c5a0639c12640fb8d4688ccb7acbd1298713ee33 lrnassar Wed Aug 14 17:56:58 2024 -0700 Running some liftOver chains requested by 2 MLQs. diff --git src/hg/makeDb/doc/susScr11/lastzRuns.txt src/hg/makeDb/doc/susScr11/lastzRuns.txt index 8a7c9f4..8e5fa17 100644 --- src/hg/makeDb/doc/susScr11/lastzRuns.txt +++ src/hg/makeDb/doc/susScr11/lastzRuns.txt @@ -1,102 +1,260 @@ ############################################################################## # LASTZ sheep GCA_002844635.1 (DONE - 2021-04-20 - Hiram) mkdir /hive/data/genomes/susScr11/bed/lastzGCA_002844635.1.2021-04-20 cd /hive/data/genomes/susScr11/bed/lastzGCA_002844635.1.2021-04-20 printf '# GCA_002844635.1 vs hg38 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_T=2 BLASTZ_O=400 BLASTZ_E=30 BLASTZ_M=254 # default BLASTZ_Q score matrix: # A C G T # A 91 -114 -31 -123 # C -114 100 -125 -31 # G -31 -125 100 -114 # T -123 -31 -114 91 # TARGET: Human Hg38 SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: sheep GCA_002844635.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCA_002844635.1/GCA_002844635.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCA_002844635.1/GCA_002844635.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCA_002844635.1.2021-04-20 TMPDIR=/dev/shm ' > DEF export targetDb="hg38" export asmId="GCA_002844635.1" export gcPath="GCA/002/844/635" cd /hive/data/genomes/$targetDb/bed/lastz${asmId}.2021-04-20 time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -syntenicNet -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 cat fb.${targetDb}.chain.${asmId}Link.txt cat fb.${targetDb}.chainSyn.${asmId}Link.txt grep -w real do.log | sed -e 's/^/ # /;' # real 318m24.582s sed -e 's/^/ # /;' fb.$targetDb.chain.${asmId}Link.txt # 2431952924 bases of 2501912388 (97.204%) in intersection sed -e 's/^/ # /;' fb.$targetDb.chainSyn.${asmId}Link.txt # 2409981908 bases of 2501912388 (96.326%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \ -querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \ $targetDb ${asmId}) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 93m2.731s sed -e 's/^/ # /;' fb.$targetDb.chainRBest.$asmId.txt # 2381230203 bases of 2501912388 (95.176%) in intersection ## Overall time for the above: # real 411m27.346s ### the swap to the assembly hub export target="susScr11" export Target="SusScr11" export query="GCA_002844635.1" export asmId="GCA_002844635.1_USMARCv1.0" export gcPath="GCA/002/844/635" mkdir -p /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \ /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 90m38.556s sed -e 's/^/ # /;' fb.${query}.chain.${Target}Link.txt # 2543057365 bases of 2755438182 (92.292%) in intersection sed -e 's/^/ # /;' fb.${query}.chainSyn.${Target}Link.txt # 2514166037 bases of 2755438182 (91.244%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \ $query $target) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 86m43.960s sed -e 's/^/ # /;' fb.${query}.chainRBest.${Target}.txt # 2388751543 bases of 2755438182 (86.692%) in intersection # Complete run time for all the swap operation: # real 285m1.340s ############################################################################## +# LASTZ Pig SusScr11 vs. Cow BosTau9 +# (DONE - 2024-08-09 - lrnassar) + + mkdir /hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09 + cd /hive/data/genomes/susScr11/bed/lastzBosTau9.2024-08-09 + + printf '# Cow BosTau9 vs. Pig SusScr11 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Pig susScr11 +SEQ1_DIR=/hive/data/genomes/susScr11/susScr11.2bit +SEQ1_LEN=/hive/data/genomes/susScr11/chrom.sizes +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/susScr11/bed/lastzBosTau9.2024-08-09 +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 844m2.282s + + sed -e 's/^/ # /;' fb.susScr11.chainBosTau9Link.txt + # 1542224987 bases of 2472073034 (62.386%) in intersection + sed -e 's/^/ # /;' fb.susScr11.chainSynBosTau9Link.txt + # 1458188575 bases of 2472073034 (58.986%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + susScr11 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 379m32.380s + + sed -e 's/^/ # /;' fb.susScr11.chainRBest.BosTau9.txt + # 1451300013 bases of 2472073034 (58.708%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/blastz.susScr11.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/susScr11/bed/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 237m58.241s + + sed -e 's/^/ # /;' fb.bosTau9.chainSusScr11Link.txt + # 1542795700 bases of 2715853792 (56.807%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynSusScr11Link.txt + # 1464525591 bases of 2715853792 (53.925%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + bosTau9 susScr11) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 418m4.992s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.SusScr11.txt + # 1452583914 bases of 2715853792 (53.485%) in intersection + +############################################################################## +# LASTZ Pig SusScr11 vs. goat GCF_001704415.2 +# (DONE - 2024-08-12 - lrnassar) + + mkdir /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12 + cd /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12 + + printf '# goat GCF_001704415.2 vs. Pig SusScr11 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Pig susScr11 +SEQ1_DIR=/hive/data/genomes/susScr11/susScr11.2bit +SEQ1_LEN=/hive/data/genomes/susScr11/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_001704415.2_ARS1.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 568m2.570s + + sed -e 's/^/ # /;' fb.susScr11.chainGCF_001704415.2Link.txt + # 1532623567 bases of 2501912388 (61.258%) in intersection + sed -e 's/^/ # /;' fb.susScr11.chainSynGCF_001704415.2Link.txt + # 1448119731 bases of 2501912388 (57.881%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + susScr11 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 495m38.221s + + sed -e 's/^/ # /;' fb.susScr11.chainRBest.GCF_001704415.2.txt + # 1444668348 bases of 2501912388 (57.743%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.susScr11.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/susScr11/bed/lastzGCF_001704415.2.2024-08-12/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 413m9.780s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSusScr11Link.txt + # 1557596633 bases of 2922617086 (53.295%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynSusScr11Link.txt + # 1455695959 bases of 2922617086 (49.808%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + GCF_001704415.2 susScr11) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 578m18.029s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.SusScr11.txt + # 1446482758 bases of 2922617086 (49.493%) in intersection + +##############################################################################