e29a2749a1dd0fc28c17cd45270edbf151cbd532 hiram Wed Oct 13 10:11:15 2021 -0700 per user request rheMac2 and rheMac10 chainNet to macFas5 refs #28318 diff --git src/hg/makeDb/doc/macFas5/lastzRuns.txt src/hg/makeDb/doc/macFas5/lastzRuns.txt index 2deb73c..64dcc24 100644 --- src/hg/makeDb/doc/macFas5/lastzRuns.txt +++ src/hg/makeDb/doc/macFas5/lastzRuns.txt @@ -1,151 +1,252 @@ # for emacs: -*- mode: sh; -*- ######################################################################### # LASTZ Crab-eating macaque/macFas5 Green monkey/chlSab1 - # (DONE - 2014-05-15 - Hiram) mkdir /hive/data/genomes/macFas5/bed/lastzChlSab1.2014-05-15 cd /hive/data/genomes/macFas5/bed/lastzChlSab1.2014-05-15 cat << '_EOF_' > DEF # Crab-eating macaque vs. Green monkey # parameters used are from the human-chimp tuning from long ago BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.52/bin/lastz BLASTZ_M=245 BLASTZ_O=600 BLASTZ_E=150 BLASTZ_T=2 BLASTZ_Y=15000 BLASTZ_K=4500 BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q # A C G T # 90 -330 -236 -356 # -330 100 -318 -236 # -236 -318 100 -330 # -356 -236 -330 90 # TARGET: Crab-eating macaque SEQ1_DIR=/hive/data/genomes/macFas5/macFas5.2bit SEQ1_LEN=/hive/data/genomes/macFas5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=50 # QUERY: Green monkey chlSab1 SEQ2_DIR=/hive/data/genomes/chlSab1/chlSab1.2bit SEQ2_LEN=/hive/data/genomes/chlSab1/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LAP=0 SEQ2_LIMIT=200 BASE=/hive/data/genomes/macFas5/bed/lastzChlSab1.2014-05-15 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 595m54.836s cat fb.macFas5.chainChlSab1Link.txt # 2602112483 bases of 2803866698 (92.804%) in intersection time (doRecipBest.pl -buildDir=`pwd` macFas5 chlSab1) > rbest.log 2>&1 & # real 73m55.625s # and for the swap: mkdir /hive/data/genomes/chlSab1/bed/blastz.macFas5.swap cd /hive/data/genomes/chlSab1/bed/blastz.macFas5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/macFas5/bed/lastzChlSab1.2014-05-15/DEF \ -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -swap -syntenicNet) > do.log 2>&1 XXX - running - Wed Jan 21 09:38:12 PST 2015 # real 117m56.319s cat fb.chlSab1.chainMacFas5Link.txt # 2665801248 bases of 2725905606 (97.795%) in intersection time (doRecipBest.pl -buildDir=`pwd` chlSab1 macFas5) > rbest.log 2>&1 # real 79m30.931s ######################################################################### # LASTZ Crab-eating macaque/macFas5 Green monkey/papHam1 - # (DONE - 2014-05-15 - Hiram) mkdir /hive/data/genomes/macFas5/bed/lastzPapHam1.2014-05-15 cd /hive/data/genomes/macFas5/bed/lastzPapHam1.2014-05-15 cat << '_EOF_' > DEF # Crab-eating macaque vs. Baboon # parameters used are from the human-chimp tuning from long ago BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.52/bin/lastz BLASTZ_M=245 BLASTZ_O=600 BLASTZ_E=150 BLASTZ_T=2 BLASTZ_Y=15000 BLASTZ_K=4500 BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q # A C G T # 90 -330 -236 -356 # -330 100 -318 -236 # -236 -318 100 -330 # -356 -236 -330 90 # TARGET: Crab-eating macaque SEQ1_DIR=/hive/data/genomes/macFas5/macFas5.2bit SEQ1_LEN=/hive/data/genomes/macFas5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=50 # QUERY: Baboon papHam1 SEQ2_DIR=/hive/data/genomes/papHam1/papHam1.2bit SEQ2_LEN=/hive/data/genomes/papHam1/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LAP=0 SEQ2_LIMIT=1500 BASE=/hive/data/genomes/macFas5/bed/lastzPapHam1.2014-05-15 