2eb7675b61bc79306e6ec54839140d2b40b31bf5 hiram Mon May 24 12:19:29 2021 -0700 canFam6 dog Tasha browser completed refs #27546 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 8296bb1..3dcdfa5 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -18364,15 +18364,83 @@ time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \ $query $target) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 246m55.342s sed -e 's/^/ # /;' fb.${query}.chainRBest.${Target}.txt # 2078102689 bases of 2553121441 (81.395%) in intersection # Complete run time for all the swap operation: # real 367m14.987s ############################################################################## +# LASTZ dog boxer Tasha canFam6 (DONE - 2021-05-17 - Hiram) + # establish a screen to control this job + mkdir /hive/data/genomes/mm10/bed/lastzCanFam6.2021-05-17 + cd /hive/data/genomes/mm10/bed/lastzCanFam6.2021-05-17 + + printf '# boxer Tasha canFam6 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: boxer Tasha canFam6 +SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit +SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes +SEQ2_CHUNK=10000000 +SEQ2_LIMIT=20 +SEQ2_LAP=0 + +BASE=/hive/data/genomes/mm10/bed/lastzCanFam6.2021-05-17 +TMPDIR=/dev/shm +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl `pwd`/DEF \ + -verbose=2 -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & + # real 276m30.999s + + sed -e 's/^/ # /;' fb.mm10.chainCanFam6Link.txt + # 791039766 bases of 2739603606 (28.874%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynCanFam6Link.txt + # 747308674 bases of 2739603606 (27.278%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam6 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 260m22.664s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.CanFam6.txt + # 731553248 bases of 2739603606 (26.703%) in intersection + + mkdir /hive/data/genomes/canFam6/bed/blastz.mm10.swap + cd /hive/data/genomes/canFam6/bed/blastz.mm10.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzCanFam6.2021-05-17/DEF \ + -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & + # real 48m21.892s + + sed -e 's/^/ # /;' fb.canFam6.chainMm10Link.txt + # 747891292 bases of 2312743346 (32.338%) in intersection + sed -e 's/^/ # /;' fb.canFam6.chainSynMm10Link.txt + # 721253430 bases of 2312743346 (31.186%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev canFam6 mm10 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 165m54.013s + + sed -e 's/^/ # /;' fb.canFam6.chainRBest.Mm10.txt + # 730713145 bases of 2312743346 (31.595%) in intersection + +##############################################################################