ba189ec1cc8a311148dcf7d28a6705d998f3add5 gperez2 Sun Nov 9 17:19:46 2025 -0800 GCF_014441545.1 to canFam6, susScr11 to GCF_009873245.2 lastz/chain/net run for users, refs #36578 #36546 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 5572fa113e7..fbf5f5843f4 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -4639,15 +4639,175 @@ sed -e 's/^/ # /;' fb.GCA_013371645.1.chainSynMm10Link.txt # 641679346 bases of 2780373160 (23.079%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/013/371/645/GCA_013371645.1/GCA_013371645.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/013/371/645/GCA_013371645.1/GCA_013371645.1.chrom.sizes.txt" \ GCA_013371645.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 237m25.924s sed -e 's/^/ # /;' fb.GCA_013371645.1.chainRBest.Mm10.txt # 644732272 bases of 2780373160 (23.189%) in intersection ############################################################################## +# LASTZ dog GCF_014441545.1 vs. Dog CanFam6 +# (DONE - 2025-10-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam6.2025-10-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam6.2025-10-24 + + printf '# Dog CanFam6 vs. dog GCF_014441545.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: dog 2020-09-03 GCF_014441545.1_ROS_Cfam_1.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Dog canFam6 +SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit +SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam6.2025-10-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_014441545.1_ROS_Cfam_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 486m53.494s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainCanFam6Link.txt + # 2331387220 bases of 2396858295 (97.268%) in intersection + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainSynCanFam6Link.txt + # 2320210083 bases of 2396858295 (96.802%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + \ + GCF_014441545.1 canFam6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 47m15.051s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainRBest.CanFam6.txt + # 2273405625 bases of 2396858295 (94.849%) in intersection + + ### and for the swap + + cd /hive/data/genomes/canFam6/bed/blastz.GCF_014441545.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_014441545.1_ROS_Cfam_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam6.2025-10-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 89m24.938s + + sed -e 's/^/ # /;' fb.canFam6.chainGCF_014441545.1Link.txt + # 2284422310 bases of 2312802198 (98.773%) in intersection + sed -e 's/^/ # /;' fb.canFam6.chainSynGCF_014441545.1Link.txt + # 2275054517 bases of 2312802198 (98.368%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + \ + canFam6 GCF_014441545.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 47m44.434s + + sed -e 's/^/ # /;' fb.canFam6.chainRBest.GCF_014441545.1.txt + # 2273730636 bases of 2312802198 (98.311%) in intersection + +############################################################################## +# LASTZ Pig SusScr11 vs. blue whale GCF_009873245.2 +# (DONE - 2025-10-29 - Gerardo) + + mkdir /hive/data/genomes/susScr11/bed/lastzGCF_009873245.2.2025-10-27 + cd /hive/data/genomes/susScr11/bed/lastzGCF_009873245.2.2025-10-27 + + printf '# blue whale GCF_009873245.2 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: blue whale 2020-10-02 GCF_009873245.2_mBalMus1.pri.v3 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/susScr11/bed/lastzGCF_009873245.2.2025-10-27 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_009873245.2_mBalMus1.pri.v3 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 441m52.407s + + sed -e 's/^/ # /;' fb.susScr11.chainGCF_009873245.2Link.txt + # 1725370768 bases of 2501912388 (68.962%) in intersection + sed -e 's/^/ # /;' fb.susScr11.chainSynGCF_009873245.2Link.txt + # 1619553238 bases of 2501912388 (64.733%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.chrom.sizes.txt" \ + susScr11 GCF_009873245.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 307m8.258s + + sed -e 's/^/ # /;' fb.susScr11.chainRBest.GCF_009873245.2.txt + # 1618105671 bases of 2501912388 (64.675%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/009/873/245/GCF_009873245.2_mBalMus1.pri.v3/trackData/blastz.susScr11.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_009873245.2_mBalMus1.pri.v3 /hive/data/genomes/susScr11/bed/lastzGCF_009873245.2.2025-10-27/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 245m25.645s + + sed -e 's/^/ # /;' fb.GCF_009873245.2.chainSusScr11Link.txt + # 1810739896 bases of 2374868943 (76.246%) in intersection + sed -e 's/^/ # /;' fb.GCF_009873245.2.chainSynSusScr11Link.txt + # 1596415268 bases of 2374868943 (67.221%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.chrom.sizes.txt" \ + GCF_009873245.2 susScr11) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 333m23.268s + + sed -e 's/^/ # /;' fb.GCF_009873245.2.chainRBest.SusScr11.txt + # 1613579672 bases of 2374868943 (67.944%) in intersection + +##############################################################################