baf2428c31c95c077cc7048911f4ecdc30732612 gperez2 Sat Nov 11 13:19:58 2023 -0800 chicken GCF_016699485.2 vs. Chicken GalGal5, lastz/chain/net run for user, refs #31969 diff --git src/hg/makeDb/doc/galGal5/lastzRuns.txt src/hg/makeDb/doc/galGal5/lastzRuns.txt index f7d24c9..aa2ed73 100644 --- src/hg/makeDb/doc/galGal5/lastzRuns.txt +++ src/hg/makeDb/doc/galGal5/lastzRuns.txt @@ -1,310 +1,393 @@ ######################################################################### # LASTZ rat/rn6 vs. chicken/galGal5 - (DONE - 2016-05-03 - Hiram) mkdir /hive/data/genomes/rn6/bed/lastzGalGal5.2016-05-03 cd /hive/data/genomes/rn6/bed/lastzGalGal5.2016-05-03 printf '# Rat vs. chicken BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_O=400 BLASTZ_E=30 BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_M=50 BLASTZ_Q=/scratch/data/blastz/HoxD55.q # A C G T # 91 -90 -25 -100 # -90 100 -100 -25 # -25 -100 100 -90 # -100 -25 -90 91 # TARGET: Rat Rn6 SEQ1_DIR=/hive/data/genomes/rn6/rn6.2bit SEQ1_LEN=/hive/data/genomes/rn6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=15 # QUERY: chicken galGal5 SEQ2_DIR=/hive/data/genomes/galGal5/galGal5.2bit SEQ2_LEN=/hive/data/genomes/galGal5/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LIMIT=100 SEQ2_LAP=0 BASE=/hive/data/genomes/rn6/bed/lastzGalGal5.2016-05-03 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 284m1.002s cat fb.rn6.chainGalGal5Link.txt # 108740749 bases of 2729860805 (3.983%) in intersection time (doRecipBest.pl -buildDir=`pwd` rn6 galGal5) > rbest.log 2>&1 & # real 206m46.355s # and for the swap: mkdir /hive/data/genomes/galGal5/bed/blastz.rn6.swap cd /hive/data/genomes/galGal5/bed/blastz.rn6.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/rn6/bed/lastzGalGal5.2016-05-03/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 16m43.312s cat fb.galGal5.chainRn6Link.txt # 95694615 bases of 1218501075 (7.853%) in intersection time (doRecipBest.pl -buildDir=`pwd` galGal5 rn6) > rbest.log 2>&1 # real 171m15.342s ######################################################################### # LASTZ zebrafish/danRer10 vs. chicken/galGal5 - (DONE - 2016-05-03 - Hiram) mkdir /hive/data/genomes/danRer10/bed/lastzGalGal5.2016-05-03 cd /hive/data/genomes/danRer10/bed/lastzGalGal5.2016-05-03 printf '# zebrafish vs. chicken BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_O=400 BLASTZ_E=30 BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_M=50 BLASTZ_Q=/scratch/data/blastz/HoxD55.q # A C G T # 91 -90 -25 -100 # -90 100 -100 -25 # -25 -100 100 -90 # -100 -25 -90 91 # TARGET: Rat DanRer10 SEQ1_DIR=/hive/data/genomes/danRer10/danRer10.2bit SEQ1_LEN=/hive/data/genomes/danRer10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=15 # QUERY: chicken galGal5 SEQ2_DIR=/hive/data/genomes/galGal5/galGal5.2bit SEQ2_LEN=/hive/data/genomes/galGal5/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=100 SEQ2_LAP=0 BASE=/hive/data/genomes/danRer10/bed/lastzGalGal5.2016-05-03 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 222m22.795s cat fb.danRer10.chainGalGal5Link.txt # 58108752 bases of 1369683683 (4.242%) in intersection time (doRecipBest.pl -buildDir=`pwd` danRer10 galGal5) > rbest.log 2>&1 & # real 92m11.817s # and for the swap: mkdir /hive/data/genomes/galGal5/bed/blastz.danRer10.swap cd /hive/data/genomes/galGal5/bed/blastz.danRer10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/danRer10/bed/lastzGalGal5.2016-05-03/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 8m52.412s cat fb.galGal5.chainDanRer10Link.txt # 49128539 bases of 1218501075 (4.032%) in intersection time (doRecipBest.pl -buildDir=`pwd` galGal5 danRer10) > rbest.log 2>&1 # real 83m20.585s ######################################################################### # LASTZ chicken/galGal5 vs. Chinese softshell turtle - (DONE - 2016-05-10 - Hiram) mkdir /hive/data/genomes/galGal5/bed/lastzPelSin1.2016-05-10 cd /hive/data/genomes/galGal5/bed/lastzPelSin1.2016-05-10 printf '# chicken vs. Chinese softshell turtle BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: chicken galGal5 SEQ1_DIR=/hive/data/genomes/galGal5/galGal5.2bit SEQ1_LEN=/hive/data/genomes/galGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=100 SEQ1_LAP=10000 # QUERY: Chinese softshell turtle pelSin1 SEQ2_DIR=/hive/data/genomes/pelSin1/pelSin1.2bit SEQ2_LEN=/hive/data/genomes/pelSin1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/galGal5/bed/lastzPelSin1.2016-05-10 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 137m44.965s cat fb.galGal5.chainPelSin1Link.txt # 269146297 bases of 1218501075 (22.088%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galGal5 pelSin1) \ > rbest.log 2>&1 & # real 68m22.787s # and for the swap: mkdir /hive/data/genomes/pelSin1/bed/blastz.galGal5.swap cd /hive/data/genomes/pelSin1/bed/blastz.galGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/galGal5/bed/lastzPelSin1.2016-05-10/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 38m32.377s cat