185bb036795666bc9d4d62d962f46eb318f588e0 hiram Fri Aug 30 10:58:44 2019 -0700 completed and in pushQ refs #23771 diff --git src/hg/makeDb/doc/rheMac10/initialBuild.txt src/hg/makeDb/doc/rheMac10/initialBuild.txt index 9e6c0d4..886f3af 100644 --- src/hg/makeDb/doc/rheMac10/initialBuild.txt +++ src/hg/makeDb/doc/rheMac10/initialBuild.txt @@ -448,31 +448,31 @@ fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 2939 =? 2939 OK # checking genbank: 2939 =? 2939 OK # verify chrM is here properly: grep chrM rheMac10.chromAlias.tab # AY612638.1 chrM genbank # NC_005943.1 chrM refseq hgLoadSqlTab rheMac10 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ rheMac10.chromAlias.tab ######################################################################### -# fixup search rule for assembly track/gold table (TBD - 2019-07-01 - Hiram) +# fixup search rule for assembly track/gold table (DONE - 2019-07-03 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/rhesus/rheMac10 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" rheMac10 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 2 AC.10 2 AC.11 1 AC.13 1 AC.17 4 AC.2 36 AC.3 22 AC.4 8 AC.5 2 AC.6 5 AC.7 4 AC.8 @@ -489,32 +489,30 @@ hgsql -N -e "select frag from gold;" rheMac10 \ | egrep -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l # 3268 hgsql -N -e "select frag from gold;" rheMac10 \ | egrep -v -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/rheMac10/trackDb.ra searchTable gold shortCircuit 1 termRegex [ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 -XXX - TBD - # verify searches work in the position box ########################################################################## # running repeat masker (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/repeatMasker cd /hive/data/genomes/rheMac10/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku rheMac10) > do.log 2>&1 # real 500m43.380s cat faSize.rmsk.txt # 2971331530 bases (34438805 N's 2936892725 real 1399379596 upper # 1537513129 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) @@ -604,50 +602,48 @@ # 2971331530 bases (34438805 N's 2936892725 real 1792976685 upper # 1143916040 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) # max 223616942 (chr1) median 26547 # %38.50 masked total, %38.95 masked real cat fb.rheMac10.rmsk.windowmaskerSdust.txt # 909614480 bases of 2971331530 (30.613%) in intersection ########################################################################## # cpgIslands - (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/cpgIslands cd /hive/data/genomes/rheMac10/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:51:16 PDT 2019 - # real 2m5.105s + # real 3m51.796s cat fb.rheMac10.cpgIslandExt.txt - # 16395346 bases of 1055588482 (1.553%) in intersection + # 21622534 bases of 2936892733 (0.736%) in intersection ############################################################################## # genscan - (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/genscan cd /hive/data/genomes/rheMac10/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:51:42 PDT 2019 - # real 88m34.900s + # real 134m51.892s cat fb.rheMac10.genscan.txt - # 23911678 bases of 1055588482 (2.265%) in intersection + # 53848328 bases of 2936892733 (1.834%) in intersection cat fb.rheMac10.genscanSubopt.txt - # 24521608 bases of 1055588482 (2.323%) in intersection + # 52550217 bases of 2936892733 (1.789%) in intersection ######################################################################### # Create kluster run files (DONE - 2019-07-01 - Hiram) # numerator is rheMac10 gapless bases "real" as reported by: featureBits -noRandom -noHap rheMac10 gap # 32449617 bases of 2821543288 (1.150%) 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 \( 2821543288 / 2861349177 \) \* 1024 # ( 2821543288 / 2861349177 ) * 1024 = 1009.754542 @@ -665,97 +661,133 @@ # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' rheMac10 \ | sort -k7,7nr | ave -col=7 stdin # min 100.000000 # max 1000000.000000 # minimum gap size is 100 and produces a reasonable number of lifts gapToLift -verbose=2 -minGap=100 rheMac10 jkStuff/rheMac10.nonBridged.lft \ -bedFile=jkStuff/rheMac10.nonBridged.bed wc -l jkStuff/rheMac10.nonBri* # 2979 jkStuff/rheMac10.nonBridged.bed # 2979 jkStuff/rheMac10.nonBridged.lft ######################################################################## -# lastz/chain/net swap human/hg38 (TBD - 2018-10-12 - Hiram) +# lastz/chain/net swap