c139f35504866c1dcf0eec5e3e07a83da8866fe5 mspeir Tue Jan 16 19:49:03 2024 -0800 adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804 diff --git src/hg/makeDb/doc/bosTau9/lastzRuns.txt src/hg/makeDb/doc/bosTau9/lastzRuns.txt index 2dd64a3..109fcb4 100644 --- src/hg/makeDb/doc/bosTau9/lastzRuns.txt +++ src/hg/makeDb/doc/bosTau9/lastzRuns.txt @@ -168,15 +168,155 @@ \ 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 ############################################################################## +# LASTZ water buffalo GCF_019923935.1 vs. Cow BosTau9 +# (DONE - 2024-01-05 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + + printf '# Cow BosTau9 vs. water buffalo GCF_019923935.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 2623m44.119s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainBosTau9Link.txt + # 2522886084 bases of 2622460639 (96.203%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynBosTau9Link.txt + # 2484746893 bases of 2622460639 (94.749%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ + \ + GCF_019923935.1 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 146m41.533s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.BosTau9.txt + # 2476483890 bases of 2622460639 (94.434%) in intersection + + ### and for the swap +# swap into: /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap +# running /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap/runSwap.sh +# do not find qTdb 'xxx' +############################################################################## +# LASTZ water buffalo GCF_019923935.1 vs. Cow BosTau9 +# (DONE - 2024-01-05 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + + printf '# Cow BosTau9 vs. water buffalo GCF_019923935.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 2623m44.119s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainBosTau9Link.txt + # 2522886084 bases of 2622460639 (96.203%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynBosTau9Link.txt + # 2484746893 bases of 2622460639 (94.749%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ + \ + GCF_019923935.1 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 146m41.533s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.BosTau9.txt + # 2476483890 bases of 2622460639 (94.434%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/blastz.GCF_019923935.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05/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 1392m58.161s + + sed -e 's/^/ # /;' fb.bosTau9.chainGCF_019923935.1Link.txt + # 2549407306 bases of 2715853792 (93.871%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_019923935.1Link.txt + # 2510417468 bases of 2715853792 (92.436%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-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 + +##############################################################################