bc46f17c49d80193157e45e9916ff3032598a245 hiram Tue Dec 12 07:45:44 2023 -0800 lastz chain net hg38 to hs1 refs #31977 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index 895a954..74f9b92 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -13807,16 +13807,103 @@ \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \ GCA_011100615.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 140m55.957s sed -e 's/^/ # /;' fb.GCA_011100615.1.chainRBest.Hg38.txt # 2394259873 bases of 2906138557 (82.386%) in intersection real 512m28.587s user 0m0.989s sys 0m1.306s + +############################################################################## +# LASTZ Human Hg38 vs. Human Hs1 +# (DONE - 2022-09-26 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21 + cd /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21 + + printf '# Human Hs1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +BLASTZ_T=2 +BLASTZ_O=600 +BLASTZ_E=150 +BLASTZ_M=254 +BLASTZ_K=4500 +BLASTZ_Y=15000 +BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q +# A C G T +# A 90 -330 -236 -356 +# C -330 100 -318 -236 +# G -236 -318 100 -330 +# T -356 -236 -330 90 + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Human hs1 +SEQ2_DIR=/hive/data/genomes/hs1/hs1.2bit +SEQ2_LEN=/hive/data/genomes/hs1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzHs1.2022-09-21 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.hg38.chainHs1Link.txt + # 3037208207 bases of 3110768607 (97.635%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynHs1Link.txt + # 3034364239 bases of 3110768607 (97.544%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + hg38 hs1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.hg38.chainRBest.Hs1.txt + + ### and for the swap + + cd /hive/data/genomes/hs1/bed/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21/DEF -swapDir=`pwd` \ +-syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 134m42.390s + + sed -e 's/^/ # /;' fb.hs1.chainHg38Link.txt + # 2906145588 bases of 3117292070 (93.227%) in intersection + sed -e 's/^/ # /;' fb.hs1.chainSynHg38Link.txt + # 2896674405 bases of 3117292070 (92.923%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + hs1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 88m35.809s + + sed -e 's/^/ # /;' fb.hs1.chainRBest.Hg38.txt + # 2863655887 bases of 3117292070 (91.864%) in intersection + ##############################################################################