human/hg38 (DONE - 2019-07-03 - Hiram) # original alignment - cd /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12 + cd /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03 cat fb.hg38.chainRheMac10Link.txt - # 154079940 bases of 3095998939 (4.977%) in intersection + # 2596157811 bases of 3095998939 (83.855%) in intersection cat fb.hg38.chainSynRheMac10Link.txt - # 95877644 bases of 3095998939 (3.097%) in intersection + # 2564291936 bases of 3095998939 (82.826%) in intersection cat fb.hg38.chainRBest.RheMac10.txt - # 106665747 bases of 3095998939 (3.445%) in intersection + # 2422981614 bases of 3095998939 (78.262%) in intersection # and for the swap: mkdir /hive/data/genomes/rheMac10/bed/blastz.hg38.swap cd /hive/data/genomes/rheMac10/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 - # real 9m45.514s + # real 61m39.505s cat fb.rheMac10.chainHg38Link.txt - # 120955955 bases of 1055588482 (11.459%) in intersection - + # 2485840115 bases of 2936892733 (84.642%) in intersection cat fb.rheMac10.chainSynHg38Link.txt - # 92597630 bases of 1055588482 (8.772%) in intersection + # 2465210442 bases of 2936892733 (83.939%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1 & - # real 139m24.408s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1 + # real 126m29.919s cat fb.rheMac10.chainRBest.Hg38.txt - # 106294585 bases of 1055588482 (10.070%) in intersection + # 2424028492 bases of 2936892733 (82.537%) in intersection ######################################################################### -# lastz/chain/net swap mouse/mm10 (TBD - 2018-10-12 - Hiram) +# lastz/chain/net swap mouse/mm10 (DONE - 2019-07-09 - Hiram) # original alignment - cd /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12 + cd /hive/data/genomes/mm10/bed/lastzRheMac10.2019-07-03 + cat fb.mm10.chainRheMac10Link.txt - # 101151132 bases of 2652783500 (3.813%) in intersection + # 923559693 bases of 2652783500 (34.815%) in intersection cat fb.mm10.chainSynRheMac10Link.txt - # 70707720 bases of 2652783500 (2.665%) in intersection + # 878479553 bases of 2652783500 (33.115%) in intersection cat fb.mm10.chainRBest.RheMac10.txt - # 79649474 bases of 2652783500 (3.002%) in intersection + # 879885863 bases of 2652783500 (33.168%) in intersection - # and for the swap: mkdir /hive/data/genomes/rheMac10/bed/blastz.mm10.swap cd /hive/data/genomes/rheMac10/bed/blastz.mm10.swap - time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/mm10/bed/lastzRheMac10.2019-07-03/DEF \ + -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ - -syntenicNet) > swap.log 2>&1 - # real 6m41.043s + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 52m48.045s cat fb.rheMac10.chainMm10Link.txt - # 88539346 bases of 1055588482 (8.388%) in intersection + # 918551088 bases of 2936892733 (31.276%) in intersection + cat fb.rheMac10.chainSynMm10Link.txt + # 876230433 bases of 2936892733 (29.835%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 & - # real 94m11.007s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 + # real 303m40.303s cat fb.rheMac10.chainRBest.Mm10.txt - # 79474812 bases of 1055588482 (7.529%) in intersection + # 878542993 bases of 2936892733 (29.914%) in intersection + ######################################################################### +# lastz/chain/net swap human/hg19 (DONE - 2019-07-09 - Hiram) + + # original alignment + cd /hive/data/genomes/hg19/bed/lastzRheMac10.2019-07-09 + + cat fb.hg19.chainRheMac10Link.txt + # 2604364199 bases of 2991694177 (87.053%) in intersection + cat fb.hg19.chainSynRheMac10Link.txt + # 2570126144 bases of 2991694177 (85.909%) in intersection + cat fb.hg19.chainRBest.RheMac10.txt + # 2421810991 bases of 2991694177 (80.951%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/rheMac10/bed/blastz.hg19.swap + cd /hive/data/genomes/rheMac10/bed/blastz.hg19.