50871bdc58d90912e30fdb66e2523de383ada100 hiram Sat Apr 1 19:07:44 2023 -0700 record of lastz runs HPRC genomes to hg38 refs #30508 diff --git src/hg/makeDb/doc/hg38/hprcLastz.txt src/hg/makeDb/doc/hg38/hprcLastz.txt new file mode 100644 index 0000000..1168ce3 --- /dev/null +++ src/hg/makeDb/doc/hg38/hprcLastz.txt @@ -0,0 +1,417 @@ +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018503255.1 +# (DONE - 2023-03-29 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29 + cd /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29 + + printf '# human GCA_018503255.1 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 2021-05-26 GCA_018503255.1_NA18906.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018503255.1_NA18906.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 150m39.450s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018503255.1Link.txt + # 3048440296 bases of 3299210039 (92.399%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018503255.1Link.txt + # 3044280661 bases of 3299210039 (92.273%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt" \ + hg38 GCA_018503255.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 69m12.500s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018503255.1.txt + # 2838452762 bases of 3299210039 (86.034%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/503/255/GCA_018503255.1_NA18906.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018503255.1_NA18906.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018503255.1.2023-03-29/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 120m43.527s + + sed -e 's/^/ # /;' fb.GCA_018503255.1.chainHg38Link.txt + # 2884269653 bases of 3055692855 (94.390%) in intersection + sed -e 's/^/ # /;' fb.GCA_018503255.1.chainSynHg38Link.txt + # 2877890032 bases of 3055692855 (94.181%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/503/255/GCA_018503255.1/GCA_018503255.1.chrom.sizes.txt" \ + GCA_018503255.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 79m48.978s + + sed -e 's/^/ # /;' fb.GCA_018503255.1.chainRBest.Hg38.txt + # 2833510609 bases of 3055692855 (92.729%) in intersection + +real 420m25.386s +user 0m1.028s +sys 0m1.944s + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472605.1 +# (DONE - 2023-03-30 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-03-30 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-03-30 + + printf '# human GCA_018472605.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# 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 2021-05-24 GCA_018472605.1_HG00621.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-03-30 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472605.1_HG00621.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 798m40.421s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472605.1Link.txt + # 3055745656 bases of 3299210039 (92.621%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472605.1Link.txt + # 3049259997 bases of 3299210039 (92.424%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt" \ + hg38 GCA_018472605.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 76m42.486s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472605.1.txt + # 2839060081 bases of 3299210039 (86.053%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/605/GCA_018472605.1_HG00621.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472605.1_HG00621.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-03-30/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 169m14.429s + + sed -e 's/^/ # /;' fb.GCA_018472605.1.chainHg38Link.txt + # 2871721741 bases of 3023026071 (94.995%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472605.1.chainSynHg38Link.txt + # 2864101252 bases of 3023026071 (94.743%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/605/GCA_018472605.1/GCA_018472605.1.chrom.sizes.txt" \ + GCA_018472605.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 77m15.470s + + sed -e 's/^/ # /;' fb.GCA_018472605.1.chainRBest.Hg38.txt + # 2836466120 bases of 3023026071 (93.829%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472595.1 +# (DONE - 2023-03-30 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-03-30 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-03-30 + + printf '# human GCA_018472595.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# 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 2021-05-24 GCA_018472595.1_HG00438.alt.pat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-03-30 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472595.1_HG00438.alt.pat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 807m55.173s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472595.1Link.txt + # 3055520777 bases of 3299210039 (92.614%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472595.1Link.txt + # 3049078073 bases of 3299210039 (92.418%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt" \ + hg38 GCA_018472595.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 75m9.076s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472595.1.txt + # 2842484819 bases of 3299210039 (86.157%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/595/GCA_018472595.1_HG00438.alt.pat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472595.1_HG00438.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-03-30/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 171m33.671s + + sed -e 's/^/ # /;' fb.GCA_018472595.1.chainHg38Link.txt + # 2878753022 bases of 3025118465 (95.162%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472595.1.chainSynHg38Link.txt + # 2870163712 bases of 3025118465 (94.878%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/595/GCA_018472595.1/GCA_018472595.1.chrom.sizes.txt" \ + GCA_018472595.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 74m2.644s + + sed -e 's/^/ # /;' fb.GCA_018472595.1.chainRBest.Hg38.txt + # 2838720611 bases of 3025118465 (93.838%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018471515.1 +# (DONE - 2023-03-30 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-03-30 + cd /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-03-30 + + printf '# human GCA_018471515.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# 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 2021-05-24 GCA_018471515.1_HG00438.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-03-30 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018471515.1_HG00438.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 972m7.613s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018471515.1Link.txt + # 3055194922 bases of 3299210039 (92.604%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471515.1Link.txt + # 3048738864 bases of 3299210039 (92.408%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt" \ + hg38 GCA_018471515.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 72m41.002s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471515.1.txt + # 2839646889 bases of 3299210039 (86.071%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/515/GCA_018471515.1_HG00438.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018471515.1_HG00438.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-03-30/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 165m20.253s + + sed -e 's/^/ # /;' fb.GCA_018471515.1.chainHg38Link.txt + # 2877981247 bases of 3035735720 (94.803%) in intersection + sed -e 's/^/ # /;' fb.GCA_018471515.1.chainSynHg38Link.txt + # 2869825707 bases of 3035735720 (94.535%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/515/GCA_018471515.1/GCA_018471515.1.chrom.sizes.txt" \ + GCA_018471515.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 74m54.798s + + sed -e 's/^/ # /;' fb.GCA_018471515.1.chainRBest.Hg38.txt + # 2837483390 bases of 3035735720 (93.469%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472565.1 +# (DONE - 2023-03-31 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-03-31 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-03-31 + + printf '# human GCA_018472565.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# 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 2021-05-24 GCA_018472565.1_HG00673.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-03-31 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472565.1_HG00673.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 896m16.971s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472565.1Link.txt + # 3055196954 bases of 3299210039 (92.604%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472565.1Link.txt + # 3048689678 bases of 3299210039 (92.407%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt" \ + hg38 GCA_018472565.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 78m30.447s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472565.1.txt + # 2842232990 bases of 3299210039 (86.149%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/565/GCA_018472565.1_HG00673.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472565.1_HG00673.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-03-31/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 182m45.578s + + sed -e 's/^/ # /;' fb.GCA_018472565.1.chainHg38Link.txt + # 2884263199 bases of 3053585067 (94.455%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472565.1.chainSynHg38Link.txt + # 2876160791 bases of 3053585067 (94.190%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/565/GCA_018472565.1/GCA_018472565.1.chrom.sizes.txt" \ + GCA_018472565.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 81m37.111s + + sed -e 's/^/ # /;' fb.GCA_018472565.1.chainRBest.Hg38.txt + # 2839163719 bases of 3053585067 (92.978%) in intersection + +##############################################################################