f6bb7fb8b0af020a2d602824f74d84d516bd96fb hiram Thu Jul 30 15:12:36 2020 -0700 liftOver mm10 to mm39 to mm10 completed refs #22271 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 9143ae1..9035587 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -17891,15 +17891,104 @@ # real 55m23.982s cat fb.panPan3.chainMm10Link.txt # 954214151 bases of 3015350297 (31.645%) in intersection cat fb.panPan3.chainSynMm10Link.txt # 887980807 bases of 3015350297 (29.449%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` panPan3 mm10) \ > rbest.log 2>&1 # real 305m11.756s cat fb.panPan3.chainRBest.Mm10.txt # 889360051 bases of 3015350297 (29.494%) in intersection ############################################################################## +# LASTZ Great Dane canFam5 (DONE - 2020-07-29 - Hiram) + # establish a screen to control this job + mkdir /hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29 + cd /hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29 + + printf '# German shepard canFam5 vs mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +BLASTZ_M=254 + +# TARGET: Mouse Mm10 +SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: German shepard canFam5 +SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit +SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes +SEQ2_CHUNK=10000000 +SEQ2_LIMIT=20 +SEQ2_LAP=0 + +BASE=/hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ + -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & +XXX - running - Wed Jul 29 13:30:41 PDT 2020 + # real 483m10.607s + + cat fb.mm10.chainCanFam5Link.txt + # 777883731 bases of 2652783500 (29.323%) in intersection + cat fb.mm10.chainSynCanFam5Link.txt + # 736602602 bases of 2652783500 (27.767%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam5 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 219m16.168s + + cat fb.mm10.chainRBest.CanFam5.txt + # 741307883 bases of 2652783500 (27.945%) in intersection + + mkdir /hive/data/genomes/canFam5/bed/blastz.mm10.swap + cd /hive/data/genomes/canFam5/bed/blastz.mm10.swap + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzCanFam5.2020-07-29/DEF \ + -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & + # real 50m20.639s + + cat fb.canFam5.chainMm10Link.txt + # 772902855 bases of 2481941580 (31.141%) in intersection + cat fb.canFam5.chainSynMm10Link.txt + # 737924732 bases of 2481941580 (29.732%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev canFam5 mm10 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 173m38.016s + + cat fb.canFam5.chainRBest.Mm10.txt + # 740357755 bases of 2481941580 (29.830%) in intersection + +############################################################################## +# LIFTOVER TO mm39 (DONE - 2020-07-30 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/mm10/bed/blat.mm39.2020-07-30 + cd /hive/data/genomes/mm10/bed/blat.mm39.2020-07-30 + doSameSpeciesLiftOver.pl -verbose=2 \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \ + -target2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -targetSizes=/hive/data/genomes/mm10/chrom.sizes \ + mm10 mm39 + time (doSameSpeciesLiftOver.pl -verbose=2 \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -targetSizes=/hive/data/genomes/mm10/chrom.sizes \ + -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \ + mm10 mm39) > doLiftOverToMm39.log 2>&1 + # real 257m19.983s + + # see if the liftOver menus function in the browser from mm10 to mm39 + +##############################################################################