ca5e96d3ef0bc2d2f995a912dc4f7b5fdf432e4e hiram Wed Apr 5 16:46:20 2023 -0700 catching up with completed lastz/chain/net refs #30912 diff --git src/hg/makeDb/doc/hg38/hprcLastz.txt src/hg/makeDb/doc/hg38/hprcLastz.txt index db17523..bc90392 100644 --- src/hg/makeDb/doc/hg38/hprcLastz.txt +++ src/hg/makeDb/doc/hg38/hprcLastz.txt @@ -1,2492 +1,2584 @@ ############################################################################## # 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_018506975.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018506975.1.2023-04-02 printf '# human GCA_018506975.1 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_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_018506975.1.2023-04-02 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 200m27.588s sed -e 's/^/ # /;' fb.hg38.chainGCA_018506975.1Link.txt # 3049128877 bases of 3299210039 (92.420%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018506975.1Link.txt # 3044461418 bases of 3299210039 (92.278%) 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 75m37.537s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018506975.1.txt # 2836999770 bases of 3299210039 (85.990%) 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_018506975.1.2023-04-02/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 126m45.101s sed -e 's/^/ # /;' fb.GCA_018506975.1.chainHg38Link.txt # 2873379328 bases of 3026533161 (94.940%) in intersection sed -e 's/^/ # /;' fb.GCA_018506975.1.chainSynHg38Link.txt # 2868194843 bases of 3026533161 (94.768%) 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 78m1.144s sed -e 's/^/ # /;' fb.GCA_018506975.1.chainRBest.Hg38.txt # 2836972314 bases of 3026533161 (93.737%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472765.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018472765.1.2023-04-02 printf '# human GCA_018472765.1 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 2021-05-24 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_018472765.1.2023-04-02 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 209m52.286s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472765.1Link.txt # 3048755024 bases of 3299210039 (92.409%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472765.1Link.txt # 3044190998 bases of 3299210039 (92.270%) 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 77m28.446s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472765.1.txt # 2838856012 bases of 3299210039 (86.047%) 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_018472765.1.2023-04-02/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 126m15.652s sed -e 's/^/ # /;' fb.GCA_018472765.1.chainHg38Link.txt # 2870973013 bases of 3037795105 (94.508%) in intersection sed -e 's/^/ # /;' fb.GCA_018472765.1.chainSynHg38Link.txt # 2864846067 bases of 3037795105 (94.307%) 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 77m45.108s sed -e 's/^/ # /;' fb.GCA_018472765.1.chainRBest.Hg38.txt # 2836134995 bases of 3037795105 (93.362%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018506955.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02 printf '# human GCA_018506955.1 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_018506955.1_HG00733.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018506955.1_HG00733.alt.pat.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 201m16.524s sed -e 's/^/ # /;' fb.hg38.chainGCA_018506955.1Link.txt # 3049046848 bases of 3299210039 (92.417%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018506955.1Link.txt # 3045133832 bases of 3299210039 (92.299%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt" \ hg38 GCA_018506955.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 75m46.689s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018506955.1.txt # 2839895561 bases of 3299210039 (86.078%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/506/955/GCA_018506955.1_HG00733.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018506955.1_HG00733.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018506955.1.2023-04-02/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 127m14.540s sed -e 's/^/ # /;' fb.GCA_018506955.1.chainHg38Link.txt # 2875810655 bases of 3042264782 (94.529%) in intersection sed -e 's/^/ # /;' fb.GCA_018506955.1.chainSynHg38Link.txt # 2869822512 bases of 3042264782 (94.332%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/506/955/GCA_018506955.1/GCA_018506955.1.chrom.sizes.txt" \ GCA_018506955.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 78m3.234s sed -e 's/^/ # /;' fb.GCA_018506955.1.chainRBest.Hg38.txt # 2839456755 bases of 3042264782 (93.334%) in intersection real 482m24.334s user 0m2.606s sys 0m1.701s ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472715.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02 printf '# human GCA_018472715.1 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 2021-05-24 GCA_018472715.1_HG00735.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018472715.1_HG00735.alt.pat.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 204m26.710s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472715.1Link.txt # 3049832328 bases of 3299210039 (92.441%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472715.1Link.txt # 3045548758 bases of 3299210039 (92.311%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt" \ hg38 GCA_018472715.