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 525m11.457s # real 73m16.304s cat fb.macFas5.chainPapHam1Link.txt # 2486618688 bases of 2803866698 (88.685%) in intersection time (doRecipBest.pl -buildDir=`pwd` macFas5 papHam1) > rbest.log 2>&1 & # real 109m2.057s # and for the swap: (DONE - 2015-01-26 - Hiram) mkdir /hive/data/genomes/papHam1/bed/blastz.macFas5.swap cd /hive/data/genomes/papHam1/bed/blastz.macFas5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/macFas5/bed/lastzPapHam1.2014-05-15/DEF \ -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -swap -syntenicNet) > do.log 2>&1 # real 619m9.663s cat fb.papHam1.chainMacFas5Link.txt # 2522131870 bases of 2741849051 (91.987%) in intersection time (doRecipBest.pl -buildDir=`pwd` papHam1 macFas5) > rbest.log 2>&1 # real 244m37.728s -######################################################################### +############################################################################## +# LASTZ Crab-eating macaque MacFas5 vs. Rhesus RheMac2 +# (DONE - 2021-10-12 - hiram) + + cd /cluster/home/hiram/kent/src/hg/makeDb/doc/macFas5 + + time (~/kent/src/hg/utils/automation/pairLastz.sh macFas5 rheMac2 \ + primate primate) > macFas5.rheMac2.log 2>&1 & + # real 366m28.349s + # user 0m1.422s + # sys 0m1.082s + + # the following make doc is in that log file, copied here: + + mkdir /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12 + cd /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12 + + printf '# Rhesus RheMac2 vs. Crab-eating macaque MacFas5 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +BLASTZ_T=2 +BLASTZ_O=600 +BLASTZ_E=150 +BLASTZ_M=254 +BLASTZ_K=4500 +BLASTZ_Y=15000 +BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q +# A C G T +# A 90 -330 -236 -356 +# C -330 100 -318 -236 +# G -236 -318 100 -330 +# T -356 -236 -330 90 + +# TARGET: Crab-eating macaque MacFas5 +SEQ1_DIR=/hive/data/genomes/macFas5/macFas5.2bit +SEQ1_LEN=/hive/data/genomes/macFas5/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Rhesus RheMac2 +SEQ2_DIR=/hive/data/genomes/rheMac2/rheMac2.2bit +SEQ2_LEN=/hive/data/genomes/rheMac2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 158m45.932s + + sed -e 's/^/ # /;' fb.macFas5.chainRheMac2Link.txt + # 2614119665 bases of 2803866698 (93.233%) in intersection + sed -e 's/^/ # /;' fb.macFas5.chainSynRheMac2Link.txt + # 2604737022 bases of 2803866698 (92.898%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + macFas5 rheMac2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 77m6.953s + + sed -e 's/^/ # /;' fb.macFas5.chainRBest.RheMac2.txt + # 2596696673 bases of 2803866698 (92.611%) in intersection + + ### and for the swap + + cd /hive/data/genomes/rheMac2/bed/blastz.macFas5.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/macFas5/bed/lastzRheMac2.2021-10-12/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 76m2.171s + + sed -e 's/^/ # /;' fb.rheMac2.chainMacFas5Link.txt + # 2600572513 bases of 2646704109 (98.257%) in intersection + sed -e 's/^/ # /;' fb.rheMac2.chainSynMacFas5Link.txt + # 2595637716 bases of 2646704109 (98.071%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + rheMac2 macFas5) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 54m32.803s + + sed -e 's/^/ # /;' fb.rheMac2.chainRBest.MacFas5.txt + # 2596730835 bases of 2646704109 (98.112%) in intersection + + +##############################################################################