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 @@ -1,182 +1,322 @@ ######################################################################### # 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 ############################################################################## +# 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 + +##############################################################################