fb.pelSin1.chainGalGal5Link.txt # 275358706 bases of 2106639384 (13.071%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` pelSin1 galGal5) \ > rbest.log 2>&1 # real 132m33.263s ######################################################################### # LASTZ chicken/galGal5 vs. turkey - (DONE - 2017-01-19 - Hiram) mkdir /hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19 cd /hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19 printf '# chicken vs. turkey BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: chicken galGal5 SEQ1_DIR=/hive/data/genomes/galGal5/galGal5.2bit SEQ1_LEN=/hive/data/genomes/galGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=100 SEQ1_LAP=10000 # QUERY: turkey melGal5 SEQ2_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ2_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 620m42.543s cat fb.galGal5.chainMelGal5Link.txt # 1029400481 bases of 1218501075 (84.481%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galGal5 melGal5) \ > rbest.log 2>&1 & # real 312m39.922s # and for the swap: mkdir /hive/data/genomes/melGal5/bed/blastz.galGal5.swap cd /hive/data/genomes/melGal5/bed/blastz.galGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 284m22.838s cat fb.melGal5.chainGalGal5Link.txt # 984928299 bases of 1093044709 (90.109%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 galGal5) \ > rbest.log 2>&1 # real 487m51.030s ######################################################################### # LASTZ Golden eagle/aquChr2 vs. chicken/galGal5 - (DONE - 2017-03-17 - Hiram) mkdir /hive/data/genomes/galGal5/bed/lastzAquChr2.2017-03-17 cd /hive/data/genomes/galGal5/bed/lastzAquChr2.2017-03-17 printf '# Golden eagle vs. chicken BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: chicken galGal5 SEQ1_DIR=/hive/data/genomes/galGal5/galGal5.2bit SEQ1_LEN=/hive/data/genomes/galGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=50 SEQ1_LAP=10000 # QUERY: Golden eagle aquChr2 SEQ2_DIR=/hive/data/genomes/aquChr2/aquChr2.2bit SEQ2_LEN=/hive/data/genomes/aquChr2/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=20 BASE=/hive/data/genomes/galGal5/bed/lastzAquChr2.2017-03-17 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 181m2.296s cat fb.galGal5.chainAquChr2Link.txt # 919609897 bases of 1218501075 (75.471%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galGal5 aquChr2) \ > rbest.log 2>&1 & # real 183m23.066s # and for the swap: mkdir /hive/data/genomes/aquChr2/bed/blastz.galGal5.swap cd /hive/data/genomes/aquChr2/bed/blastz.galGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/galGal5/bed/lastzAquChr2.2017-03-17/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 60m38.086s cat fb.aquChr2.chainGalGal5Link.txt # 854022282 bases of 1180019022 (72.374%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` aquChr2 galGal5) \ > rbest.log 2>&1 # real 167m4.022s ######################################################################### +# LASTZ chicken GCF_016699485.2 vs. Chicken GalGal5 +# (DONE - 2023-08-15 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGalGal5.2023-08-15 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGalGal5.2023-08-15 + + printf '# Chicken GalGal5 vs. chicken GCF_016699485.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: chicken 2021-01-19 GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Chicken galGal5 +SEQ2_DIR=/hive/data/genomes/galGal5/galGal5.2bit +SEQ2_LEN=/hive/data/genomes/galGal5/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGalGal5.2023-08-15 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 232m0.504s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainGalGal5Link.txt + # 1036760370 bases of 1053332251 (98.427%) in intersection + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainSynGalGal5Link.txt + # 1015115099 bases of 1053332251 (96.372%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \ + \ + GCF_016699485.2 galGal5) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 33m10.138s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainRBest.GalGal5.txt + # 1014531342 bases of 1053332251 (96.316%) in intersection + + ### and for the swap + + cd /hive/data/genomes/galGal5/bed/blastz.GCF_016699485.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGalGal5.2023-08-15/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 79m10.913s + + sed -e 's/^/ # /;' fb.galGal5.chainGCF_016699485.2Link.txt + # 1125580117 bases of 1230258557 (91.491%) in intersection + sed -e 's/^/ # /;' fb.galGal5.chainSynGCF_016699485.2Link.txt + # 1109811364 bases of 1230258557 (90.210%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \ + \ + galGal5 GCF_016699485.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 42m6.153s + + sed -e 's/^/ # /;' fb.galGal5.chainRBest.GCF_016699485.2.txt + # 1021179381 bases of 1230258557 (83.005%) in intersection + +real 386m37.712s +user 0m3.674s +sys 0m4.972s +##############################################################################