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 76m11.079s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472715.1.txt # 2838794506 bases of 3299210039 (86.045%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/715/GCA_018472715.1_HG00735.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018472715.1_HG00735.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472715.1.2023-04-02/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 126m58.305s sed -e 's/^/ # /;' fb.GCA_018472715.1.chainHg38Link.txt # 2870517837 bases of 3033541617 (94.626%) in intersection sed -e 's/^/ # /;' fb.GCA_018472715.1.chainSynHg38Link.txt # 2864517688 bases of 3033541617 (94.428%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/715/GCA_018472715.1/GCA_018472715.1.chrom.sizes.txt" \ GCA_018472715.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 78m29.627s sed -e 's/^/ # /;' fb.GCA_018472715.1.chainRBest.Hg38.txt # 2835565639 bases of 3033541617 (93.474%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471095.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02 printf '# human GCA_018471095.1 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 2021-05-24 GCA_018471095.1_HG00741.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018471095.1_HG00741.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 175m18.932s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471095.1Link.txt # 3048859071 bases of 3299210039 (92.412%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471095.1Link.txt # 3044347720 bases of 3299210039 (92.275%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt" \ hg38 GCA_018471095.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 73m55.452s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471095.1.txt # 2837688913 bases of 3299210039 (86.011%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/095/GCA_018471095.1_HG00741.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018471095.1_HG00741.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471095.1.2023-04-02/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 128m25.672s sed -e 's/^/ # /;' fb.GCA_018471095.1.chainHg38Link.txt # 2872162291 bases of 3036701854 (94.582%) in intersection sed -e 's/^/ # /;' fb.GCA_018471095.1.chainSynHg38Link.txt # 2865992480 bases of 3036701854 (94.378%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/095/GCA_018471095.1/GCA_018471095.1.chrom.sizes.txt" \ GCA_018471095.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m7.797s sed -e 's/^/ # /;' fb.GCA_018471095.1.chainRBest.Hg38.txt # 2835910744 bases of 3036701854 (93.388%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472685.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02 printf '# human GCA_018472685.1 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 2021-05-24 GCA_018472685.1_HG01071.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018472685.1_HG01071.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 183m14.390s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472685.1Link.txt # 3047519463 bases of 3299210039 (92.371%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472685.1Link.txt # 3043196829 bases of 3299210039 (92.240%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt" \ hg38 GCA_018472685.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 75m34.874s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472685.1.txt # 2836768261 bases of 3299210039 (85.983%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/685/GCA_018472685.1_HG01071.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018472685.1_HG01071.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472685.1.2023-04-02/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 130m36.307s sed -e 's/^/ # /;' fb.GCA_018472685.1.chainHg38Link.txt # 2868617976 bases of 3012710110 (95.217%) in intersection sed -e 's/^/ # /;' fb.GCA_018472685.1.chainSynHg38Link.txt # 2862952792 bases of 3012710110 (95.029%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/685/GCA_018472685.1/GCA_018472685.1.chrom.sizes.txt" \ GCA_018472685.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 80m25.524s sed -e 's/^/ # /;' fb.GCA_018472685.1.chainRBest.Hg38.txt # 2833591390 bases of 3012710110 (94.055%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471105.1 # (DONE - 2023-04-02 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02 cd /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02 printf '# human GCA_018471105.1 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 2021-05-24 GCA_018471105.1_HG00741.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018471105.1_HG00741.alt.pat.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 182m2.727s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471105.1Link.txt # 3047619516 bases of 3299210039 (92.374%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471105.1Link.txt # 3043638122 bases of 3299210039 (92.254%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt" \ hg38 GCA_018471105.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 75m1.197s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471105.1.txt # 2837413728 bases of 3299210039 (86.003%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/105/GCA_018471105.1_HG00741.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018471105.1_HG00741.