e303c9b8fc40e8cc55a0186148cef1d54108c126 gperez2 Fri Nov 12 17:24:03 2021 -0800 sheep GCF_002742125.1 vs. OviAri4 lastz/chain/net run for user, refs #28463 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index e37d669..0fca4ba 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -838,15 +838,114 @@ -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ GCF_000349665.1 rn6) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 488m35.716s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRBest.Rn6.txt # 1350825251 bases of 2504925039 (53.927%) in intersection real 1989m11.755s user 0m1.959s sys 0m2.860s ############################################################################## +# LASTZ sheep GCF_002742125.1 vs. Sheep OviAri4 (DONE- 2021-11-08 - 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 \ + GCF_002742125.1_Oar_rambouillet_v1.0 oviAri4 mammal mammal) \ + > sheepLiftOver_20211108.log 2>&1 & + # check the total time +grep -w real sheepLiftOver_20211108.log | tail -1 | sed -e 's/^/ # /;' + # real 2380m46.742s + + # this sheepLiftOver_20211108 log file happens to have a copy of the make doc, as well + # as the copy of the make doc left in the target assembly directory: +# /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08/makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/sheepLiftOver_20211108.log + +############################################################################## +# LASTZ sheep GCF_002742125.1 vs. Sheep OviAri4 +# (DONE - 2021-11-08 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 + + printf '# Sheep OviAri4 vs. sheep GCF_002742125.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sheep GCF_002742125.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Sheep OviAri4 +SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit +SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1306m58.735s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainOviAri4Link.txt + # 2751767534 bases of 2869914396 (95.883%) in intersection + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynOviAri4Link.txt + # 2683354898 bases of 2869914396 (93.499%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ + \ + GCF_002742125.1 oviAri4) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 134m53.482s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.OviAri4.txt + # 2516745591 bases of 2869914396 (87.694%) in intersection + + ### and for the swap + + cd /hive/data/genomes/oviAri4/bed/blastz.GCF_002742125.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08/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 813m49.535s + + sed -e 's/^/ # /;' fb.oviAri4.chainGCF_002742125.1Link.txt + # 2554085476 bases of 2615516299 (97.651%) in intersection + sed -e 's/^/ # /;' fb.oviAri4.chainSynGCF_002742125.1Link.txt + # 2527079442 bases of 2615516299 (96.619%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ + \ + oviAri4 GCF_002742125.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 125m4.180s + + sed -e 's/^/ # /;' fb.oviAri4.chainRBest.GCF_002742125.1.txt + # 2520434078 bases of 2615516299 (96.365%) in intersection