3d5b0dec29544546bf7e8be1d923433bc5d28428 hiram Thu Nov 28 11:04:34 2019 -0800 done with regenCho1 chainNet refs #24524 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index 7af83b0..67a20e3 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -12271,58 +12271,56 @@ TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 & # real 162m40.237s cat fb.hg38.chainRegenRn1Link.txt # 863041482 bases of 3095998939 (27.876%) in intersection cat fb.hg38.chainSynRegenRn1Link.txt # 809332351 bases of 3095998939 (26.141%) in intersection time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 regenRn1) > rbest.log 2>&1 & -XXX - running - Fri Sep 13 11:41:44 PDT 2019 - # real 328m4.069s + # real 261m19.645s cat fb.hg38.chainRBest.RegenRn1.txt - # 857127621 bases of 3095998939 (27.685%) in intersection + # 792532873 bases of 3095998939 (25.599%) in intersection # and for the swap: mkdir /hive/data/genomes/regenRn1/bed/blastz.hg38.swap cd /hive/data/genomes/regenRn1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 63m47.773s cat fb.regenRn1.chainHg38Link.txt # 827167139 bases of 2282482188 (36.240%) in intersection cat fb.regenRn1.chainSynHg38Link.txt # 788025130 bases of 2282482188 (34.525%) in intersection time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 hg38) > rbest.log 2>&1 -XXX - running - Fri Sep 13 12:07:31 PDT 2019 - # real 300m30.411s + # real 300m50.570s cat fb.regenRn1.chainRBest.Hg38.txt - # 858923025 bases of 2534810853 (33.885%) in intersection + # 793987134 bases of 2282482188 (34.786%) in intersection ######################################################################### # LASTZ human/hg38 Gorilla/gorGor6 - (DONE - 2019-11-20 - Hiram) mkdir /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20 cd /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20 printf '# human vs gorilla BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/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 @@ -12379,19 +12377,94 @@ time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 63m46.473s cat fb.gorGor6.chainHg38Link.txt # 2738870921 bases of 2999027915 (91.325%) in intersection cat fb.gorGor6.chainSynHg38Link.txt # 2728591501 bases of 2999027915 (90.983%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` gorGor6 hg38) \ > rbest.log 2>&1 -XXX - running - Tue Nov 26 11:55:51 PST 2019 - # real 125m35.459s + # real 62m14.470s -########################################################################### + cat fb.gorGor6.chainRBest.Hg38.txt + # 2697792568 bases of 2999027915 (89.956%) in intersection + +############################################################################# +# LASTZ human/hg38 vs. Chinese hamster CHO-K1 cell line/regenCho1 +# (DONE - 2019-11-26 - Hiram) + + mkdir /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26 + cd /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26 + + printf '# human vs Chinese hamster ovary CHO-K1 cell line +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz +BLASTZ_M=254 + +# TARGET: human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit +SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes +SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift +SEQ1_CHUNK=40000000 +SEQ1_LIMIT=20 +SEQ1_LAP=10000 + +# QUERY: Chinese hamster ovary CHO-K1 cell line regenCho1 +SEQ2_DIR=/hive/data/genomes/regenCho1/regenCho1.2bit +SEQ2_LEN=/hive/data/genomes/regenCho1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LIMIT=20 +SEQ2_LAP=0 + +BASE=/hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ + -chainMinScore=3000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -noDbNameCheck -syntenicNet) > do.log 2>&1 + # real 376m47.828s + + cat fb.hg38.chainRegenCho1Link.txt + # 979733899 bases of 3095998939 (31.645%) in intersection + cat fb.hg38.chainSynRegenCho1Link.txt + # 917104031 bases of 3095998939 (29.622%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + hg38 regenCho1) > rbest.log 2>&1 & + # real 259m42.688s + + cat fb.hg38.chainRBest.RegenCho1.txt + # 901006295 bases of 3095998939 (29.102%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/regenCho1/bed/blastz.hg38.swap + cd /hive/data/genomes/regenCho1/bed/blastz.hg38.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26/DEF \ + -swap -chainMinScore=3000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -noDbNameCheck -syntenicNet) > swap.log 2>&1 + # real 79m18.904s + + cat fb.regenCho1.chainHg38Link.txt + # 956720146 bases of 2266312740 (42.215%) in intersection + cat fb.regenCho1.chainSynHg38Link.txt + # 895755077 bases of 2266312740 (39.525%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + regenCho1 hg38) > rbest.log 2>&1 & + # real 289m24.440s + + cat fb.regenCho1.chainRBest.Hg38.txt + # 902782523 bases of 2266312740 (39.835%) in intersection + +#########################################################################