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471105.1.2023-04-02/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 132m1.463s sed -e 's/^/ # /;' fb.GCA_018471105.1.chainHg38Link.txt # 2869710420 bases of 3029878036 (94.714%) in intersection sed -e 's/^/ # /;' fb.GCA_018471105.1.chainSynHg38Link.txt # 2864242851 bases of 3029878036 (94.533%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/105/GCA_018471105.1/GCA_018471105.1.chrom.sizes.txt" \ GCA_018471105.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m3.458s sed -e 's/^/ # /;' fb.GCA_018471105.1.chainRBest.Hg38.txt # 2835965394 bases of 3029878036 (93.600%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472725.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03 printf '# human GCA_018472725.1 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 2021-05-24 GCA_018472725.1_HG01071.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018472725.1_HG01071.alt.pat.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 160m24.666s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472725.1Link.txt # 3048680762 bases of 3299210039 (92.406%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472725.1Link.txt # 3044321333 bases of 3299210039 (92.274%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt" \ hg38 GCA_018472725.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 77m30.892s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472725.1.txt # 2837612037 bases of 3299210039 (86.009%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/725/GCA_018472725.1_HG01071.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018472725.1_HG01071.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472725.1.2023-04-03/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 131m40.602s sed -e 's/^/ # /;' fb.GCA_018472725.1.chainHg38Link.txt # 2872704373 bases of 3057222025 (93.965%) in intersection sed -e 's/^/ # /;' fb.GCA_018472725.1.chainSynHg38Link.txt # 2866971315 bases of 3057222025 (93.777%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/725/GCA_018472725.1/GCA_018472725.1.chrom.sizes.txt" \ GCA_018472725.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m9.750s sed -e 's/^/ # /;' fb.GCA_018472725.1.chainRBest.Hg38.txt # 2835295801 bases of 3057222025 (92.741%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471345.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03 printf '# human GCA_018471345.1 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 2021-05-24 GCA_018471345.1_HG01106.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018471345.1_HG01106.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 163m27.915s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471345.1Link.txt # 3052479767 bases of 3299210039 (92.522%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471345.1Link.txt # 3047870251 bases of 3299210039 (92.382%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt" \ hg38 GCA_018471345.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 78m56.306s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471345.1.txt # 2839586059 bases of 3299210039 (86.069%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/345/GCA_018471345.1_HG01106.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018471345.1_HG01106.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471345.1.2023-04-03/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 136m8.430s sed -e 's/^/ # /;' fb.GCA_018471345.1.chainHg38Link.txt # 2870939240 bases of 3035845582 (94.568%) in intersection sed -e 's/^/ # /;' fb.GCA_018471345.1.chainSynHg38Link.txt # 2864604476 bases of 3035845582 (94.359%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/345/GCA_018471345.1/GCA_018471345.1.chrom.sizes.txt" \ GCA_018471345.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m1.908s sed -e 's/^/ # /;' fb.GCA_018471345.1.chainRBest.Hg38.txt # 2838573475 bases of 3035845582 (93.502%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472605.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472605.1.2023-04-03 printf '# human GCA_018472605.1 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 2021-05-24 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_018472605.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 189m7.217s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472605.1Link.txt # 3048862121 bases of 3299210039 (92.412%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472605.1Link.txt # 3044640548 bases of 3299210039 (92.284%) 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 79m0.667s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472605.1.txt # 2836238209 bases of 3299210039 (85.967%) 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_018472605.1.2023-04-03/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 136m8.411s sed -e 's/^/ # /;' fb.GCA_018472605.1.chainHg38Link.txt # 2864962762 bases of 3023026071 (94.771%) in intersection sed -e 's/^/ # /;' fb.GCA_018472605.1.chainSynHg38Link.txt # 2859512924 bases of 3023026071 (94.591%) 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 82m40.326s sed -e 's/^/ # /;' fb.GCA_018472605.1.chainRBest.Hg38.txt # 2834151666 bases of 3023026071 (93.752%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471515.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018471515.1.2023-04-03 printf '# human GCA_018471515.1 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 2021-05-24 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_018471515.