394ef72060f80bfaa2ec5186aa2cb8672c5460fc gperez2 Sat Mar 11 14:02:09 2023 -0800 mm10 vs. GCA_001624675.1/GCA_001632575.1 lastz/chain/net runs for user, refs #30492 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 0fa2693..7aff1ff 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -2032,15 +2032,182 @@ -target2bit="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.chrom.sizes.txt" \ GCF_024166365.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 410m24.376s sed -e 's/^/ # /;' fb.GCF_024166365.1.chainRBest.Hg38.txt # 1284042505 bases of 3401247148 (37.752%) in intersection real 1579m17.153s user 0m0.974s sys 0m1.004s ############################################################################## +# LASTZ house mouse GCA_001624675.1 vs. Mouse Mm10 +# (DONE - 2023-02-06 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 + cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 + + printf '# Mouse Mm10 vs. house mouse GCA_001624675.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: house mouse 2016-04-26 GCA_001624675.1_NOD_ShiLtJ_v1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.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/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_001624675.1_NOD_ShiLtJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 572m8.503s + + sed -e 's/^/ # /;' fb.GCA_001624675.1.chainMm10Link.txt + # 2224459292 bases of 2982063250 (74.595%) in intersection + sed -e 's/^/ # /;' fb.GCA_001624675.1.chainSynMm10Link.txt + # 2209813247 bases of 2982063250 (74.104%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.chrom.sizes.txt" \ + \ + GCA_001624675.1 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 81m3.164s + + sed -e 's/^/ # /;' fb.GCA_001624675.1.chainRBest.Mm10.txt + # 2205696172 bases of 2982063250 (73.965%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm10/bed/blastz.GCA_001624675.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_001624675.1_NOD_ShiLtJ_v1 /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06/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 107m34.257s + + sed -e 's/^/ # /;' fb.mm10.chainGCA_001624675.1Link.txt + # 2406965836 bases of 2818974548 (85.384%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCA_001624675.1Link.txt + # 2302191604 bases of 2818974548 (81.668%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.chrom.sizes.txt" \ + \ + mm10 GCA_001624675.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 86m0.955s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCA_001624675.1.txt + # 2200638822 bases of 2818974548 (78.065%) in intersection + + +real 846m47.401s +user 0m1.125s +sys 0m1.575s +############################################################################## +# LASTZ Mouse Mm10 vs. house mouse GCA_001632575.1 +# (DONE - 2023-02-07 - Gerardo) + + mkdir /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 + cd /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 + + printf '# house mouse GCA_001632575.1 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: house mouse 2016-05-09 GCA_001632575.1_C3H_HeJ_v1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_001632575.1_C3H_HeJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 394m43.728s + + sed -e 's/^/ # /;' fb.mm10.chainGCA_001632575.1Link.txt + # 2458093602 bases of 2818974548 (87.198%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCA_001632575.1Link.txt + # 2360661678 bases of 2818974548 (83.742%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt" \ + mm10 GCA_001632575.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 74m28.901s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCA_001632575.1.txt + # 2254140497 bases of 2818974548 (79.963%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blastz.mm10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_001632575.1_C3H_HeJ_v1 /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07/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 110m17.627s + + sed -e 's/^/ # /;' fb.GCA_001632575.1.chainMm10Link.txt + # 2272113623 bases of 2701131316 (84.117%) in intersection + sed -e 's/^/ # /;' fb.GCA_001632575.1.chainSynMm10Link.txt + # 2260408202 bases of 2701131316 (83.684%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt" \ + GCA_001632575.1 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 72m53.272s + + sed -e 's/^/ # /;' fb.GCA_001632575.1.chainRBest.Mm10.txt + # 2258449853 bases of 2701131316 (83.611%) in intersection + +real 652m24.059s +user 0m1.118s +sys 0m1.400s +##############################################################################