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg19/bed/lastzRheMac10.2019-07-09/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 + # real 56m29.163s + + cat fb.rheMac10.chainHg19Link.txt + # 2483311773 bases of 2936892733 (84.556%) in intersection + cat fb.rheMac10.chainSynHg19Link.txt + # 2461925388 bases of 2936892733 (83.828%) in intersection + + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg19) > rbest.log 2>&1 + # real 112m15.825s + + cat fb.rheMac10.chainRBest.Hg19.txt + # 2423781773 bases of 2936892733 (82.529%) in intersection + +############################################################################## # GENBANK AUTO UPDATE (DONE - 2019-07-03 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Macaca mulatta 381495 60276 5820 # edit etc/genbank.conf to add rheMac10 just before galGal5 # rheMac10 Macaca mulatta (rhesus) (refseq assembly GCF_003339765.1) rheMac10.serverGenome = /hive/data/genomes/rheMac10/rheMac10.2bit rheMac10.ooc = /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc rheMac10.lift = /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft rheMac10.perChromTables = no @@ -791,35 +823,34 @@ git commit -m "Added rheMac10 - rhesus/Macaca mulatta refs #23771" etc/hgwdev.dbs git push make etc-update # wait a few days for genbank magic to take place, the tracks will # appear ############################################################################# # augustus gene track (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/augustus cd /hive/data/genomes/rheMac10/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:53:20 PDT 2019 - # real 48m48.597s + # real 129m48.296s cat fb.rheMac10.augustusGene.txt - # 25827925 bases of 1055588482 (2.447%) in intersection + # 50002729 bases of 2936892733 (1.703%) in intersection ######################################################################### # ncbiRefSeq (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/ncbiRefSeq cd /hive/data/genomes/rheMac10/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_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > download.log 2>&1 # real 2m3.842s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ @@ -827,91 +858,80 @@ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > process.log 2>&1 # real 2m6.030s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > load.log 2>&1 # real 0m27.175s cat fb.ncbiRefSeq.rheMac10.txt # 92462016 bases of 2936892733 (3.148%) in intersection -XXX TBD - # need to add: include ../../refSeqComposite.ra alpha + # add: include ../../refSeqComposite.ra alpha # to the rhesus/rheMac10/trackDb.ra to turn on the track in the browser - # there was one gene that claimed to have a protein, but the - # protein sequence was not included in the protein.faa file - # discovered from joinerCheck - # manual fix to blank out this one protein, to see the entry - hgsql -e 'select * from ncbiRefSeqLink where protAcc="NP_989875.1";' rheMac10 - hgsql -e 'update ncbiRefSeqLink set protAcc="" where protAcc="NP_989875.1";' rheMac10 - # this makes the 'protein' link disappear from the gene details page - # curious that this gene is marked as a non-coding gene anyway ? - # gene: FET1 at chr4:63,102,774-63,105,516- - featureBits -enrichment rheMac10 refGene ncbiRefSeq - # refGene 1.374%, ncbiRefSeq 8.397%, both 1.370%, cover 99.73%, enrich 11.88x + # refGene 0.402%, ncbiRefSeq 3.148%, both 0.402%, cover 99.90%, enrich 31.73x featureBits -enrichment rheMac10 ncbiRefSeq refGene - # ncbiRefSeq 8.397%, refGene 1.374%, both 1.370%, cover 16.32%, enrich 11.88x + # ncbiRefSeq 3.148%, refGene 0.402%, both 0.402%, cover 12.76%, enrich 31.73x featureBits -enrichment rheMac10 ncbiRefSeqCurated refGene - # ncbiRefSeqCurated 1.368%, refGene 1.374%, both 1.364%, cover 99.71%, enrich 72.59x + # ncbiRefSeqCurated 0.401%, refGene 0.402%, both 0.400%, cover 99.66%, enrich 247.79x + featureBits -enrichment rheMac10 refGene ncbiRefSeqCurated - # refGene 1.374%, ncbiRefSeqCurated 1.368%, both 1.364%, cover 99.32%, enrich 72.59x + # refGene 0.402%, ncbiRefSeqCurated 0.401%, both 0.400%, cover 99.33%, enrich 247.79x ######################################################################### # LIFTOVER TO rheMac8 (DONE - 2019-07-02 - Hiram) ssh hgwdev mkdir /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02 cd /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \ rheMac10 rheMac8 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \ rheMac10 rheMac8) > doLiftOverToRheMac8.log 2>&1 -XXX - running - Tue Jul 2 08:11:05 PDT 2019 - # real 156m30.215s + # real 268m29.927s - # see if the liftOver menus function in the browser from rheMac10 to galGal5 + # see if the liftOver menus function in the browser from rheMac10 to rheMac8 ######################################################################### -# BLATSERVERS ENTRY (TBD - 2018-10-12 - Hiram) +# BLATSERVERS ENTRY (DONE - 2019-07-09 - 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 ("rheMac10", "blat1a", "17892", "1", "0"); \ + VALUES ("rheMac10", "blat1a", "17898", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ - VALUES ("rheMac10", "blat1a", "17893", "0", "1");' \ + VALUES ("rheMac10", "blat1a", "17899", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ -## reset default position to MEPE gene (egg shell protein) -## (TBD - 2018-10-12 - Hiram) +## reset default position to same as rheMac8 +## (DONE - 2019-07-09 - Hiram) # as found from the galGal5 to rheMac10 liftOver ssh hgwdev - hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928" + hgsql -e 'update dbDb set defaultPos="chr3:70672926-70708108" where name="rheMac10";' hgcentraltest ######################################################################### # crispr 10K shoulders (TBD - 2018-10-16 - Hiram) # working on this script, adding the indexFa step: time (~/kent/src/hg/utils/automation/doCrispr.pl \ -stop=indexFa -buildDir=`pwd` -smallClusterHub=ku rheMac10 ncbiRefSeq) \ > indexFa.log 2>&1 # real 23m26.694s time (~/kent/src/hg/utils/automation/doCrispr.pl \ -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \ rheMac10 ncbiRefSeq) > guides.log 2>&1 # real 2m50.758s @@ -930,73 +950,81 @@ # 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 rheMac10 ncbiRefSeq) \ > load.log # real 307m41.143s ######################################################################### -# all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram) +# all.joiner update, downloads and in pushQ - (DONE - 2019-07-03,08-30 - Hiram) xyz cd $HOME/kent/src/hg/makeDb/schema # verify all the business is done for release ~/kent/src/hg/utils/automation/verifyBrowser.pl rheMac10 # fixup all.joiner until this is a clean output joinerCheck -database=rheMac10 -tableCoverage all.joiner joinerCheck -database=rheMac10 -times all.joiner joinerCheck -database=rheMac10 -keys all.joiner # when clean, check in: - git commit -m 'adding rules for rheMac10 refs #22113' all.joiner + git commit -m 'adding rules for rheMac10 and regenRn0 refs #23771 #21578' all.joiner git push # run up a 'make alpha' in hg/hgTables to get this all.joiner file # into the hgwdev/genome-test system cd /hive/data/genomes/rheMac10 time (makeDownloads.pl rheMac10) > downloads.log 2>&1 - # real 10m7.605s + # real 17m47.024s # now ready for pushQ entry mkdir /hive/data/genomes/rheMac10/pushQ cd /hive/data/genomes/rheMac10/pushQ - time (makePushQSql.pl -redmineList rheMac10) > rheMac10.pushQ.sql 2> stderr.out - # real 9m58.779s - - # remove the extra chainNet files from the listings: - sed -i -e "/etNig1/d" redmine.rheMac10.file.list - sed -i -e "/asAcu1/d" redmine.rheMac10.file.list - sed -i -e "/etNig1/d" redmine.rheMac10.table.list - sed -i -e "/onAlb1/d" redmine.rheMac10.table.list - sed -i -e "/asAcu1/d" redmine.rheMac10.table.list - sed -i -e "/Stickleback/d" redmine.rheMac10.releaseLog.txt - sed -i -e "/Tetraodon/d" redmine.rheMac10.releaseLog.txt - sed -i -e "/sparrow/d" redmine.rheMac10.releaseLog.txt + time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList rheMac10) > rheMac10.pushQ.sql 2> stderr.out + # real 15m52.548s + # remove the tandemDups and gapOverlap from the file list: sed -i -e "/tandemDups/d" redmine.rheMac10.table.list sed -i -e "/Tandem Dups/d" redmine.rheMac10.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.rheMac10.table.list sed -i -e "/Gap Overlaps/d" redmine.rheMac10.releaseLog.txt - # real 7m21.629s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/rheMac10/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/rheMac10/wib/quality.wib # WARNING: hgwdev does not have /gbdb/rheMac10/bbi/quality.bw # WARNING: rheMac10 does not have seq # WARNING: rheMac10 does not have extFile + + # verify the file list does correctly match to files + cat redmine.rheMac10.file.list | while read L +do + eval ls $L > /dev/null +done + # should be silent, missing files will show as errors + + # verify database tables, how many to expect: + wc -l redmine.rheMac10.table.list + # 63 redmine.rheMac10.table.list + + # how many actual: + awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.rheMac10.table.list | sh | wc -l + # 63 + + # would be a smaller number actual if some were missing + # add the path names to the listing files in the redmine issue # in the three appropriate entry boxes: # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.file.list # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.releaseLog.txt # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.table.list #########################################################################