b436b166ee021405e3acfab5c851db5192797221 gperez2 Sat Aug 5 16:36:20 2023 -0700 mouse(mm39/mm10) vs. ferret/chicken/Chimp/Gorilla/Orangutan, lastz/chain/net run for user, refs #31323 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 5a0178b..fe9199b 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -2752,15 +2752,430 @@ \ -target2bit="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/921/998/555/GCA_921998555.2/GCA_921998555.2.chrom.sizes.txt" \ GCA_921998555.2 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 61m37.296s sed -e 's/^/ # /;' fb.GCA_921998555.2.chainRBest.Mm39.txt # 2449674283 bases of 2516264171 (97.354%) in intersection real 1670m26.743s user 0m2.054s sys 0m1.924s ############################################################################## +# LASTZ Mouse Mm39 vs. chicken GCF_016699485.2 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29 + cd /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29 + + printf '# chicken GCF_016699485.2 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: chicken 2021-01-19 GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 435m53.262s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_016699485.2Link.txt + # 67189810 bases of 2728222451 (2.463%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_016699485.2Link.txt + # 48811233 bases of 2728222451 (1.789%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \ + mm39 GCF_016699485.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 51m5.222s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_016699485.2.txt + # 53298237 bases of 2728222451 (1.954%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b /hive/data/genomes/mm39/bed/lastzGCF_016699485.2.2023-05-29/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 4m5.058s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainMm39Link.txt + # 56503060 bases of 1053332251 (5.364%) in intersection + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainSynMm39Link.txt + # 48074471 bases of 1053332251 (4.564%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \ + GCF_016699485.2 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 34m39.964s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainRBest.Mm39.txt + # 53178672 bases of 1053332251 (5.049%) in intersection + +real 525m50.616s +user 0m1.738s +sys 0m2.087s +############################################################################## +# LASTZ Mouse Mm39 vs. domestic ferret GCF_011764305.1 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29 + cd /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29 + + printf '# domestic ferret GCF_011764305.1 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: domestic ferret 2020-03-27 GCF_011764305.1_ASM1176430v1.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_011764305.1_ASM1176430v1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 852m25.289s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_011764305.1Link.txt + # 763807668 bases of 2728222451 (27.997%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_011764305.1Link.txt + # 716560841 bases of 2728222451 (26.265%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt" \ + mm39 GCF_011764305.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 154m41.629s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_011764305.1.txt + # 725906862 bases of 2728222451 (26.607%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/011/764/305/GCF_011764305.1_ASM1176430v1.1/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_011764305.1_ASM1176430v1.1 /hive/data/genomes/mm39/bed/lastzGCF_011764305.1.2023-05-29/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 44m36.988s + + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainMm39Link.txt + # 761141027 bases of 2577107489 (29.535%) in intersection + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainSynMm39Link.txt + # 716305280 bases of 2577107489 (27.795%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/011/764/305/GCF_011764305.1/GCF_011764305.1.chrom.sizes.txt" \ + GCF_011764305.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 121m45.274s + + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainRBest.Mm39.txt + # 725361939 bases of 2577107489 (28.146%) in intersection + +real 1173m34.419s +user 0m2.095s +sys 0m2.301s +############################################################################## +# LASTZ Mouse Mm39 vs. Sumatran orangutan GCF_028885655.1 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29 + cd /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29 + + printf '# Sumatran orangutan GCF_028885655.1 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: Sumatran orangutan 2023-02-28 GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 940m23.193s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_028885655.1Link.txt + # 941283209 bases of 2728222451 (34.502%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_028885655.1Link.txt + # 893464035 bases of 2728222451 (32.749%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt" \ + mm39 GCF_028885655.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 275m37.724s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_028885655.1.txt + # 895752761 bases of 2728222451 (32.833%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/885/655/GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri /hive/data/genomes/mm39/bed/lastzGCF_028885655.1.2023-05-29/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 53m46.711s + + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainMm39Link.txt + # 970824025 bases of 3365490689 (28.846%) in intersection + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainSynMm39Link.txt + # 905819364 bases of 3365490689 (26.915%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/028/885/655/GCF_028885655.1/GCF_028885655.1.chrom.sizes.txt" \ + GCF_028885655.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 237m40.734s + + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainRBest.Mm39.txt + # 894076603 bases of 3365490689 (26.566%) in intersection + +real 1507m34.121s +user 0m2.845s +sys 0m2.181s +############################################################################## +# LASTZ chimpanzee GCF_028858775.1 vs. Mouse Mm39 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29 + + printf '# Mouse Mm39 vs. chimpanzee GCF_028858775.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: chimpanzee 2023-02-27 GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Mouse mm39 +SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 960m42.867s + + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainMm39Link.txt + # 1056035654 bases of 3225356997 (32.742%) in intersection + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainSynMm39Link.txt + # 903788000 bases of 3225356997 (28.021%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt" \ + \ + GCF_028858775.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 237m54.207s + + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainRBest.Mm39.txt + # 893978029 bases of 3225356997 (27.717%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm39/bed/blastz.GCF_028858775.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm39.2023-05-29/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 60m41.085s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_028858775.1Link.txt + # 940808438 bases of 2728222451 (34.484%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_028858775.1Link.txt + # 893120131 bases of 2728222451 (32.736%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/028/858/775/GCF_028858775.1/GCF_028858775.1.chrom.sizes.txt" \ + \ + mm39 GCF_028858775.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 275m57.758s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_028858775.1.txt + # 895679835 bases of 2728222451 (32.830%) in intersection + +real 1535m22.222s +user 0m3.257s +sys 0m2.265s +############################################################################## +# LASTZ western lowland gorilla GCF_029281585.1 vs. Mouse Mm39 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29 + + printf '# Mouse Mm39 vs. western lowland gorilla GCF_029281585.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: western lowland gorilla 2023-03-20 GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Mouse mm39 +SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 984m39.047s + + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainMm39Link.txt + # 1170286145 bases of 3600562452 (32.503%) in intersection + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainSynMm39Link.txt + # 902054620 bases of 3600562452 (25.053%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt" \ + \ + GCF_029281585.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 274m15.491s + + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainRBest.Mm39.txt + # 894069759 bases of 3600562452 (24.831%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm39/bed/blastz.GCF_029281585.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm39.2023-05-29/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 62m35.300s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_029281585.1Link.txt + # 941358541 bases of 2728222451 (34.504%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_029281585.1Link.txt + # 893311044 bases of 2728222451 (32.743%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt" \ + \ + mm39 GCF_029281585.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 285m21.078s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_029281585.1.txt + # 895609380 bases of 2728222451 (32.828%) in intersection + +real 1606m58.270s +user 0m4.597s +sys 0m2.305s +##############################################################################