noClass.net + + netClass -verbose=0 -noAr noClass.net regenRn1 rn6 regenRn1.rn6.net + + netFilter -minGap=10 regenRn1.rn6.net \ + | hgLoadNet -verbose=0 regenRn1 netRn6 stdin + + featureBits regenRn1 chainRn6Link > fb.regenRn1.chainRn6Link.txt 2>&1 + + cat fb.regenRn1.chainRn6Link.txt + # 2211701054 bases of 2282482188 (96.899%) in intersection ######################################################################### # LIFTOVER TO regenRn0 (DONE - 2019-09-09 - Hiram) ssh hgwdev mkdir /hive/data/genomes/regenRn1/bed/blat.regenRn0.2019-09-09 cd /hive/data/genomes/regenRn1/bed/blat.regenRn0.2019-09-09 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc \ regenRn1 regenRn0 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc \ regenRn1 regenRn0) > doLiftOverToRegenRn0.log 2>&1 # real 176m49.811s # see if the liftOver menus function in the browser from regenRn1 to galGal5 # would like to see this as a track: - time (chainToPsl regenRn1ToRegenRn0.over.chain.gz ../../chrom.sizes \ - /hive/data/genomes/regenRn0/chrom.sizes ../../regenRn1.2bit \ - /hive/data/genomes/regenRn0/regenRn0.2bit regenRn1ToRegenRn0.psl) > chainToPsl.log 2>&1 - # real 0m24.740s + hgLoadChain regenRn1 chainRegenRn0 regenRn1ToRegenRn0.over.chain.gz + # Loading 56 chains into regenRn1.chainRegenRn0 + + chainSort regenRn1ToRegenRn0.over.chain.gz stdout \ + | chainPreNet stdin \ + /hive/data/genomes/regenRn1/chrom.sizes \ + /hive/data/genomes/regenRn0/chrom.sizes stdout \ + | chainNet stdin -minSpace=1 /hive/data/genomes/regenRn1/chrom.sizes \ + /hive/data/genomes/regenRn0/chrom.sizes stdout /dev/null \ + | netSyntenic stdin noClass.net + + netClass -verbose=0 -noAr noClass.net regenRn1 regenRn0 regenRn1.regenRn0.net + + netFilter -minGap=10 regenRn1.regenRn0.net \ + | hgLoadNet -verbose=0 regenRn1 netRegenRn0 stdin + +featureBits regenRn1 chainRegenRn0Link > fb.regenRn1.chainRegenRn0Link.txt 2>&1 + + cat fb.regenRn1.chainRegenRn0Link.txt + # 2395098699 bases of 2282482188 (104.934%) in intersection ######################################################################### -# BLATSERVERS ENTRY (TBD - 2019-09-08 - Hiram) +# BLATSERVERS ENTRY (DONE - 2019-09-13 - 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 ("regenRn1", "blat1a", "17892", "1", "0"); \ + VALUES ("regenRn1", "blat1c", "17912", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ - VALUES ("regenRn1", "blat1a", "17893", "0", "1");' \ + VALUES ("regenRn1", "blat1c", "17913", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to MEPE gene (egg shell protein) ## (TBD - 2019-09-08 - Hiram) # as found from the galGal5 to regenRn1 liftOver ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928" where name="regenRn1";' hgcentraltest ######################################################################### -# crispr whole genome (WORKING - 2019-07-02 - Hiram) - mkdir /hive/data/genomes/regenRn1/bed/crisprAll - cd /hive/data/genomes/regenRn1/bed/crisprAll - - # working on this script, adding the indexFa step: - time (~/kent/src/hg/utils/automation/doCrispr.pl \ - -stop=indexFa -buildDir=`pwd` -smallClusterHub=ku regenRn1 augustusGene) \ - > indexFa.log 2>&1 -XXX - running - Tue Jul 2 11:09:39 PDT 2019 - # real 23m26.694s - - # the large shoulder argument will cause the entire genome to be scanned -~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \ - hg19 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ - -buildDir=`pwd` -smallClusterHub=hgwdev-101 -bigClusterHub=ku \ - -workhorse=hgwdev - - - time (~/kent/src/hg/utils/automation/doCrispr.pl \ - -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \ - regenRn1 ncbiRefSeq) > guides.log 2>&1 - # real 2m50.758s - - # adding the /dev/shm/ setup rsync for the indexed Fa - # performed manually to work out the procedure - time (~/kent/src/hg/utils/automation/doCrispr.pl \ - -continue=specScores -stop=specScores -buildDir=`pwd` \ - -smallClusterHub=ku regenRn1 ncbiRefSeq) > specScores.log - - # had about half of ku for about half this time: -# Completed: 884922 of 884922 jobs -# CPU time in finished jobs: 35872791s 597879.85m 9964.66h 415.19d 1.138 y -# IO & Wait Time: 899261s 14987.69m 249.79h 10.41d 0.029 y -# Average job time: 42s 0.69m 0.01h 0.00d -# Longest finished job: 88s 1.47m 0.02h 0.00d -# Submission to last job: 48045s 800.75m 13.35h 0.56d - - - time find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab - # real 236m17.220s - wc -l specScores.tab - # 66451712 specScores.tab - - time (~/kent/src/hg/utils/automation/doCrispr.pl \ - -continue=effScores -stop=load \ - -buildDir=`pwd` -smallClusterHub=ku regenRn1 ncbiRefSeq) \ - > load.log - # real 307m41.143s - -######################################################################### # all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram) xyz cd $HOME/kent/src/hg/makeDb/schema # verify all the business is done for release ~/kent/src/hg/utils/automation/verifyBrowser.pl