08ee8989aa3b4c6d48bd30d3e205705523cb6f9e gperez2 Sat Mar 30 15:00:04 2024 -0700 mm39 to GCA_921999005.2/GCA_921997125.2 lastz/chain/net run for user, refs #32859 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 5384a0a..8e69894 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -3247,15 +3247,179 @@ sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynMm39Link.txt # 657252141 bases of 2622460639 (25.062%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ GCF_019923935.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 189m53.630s sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.Mm39.txt # 666929206 bases of 2622460639 (25.431%) in intersection ############################################################################## +# LASTZ Mouse Mm39 vs. southeastern Asian house mouse GCA_921999005.2 +# (DONE - 2024-01-19 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17 + cd /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17 + + printf '# southeastern Asian house mouse GCA_921999005.2 vs. Mouse Mm39 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: southeastern Asian house mouse 2022-07-01 GCA_921999005.2_CAST_EiJ_v3 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_921999005.2_CAST_EiJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1359m58.695s + + sed -e 's/^/ # /;' fb.mm39.chainGCA_921999005.2Link.txt + # 2501251357 bases of 2728222451 (91.681%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_921999005.2Link.txt + # 2431341452 bases of 2728222451 (89.118%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt" \ + mm39 GCA_921999005.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_921999005.2.txt + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/921/999/005/GCA_921999005.2_CAST_EiJ_v3/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_921999005.2_CAST_EiJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921999005.2.2024-01-17/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 140m46.400s + + sed -e 's/^/ # /;' fb.GCA_921999005.2.chainMm39Link.txt + # 2390038015 bases of 2519863764 (94.848%) in intersection + sed -e 's/^/ # /;' fb.GCA_921999005.2.chainSynMm39Link.txt + # 2373697524 bases of 2519863764 (94.199%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/921/999/005/GCA_921999005.2/GCA_921999005.2.chrom.sizes.txt" \ + GCA_921999005.2 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 75m41.067s + + sed -e 's/^/ # /;' fb.GCA_921999005.2.chainRBest.Mm39.txt + # 2365131997 bases of 2519863764 (93.860%) in intersection + +real 216m31.324s +user 0m2.037s +sys 0m1.892s +############################################################################## +# LASTZ Mouse Mm39 vs. house mouse GCA_921997125.2 +# (DONE - 2024-01-19 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19 + cd /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19 + + printf '# house mouse GCA_921997125.2 vs. Mouse Mm39 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: house mouse 2022-07-01 GCA_921997125.2_C3H_HeJ_v3 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_921997125.2_C3H_HeJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 2979m32.120s + + sed -e 's/^/ # /;' fb.mm39.chainGCA_921997125.2Link.txt + # 2579672710 bases of 2728222451 (94.555%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_921997125.2Link.txt + # 2517293978 bases of 2728222451 (92.269%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt" \ + mm39 GCA_921997125.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 79m31.586s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_921997125.2.txt + # 2453630589 bases of 2728222451 (89.935%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/921/997/125/GCA_921997125.2_C3H_HeJ_v3/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_921997125.2_C3H_HeJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921997125.2.2024-01-19/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 148m7.378s + + sed -e 's/^/ # /;' fb.GCA_921997125.2.chainMm39Link.txt + # 2466008293 bases of 2532437445 (97.377%) in intersection + sed -e 's/^/ # /;' fb.GCA_921997125.2.chainSynMm39Link.txt + # 2459127633 bases of 2532437445 (97.105%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt" \ + GCA_921997125.2 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 59m10.825s + + sed -e 's/^/ # /;' fb.GCA_921997125.2.chainRBest.Mm39.txt + # 2454104373 bases of 2532437445 (96.907%) in intersection + +real 3266m26.008s +user 0m3.015s +sys 0m3.143s +##############################################################################