166f7ceea61ae6355730d52f2ab9edf5b3542103 hiram Sun Apr 2 14:50:37 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 index 1168ce3..019da49 100644 --- src/hg/makeDb/doc/hg38/hprcLastz.txt +++ src/hg/makeDb/doc/hg38/hprcLastz.txt @@ -1,417 +1,737 @@ ############################################################################## # 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 ############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472575.1 +# (DONE - 2023-03-31 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-03-31 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-03-31 + + printf '# human GCA_018472575.1 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_018472575.1_HG00621.alt.pat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-03-31 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472575.1_HG00621.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 1656m19.999s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472575.1Link.txt + # 2930227171 bases of 3299210039 (88.816%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472575.1Link.txt + # 2919500649 bases of 3299210039 (88.491%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt" \ + hg38 GCA_018472575.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 80m49.485s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472575.1.txt + # 2712261274 bases of 3299210039 (82.209%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/575/GCA_018472575.1_HG00621.alt.pat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472575.1_HG00621.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-03-31/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 176m35.017s + + sed -e 's/^/ # /;' fb.GCA_018472575.1.chainHg38Link.txt + # 2749841756 bases of 2905948993 (94.628%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472575.1.chainSynHg38Link.txt + # 2740982328 bases of 2905948993 (94.323%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/575/GCA_018472575.1/GCA_018472575.1.chrom.sizes.txt" \ + GCA_018472575.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 75m18.079s + + sed -e 's/^/ # /;' fb.GCA_018472575.1.chainRBest.Hg38.txt + # 2711354036 bases of 2905948993 (93.304%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472585.1 +# (DONE - 2023-03-31 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-03-31 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-03-31 + + printf '# human GCA_018472585.1 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_018472585.1_HG00673.alt.pat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-03-31 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472585.1_HG00673.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 1885m29.234s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472585.1Link.txt + # 2929448512 bases of 3299210039 (88.792%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472585.1Link.txt + # 2918442760 bases of 3299210039 (88.459%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt" \ + hg38 GCA_018472585.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 73m33.209s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472585.1.txt + # 2710429846 bases of 3299210039 (82.154%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/585/GCA_018472585.1_HG00673.alt.pat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472585.1_HG00673.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-03-31/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 178m21.195s + + sed -e 's/^/ # /;' fb.GCA_018472585.1.chainHg38Link.txt + # 2753693241 bases of 2925716157 (94.120%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472585.1.chainSynHg38Link.txt + # 2744516270 bases of 2925716157 (93.807%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/585/GCA_018472585.1/GCA_018472585.1.chrom.sizes.txt" \ + GCA_018472585.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 78m41.678s + + sed -e 's/^/ # /;' fb.GCA_018472585.1.chainRBest.Hg38.txt + # 2709952963 bases of 2925716157 (92.625%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018506975.1 +# (DONE - 2023-04-01 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-01 + cd /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-01 + + printf '# human GCA_018506975.1 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 2021-05-26 GCA_018506975.1_HG00733.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-01 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018506975.1_HG00733.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 715m15.369s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018506975.1Link.txt + # 3055939979 bases of 3299210039 (92.626%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018506975.1Link.txt + # 3049122190 bases of 3299210039 (92.420%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt" \ + hg38 GCA_018506975.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 79m55.110s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018506975.1.txt + # 2839289049 bases of 3299210039 (86.060%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/975/GCA_018506975.1_HG00733.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018506975.1_HG00733.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-01/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 185m40.016s + + sed -e 's/^/ # /;' fb.GCA_018506975.1.chainHg38Link.txt + # 2881236161 bases of 3026533161 (95.199%) in intersection + sed -e 's/^/ # /;' fb.GCA_018506975.1.chainSynHg38Link.txt + # 2873519502 bases of 3026533161 (94.944%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/975/GCA_018506975.1/GCA_018506975.1.chrom.sizes.txt" \ + GCA_018506975.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 83m22.954s + + sed -e 's/^/ # /;' fb.GCA_018506975.1.chainRBest.Hg38.txt + # 2839019594 bases of 3026533161 (93.804%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. human GCA_018472765.1 +# (DONE - 2023-04-01 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-01 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-01 + + printf '# human GCA_018472765.1 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_018472765.1_HG00735.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-01 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018472765.1_HG00735.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 773m57.328s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472765.1Link.txt + # 3055677509 bases of 3299210039 (92.618%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472765.1Link.txt + # 3048544954 bases of 3299210039 (92.402%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt" \ + hg38 GCA_018472765.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 77m29.396s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472765.1.txt + # 2842418915 bases of 3299210039 (86.155%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/765/GCA_018472765.1_HG00735.pri.mat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018472765.1_HG00735.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-01/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 186m20.625s + + sed -e 's/^/ # /;' fb.GCA_018472765.1.chainHg38Link.txt + # 2878517540 bases of 3037795105 (94.757%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472765.1.chainSynHg38Link.txt + # 2870375039 bases of 3037795105 (94.489%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/765/GCA_018472765.1/GCA_018472765.1.chrom.sizes.txt" \ + GCA_018472765.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 86m3.847s + + sed -e 's/^/ # /;' fb.GCA_018472765.1.chainRBest.Hg38.txt + # 2837794728 bases of 3037795105 (93.416%) in intersection + +##############################################################################