regenRn1 # fixup all.joiner until this is a clean output joinerCheck -database=regenRn1 -tableCoverage all.joiner joinerCheck -database=regenRn1 -times all.joiner joinerCheck -database=regenRn1 -keys all.joiner # when clean, check in: - git commit -m 'adding rules for regenRn1 refs #22113' all.joiner + git commit -m 'adding rules for regenRn1 refs #21579' all.joiner git push # run up a 'make alpha' in hg/hgTables to get this all.joiner file # into the hgwdev/genome-test system cd /hive/data/genomes/regenRn1 time (makeDownloads.pl regenRn1) > downloads.log 2>&1 +XXX - running - Tue Oct 22 08:15:47 PDT 2019 # real 10m7.605s # now ready for pushQ entry mkdir /hive/data/genomes/regenRn1/pushQ cd /hive/data/genomes/regenRn1/pushQ time (makePushQSql.pl -redmineList regenRn1) > regenRn1.pushQ.sql 2> stderr.out # real 9m58.779s # remove the extra chainNet files from the listings: sed -i -e "/etNig1/d" redmine.regenRn1.file.list sed -i -e "/asAcu1/d" redmine.regenRn1.file.list sed -i -e "/etNig1/d" redmine.regenRn1.table.list sed -i -e "/onAlb1/d" redmine.regenRn1.table.list sed -i -e "/asAcu1/d" redmine.regenRn1.table.list sed -i -e "/Stickleback/d" redmine.regenRn1.releaseLog.txt @@ -913,16 +898,95 @@ # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/regenRn1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/regenRn1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/regenRn1/bbi/quality.bw # WARNING: regenRn1 does not have seq # WARNING: regenRn1 does not have extFile # add the path names to the listing files in the redmine issue # in the three appropriate entry boxes: # /hive/data/genomes/regenRn1/pushQ/redmine.regenRn1.file.list # /hive/data/genomes/regenRn1/pushQ/redmine.regenRn1.releaseLog.txt # /hive/data/genomes/regenRn1/pushQ/redmine.regenRn1.table.list +############################################################################## +# crispr whole genome (DONE - 2019-10-15,22 - Hiram) + mkdir /hive/data/genomes/regenRn1/bed/crisprAll + cd /hive/data/genomes/regenRn1/bed/crisprAll + + # the large shoulder argument will cause the entire genome to be scanned + # and since this is a new genome, samtools fa indexing will take place + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \ + regenRn1 refGene -shoulder=250000000 -tableName=crisprAll \ + -fileServer=hgwdev -buildDir=`pwd` -smallClusterHub=hgwdev \ + -bigClusterHub=ku -workhorse=hgwdev) > ranges.log 2>&1 + # real 65m1.474s + + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ + -continue=guides -stop=guides \ + regenRn1 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) > guides.log 2>&1 + # real 5m21.112s + + # one of the jobs failed on ku, but worked OK on hgwdev stand alone +/cluster/software/bin/python \ + /hive/data/outside/crisprTrack/scripts/findGuides.py \ + /hive/data/genomes/regenRn1/bed/crisprAll/ranges/tmp/040.fa \ + /hive/data/genomes/regenRn1/chrom.sizes tmp/040.bed tmp/040.fa +Completed: 99 of 100 jobs +Crashed: 1 jobs +CPU time in finished jobs: 9475s 157.92m 2.63h 0.11d 0.000 y +IO & Wait Time: 371s 6.18m 0.10h 0.00d 0.000 y +Average job time: 99s 1.66m 0.03h 0.00d +Longest finished job: 524s 8.73m 0.15h 0.01d +Submission to last job: 539s 8.98m 0.15h 0.01d + + + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ + -continue=specScoreJobList -stop=specScores -fileServer=hgwdev \ + regenRn1 knownGene -shoulder=250000000 -tableName=crisprAll \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) > specScores.log 2>&1 + # real 4764m4.884s + # user 0m1.693s + # sys 0m1.684s + +# Number of specScores: 204371688 + +# Completed: 2733924 of 2733924 jobs +# CPU time in finished jobs: 220930932s 3682182.20m 61369.70h 2557.07d 7.006 y +# IO & Wait Time: 5388062s 89801.04m 1496.68h 62.36d 0.171 y +# Average job time: 83s 1.38m 0.02h 0.00d +# Longest finished job: 189s 3.15m 0.05h 0.00d +# Submission to last job: 228205s 3803.42m 63.39h 2.64d + + ### remember to get back to hgwdev to run this + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ + -continue=effScores -stop=load regenRn1 knownGene \ + -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) > load.log 2>&1 + # real 834m5.635s + # user 0m0.962s + # sys 0m1.894s + +# effScores: +Completed: 24067 of 24067 jobs +CPU time in finished jobs: 12223610s 203726.84m 3395.45h 141.48d 0.388 y +IO & Wait Time: 143817s 2396.95m 39.95h 1.66d 0.005 y +Average job time: 514s 8.56m 0.14h 0.01d +Longest finished job: 1269s 21.15m 0.35h 0.01d +Submission to last job: 12710s 211.83m 3.53h 0.15d + + +# offTargets: +Completed: 136697 of 136697 jobs +CPU time in finished jobs: 2016502s 33608.36m 560.14h 23.34d 0.064 y +IO & Wait Time: 2570740s 42845.67m 714.09h 29.75d 0.082 y +Average job time: 34s 0.56m 0.01h 0.00d +Longest finished job: 77s 1.28m 0.02h 0.00d +Submission to last job: 4643s 77.38m 1.29h 0.05d + #########################################################################