722f05d417cfe7733d360889b901f4d54c4a38dc hiram Thu Apr 6 15:23:14 2023 -0700 eliminate a duplicate entry refs #30912 diff --git src/hg/makeDb/doc/hg38/hprcLastz.txt src/hg/makeDb/doc/hg38/hprcLastz.txt index c6f8c0c..a3c4ded 100644 --- src/hg/makeDb/doc/hg38/hprcLastz.txt +++ src/hg/makeDb/doc/hg38/hprcLastz.txt @@ -3398,122 +3398,30 @@ sed -e 's/^/ # /;' fb.GCA_018505855.1.chainSynHg38Link.txt # 2742930636 bases of 2950246117 (92.973%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt" \ GCA_018505855.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 84m36.497s sed -e 's/^/ # /;' fb.GCA_018505855.1.chainRBest.Hg38.txt # 2707923188 bases of 2950246117 (91.786%) in intersection ############################################################################## -# LASTZ Human Hg38 vs. human GCA_018505855.1 -# (DONE - 2023-04-06 - hiram) - - mkdir /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06 - cd /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06 - - printf '# human GCA_018505855.1 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_018505855.1_HG02055.alt.pat.f1_v2 -SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit -SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt -SEQ2_CHUNK=20000000 -SEQ2_LAP=0 -SEQ2_LIMIT=100 - -BASE=/hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06 -TMPDIR=/dev/shm - -' > DEF - - time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ - -qAsmId GCA_018505855.1_HG02055.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 160m27.006s - - sed -e 's/^/ # /;' fb.hg38.chainGCA_018505855.1Link.txt - # 2920085105 bases of 3299210039 (88.509%) in intersection - sed -e 's/^/ # /;' fb.hg38.chainSynGCA_018505855.1Link.txt - # 2915187308 bases of 3299210039 (88.360%) in intersection - - time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ - \ - -query2Bit="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit" \ --querySizes="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt" \ - hg38 GCA_018505855.1) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;' - # real 75m52.496s - - sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_018505855.1.txt - # 2712237293 bases of 3299210039 (82.209%) in intersection - - ### and for the swap - - cd /hive/data/genomes/asmHubs/allBuild/GCA/018/505/855/GCA_018505855.1_HG02055.alt.pat.f1_v2/trackData/blastz.hg38.swap - - time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ - -qAsmId GCA_018505855.1_HG02055.alt.pat.f1_v2 /hive/data/genomes/hg38/bed/lastzGCA_018505855.1.2023-04-06/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 122m39.734s - - sed -e 's/^/ # /;' fb.GCA_018505855.1.chainHg38Link.txt - # 2749378239 bases of 2950246117 (93.191%) in intersection - sed -e 's/^/ # /;' fb.GCA_018505855.1.chainSynHg38Link.txt - # 2742930636 bases of 2950246117 (92.973%) in intersection -\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ - \ - -target2bit="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.2bit" \ --targetSizes="/hive/data/genomes/asmHubs/GCA/018/505/855/GCA_018505855.1/GCA_018505855.1.chrom.sizes.txt" \ - GCA_018505855.1 hg38) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;' - # real 84m36.497s - - sed -e 's/^/ # /;' fb.GCA_018505855.1.chainRBest.Hg38.txt - # 2707923188 bases of 2950246117 (91.786%) in intersection - -############################################################################## # LASTZ Human Hg38 vs. human GCA_018504055.1 # (DONE - 2023-04-06 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06 cd /hive/data/genomes/hg38/bed/lastzGCA_018504055.1.2023-04-06 printf '# human GCA_018504055.1 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