0f63b81106ac90c3e8b459a7b56cfea702ca6bce gperez2 Tue Dec 21 13:02:11 2021 -0800 sheep GCF_016772045.1 vs. oviAri3(/4)(sheep GCF_002742125.1) lastz/chain/net run for user, refs #28648 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 0fca4ba..9d994c5 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -937,15 +937,336 @@ 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 + +real 2380m46.742s +user 0m1.784s +sys 0m1.912s +############################################################################## +# LASTZ sheep GCF_016772045.1 vs. Sheep OviAri3 (DONE - 2021-12-15 -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_016772045.1_ARS-UI_Ramb_v2.0 oviAri3 mammal mammal) \ + > GCF016772045_oviAri3_20211215.log 2>&1 & + # check the total time +grep -w real GCF016772045_oviAri3_20211215.log | tail -1 | sed -e 's/^/ # /;' + # real 2508m50.449s + + # this GCF016772045_oviAri3_20211215.log 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/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15//makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/GCF016772045_oviAri3_20211215.log + +############################################################################## +# LASTZ sheep GCF_016772045.1 vs. Sheep OviAri3 +# (DONE - 2021-12-15 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 + + printf '# Sheep OviAri3 vs. sheep GCF_016772045.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sheep GCF_016772045.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Sheep OviAri3 +SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.2bit +SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1573m35.149s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainOviAri3Link.txt + # 2511613301 bases of 2628146905 (95.566%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynOviAri3Link.txt + # 2472798897 bases of 2628146905 (94.089%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + \ + GCF_016772045.1 oviAri3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 103m6.701s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.OviAri3.txt + # 2466641987 bases of 2628146905 (93.855%) in intersection + + ### and for the swap + + cd /hive/data/genomes/oviAri3/bed/blastz.GCF_016772045.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15/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 709m20.158s + + sed -e 's/^/ # /;' fb.oviAri3.chainGCF_016772045.1Link.txt + # 2499875349 bases of 2619054388 (95.450%) in intersection + sed -e 's/^/ # /;' fb.oviAri3.chainSynGCF_016772045.1Link.txt + # 2475599907 bases of 2619054388 (94.523%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + \ + oviAri3 GCF_016772045.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 122m47.847s + + sed -e 's/^/ # /;' fb.oviAri3.chainRBest.GCF_016772045.1.txt + # 2470367813 bases of 2619054388 (94.323%) in intersection + + +real 2508m50.449s +user 0m1.587s +sys 0m1.678s +############################################################################## +# LASTZ sheep GCF_016772045.1 vs. Sheep OviAri4 (DONE - 2021-12-15 -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_016772045.1_ARS-UI_Ramb_v2.0 oviAri4 mammal mammal) \ + > GCF016772045_oviAri4_20211215.log 2>&1 & + # check the total time +grep -w real GCF016772045_oviAri4_20211215.log | tail -1 | sed -e 's/^/ # /;' + # real 2669m31.448s + + # this GCF016772045_oviAri4_20211215.log 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/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15//makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/GCF016772045_oviAri4_20211215.log + +############################################################################## +# LASTZ sheep GCF_016772045.1 vs. Sheep OviAri4 +# (DONE - 2021-12-15 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 + + printf '# Sheep OviAri4 vs. sheep GCF_016772045.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sheep GCF_016772045.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.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/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1657m21.821s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainOviAri4Link.txt + # 2552765241 bases of 2628146905 (97.132%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynOviAri4Link.txt + # 2521297402 bases of 2628146905 (95.934%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + \ + GCF_016772045.1 oviAri4) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 110m56.360s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.OviAri4.txt + # 2512287192 bases of 2628146905 (95.592%) in intersection + + ### and for the swap + + cd /hive/data/genomes/oviAri4/bed/blastz.GCF_016772045.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15/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 777m47.304s + + sed -e 's/^/ # /;' fb.oviAri4.chainGCF_016772045.1Link.txt + # 2551757085 bases of 2615516299 (97.562%) in intersection + sed -e 's/^/ # /;' fb.oviAri4.chainSynGCF_016772045.1Link.txt + # 2526678124 bases of 2615516299 (96.603%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + \ + oviAri4 GCF_016772045.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 123m25.562s + + sed -e 's/^/ # /;' fb.oviAri4.chainRBest.GCF_016772045.1.txt + # 2516185710 bases of 2615516299 (96.202%) in intersection + + +real 2669m31.448s +user 0m1.595s +sys 0m1.620s +############################################################################## +# LASTZ sheep GCF_002742125.1 vs. sheep GCF_016772045.1 (DONE - 2021-12-15 -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 GCF_016772045.1_ARS-UI_Ramb_v2.0 mammal mammal) \ + > GCF002742125_GCF016772045_20211215.log 2>&1 & + # check the total time +grep -w real GCF002742125_GCF016772045_20211215.log | tail -1 | sed -e 's/^/ # /;' + # real 2656m30.586s + + # this GCF002742125_GCF016772045_20211215.log 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/lastzGCF_016772045.1.2021-12-15/makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/GCF002742125_GCF016772045_20211215.log + +############################################################################## +# LASTZ sheep GCF_002742125.1 vs. sheep GCF_016772045.1 +# (DONE - 2021-12-15 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15 + + printf '# sheep GCF_016772045.1 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 GCF_016772045.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt +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/lastzGCF_016772045.1.2021-12-15 +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 -qAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1439m18.311s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainGCF_016772045.1Link.txt + # 2838492016 bases of 2869914396 (98.905%) in intersection + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynGCF_016772045.1Link.txt + # 2803625709 bases of 2869914396 (97.690%) 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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + GCF_002742125.1 GCF_016772045.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 88m6.029s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.GCF_016772045.1.txt + # 2614623978 bases of 2869914396 (91.105%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/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 -qAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15/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 1047m12.920s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainGCF_002742125.1Link.txt + # 2622530937 bases of 2628146905 (99.786%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynGCF_002742125.1Link.txt + # 2612741995 bases of 2628146905 (99.414%) 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" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ + GCF_016772045.1 GCF_002742125.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 81m52.743s + + sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.GCF_002742125.1.txt + # 2611860239 bases of 2628146905 (99.380%) in intersection + + +real 2656m30.586s +user 0m1.556s +sys 0m1.520s