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 197m39.931s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471515.1Link.txt # 3048509903 bases of 3299210039 (92.401%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471515.1Link.txt # 3044275459 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/018/471/515/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 78m24.518s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471515.1.txt # 2837640885 bases of 3299210039 (86.010%) 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_018471515.1.2023-04-03/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 136m4.523s sed -e 's/^/ # /;' fb.GCA_018471515.1.chainHg38Link.txt # 2870944460 bases of 3035735720 (94.572%) in intersection sed -e 's/^/ # /;' fb.GCA_018471515.1.chainSynHg38Link.txt # 2865099920 bases of 3035735720 (94.379%) 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 82m16.558s sed -e 's/^/ # /;' fb.GCA_018471515.1.chainRBest.Hg38.txt # 2835732395 bases of 3035735720 (93.412%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472595.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472595.1.2023-04-03 printf '# human GCA_018472595.1 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 2021-05-24 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_018472595.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 196m7.811s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472595.1Link.txt # 3048581733 bases of 3299210039 (92.403%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472595.1Link.txt # 3044528695 bases of 3299210039 (92.281%) 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 78m33.317s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472595.1.txt # 2840594342 bases of 3299210039 (86.099%) 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_018472595.1.2023-04-03/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 137m31.327s sed -e 's/^/ # /;' fb.GCA_018472595.1.chainHg38Link.txt # 2871502587 bases of 3025118465 (94.922%) in intersection sed -e 's/^/ # /;' fb.GCA_018472595.1.chainSynHg38Link.txt # 2865278629 bases of 3025118465 (94.716%) 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 82m56.603s sed -e 's/^/ # /;' fb.GCA_018472595.1.chainRBest.Hg38.txt # 2836658931 bases of 3025118465 (93.770%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472575.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472575.1.2023-04-03 printf '# human GCA_018472575.1 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 2021-05-24 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_018472575.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 176m47.456s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472575.1Link.txt # 2920833052 bases of 3299210039 (88.531%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472575.1Link.txt # 2916328121 bases of 3299210039 (88.395%) 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 76m25.435s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472575.1.txt # 2710256427 bases of 3299210039 (82.149%) 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_018472575.1.2023-04-03/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 125m33.570s sed -e 's/^/ # /;' fb.GCA_018472575.1.chainHg38Link.txt # 2739127249 bases of 2905948993 (94.259%) in intersection sed -e 's/^/ # /;' fb.GCA_018472575.1.chainSynHg38Link.txt # 2733323310 bases of 2905948993 (94.060%) 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 76m16.094s sed -e 's/^/ # /;' fb.GCA_018472575.1.chainRBest.Hg38.txt # 2709554231 bases of 2905948993 (93.242%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472585.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472585.1.2023-04-03 printf '# human GCA_018472585.1 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 2021-05-24 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_018472585.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 181m4.915s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472585.1Link.txt # 2919592068 bases of 3299210039 (88.494%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472585.1Link.txt # 2914421362 bases of 3299210039 (88.337%) 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 74m31.767s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472585.1.txt # 2707836905 bases of 3299210039 (82.075%) 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_018472585.1.2023-04-03/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 126m45.526s sed -e 's/^/ # /;' fb.GCA_018472585.1.chainHg38Link.txt # 2741986527 bases of 2925716157 (93.720%) in intersection sed -e 's/^/ # /;' fb.GCA_018472585.1.chainSynHg38Link.txt # 2736302463 bases of 2925716157 (93.526%) 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 73m6.616s sed -e 's/^/ # /;' fb.GCA_018472585.1.chainRBest.Hg38.txt # 2707556807 bases of 2925716157 (92.543%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018472565.1 # (DONE - 2023-04-03 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03 cd /hive/data/genomes/hg38/bed/lastzGCA_018472565.1.2023-04-03 printf '# human GCA_018472565.1 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 2021-05-24 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_018472565.1.2023-04-03 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=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 193m23.535s sed -e 's/^/ # /;' fb.hg38.chainGCA_018472565.1Link.txt # 3048046135 bases of 3299210039 (92.387%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472565.1Link.txt # 3043672595 bases of 3299210039 (92.255%) 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 77m57.561s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472565.1.txt # 2839459324 bases of 3299210039 (86.065%) 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_018472565.1.2023-04-03/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 135m7.995s sed -e 's/^/ # /;' fb.GCA_018472565.1.chainHg38Link.txt # 2875683503 bases of 3053585067 (94.174%) in intersection sed -e 's/^/ # /;' fb.GCA_018472565.1.chainSynHg38Link.txt # 2869784047 bases of 3053585067 (93.981%) 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 79m55.124s sed -e 's/^/ # /;' fb.GCA_018472565.1.chainRBest.Hg38.txt # 2835964470 bases of 3053585067 (92.873%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018504645.1 # (DONE - 2023-04-04 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04 cd /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04 printf '# human GCA_018504645.1 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_018504645.1_HG01109.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018504645.1_HG01109.alt.pat.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 203m4.556s sed -e 's/^/ # /;' fb.hg38.chainGCA_018504645.1Link.txt # 2920217350 bases of 3299210039 (88.513%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018504645.1Link.txt # 2915634332 bases of 3299210039 (88.374%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt" \ hg38 GCA_018504645.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m18.405s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018504645.1.txt # 2712395314 bases of 3299210039 (82.213%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/645/GCA_018504645.1_HG01109.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018504645.1_HG01109.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504645.1.2023-04-04/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 130m58.222s sed -e 's/^/ # /;' fb.GCA_018504645.1.chainHg38Link.txt # 2747539796 bases of 2921876128 (94.033%) in intersection sed -e 's/^/ # /;' fb.GCA_018504645.1.chainSynHg38Link.txt # 2742166983 bases of 2921876128 (93.850%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/645/GCA_018504645.1/GCA_018504645.1.chrom.sizes.txt" \ GCA_018504645.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 75m24.687s sed -e 's/^/ # /;' fb.GCA_018504645.1.chainRBest.Hg38.txt # 2711590537 bases of 2921876128 (92.803%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471075.1 # (DONE - 2023-04-04 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04 cd /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04 printf '# human GCA_018471075.1 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 2021-05-24 GCA_018471075.1_HG01106.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018471075.1_HG01106.alt.pat.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 209m12.834s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471075.1Link.txt # 2920665557 bases of 3299210039 (88.526%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471075.1Link.txt # 2915808493 bases of 3299210039 (88.379%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt" \ hg38 GCA_018471075.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 79m53.525s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471075.1.txt # 2711607125 bases of 3299210039 (82.190%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/075/GCA_018471075.1_HG01106.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018471075.1_HG01106.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471075.1.2023-04-04/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 132m43.054s sed -e 's/^/ # /;' fb.GCA_018471075.1.chainHg38Link.txt # 2744444887 bases of 2927007346 (93.763%) in intersection sed -e 's/^/ # /;' fb.GCA_018471075.1.chainSynHg38Link.txt # 2738739772 bases of 2927007346 (93.568%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/075/GCA_018471075.1/GCA_018471075.1.chrom.sizes.txt" \ GCA_018471075.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 76m15.192s sed -e 's/^/ # /;' fb.GCA_018471075.1.chainRBest.Hg38.txt # 2710147089 bases of 2927007346 (92.591%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018471065.1 # (DONE - 2023-04-04 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04 cd /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04 printf '# human GCA_018471065.1 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 2021-05-24 GCA_018471065.1_HG01175.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018471065.1_HG01175.alt.pat.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 166m0.387s sed -e 's/^/ # /;' fb.hg38.chainGCA_018471065.1Link.txt # 3047883175 bases of 3299210039 (92.382%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018471065.1Link.txt # 3043689722 bases of 3299210039 (92.255%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt" \ hg38 GCA_018471065.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 69m45.945s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018471065.1.txt # 2837540130 bases of 3299210039 (86.007%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/471/065/GCA_018471065.1_HG01175.