######################################################################### # LASTZ turkey/melGal5 vs. zebrafish - (DONE - 2017-01-19 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzDanRer10.2017-01-19 cd /hive/data/genomes/melGal5/bed/lastzDanRer10.2017-01-19 printf '# turkey vs. zebrafish BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=200 SEQ1_LAP=10000 # QUERY: zebrafish danRer10 SEQ2_DIR=/hive/data/genomes/danRer10/danRer10.2bit SEQ2_LEN=/hive/data/genomes/danRer10/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/melGal5/bed/lastzDanRer10.2017-01-19 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 298m19.694s cat fb.melGal5.chainDanRer10Link.txt # 26799847 bases of 1093044709 (2.452%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 danRer10) \ > rbest.log 2>&1 & # real 115m59.033s # and for the swap: mkdir /hive/data/genomes/danRer10/bed/blastz.melGal5.swap cd /hive/data/genomes/danRer10/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzDanRer10.2017-01-19/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 4m25.214s cat fb.danRer10.chainMelGal5Link.txt # 35212655 bases of 1369683683 (2.571%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` danRer10 melGal5) \ > rbest.log 2>&1 # real 129m59.859s ######################################################################### # LASTZ turkey/melGal5 vs. frog - (DONE - 2017-01-19 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzXenTro7.2017-01-19 cd /hive/data/genomes/melGal5/bed/lastzXenTro7.2017-01-19 printf '# turkey vs. frog BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=300 SEQ1_LAP=10000 # QUERY: frog xenTro7 SEQ2_DIR=/hive/data/genomes/xenTro7/xenTro7.2bit SEQ2_LEN=/hive/data/genomes/xenTro7/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/melGal5/bed/lastzXenTro7.2017-01-19 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 319m41.125s cat fb.melGal5.chainXenTro7Link.txt # 39051789 bases of 1093044709 (3.573%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 xenTro7) \ > rbest.log 2>&1 & # real 202m32.347s # and for the swap: mkdir /hive/data/genomes/xenTro7/bed/blastz.melGal5.swap cd /hive/data/genomes/xenTro7/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzXenTro7.2017-01-19/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 5m0.297s cat fb.xenTro7.chainMelGal5Link.txt # 45799596 bases of 1365936747 (3.353%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro7 melGal5) \ > rbest.log 2>&1 # real 204m15.717s ######################################################################### # LASTZ turkey/melGal5 vs. medium ground finch - (DONE - 2017-01-20 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 cd /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 printf '# turkey vs. Medium ground finch BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=500 SEQ1_LAP=10000 # QUERY: Medium ground finch geoFor1 SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=200 BASE=/hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 403m51.968s cat fb.melGal5.chainGeoFor1Link.txt # 740714391 bases of 1093044709 (67.766%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 geoFor1) \ > rbest.log 2>&1 & # real 333m12.871s # lost the rbest.log file # and for the swap: mkdir /hive/data/genomes/geoFor1/bed/blastz.melGal5.swap cd /hive/data/genomes/geoFor1/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 65m39.225s cat fb.geoFor1.chainMelGal5Link.txt # 725536636 bases of 1041286029 (69.677%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` geoFor1 melGal5) \ > rbest.log 2>&1 # real 291m40.237s ######################################################################### # LASTZ turkey/melGal5 vs. medium ground finch - (DONE - 2017-01-20 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 cd /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 printf '# turkey vs. Peregrine falcon BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=400 SEQ1_LAP=10000 # QUERY: Peregrine falcon falPer1 SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=80 BASE=/hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 422m43.269s cat fb.melGal5.chainFalPer1Link.txt # 854639905 bases of 1093044709 (78.189%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 falPer1) \ > rbest.log 2>&1 & # real 336m8.770s # and for the swap: mkdir /hive/data/genomes/falPer1/bed/blastz.melGal5.swap cd /hive/data/genomes/falPer1/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 64m19.073s cat fb.falPer1.chainMelGal5Link.txt # 826670414 bases of 1153404357 (71.672%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` falPer1 melGal5) \ > rbest.log 2>&1 # real 247m39.409s ######################################################################### # swap lastz/chainNet from galGal5 chicken (DONE - 2017-01-19 - Hiram) # alignment of melGal5 to galGal5: cd /hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19 cat fb.galGal5.chainMelGal5Link.txt # 1029400481 bases of 1218501075 (84.481%) in intersection # and for the swap: mkdir /hive/data/genomes/melGal5/bed/blastz.galGal5.swap cd /hive/data/genomes/melGal5/bed/blastz.galGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/galGal5/bed/lastzMelGal5.2017-01-19/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 284m22.838s cat fb.melGal5.chainGalGal5Link.txt # 984928299 bases of 1093044709 (90.109%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 galGal5) \ > rbest.log 2>&1 # real 487m51.030s ######################################################################### # LASTZ turkey/melGal5 vs. Peregrine falcon - (DONE - 2017-01-20 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 cd /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 printf '# turkey vs. Peregrine falcon BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=400 SEQ1_LAP=10000 # QUERY: Peregrine falcon falPer1 SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=80 BASE=/hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 422m43.269s cat fb.melGal5.chainFalPer1Link.txt # 854639905 bases of 1093044709 (78.189%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 falPer1) \ > rbest.log 2>&1 & # real 336m8.770s # and for the swap: mkdir /hive/data/genomes/falPer1/bed/blastz.melGal5.swap cd /hive/data/genomes/falPer1/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 64m19.073s cat fb.falPer1.chainMelGal5Link.txt # 826670414 bases of 1153404357 (71.672%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` falPer1 melGal5) \ > rbest.log 2>&1 # real 247m39.409s ######################################################################### # LASTZ turkey/melGal5 vs. Medium ground finch - (DONE - 2017-01-20 - Hiram) mkdir /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 cd /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 printf '# turkey vs. Medium ground finch BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: turkey melGal5 SEQ1_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ1_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LIMIT=400 SEQ1_LAP=10000 # QUERY: Medium ground finch geoFor1 SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=80 BASE=/hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > do.log 2>&1 # real 403m51.968s cat fb.melGal5.chainGeoFor1Link.txt # 740714391 bases of 1093044709 (67.766%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 geoFor1) \ > rbest.log 2>&1 & # lost log file # and for the swap: mkdir /hive/data/genomes/geoFor1/bed/blastz.melGal5.swap cd /hive/data/genomes/geoFor1/bed/blastz.melGal5.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/melGal5/bed/lastzGeoFor1.2017-01-20/DEF \ -swap -chainMinScore=5000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 65m39.225s cat fb.geoFor1.chainMelGal5Link.txt # 725536636 bases of 1041286029 (69.677%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` geoFor1 melGal5) \ > rbest.log 2>&1 # real 291m40.237s #########################################################################