06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 0627318..bd58490 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -3483,45 +3483,80 @@ # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable # number of jobs, 50,000 to something under 100,000 # Can't do this when there are only the single small set of chroms time nice -n +19 doBlastzChainNet.pl -verbose=2 \ `pwd`/DEF \ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 & # real 1792m40.071s cat fb.mm10.chainMonDom5Link.txt # 254245903 bases of 2652783500 (9.584%) in intersection # set sym link to indicate this is the lastz for this genome: cd /hive/data/genomes/mm10/bed ln -s lastzMonDom5.2012-03-29 lastz.monDom5 + # add syntenic net and recip best per user request 2020-11 - Hiram + time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ + -continue=syntenicNet -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > synNet.log 2>&1 & + # real 4m58.921s + + cat fb.mm10.chainSynMonDom5Link.txt + # 181282548 bases of 2652783500 (6.834%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev mm10 monDom5 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 1024m21.233s + + cat fb.mm10.chainRBest.MonDom5.txt + # 208921944 bases of 2652783500 (7.876%) in intersection + + # and for the swap mkdir /hive/data/genomes/monDom5/bed/blastz.mm10.swap cd /hive/data/genomes/monDom5/bed/blastz.mm10.swap time nice -n +19 doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzMonDom5.2012-03-29/DEF \ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \ -swap -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 & # real 73m49.230s cat fb.monDom5.chainMm10Link.txt # 252291401 bases of 3501660299 (7.205%) in intersection # set sym link to indicate this is the lastz for this genome: cd /hive/data/genomes/monDom5/bed ln -s blastz.mm10.swap lastz.mm10 + # add syntenic net and recip best per user request 2020-11 - Hiram + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzMonDom5.2012-03-29/DEF \ + -continue=syntenicNet -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > synNet.log 2>&1 & + # real 4m52.417s + cat fb.monDom5.chainMm10Link.txt + # 252291401 bases of 3501660299 (7.205%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev monDom5 mm10 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 1013m15.298s + + cat fb.monDom5.chainRBest.Mm10.txt + # 209696912 bases of 3501660299 (5.988%) in intersection + ######################################################################### # lastz Tasmanian Devil sarHar1 (DONE - 2012-03-29 - Hiram) # establish a screen to control this job with a name to indicate what it is screen -S mm10SarHar1 mkdir /hive/data/genomes/mm10/bed/lastzSarHar1.2012-03-29 cd /hive/data/genomes/mm10/bed/lastzSarHar1.2012-03-29 cat << '_EOF_' > DEF # Mouse vs. tasmanian devil BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_Q=/scratch/data/blastz/HoxD55.q @@ -3671,45 +3706,73 @@ # adjust the SEQ2_LIMIT with -stop=partition to get a reasonable # number of jobs, 50,000 to something under 100,000 # when not present, SEQ2_LIMIT is a default 100 time nice -n +19 doBlastzChainNet.pl -verbose=2 \ `pwd`/DEF \ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 & # real 1264m1.056s cat fb.mm10.chainOrnAna1Link.txt # 141873792 bases of 2652783500 (5.348%) in intersection # set sym link to indicate this is the lastz for this genome: cd /hive/data/genomes/mm10/bed ln -s lastzOrnAna1.2012-03-29 lastz.ornAna1 + # add syntenic net and recip best per user request 2020-11 - Hiram + time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ + -continue=syntenicNet -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > synNet.log 2>&1 & + # real 2m3.337s + + time (doRecipBest.pl -load -workhorse=hgwdev mm10 ornAna1 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 196m25.100s + # and for the swap mkdir /hive/data/genomes/ornAna1/bed/blastz.mm10.swap cd /hive/data/genomes/ornAna1/bed/blastz.mm10.swap time nice -n +19 doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzOrnAna1.2012-03-29/DEF \ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \ -swap -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 & # real 49m45.308s cat fb.ornAna1.chainMm10Link.txt # 135101083 bases of 1842236818 (7.334%) in intersection # set sym link to indicate this is the lastz for this genome: cd /hive/data/genomes/ornAna1/bed ln -s blastz.mm10.swap lastz.mm10 + # add syntenic net and recip best per user request 2020-11 - Hiram + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzOrnAna1.2012-03-29/DEF \ + -continue=syntenicNet -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > synNet.log 2>&1 & + # real 3m17.422s + cat fb.ornAna1.chainSynMm10Link.txt + # 76550450 bases of 1842236818 (4.155%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev ornAna1 mm10 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 207m50.665s + + cat fb.ornAna1.chainRBest.Mm10.txt + # 114682047 bases of 1842236818 (6.225%) in intersection + ######################################################################### # lastz turtle chrPic1 (DONE - 2012-03-29 - Hiram) # establish a screen to control this job with a name to indicate what it is screen -S mm10ChrPic1 mkdir /hive/data/genomes/mm10/bed/lastzChrPic1.2012-03-29 cd /hive/data/genomes/mm10/bed/lastzChrPic1.2012-03-29 cat << '_EOF_' > DEF # Mouse vs. turtle BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.02/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_Q=/scratch/data/blastz/HoxD55.q