5dbad70c3a1445cc3a505b451c623f9aa7bcca3b hiram Mon Aug 17 12:46:26 2020 -0700 lastz chainNet hg38 to canFam5 in progress refs #25917 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index 2ca3a12..f83d11f 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -12684,15 +12684,91 @@ -syntenicNet) > swap.log 2>&1 # real 73m50.456s cat fb.panPan3.chainHg38Link.txt # 2777869191 bases of 3015350297 (92.124%) in intersection cat fb.panPan3.chainSynHg38Link.txt # 2768018012 bases of 3015350297 (91.798%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ panPan3 hg38) > rbest.log 2>&1 & # real 66m52.340s cat fb.panPan3.chainRBest.Hg38.txt # 2732415393 bases of 3015350297 (90.617%) in intersection ######################################################################### +# LASTZ human/hg38 vs. Great Dane/canFam5 +# (DONE - 2020-07-29 - Hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29 + cd /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29 + + printf '# human vs. Great Dane +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +BLASTZ_M=254 + +# TARGET: human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit +SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes +SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift +SEQ1_CHUNK=40000000 +SEQ1_LIMIT=20 +SEQ1_LAP=10000 + +# QUERY: Great Dane Zoey/canFam5 +SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit +SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LIMIT=20 +SEQ2_LAP=0 + +BASE=/hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ + -chainMinScore=3000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -syntenicNet) > do.log 2>&1 + # real 1038m20.721s + + cat fb.hg38.chainCanFam5Link.txt + # 1545648756 bases of 3110768607 (49.687%) in intersection + + cat fb.hg38.chainSynCanFam5Link.txt + # 1484758745 bases of 3110768607 (47.730%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + hg38 canFam5) > rbest.log 2>&1 & +XXX - running - Mon Aug 17 12:41:45 PDT 2020 + # real 310m32.196s + + cat fb.hg38.chainRBest.CanFam5.txt + # 1425406620 bases of 3110768607 (45.822%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/canFam5/bed/blastz.hg38.swap + cd /hive/data/genomes/canFam5/bed/blastz.hg38.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29/DEF \ + -swap -chainMinScore=3000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 +XXX - running - Mon Aug 17 12:42:53 PDT 2020 + # real 99m10.990s + + cat fb.canFam5.chainHg38Link.txt + # 1493209286 bases of 2481941580 (60.163%) in intersection + cat fb.canFam5.chainSynHg38Link.txt + # 1448164376 bases of 2481941580 (58.348%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + canFam5 hg38) > rbest.log 2>&1 & + # real 257m59.713s + + cat fb.canFam5.chainRBest.Hg38.txt + # 1425296830 bases of 2481941580 (57.427%) in intersection + +#########################################################################