992301fd95080179b4b58ccddc4d59584a5c4e3d gperez2 Sun Oct 6 23:06:23 2024 -0700 hg38 to GCF_950295315.1/GCF_002263795.3/GCF_011100685.1 lastz/chain/net run for users, refs #34429 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index ccde1c5..cba116a 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -15014,15 +15014,265 @@ sed -e 's/^/ # /;' fb.GCF_000767855.1.chainSynHg38Link.txt # 1372565487 bases of 1992663268 (68.881%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \ GCF_000767855.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 166m30.684s sed -e 's/^/ # /;' fb.GCF_000767855.1.chainRBest.Hg38.txt # 1373576819 bases of 1992663268 (68.932%) in intersection ############################################################################## +# LASTZ Human Hg38 vs. western European hedgehog GCF_950295315.1 +# (DONE - 2024-09-14 - Gerardo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14 + cd /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14 + + printf '# western European hedgehog GCF_950295315.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: western European hedgehog 2023-05-01 GCF_950295315.1_mEriEur2.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_950295315.1_mEriEur2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1070m35.939s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_950295315.1Link.txt + # 779724539 bases of 3299210039 (23.634%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_950295315.1Link.txt + # 720598955 bases of 3299210039 (21.842%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \ + hg38 GCF_950295315.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 238m8.840s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_950295315.1.txt + # 695639959 bases of 3299210039 (21.085%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_950295315.1_mEriEur2.1 /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 49m21.433s + + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainHg38Link.txt + # 718540551 bases of 2720683831 (26.410%) in intersection + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainSynHg38Link.txt + # 684033491 bases of 2720683831 (25.142%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \ + GCF_950295315.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 222m21.349s + + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainRBest.Hg38.txt + # 696207129 bases of 2720683831 (25.589%) in intersection + + +real 1581m9.953s +user 0m4.705s +sys 0m20.521s +############################################################################## +# LASTZ Human Hg38 vs. domestic cattle GCF_002263795.3 +# (DONE - 2024-09-14 - Gerardo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14 + cd /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14 + + printf '# domestic cattle GCF_002263795.3 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1360m45.921s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_002263795.3Link.txt + # 1437599863 bases of 3299210039 (43.574%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_002263795.3Link.txt + # 1371275838 bases of 3299210039 (41.564%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + hg38 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 291m17.080s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_002263795.3.txt + # 1287906858 bases of 3299210039 (39.037%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 94m25.389s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainHg38Link.txt + # 1351306335 bases of 2770686120 (48.772%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynHg38Link.txt + # 1304221756 bases of 2770686120 (47.072%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_002263795.3 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 309m22.281s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.Hg38.txt + # 1288620776 bases of 2770686120 (46.509%) in intersection + +real 2055m58.482s +user 0m3.619s +sys 0m9.300s +############################################################################## +# LASTZ Human Hg38 vs. dog GCF_011100685.1 +# (DONE - 2024-09-14 - Gerardo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14 + cd /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14 + + printf '# dog GCF_011100685.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: dog 2020-03-10 GCF_011100685.1_UU_Cfam_GSD_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1637m0.994s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_011100685.1Link.txt + # 1588231052 bases of 3299210039 (48.140%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_011100685.1Link.txt + # 1521346162 bases of 3299210039 (46.112%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \ + hg38 GCF_011100685.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 281m48.990s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_011100685.1.txt + # 1425161610 bases of 3299210039 (43.197%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/011/100/685/GCF_011100685.1_UU_Cfam_GSD_1.0/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 125m45.802s + + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainHg38Link.txt + # 1492725079 bases of 2481983352 (60.142%) in intersection + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainSynHg38Link.txt + # 1447552241 bases of 2481983352 (58.322%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \ + GCF_011100685.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 255m23.446s + + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainRBest.Hg38.txt + # 1425408450 bases of 2481983352 (57.430%) in intersection + +real 2300m12.938s +user 0m2.731s +sys 0m12.713s +##############################################################################