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/rheMac10/lastzRuns.txt src/hg/makeDb/doc/rheMac10/lastzRuns.txt index f3b5f67..c8b66a2 100644 --- src/hg/makeDb/doc/rheMac10/lastzRuns.txt +++ src/hg/makeDb/doc/rheMac10/lastzRuns.txt @@ -1,66 +1,166 @@ ############################################################################## # LASTZ Rat rn6 (DONE - 2020-10-20 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20 cd /hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20 printf '# rat vs rhesus BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Rhesus RheMac10 SEQ1_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit SEQ1_LEN=/hive/data/genomes/rheMac10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rat Rn6 SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit SEQ2_LEN=/hive/data/genomes/rn6/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=500 BASE=/hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20 TMPDIR=/dev/shm ' > DEF # establish a screen to control this job screen -S rheMac10Rn6 time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & # real 278m29.024s cat fb.rheMac10.chainRn6Link.txt # 901231172 bases of 2936892733 (30.687%) in intersection cat fb.rheMac10.chainSynRn6Link.txt # 854008376 bases of 2936892733 (29.079%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ rheMac10 rn6) > rbest.log 2>&1 & # real 293m29.540s cat fb.rheMac10.chainRBest.Rn6.txt # 860406990 bases of 2936892733 (29.297%) in intersection mkdir /hive/data/genomes/rn6/bed/blastz.rheMac10.swap cd /hive/data/genomes/rn6/bed/blastz.rheMac10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/rheMac10/bed/lastzRn6.2020-10-20/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 61m59.379s cat fb.rn6.chainRheMac10Link.txt # 938991388 bases of 2729860805 (34.397%) in intersection cat fb.rn6.chainSynRheMac10Link.txt # 873546846 bases of 2729860805 (32.000%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ rn6 rheMac10) > rbest.log 2>&1 # real 358m51.937s cat fb.rn6.chainRBest.RheMac10.txt # 861947799 bases of 2729860805 (31.575%) in intersection -######################################################################### +############################################################################## +# LASTZ Rhesus RheMac10 vs. Crab-eating macaque MacFas5 +# (DONE - 2021-10-12 - hiram) + + cd /cluster/home/hiram/kent/src/hg/makeDb/doc/rheMac10 + time (~/kent/src/hg/utils/automation/pairLastz.sh rheMac10 macFas5 \ + primate primate) > rheMac10.macFas5.log 2>&1 & + # real 422m56.515s + # user 0m1.550s + # sys 0m1.626s + + # the following make doc is in that log file, copied here: + + mkdir /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12 + cd /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12 + + printf '# Crab-eating macaque MacFas5 vs. Rhesus RheMac10 +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: Rhesus RheMac10 +SEQ1_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit +SEQ1_LEN=/hive/data/genomes/rheMac10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Crab-eating macaque MacFas5 +SEQ2_DIR=/hive/data/genomes/macFas5/macFas5.2bit +SEQ2_LEN=/hive/data/genomes/macFas5/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12 +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 188m26.969s + + sed -e 's/^/ # /;' fb.rheMac10.chainMacFas5Link.txt + # 2784170031 bases of 2936892733 (94.800%) in intersection + sed -e 's/^/ # /;' fb.rheMac10.chainSynMacFas5Link.txt + # 2760382026 bases of 2936892733 (93.990%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + rheMac10 macFas5) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 96m55.151s + + sed -e 's/^/ # /;' fb.rheMac10.chainRBest.MacFas5.txt + # 2728786009 bases of 2936892733 (92.914%) in intersection + + ### and for the swap + + cd /hive/data/genomes/macFas5/bed/blastz.rheMac10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/rheMac10/bed/lastzMacFas5.2021-10-12/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 71m1.507s + + sed -e 's/^/ # /;' fb.macFas5.chainRheMac10Link.txt + # 2739714634 bases of 2803866698 (97.712%) in intersection + sed -e 's/^/ # /;' fb.macFas5.chainSynRheMac10Link.txt + # 2729711862 bases of 2803866698 (97.355%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + macFas5 rheMac10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 66m32.559s + + sed -e 's/^/ # /;' fb.macFas5.chainRBest.RheMac10.txt + # 2730109619 bases of 2803866698 (97.369%) in intersection + +############################################################################## +