116b53aa88a02bcecec4ce0362a8277eec749073 gperez2 Wed Dec 20 23:06:53 2023 -0800 panTro6 vs. macFas5, lastz/chain/net run for user, refs #32760 diff --git src/hg/makeDb/doc/macFas5/lastzRuns.txt src/hg/makeDb/doc/macFas5/lastzRuns.txt index ec63cb0..de8ae7f 100644 --- src/hg/makeDb/doc/macFas5/lastzRuns.txt +++ src/hg/makeDb/doc/macFas5/lastzRuns.txt @@ -333,15 +333,108 @@ -query2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \ \ macFas5 GCA_011100615.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 72m23.439s sed -e 's/^/ # /;' fb.macFas5.chainRBest.GCA_011100615.1.txt # 2680072146 bases of 2946843737 (90.947%) in intersection real 354m14.218s user 0m3.158s sys 0m3.325s ############################################################################## +# LASTZ Chimp PanTro6 vs. Crab-eating macaque MacFas5 +# (DONE - 2023-12-11 - gperez2) + + mkdir /hive/data/genomes/panTro6/bed/lastzMacFas5.2023-12-11 + cd /hive/data/genomes/panTro6/bed/lastzMacFas5.2023-12-11 + + printf '# Crab-eating macaque MacFas5 vs. Chimp PanTro6 +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: Chimp panTro6 +SEQ1_DIR=/hive/data/genomes/panTro6/panTro6.2bit +SEQ1_LEN=/hive/data/genomes/panTro6/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/panTro6/bed/lastzMacFas5.2023-12-11 +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 93m4.325s + + sed -e 's/^/ # /;' fb.panTro6.chainMacFas5Link.txt + # 2482510656 bases of 3018592990 (82.241%) in intersection + sed -e 's/^/ # /;' fb.panTro6.chainSynMacFas5Link.txt + # 2446198446 bases of 3018592990 (81.038%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + panTro6 macFas5) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 113m36.180s + + sed -e 's/^/ # /;' fb.panTro6.chainRBest.MacFas5.txt + # 2400158905 bases of 3018592990 (79.513%) in intersection + + ### and for the swap + + cd /hive/data/genomes/macFas5/bed/blastz.panTro6.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/panTro6/bed/lastzMacFas5.2023-12-11/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 57m31.785s + + sed -e 's/^/ # /;' fb.macFas5.chainPanTro6Link.txt + # 2430179833 bases of 2803866698 (86.672%) in intersection + sed -e 's/^/ # /;' fb.macFas5.chainSynPanTro6Link.txt + # 2406117748 bases of 2803866698 (85.814%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + macFas5 panTro6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 106m35.531s + + sed -e 's/^/ # /;' fb.macFas5.chainRBest.PanTro6.txt + # 2400398207 bases of 2803866698 (85.610%) in intersection + +real 370m48.159s +user 0m1.744s +sys 0m1.977s +##############################################################################