2fd3b8fcf0d2e0e4e2315ddcd66f2a94d8987e74 hiram Tue Mar 21 11:11:06 2023 -0700 lastz to GCF_003369695.1 refs #30648 diff --git src/hg/makeDb/doc/bosTau9/lastzRuns.txt src/hg/makeDb/doc/bosTau9/lastzRuns.txt index 9ac6182..2dd64a3 100644 --- src/hg/makeDb/doc/bosTau9/lastzRuns.txt +++ src/hg/makeDb/doc/bosTau9/lastzRuns.txt @@ -1,95 +1,182 @@ ######################################################################### # LASTZ Cow BosTau9 vs. Cow BosTau5 (DONE - 2022-02-25 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ bosTau9 bosTau5 mammal mammal) \ > bosTau9_bosTau5_20220225_secondTime.log 2>&1 & # check the total time grep -w real bosTau9_bosTau5_20220225_secondTime.log | tail -1 | sed -e 's/^/ # /;' # real 675m26.699s ######################################################################### # LASTZ Cow BosTau9 vs. Cow BosTau5 # (DONE - 2022-02-25 - Gerardo) mkdir /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18 cd /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18 printf '# Cow BosTau5 vs. Cow BosTau9 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Cow BosTau9 SEQ1_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit SEQ1_LEN=/hive/data/genomes/bosTau9/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Cow BosTau5 SEQ2_DIR=/hive/data/genomes/bosTau5/bosTau5.2bit SEQ2_LEN=/hive/data/genomes/bosTau5/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 543m53.934s sed -e 's/^/ # /;' fb.bosTau9.chainBosTau5Link.txt # 2595387173 bases of 2715853792 (95.564%) in intersection sed -e 's/^/ # /;' fb.bosTau9.chainSynBosTau5Link.txt # 2560256591 bases of 2715853792 (94.271%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ bosTau9 bosTau5) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 74m31.401s sed -e 's/^/ # /;' fb.bosTau9.chainRBest.BosTau5.txt # 2540513150 bases of 2715853792 (93.544%) in intersection ### and for the swap cd /hive/data/genomes/bosTau5/bed/blastz.bosTau9.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ /hive/data/genomes/bosTau9/bed/lastzBosTau5.2022-02-18/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 601m9.542s sed -e 's/^/ # /;' fb.bosTau5.chainBosTau9Link.txt # 2706702737 bases of 2732505379 (99.056%) in intersection sed -e 's/^/ # /;' fb.bosTau5.chainSynBosTau9Link.txt # 2673116410 bases of 2732505379 (97.827%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ bosTau5 bosTau9) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 74m16.598s sed -e 's/^/ # /;' fb.bosTau5.chainRBest.BosTau9.txt # 2543778039 bases of 2732505379 (93.093%) in intersection -############################################################################## real 675m26.699s user 0m0.945s sys 0m1.486s + +############################################################################## +############################################################################## +# LASTZ hybrid cattle GCF_003369695.1 vs. Cow BosTau9 redmine30648 +# (DONE - 2023-03-17 - hiram) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24 + + printf '# Cow BosTau9 vs. hybrid cattle GCF_003369695.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: hybrid cattle 2018-11-30 GCF_003369695.1_UOA_Brahman_1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Cow bosTau9 +SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit +SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_003369695.1_UOA_Brahman_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 469m2.411s + + sed -e 's/^/ # /;' fb.GCF_003369695.1.chainBosTau9Link.txt + # 2657463787 bases of 2680953056 (99.124%) in intersection + sed -e 's/^/ # /;' fb.GCF_003369695.1.chainSynBosTau9Link.txt + # 2644164750 bases of 2680953056 (98.628%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt" \ + \ + GCF_003369695.1 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 65m55.031s + + sed -e 's/^/ # /;' fb.GCF_003369695.1.chainRBest.BosTau9.txt + # 2603287922 bases of 2680953056 (97.103%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/blastz.GCF_003369695.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_003369695.1_UOA_Brahman_1 /hive/data/genomes/asmHubs/allBuild/GCF/003/369/695/GCF_003369695.1_UOA_Brahman_1/trackData/lastzBosTau9.2023-02-24/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 558m50.584s + + sed -e 's/^/ # /;' fb.bosTau9.chainGCF_003369695.1Link.txt + # 2642343563 bases of 2715853792 (97.293%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_003369695.1Link.txt + # 2630064290 bases of 2715853792 (96.841%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/003/369/695/GCF_003369695.1/GCF_003369695.1.chrom.sizes.txt" \ + \ + bosTau9 GCF_003369695.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 72m1.651s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_003369695.1.txt + # 2603923510 bases of 2715853792 (95.879%) in intersection + + +real 630m53.197s +user 0m0.615s +sys 0m0.648s + +##############################################################################