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/mm10.txt src/hg/makeDb/doc/mm10.txt index 09bee25..984cba5 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -19229,15 +19229,175 @@ cd /gbdb/mm10 mkdir vistaEnhancers; cd vistaEnhancers # Making symlink for big files ln -s /hive/data/outside/vistaEnhancers/mm10/vistaEnhancers.bb cd ~/kent/src/hg/makeDb/trackDb/mouse/mm10 vi trackDb.ra ############################################################################# ############################################################################# # JASPAR 2024 bigBed update 11/13/24 cd /hive/data/genomes/mm10/bed/jaspar wget https://frigg.uio.no/JASPAR/JASPAR_genome_browser_tracks/current/mm10/JASPAR2024_mm10.bb mv JASPAR2024_mm10.bb JASPAR2024.bb ln -s JASPAR2024.bb /gbdb/mm10/jaspar/JASPAR2024.bb + +############################################################################## +# LASTZ Mouse Mm10 vs. water buffalo GCF_019923935.1 +# (DONE - 2024-01-03 - mspeir) + + mkdir /hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 + cd /hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 + + printf '# water buffalo GCF_019923935.1 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: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId 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 198m37.349s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_019923935.1Link.txt + # 726061208 bases of 2818974548 (25.756%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_019923935.1Link.txt + # 676398917 bases of 2818974548 (23.995%) 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" \ + mm10 GCF_019923935.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 221m47.012s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_019923935.1.txt + # 667467634 bases of 2818974548 (23.678%) in intersection + + ### and for the swap +# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.mm10.swap +# running /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.mm10.swap/runSwap.sh ++ cd /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ export defaultName=GCF_019923935.1_NDDB_SH_1 ++ defaultName=GCF_019923935.1_NDDB_SH_1 ++ export asmId=GCF_019923935.1_NDDB_SH_1 ++ asmId=GCF_019923935.1_NDDB_SH_1 ++ export buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.txt ++ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.txt . ++ '[' -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb ']' ++ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.bb ++ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb . ++ /cluster/home/mspeir/kent/src/hg/utils/automation/asmHubTrackDb.sh GCF_019923935.1_NDDB_SH_1 GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 +# no ensGene found +composite chainNet +constructing synNet.bb links GCF_019923935.1_NDDB_SH_1 hg38 +constructing rbestNet.bb links GCF_019923935.1_NDDB_SH_1 hg38 +constructing synNet.bb links GCF_019923935.1_NDDB_SH_1 mm10 +constructing rbestNet.bb links GCF_019923935.1_NDDB_SH_1 mm10 +############################################################################## +# LASTZ Mouse Mm10 vs. water buffalo GCF_019923935.1 +# (DONE - 2024-01-03 - mspeir) + + mkdir /hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 + cd /hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 + + printf '# water buffalo GCF_019923935.1 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: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId 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 198m37.349s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_019923935.1Link.txt + # 726061208 bases of 2818974548 (25.756%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_019923935.1Link.txt + # 676398917 bases of 2818974548 (23.995%) 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" \ + mm10 GCF_019923935.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 221m47.012s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_019923935.1.txt + # 667467634 bases of 2818974548 (23.678%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.mm10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/mm10/bed/lastzGCF_019923935.1.2024-01-03/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 109m24.788s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainMm10Link.txt + # 692375708 bases of 2622460639 (26.402%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynMm10Link.txt + # 657128856 bases of 2622460639 (25.058%) 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 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 195m35.449s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.Mm10.txt + # 666765450 bases of 2622460639 (25.425%) in intersection + +real 725m31.677s +user 0m3.111s +sys 0m2.760s + +##############################################################################