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018471065.1_HG01175.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018471065.1.2023-04-04/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 115m9.563s sed -e 's/^/ # /;' fb.GCA_018471065.1.chainHg38Link.txt # 2867069552 bases of 3030026811 (94.622%) in intersection sed -e 's/^/ # /;' fb.GCA_018471065.1.chainSynHg38Link.txt # 2861422546 bases of 3030026811 (94.436%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/471/065/GCA_018471065.1/GCA_018471065.1.chrom.sizes.txt" \ GCA_018471065.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 69m34.161s sed -e 's/^/ # /;' fb.GCA_018471065.1.chainRBest.Hg38.txt # 2835565461 bases of 3030026811 (93.582%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018504045.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05 printf '# human GCA_018504045.1 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_018504045.1_HG01243.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018504045.1_HG01243.alt.pat.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 150m59.122s sed -e 's/^/ # /;' fb.hg38.chainGCA_018504045.1Link.txt # 2919254671 bases of 3299210039 (88.483%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018504045.1Link.txt # 2913695572 bases of 3299210039 (88.315%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt" \ hg38 GCA_018504045.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 72m53.423s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018504045.1.txt # 2709479193 bases of 3299210039 (82.125%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/504/045/GCA_018504045.1_HG01243.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018504045.1_HG01243.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018504045.1.2023-04-05/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 119m46.883s sed -e 's/^/ # /;' fb.GCA_018504045.1.chainHg38Link.txt # 2743073817 bases of 2908728425 (94.305%) in intersection sed -e 's/^/ # /;' fb.GCA_018504045.1.chainSynHg38Link.txt # 2737254676 bases of 2908728425 (94.105%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/045/GCA_018504045.1/GCA_018504045.1.chrom.sizes.txt" \ GCA_018504045.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 72m42.690s sed -e 's/^/ # /;' fb.GCA_018504045.1.chainRBest.Hg38.txt # 2706781589 bases of 2908728425 (93.057%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469405.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05 printf '# human GCA_018469405.1 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 2021-05-24 GCA_018469405.1_HG01258.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469405.1_HG01258.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 156m49.282s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469405.1Link.txt # 3049729340 bases of 3299210039 (92.438%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469405.1Link.txt # 3045207974 bases of 3299210039 (92.301%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt" \ hg38 GCA_018469405.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 75m50.802s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469405.1.txt # 2836720842 bases of 3299210039 (85.982%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/405/GCA_018469405.1_HG01258.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469405.1_HG01258.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469405.1.2023-04-05/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 126m38.759s sed -e 's/^/ # /;' fb.GCA_018469405.1.chainHg38Link.txt # 2873269175 bases of 3032420282 (94.752%) in intersection sed -e 's/^/ # /;' fb.GCA_018469405.1.chainSynHg38Link.txt # 2867398349 bases of 3032420282 (94.558%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/405/GCA_018469405.1/GCA_018469405.1.chrom.sizes.txt" \ GCA_018469405.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 78m41.856s sed -e 's/^/ # /;' fb.GCA_018469405.1.chainRBest.Hg38.txt # 2835173854 bases of 3032420282 (93.495%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469675.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05 printf '# human GCA_018469675.1 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 2021-05-24 GCA_018469675.1_HG01258.alt.pat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469675.1_HG01258.alt.pat.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 162m37.126s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469675.1Link.txt # 2920623841 bases of 3299210039 (88.525%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469675.1Link.txt # 2915334531 bases of 3299210039 (88.365%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt" \ hg38 GCA_018469675.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 76m17.382s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469675.1.txt # 2711692640 bases of 3299210039 (82.192%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/675/GCA_018469675.1_HG01258.alt.pat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469675.1_HG01258.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469675.1.2023-04-05/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 119m29.520s sed -e 's/^/ # /;' fb.GCA_018469675.1.chainHg38Link.txt # 2742067216 bases of 2915178237 (94.062%) in intersection sed -e 's/^/ # /;' fb.GCA_018469675.1.chainSynHg38Link.txt # 2736192130 bases of 2915178237 (93.860%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/675/GCA_018469675.1/GCA_018469675.1.chrom.sizes.txt" \ GCA_018469675.