66a8e56296308c7ed601e188dd9374ebe4b3c5ec hiram Fri Jun 5 09:42:01 2020 -0700 finished lastz/chain/net to assembly hub sequence per user request refs #25625 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index a12e314..4dee6ba 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -17725,85 +17725,81 @@ # QUERY: woodchuck/Marmota monax/GCA_901343595.1 SEQ2_DIR=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit SEQ2_LEN=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -noDbNameCheck -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & -XXX - running - Fri May 29 17:11:31 PDT 2020 - # real 98m5.996s - - # slight problem with the resulting chain table name: - # chainGCA_901343595.1_MONAX5 - # can not have a table name with .1 like that, MySQL thought - # that was database chainGCA_901343595 taable 1_MONAX5 - # fixed up loadUp.csh to do that correctly with name: - # chainGCA_901343595v1_MONAX5 - # would need to change the SEQ2_DIR name - # make some symLinks and have settings: -# SEQ2_DIR=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit -# SEQ2_LEN=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes - # real 483m10.607s - time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ - -continue=download -noDbNameCheck -syntenicNet \ - -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ - -chainMinScore=3000 -chainLinearGap=medium) > download.log 2>&1 & + # real 125m59.598s cat fb.mm10.chainGCA_901343595v1_MONAX5Link.txt # 923698956 bases of 2652783500 (34.820%) in intersection + cat fb.mm10.chainSynGCA_901343595v1_MONAX5Link.txt + # 851857022 bases of 2652783500 (32.112%) in intersection - cat fb.mm10.chainCanFam4Link.txt - # 777883731 bases of 2652783500 (29.323%) in intersection - cat fb.mm10.chainSynCanFam4Link.txt - # 736602602 bases of 2652783500 (27.767%) in intersection - - - time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam4 \ + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load \ + -workhorse=hgwdev mm10 GCA_901343595v1_MONAX5 \ + -query2Bit=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit \ + -querySizes=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & - # real 219m16.168s + # real 226m4.391s - cat fb.mm10.chainRBest.CanFam4.txt - # 741307883 bases of 2652783500 (27.945%) in intersection + cat fb.mm10.chainRBest.GCA_901343595v1_MONAX5.txt + # 877175980 bases of 2652783500 (33.066%) in intersection - mkdir /hive/data/genomes/canFam4/bed/blastz.mm10.swap - cd /hive/data/genomes/canFam4/bed/blastz.mm10.swap + mkdir /hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/trackData/blastz.mm10.swap + cd /hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/trackData/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/mm10/bed/lastzCanFam4.2020-05-29/DEF \ + /hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/DEF \ + -noDbNameCheck -swapDir=`pwd` -skipDownload -trackHub \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & - # real 50m20.639s - cat fb.canFam4.chainMm10Link.txt - # 772902855 bases of 2481941580 (31.141%) in intersection - cat fb.canFam4.chainSynMm10Link.txt - # 737924732 bases of 2481941580 (29.732%) in intersection - - time (doRecipBest.pl -load -workhorse=hgwdev canFam4 mm10 \ + # real 25m28.210s + # ran into problem of expired certificate at genome-source.gi.ucsc.edu + # finished netChains.csh manually, then continuing: + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/DEF \ + -noDbNameCheck -swapDir=`pwd` -skipDownload -trackHub \ + -continue=load -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > load.log 2>&1 & + # real 37m23.399s + + cat fb.GCA_901343595v1_MONAX5.chain.Mm10Link.txt + # 974411924 bases of 2625891882 (37.108%) in intersection + cat fb.GCA_901343595v1_MONAX5.chainSyn.Mm10Link.txt + # 865165537 bases of 2625891882 (32.947%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load \ + -skipDownload -trackHub -workhorse=hgwdev GCA_901343595v1_MONAX5 mm10 \ + -target2Bit=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit \ + -targetSizes=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & - # real 173m38.016s + # real 277m4.130s - cat fb.canFam4.chainRBest.Mm10.txt - # 740357755 bases of 2481941580 (29.830%) in intersection + cat fb.GCA_901343595v1_MONAX5.chainRBest.Mm10.txt + # 877160501 bases of 2625891882 (33.404%) in intersection ############################################################################## # ENCODE Registry of Candidate cis-Regulatory Elements # # 2020-05-12 kate # # From ENCODE 3 Data Analysis Center at U Mass Med Center (Zlab) # Data contacts: Henry Pratt, Jill Moore, Zhiping Weng PI # # RM #24668 # # Download BED file (hosted on their integrative hub) cd /hive/data/outside/encode3/ccre mkdir mouse