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/mm10.txt src/hg/makeDb/doc/mm10.txt index 165a7ef..cbb267d 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -18769,15 +18769,430 @@ mkdir fantom5 cd fantom5 # Making symlinks for big files for file in $(ls /hive/data/outside/fantom5/riken_f5/mm10/*.b*) ; do ln -s $file; done cd /hive/data/outside/fantom5/riken_f5/mm10/ cp trackDb.txt fantom5.ra vi fantom5.ra # Indented subtracks # Changing bigDataUrl # Removing non-alpha characters cd ~/kent/src/hg/makeDb/trackDb/mouse/mm10/ cp /hive/data/outside/fantom5/riken_f5/hg38/fantom5.ra . vi trackDb.ra #include fantom5.ra alpha ############################################################################## +# LASTZ Mouse Mm10 vs. chicken GCF_016699485.2 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm10/bed/lastzGCF_016699485.2.2023-05-29 + cd /hive/data/genomes/mm10/bed/lastzGCF_016699485.2.2023-05-29 + + printf '# chicken GCF_016699485.2 vs. Mouse Mm10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm10 +SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ1_LEN=/hive/data/genomes/mm10/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/mm10/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 460m9.556s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_016699485.2Link.txt + # 69911555 bases of 2818974548 (2.480%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_016699485.2Link.txt + # 50043505 bases of 2818974548 (1.775%) 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" \ + mm10 GCF_016699485.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 51m15.277s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_016699485.2.txt + # 53269354 bases of 2818974548 (1.890%) 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.mm10.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/mm10/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 3m59.186s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainMm10Link.txt + # 56470179 bases of 1053332251 (5.361%) in intersection + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainSynMm10Link.txt + # 48075570 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 34m17.704s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainRBest.Mm10.txt + # 53161662 bases of 1053332251 (5.047%) in intersection + +real 549m48.888s +user 0m1.670s +sys 0m2.038s +############################################################################## +# LASTZ Mouse Mm10 vs. domestic ferret GCF_011764305.1 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm10/bed/lastzGCF_011764305.1.2023-05-29 + cd /hive/data/genomes/mm10/bed/lastzGCF_011764305.1.2023-05-29 + + printf '# domestic ferret GCF_011764305.1 vs. Mouse Mm10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm10 +SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ1_LEN=/hive/data/genomes/mm10/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/mm10/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 887m53.003s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_011764305.1Link.txt + # 786269484 bases of 2818974548 (27.892%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_011764305.1Link.txt + # 736073378 bases of 2818974548 (26.111%) 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" \ + mm10 GCF_011764305.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 136m18.830s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_011764305.1.txt + # 725535934 bases of 2818974548 (25.738%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/011/764/305/GCF_011764305.1_ASM1176430v1.1/trackData/blastz.mm10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_011764305.1_ASM1176430v1.1 /hive/data/genomes/mm10/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 45m42.440s + + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainMm10Link.txt + # 755800573 bases of 2577107489 (29.327%) in intersection + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainSynMm10Link.txt + # 716112438 bases of 2577107489 (27.787%) 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 115m58.410s + + sed -e 's/^/ # /;' fb.GCF_011764305.1.chainRBest.Mm10.txt + # 724974151 bases of 2577107489 (28.131%) in intersection + +real 1185m57.217s +user 0m2.091s +sys 0m2.151s +############################################################################## +# LASTZ Mouse Mm10 vs. Sumatran orangutan GCF_028885655.1 +# (DONE - 2023-05-29 - Gerardo) + + mkdir /hive/data/genomes/mm10/bed/lastzGCF_028885655.1.2023-05-29 + cd /hive/data/genomes/mm10/bed/lastzGCF_028885655.1.2023-05-29 + + printf '# Sumatran orangutan GCF_028885655.1 vs. Mouse Mm10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm10 +SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ1_LEN=/hive/data/genomes/mm10/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/mm10/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 935m21.904s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_028885655.1Link.txt + # 968671735 bases of 2818974548 (34.363%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_028885655.1Link.txt + # 917832766 bases of 2818974548 (32.559%) 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" \ + mm10 GCF_028885655.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 249m25.816s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_028885655.1.txt + # 895237861 bases of 2818974548 (31.758%) 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.mm10.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/mm10/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 53m48.020s + + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainMm10Link.txt + # 969760022 bases of 3365490689 (28.815%) in intersection + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainSynMm10Link.txt + # 905523135 bases of 3365490689 (26.906%) 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 232m8.721s + + sed -e 's/^/ # /;' fb.GCF_028885655.1.chainRBest.Mm10.txt + # 893784537 bases of 3365490689 (26.557%) in intersection + +real 1470m50.153s +user 0m2.905s +sys 0m2.377s +############################################################################## +# LASTZ chimpanzee GCF_028858775.1 vs. Mouse Mm10 +# (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/lastzMm10.2023-05-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/858/775/GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri/trackData/lastzMm10.2023-05-29 + + printf '# Mouse Mm10 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 mm10 +SEQ2_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ2_LEN=/hive/data/genomes/mm10/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/lastzMm10.2023-05-29 +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 962m5.922s + + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainMm10Link.txt + # 1052550747 bases of 3225356997 (32.634%) in intersection + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainSynMm10Link.txt + # 903800311 bases of 3225356997 (28.022%) 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 253m21.822s + + sed -e 's/^/ # /;' fb.GCF_028858775.1.chainRBest.Mm10.txt + # 893733597 bases of 3225356997 (27.710%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm10/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/lastzMm10.2023-05-29/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 53m57.464s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_028858775.1Link.txt + # 968374021 bases of 2818974548 (34.352%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_028858775.1Link.txt + # 917752702 bases of 2818974548 (32.556%) 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" \ + \ + mm10 GCF_028858775.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 260m16.557s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_028858775.1.txt + # 895305709 bases of 2818974548 (31.760%) in intersection + +real 1529m47.858s +user 0m3.258s +sys 0m2.169s +############################################################################## +# LASTZ western lowland gorilla GCF_029281585.1 vs. Mouse Mm10 +# (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/lastzMm10.2023-05-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/029/281/585/GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri/trackData/lastzMm10.2023-05-29 + + printf '# Mouse Mm10 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 mm10 +SEQ2_DIR=/hive/data/genomes/mm10/mm10.2bit +SEQ2_LEN=/hive/data/genomes/mm10/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/lastzMm10.2023-05-29 +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 969m31.867s + + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainMm10Link.txt + # 1163587557 bases of 3600562452 (32.317%) in intersection + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainSynMm10Link.txt + # 901996582 bases of 3600562452 (25.052%) 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 267m18.829s + + sed -e 's/^/ # /;' fb.GCF_029281585.1.chainRBest.Mm10.txt + # 893796215 bases of 3600562452 (24.824%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm10/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/lastzMm10.2023-05-29/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 54m56.098s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_029281585.1Link.txt + # 969007315 bases of 2818974548 (34.374%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_029281585.1Link.txt + # 917900547 bases of 2818974548 (32.562%) 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" \ + \ + mm10 GCF_029281585.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 270m58.663s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_029281585.1.txt + # 895198565 bases of 2818974548 (31.756%) in intersection + +real 1562m52.789s +user 0m4.517s +sys 0m2.098s +##############################################################################