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 72m13.307s sed -e 's/^/ # /;' fb.GCA_018469675.1.chainRBest.Hg38.txt # 2708251212 bases of 2915178237 (92.902%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469685.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05 printf '# human GCA_018469685.1 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 2021-05-24 GCA_018469685.1_HG01361.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469685.1_HG01361.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 171m14.537s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469685.1Link.txt # 3048195466 bases of 3299210039 (92.392%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469685.1Link.txt # 3043159939 bases of 3299210039 (92.239%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt" \ hg38 GCA_018469685.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 73m22.770s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469685.1.txt # 2833943818 bases of 3299210039 (85.898%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/685/GCA_018469685.1_HG01361.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469685.1_HG01361.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469685.1.2023-04-05/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 123m21.537s sed -e 's/^/ # /;' fb.GCA_018469685.1.chainHg38Link.txt # 2863544355 bases of 3025313608 (94.653%) in intersection sed -e 's/^/ # /;' fb.GCA_018469685.1.chainSynHg38Link.txt # 2858105884 bases of 3025313608 (94.473%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/685/GCA_018469685.1/GCA_018469685.1.chrom.sizes.txt" \ GCA_018469685.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 79m30.190s sed -e 's/^/ # /;' fb.GCA_018469685.1.chainRBest.Hg38.txt # 2830977232 bases of 3025313608 (93.576%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469665.1 # (DONE - 2023-04-04 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04 cd /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04 printf '# human GCA_018469665.1 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 2021-05-24 GCA_018469665.1_HG01123.pri.mat.f1_v2.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469665.1_HG01123.pri.mat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 213m6.351s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469665.1Link.txt # 3048844569 bases of 3299210039 (92.411%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469665.1Link.txt # 3044500979 bases of 3299210039 (92.280%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt" \ hg38 GCA_018469665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 85m45.377s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469665.1.txt # 2836682774 bases of 3299210039 (85.981%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/665/GCA_018469665.1_HG01123.pri.mat.f1_v2.1/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469665.1_HG01123.pri.mat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469665.1.2023-04-04/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 133m41.257s sed -e 's/^/ # /;' fb.GCA_018469665.1.chainHg38Link.txt # 2865875487 bases of 3012822948 (95.123%) in intersection sed -e 's/^/ # /;' fb.GCA_018469665.1.chainSynHg38Link.txt # 2860544697 bases of 3012822948 (94.946%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/665/GCA_018469665.1/GCA_018469665.1.chrom.sizes.txt" \ GCA_018469665.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 80m1.738s sed -e 's/^/ # /;' fb.GCA_018469665.1.chainRBest.Hg38.txt # 2834465468 bases of 3012822948 (94.080%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469865.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05 printf '# human GCA_018469865.1 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 2021-05-24 GCA_018469865.1_HG01358.pri.mat.f1_v2.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469865.1_HG01358.pri.mat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 168m13.600s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469865.1Link.txt # 3047657353 bases of 3299210039 (92.375%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469865.1Link.txt # 3043194543 bases of 3299210039 (92.240%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt" \ hg38 GCA_018469865.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 77m3.311s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469865.1.txt # 2838079272 bases of 3299210039 (86.023%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/865/GCA_018469865.1_HG01358.pri.mat.f1_v2.1/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469865.1_HG01358.pri.mat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469865.1.2023-04-05/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 123m12.696s sed -e 's/^/ # /;' fb.GCA_018469865.1.chainHg38Link.txt # 2865143593 bases of 3029587694 (94.572%) in intersection sed -e 's/^/ # /;' fb.GCA_018469865.1.chainSynHg38Link.txt # 2859636823 bases of 3029587694 (94.390%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/865/GCA_018469865.1/GCA_018469865.1.chrom.sizes.txt" \ GCA_018469865.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 74m43.717s sed -e 's/^/ # /;' fb.GCA_018469865.1.chainRBest.Hg38.txt # 2834353735 bases of 3029587694 (93.556%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018469965.