############################################################################# # LASTZ Malayan flying lemur/galVar1 - (DONE - 2017-03-09 - Hiram) mkdir /hive/data/genomes/tupChi1/bed/lastzGalVar1.2017-03-09 cd /hive/data/genomes/tupChi1/bed/lastzGalVar1.2017-03-09 printf '# Chinese tree shrew vs Malayan flying lemur BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: Chinese tree shrew tupChi1 SEQ1_DIR=/hive/data/genomes/tupChi1/tupChi1.2bit SEQ1_LEN=/hive/data/genomes/tupChi1/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=1000 SEQ1_LAP=10000 # TARGET: Malayan flying lemur galVar1 SEQ2_DIR=/hive/data/genomes/galVar1/galVar1.2bit SEQ2_LEN=/hive/data/genomes/galVar1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LIMIT=800 SEQ2_LAP=0 BASE=/hive/data/genomes/tupChi1/bed/lastzGalVar1.2017-03-09 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 440m32.995s cat fb.tupChi1.chainGalVar1Link.txt # 1414140103 bases of 2706389135 (52.252%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupChi1 galVar1) \ > rbest.log 2>&1 & # real 81m49.289s # and for the swap: mkdir /hive/data/genomes/galVar1/bed/blastz.tupChi1.swap cd /hive/data/genomes/galVar1/bed/blastz.tupChi1.swap time (doBlastzChainNet.pl -verbose=2 -swap \ /hive/data/genomes/tupChi1/bed/lastzGalVar1.2017-03-09/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 320m48.042s cat fb.galVar1.chainTupChi1Link.txt # 1491449851 bases of 2802917674 (53.211%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galVar1 tupChi1) \ > rbest.log 2>&1 # real 146m1.658s ######################################################################### # swap lastz/chain/net (DONE - 2017-03-09 - Hiram) # original alignment cd /hive/data/genomes/mm10/bed/lastzTupChi1.2017-03-09 cat fb.mm10.chainTupChi1Link.txt # 683463709 bases of 2652783500 (25.764%) in intersection # and for the swap: mkdir /hive/data/genomes/tupChi1/bed/blastz.mm10.swap cd /hive/data/genomes/tupChi1/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzTupChi1.2017-03-09/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 71m4.702s cat fb.tupChi1.chainMm10Link.txt # 708757944 bases of 2706389135 (26.188%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupChi1 mm10) \ > rbest.log 2>&1 # real 508m10.564s ############################################################################# # swap lastz/chain/net hg19/human (DONE - 2013-07-07 - Hiram) # original alignment /hive/data/genomes/hg19/bed/lastzTupChi1.2013-07-05 cat fb.hg19.chainTupChi1Link.txt # 1348933101 bases of 2897316137 (46.558%) in intersection # running the swap mkdir /hive/data/genomes/tupChi1/bed/blastz.hg19.swap cd /hive/data/genomes/tupChi1/bed/blastz.hg19.swap time nice -n +19 doBlastzChainNet.pl -verbose=2 \ -swap /hive/data/genomes/hg19/bed/lastzTupChi1.2013-07-05/DEF \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \ -syntenicNet > swap.log 2>&1 # real 118m8.921s cat fb.tupChi1.chainHg19Link.txt # 1360938926 bases of 2706389135 (50.286%) in intersection cd /hive/data/genomes/tupChi1/bed ln -s blastz.hg19.swap lastz.hg19 doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupChi1 hg19 # real 745m37.336s ######################################################################### # swap lastz/chain/net hg38/human (DONE - 2015-02-17 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17 cat fb.hg38.chainTupChi1Link.txt # 1379994626 bases of 3049335806 (45.256%) in intersection # and for the swap: mkdir /hive/data/genomes/tupChi1/bed/blastz.hg38.swap cd /hive/data/genomes/tupChi1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 119m54.935s cat fb.tupChi1.chainHg38Link.txt # 1362665822 bases of 2706389135 (50.350%) in intersection time (doRecipBest.pl -buildDir=`pwd` tupChi1 hg38) > rbest.log 2>&1 # real 43m38.032s ######################################################################### # lastz/chain/net tupBel1/tree shrew (DONE - 2017-03-07 - Hiram) mkdir /hive/data/genomes/tupChi1/bed/lastzTupBel1.2017-03-07 cd /hive/data/genomes/tupChi1/bed/lastzTupBel1.2017-03-07 printf '# Chinese tree shrew vs. tree shrew BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: Chinese tree shrew tupChi1 hg38 SEQ1_DIR=/hive/data/genomes/tupChi1/tupChi1.2bit SEQ1_LEN=/hive/data/genomes/tupChi1/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=300 SEQ1_LAP=10000 # QUERY: tree shrew tupBel1 SEQ2_DIR=/hive/data/genomes/tupBel1/tupBel1.2bit SEQ2_LEN=/hive/data/genomes/tupBel1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LIMIT=1000 SEQ2_LAP=0 BASE=/hive/data/genomes/tupChi1/bed/lastzTupBel1.2017-03-07 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # failed during chaining due to 10 Gb process memory limit # real 226m29.056s # finish last chain job on hgwdev with plenty of memory time ./chain.csh part124.lst chain/part124.lst.chain # real 287m42.860s # continuing: time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku \ -bigClusterHub=ku -syntenicNet \ -continue=chainMerge) > chainMerge.log 2>&1 # real 648m50.732s cat fb.tupChi1.chainTupBel1Link.txt # 2141976820 bases of 2706389135 (79.145%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupChi1 galVar1) \ > rbest.log 2>&1 & # real real 81m58.778s # and for the swap: mkdir /hive/data/genomes/tupBel1/bed/blastz.tupChi1.swap cd /hive/data/genomes/tupBel1/bed/blastz.tupChi1.swap time (doBlastzChainNet.pl -verbose=2 -swap \ /hive/data/genomes/tupChi1/bed/lastzGalVar1.2017-03-09/DEF -verbose=2 \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 925m18.998s cat fb.tupBel1.chainTupChi1Link.txt # 2098821387 bases of 2137225476 (98.203%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupBel1 tupChi1) \ > rbest.log 2>&1 # real 188m5.418s #########################################################################