c5a0639c12640fb8d4688ccb7acbd1298713ee33 lrnassar Wed Aug 14 17:56:58 2024 -0700 Running some liftOver chains requested by 2 MLQs. diff --git src/hg/makeDb/doc/bosTau9/lastzRuns.txt src/hg/makeDb/doc/bosTau9/lastzRuns.txt index 109fcb4..23f4ea6 100644 --- src/hg/makeDb/doc/bosTau9/lastzRuns.txt +++ src/hg/makeDb/doc/bosTau9/lastzRuns.txt @@ -308,15 +308,176 @@ -querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ \ bosTau9 GCF_019923935.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 124m20.231s sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_019923935.1.txt # 2476775898 bases of 2715853792 (91.197%) in intersection real 4287m53.907s user 0m2.895s sys 0m2.314s ############################################################################## + +############################################################################## +# LASTZ Cow BosTau9 vs. Horse EquCab3 +# (DONE - 2024-08-09 - lrnassar) + + mkdir /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09 + cd /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09 + + printf '# Horse EquCab3 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: Horse equCab3 +SEQ2_DIR=/hive/data/genomes/equCab3/equCab3.2bit +SEQ2_LEN=/hive/data/genomes/equCab3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09 +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 846m27.399s + + sed -e 's/^/ # /;' fb.bosTau9.chainEquCab3Link.txt + # 1554179648 bases of 2715853792 (57.226%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynEquCab3Link.txt + # 1502506284 bases of 2715853792 (55.324%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + bosTau9 equCab3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 244m38.025s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.EquCab3.txt + # 1481921961 bases of 2715853792 (54.566%) in intersection + + ### and for the swap + + cd /hive/data/genomes/equCab3/bed/blastz.bosTau9.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/bosTau9/bed/lastzEquCab3.2024-08-09/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 151m32.417s + + sed -e 's/^/ # /;' fb.equCab3.chainBosTau9Link.txt + # 1588535515 bases of 2497530654 (63.604%) in intersection + sed -e 's/^/ # /;' fb.equCab3.chainSynBosTau9Link.txt + # 1536072990 bases of 2497530654 (61.504%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + equCab3 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 198m27.720s + + sed -e 's/^/ # /;' fb.equCab3.chainRBest.BosTau9.txt + # 1481165695 bases of 2497530654 (59.305%) in intersection + +############################################################################## + +# LASTZ sheep GCF_016772045.2 vs. Cow BosTau9 +# (DONE - 2024-08-09 - lrnassar) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09 + + printf '# Cow BosTau9 vs. sheep GCF_016772045.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.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/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1131m30.899s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainBosTau9Link.txt + # 2345286242 bases of 2654063983 (88.366%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainSynBosTau9Link.txt + # 2290967435 bases of 2654063983 (86.319%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ + \ + GCF_016772045.2 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 225m50.587s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainRBest.BosTau9.txt + # 2278884591 bases of 2654063983 (85.864%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/blastz.GCF_016772045.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzBosTau9.2024-08-09/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 447m1.738s + + sed -e 's/^/ # /;' fb.bosTau9.chainGCF_016772045.2Link.txt + # 2366545255 bases of 2715853792 (87.138%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_016772045.2Link.txt + # 2307155872 bases of 2715853792 (84.951%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ + \ + bosTau9 GCF_016772045.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 221m53.772s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_016772045.2.txt + # 2279192983 bases of 2715853792 (83.922%) in intersection + +##############################################################################