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05 printf '# human GCA_018469965.1 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 2021-05-24 GCA_018469965.1_HG01358.alt.pat.f1_v2.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018469965.1_HG01358.alt.pat.f1_v2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 143m44.220s sed -e 's/^/ # /;' fb.hg38.chainGCA_018469965.1Link.txt # 2920305964 bases of 3299210039 (88.515%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469965.1Link.txt # 2915298077 bases of 3299210039 (88.364%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt" \ hg38 GCA_018469965.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 76m41.070s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469965.1.txt # 2712668877 bases of 3299210039 (82.222%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/965/GCA_018469965.1_HG01358.alt.pat.f1_v2.1/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018469965.1_HG01358.alt.pat.f1_v2.1 /hive/data/genomes/hg38/bed/lastzGCA_018469965.1.2023-04-05/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 112m18.392s sed -e 's/^/ # /;' fb.GCA_018469965.1.chainHg38Link.txt # 2748397653 bases of 2932540871 (93.721%) in intersection sed -e 's/^/ # /;' fb.GCA_018469965.1.chainSynHg38Link.txt # 2742649822 bases of 2932540871 (93.525%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/965/GCA_018469965.1/GCA_018469965.1.chrom.sizes.txt" \ GCA_018469965.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 76m24.412s sed -e 's/^/ # /;' fb.GCA_018469965.1.chainRBest.Hg38.txt # 2710789449 bases of 2932540871 (92.438%) in intersection ############################################################################## # LASTZ Human Hg38 vs. human GCA_018467155.1 # (DONE - 2023-04-05 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05 cd /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05 printf '# human GCA_018467155.1 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 2021-05-24 GCA_018467155.1_HG01891.pri.mat.f1_v2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_018467155.1_HG01891.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 167m43.516s sed -e 's/^/ # /;' fb.hg38.chainGCA_018467155.1Link.txt # 3047773145 bases of 3299210039 (92.379%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018467155.1Link.txt # 3042967052 bases of 3299210039 (92.233%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt" \ hg38 GCA_018467155.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 69m46.717s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018467155.1.txt # 2834653179 bases of 3299210039 (85.919%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/018/467/155/GCA_018467155.1_HG01891.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_018467155.1_HG01891.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018467155.1.2023-04-05/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 125m58.945s sed -e 's/^/ # /;' fb.GCA_018467155.1.chainHg38Link.txt # 2866986413 bases of 3022952778 (94.841%) in intersection sed -e 's/^/ # /;' fb.GCA_018467155.1.chainSynHg38Link.txt # 2861260988 bases of 3022952778 (94.651%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/467/155/GCA_018467155.1/GCA_018467155.1.chrom.sizes.txt" \ GCA_018467155.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 77m35.492s sed -e 's/^/ # /;' fb.GCA_018467155.1.chainRBest.Hg38.txt # 2832748344 bases of 3022952778 (93.708%) in intersection ############################################################################## +# LASTZ Human Hg38 vs. human GCA_018469705.1 +# (DONE - 2023-04-05 - hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05 + cd /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05 + + printf '# human GCA_018469705.1 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 2021-05-24 GCA_018469705.1_HG01361.alt.pat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_018469705.1_HG01361.alt.pat.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 181m59.456s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_018469705.1Link.txt + # 3048539612 bases of 3299210039 (92.402%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018469705.1Link.txt + # 3044490947 bases of 3299210039 (92.279%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt" \ + hg38 GCA_018469705.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 78m20.100s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018469705.1.txt + # 2837562648 bases of 3299210039 (86.007%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/469/705/GCA_018469705.1_HG01361.alt.pat.f1_v2/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_018469705.1_HG01361.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018469705.1.2023-04-05/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 127m44.548s + + sed -e 's/^/ # /;' fb.GCA_018469705.1.chainHg38Link.txt + # 2865148414 bases of 3010067136 (95.186%) in intersection + sed -e 's/^/ # /;' fb.GCA_018469705.1.chainSynHg38Link.txt + # 2859768016 bases of 3010067136 (95.007%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/469/705/GCA_018469705.1/GCA_018469705.1.chrom.sizes.txt" \ + GCA_018469705.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 76m30.039s + + sed -e 's/^/ # /;' fb.GCA_018469705.1.chainRBest.Hg38.txt + # 2835320194 bases of 3010067136 (94.195%) in intersection + +##############################################################################