9a9b4e595e833b4f0f52875567b7e68c7f2270b8 hiram Thu Apr 6 15:10:55 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 0d8ff05..c6f8c0c 100644 --- src/hg/makeDb/doc/hg38/hprcLastz.txt +++ src/hg/makeDb/doc/hg38/hprcLastz.txt @@ -3582,107 +3582,107 @@ sed -e 's/^/ # /;' fb.GCA_018504055.1.chainSynHg38Link.txt # 2864430996 bases of 3024505444 (94.707%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/504/055/GCA_018504055.1/GCA_018504055.1.chrom.sizes.txt" \ GCA_018504055.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 77m53.994s sed -e 's/^/ # /;' fb.GCA_018504055.1.chainRBest.Hg38.txt # 2835545942 bases of 3024505444 (93.752%) in intersection ############################################################################## -# LASTZ Human Hg38 vs. human GCA_018505825.1 -# (DONE - 2023-04-06 - hiram) +# LASTZ Human Hg38 vs. human GCA_018472695.1 +# (DONE - 2023-04-05 - hiram) - mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06 - cd /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06 + mkdir /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05 + cd /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05 - printf '# human GCA_018505825.1 vs. Human Hg38 + printf '# human GCA_018472695.1 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_018505825.1_HG02109.pri.mat.f1_v2 -SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit -SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt +# QUERY: human 2021-05-24 GCA_018472695.1_HG01928.pri.mat.f1_v2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 -BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06 +BASE=/hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ - -qAsmId GCA_018505825.1_HG02109.pri.mat.f1_v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -qAsmId GCA_018472695.1_HG01928.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 159m28.473s + # real 159m39.178s - sed -e 's/^/ # /;' fb.hg38.chainGCA_018505825.1Link.txt - # 3048266987 bases of 3299210039 (92.394%) in intersection - sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018505825.1Link.txt - # 3044144120 bases of 3299210039 (92.269%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainGCA_018472695.1Link.txt + # 3048263455 bases of 3299210039 (92.394%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018472695.1Link.txt + # 3043984227 bases of 3299210039 (92.264%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ - -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit" \ --querySizes="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt" \ - hg38 GCA_018505825.1) > rbest.log 2>&1 + -query2Bit="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt" \ + hg38 GCA_018472695.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' - # real 78m14.803s + # real 76m32.710s - sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018505825.1.txt - # 2837240177 bases of 3299210039 (85.998%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018472695.1.txt + # 2836761152 bases of 3299210039 (85.983%) in intersection ### and for the swap - cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/825/GCA_018505825.1_HG02109.pri.mat.f1_v2/trackData/blastz.hg38.swap + cd /hive/data/genomes/asmHubs/allBuild/GCA/018/472/695/GCA_018472695.1_HG01928.pri.mat.f1_v2/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ - -qAsmId GCA_018505825.1_HG02109.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505825.1.2023-04-06/DEF -swapDir=`pwd` \ + -qAsmId GCA_018472695.1_HG01928.pri.mat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018472695.1.2023-04-05/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 130m6.019s + # real 124m6.184s - sed -e 's/^/ # /;' fb.GCA_018505825.1.chainHg38Link.txt - # 2870938986 bases of 3026115826 (94.872%) in intersection - sed -e 's/^/ # /;' fb.GCA_018505825.1.chainSynHg38Link.txt - # 2865131757 bases of 3026115826 (94.680%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472695.1.chainHg38Link.txt + # 2861018135 bases of 3025961049 (94.549%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472695.1.chainSynHg38Link.txt + # 2855644289 bases of 3025961049 (94.371%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ - -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.2bit" \ --targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/825/GCA_018505825.1/GCA_018505825.1.chrom.sizes.txt" \ - GCA_018505825.1 hg38) > rbest.log 2>&1 + -target2bit="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/018/472/695/GCA_018472695.1/GCA_018472695.1.chrom.sizes.txt" \ + GCA_018472695.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' - # real 80m15.495s + # real 68m26.475s - sed -e 's/^/ # /;' fb.GCA_018505825.1.chainRBest.Hg38.txt - # 2835084887 bases of 3026115826 (93.687%) in intersection + sed -e 's/^/ # /;' fb.GCA_018472695.1.chainRBest.Hg38.txt + # 2834035035 bases of 3025961049 (93.657%) in intersection ##############################################################################