######################################################################### # LASTZ C. japonica/caeJap4 - (DONE - 2015-06-25 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaeJap4.2015-06-25 cd /hive/data/genomes/ce11/bed/lastzCaeJap4.2015-06-25 cat << '_EOF_' > DEF # ce11 vs caeJap4 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: C. japonica caeJap4 SEQ2_DIR=/scratch/data/caeJap4/caeJap4.2bit SEQ2_LEN=/scratch/data/caeJap4/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaeJap4.2015-06-25 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 16m5.192s cat fb.ce11.chainCaeJap4Link.txt # 27788713 bases of 100286401 (27.709%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caeJap4) > rbest.log 2>&1 & # real 1m14.336s (lost the rbest.log) # and for the swap: mkdir /hive/data/genomes/caeJap4/bed/blastz.ce11.swap cd /hive/data/genomes/caeJap4/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaeJap4.2015-06-25/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m23.708s cat fb.caeJap4.chainCe11Link.txt # 30092433 bases of 154057934 (19.533%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeJap4 ce11) \ > rbest.log 2>&1 # real 2m9.571s ######################################################################### # LASTZ M. hapla/melHap1 - (DONE - 2015-06-26 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzMelHap1.2015-06-26 cd /hive/data/genomes/ce11/bed/lastzMelHap1.2015-06-26 cat << '_EOF_' > DEF # ce11 vs melHap1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Meloidogyne hapla melHap1 SEQ2_DIR=/scratch/data/melHap1/melHap1.2bit SEQ2_LEN=/scratch/data/melHap1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzMelHap1.2015-06-26 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 4m26.505s cat fb.ce11.chainMelHap1Link.txt # 3927661 bases of 100286401 (3.916%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 melHap1) > rbest.log 2>&1 & # real 0m26.480s # and for the swap: mkdir /hive/data/genomes/melHap1/bed/blastz.ce11.swap cd /hive/data/genomes/melHap1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzMelHap1.2015-06-26/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m50.085s cat fb.melHap1.chainCe11Link.txt # 3626430 bases of 53017507 (6.840%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 ce11) \ > rbest.log 2>&1 # real 0m28.275s ######################################################################### # LASTZ C. angaria/caeAng2 - (DONE - 2015-06-30 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaeAng2.2015-06-30 cd /hive/data/genomes/ce11/bed/lastzCaeAng2.2015-06-30 cat << '_EOF_' > DEF # ce11 vs caeAng2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: C. angaria caeAng2 SEQ2_DIR=/hive/data/genomes/caeAng2/caeAng2.2bit SEQ2_LEN=/hive/data/genomes/caeAng2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaeAng2.2015-06-30 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 19m36.998s cat fb.ce11.chainCaeAng2Link.txt # 17733068 bases of 100286401 (17.682%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caeAng2) > rbest.log 2>&1 & # real 1m1.211s # and for the swap: mkdir /hive/data/genomes/caeAng2/bed/blastz.ce11.swap cd /hive/data/genomes/caeAng2/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaeAng2.2015-06-30/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 8m32.125s cat fb.caeAng2.chainCe11Link.txt # 19987227 bases of 95237926 (20.987%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeAng2 ce11) \ > rbest.log 2>&1 # real 4m36.188s ######################################################################### # LASTZ M. incognita/melInc2 - (DONE - 2015-06-30 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzMelInc2.2015-06-30 cd /hive/data/genomes/ce11/bed/lastzMelInc2.2015-06-30 cat << '_EOF_' > DEF # ce11 vs melInc2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: M. incognita melInc2 SEQ2_DIR=/hive/data/genomes/melInc2/melInc2.2bit SEQ2_LEN=/hive/data/genomes/melInc2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzMelInc2.2015-06-30 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 5m19.519s cat fb.ce11.chainMelInc2Link.txt # 3526393 bases of 100286401 (3.516%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 melInc2) > rbest.log 2>&1 & # real 0m36.875s # and for the swap: mkdir /hive/data/genomes/melInc2/bed/blastz.ce11.swap cd /hive/data/genomes/melInc2/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzMelInc2.2015-06-30/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m2.321s cat fb.melInc2.chainCe11Link.txt # 4548339 bases of 82114761 (5.539%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 ce11) \ > rbest.log 2>&1 # real 0m30.384s ######################################################################### # LASTZ Panagrellus redivivus/panRed1 - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzPanRed1.2015-07-01 cd /hive/data/genomes/ce11/bed/lastzPanRed1.2015-07-01 cat << '_EOF_' > DEF # ce11 vs panRed1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Panagrellus redivivus panRed1 SEQ2_DIR=/hive/data/genomes/panRed1/panRed1.2bit SEQ2_LEN=/hive/data/genomes/panRed1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzPanRed1.2015-07-01 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 4m27.377s cat fb.ce11.chainPanRed1Link.txt # 6603624 bases of 100286401 (6.585%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 panRed1) > rbest.log 2>&1 & # real 0m33.563s # and for the swap: mkdir /hive/data/genomes/panRed1/bed/blastz.ce11.swap cd /hive/data/genomes/panRed1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzPanRed1.2015-07-01/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m53.970s cat fb.panRed1.chainCe11Link.txt # 6446092 bases of 62228262 (10.359%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 ce11) \ > rbest.log 2>&1 # real 0m38.503s ######################################################################### # LASTZ Pristionchus pacificus/priPac3 - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzPriPac3.2015-07-01 cd /hive/data/genomes/ce11/bed/lastzPriPac3.2015-07-01 cat << '_EOF_' > DEF # ce11 vs priPac3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Pristionchus pacificus priPac3 SEQ2_DIR=/hive/data/genomes/priPac3/priPac3.2bit SEQ2_LEN=/hive/data/genomes/priPac3/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzPriPac3.2015-07-01 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 16m34.215s cat fb.ce11.chainPriPac3Link.txt # 6326413 bases of 100286401 (6.308%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 priPac3) > rbest.log 2>&1 & # real 0m37.219s # and for the swap: mkdir /hive/data/genomes/priPac3/bed/blastz.ce11.swap cd /hive/data/genomes/priPac3/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzPriPac3.2015-07-01/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m13.447s cat fb.priPac3.chainCe11Link.txt # 6947156 bases of 153238914 (4.534%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 ce11) \ > rbest.log 2>&1 # real 0m48.989s ######################################################################### # LASTZ Caenorhabditis briggsae/cb4 - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCb4.2015-07-01 cd /hive/data/genomes/ce11/bed/lastzCb4.2015-07-01 cat << '_EOF_' > DEF # ce11 vs cb4 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis briggsae cb4 SEQ2_DIR=/hive/data/genomes/cb4/cb4.2bit SEQ2_LEN=/hive/data/genomes/cb4/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCb4.2015-07-01 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 11m45.085s cat fb.ce11.chainCb4Link.txt # 39496335 bases of 100286401 (39.384%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 cb4) > rbest.log 2>&1 & # real 1m44.529s # and for the swap: mkdir /hive/data/genomes/cb4/bed/blastz.ce11.swap cd /hive/data/genomes/cb4/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCb4.2015-07-01/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m3.364s cat fb.cb4.chainCe11Link.txt # 39234668 bases of 108371485 (36.204%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` cb4 ce11) \ > rbest.log 2>&1 # real 1m58.707s ######################################################################### # LASTZ Caenorhabditis brenneri/caePb3 - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaePb3.2015-07-01 cd /hive/data/genomes/ce11/bed/lastzCaePb3.2015-07-01 cat << '_EOF_' > DEF # ce11 vs caePb3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis brenneri caePb3 SEQ2_DIR=/hive/data/genomes/caePb3/caePb3.2bit SEQ2_LEN=/hive/data/genomes/caePb3/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaePb3.2015-07-01 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 14m1.774s cat fb.ce11.chainCaePb3Link.txt # 40753915 bases of 100286401 (40.638%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caePb3) > rbest.log 2>&1 & # real 1m31.030s (lost log ...) # and for the swap: mkdir /hive/data/genomes/caePb3/bed/blastz.ce11.swap cd /hive/data/genomes/caePb3/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaePb3.2015-07-01/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m54.518s cat fb.caePb3.chainCe11Link.txt # 54933712 bases of 170093652 (32.296%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caePb3 ce11) \ > rbest.log 2>&1 # real 2m14.946s ######################################################################### # LASTZ Caenorhabditis remanei/caeRem4 - (DONE - 2015-07-02 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaeRem4.2015-07-02 cd /hive/data/genomes/ce11/bed/lastzCaeRem4.2015-07-02 cat << '_EOF_' > DEF # ce11 vs caeRem4 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis remanei caeRem4 SEQ2_DIR=/hive/data/genomes/caeRem4/caeRem4.2bit SEQ2_LEN=/hive/data/genomes/caeRem4/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaeRem4.2015-07-02 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 11m45.453s cat fb.ce11.chainCaeRem4Link.txt # 41834559 bases of 100286401 (41.715%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caeRem4) > rbest.log 2>&1 & # real 1m31.160s # and for the swap: mkdir /hive/data/genomes/caeRem4/bed/blastz.ce11.swap cd /hive/data/genomes/caeRem4/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaeRem4.2015-07-02/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m26.148s cat fb.caeRem4.chainCe11Link.txt # 46250303 bases of 138406203 (33.416%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeRem4 ce11) \ > rbest.log 2>&1 # real 2m5.240s ######################################################################### # LASTZ Caenorhabditis remanei/haeCon2 - (DONE - 2015-07-07 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzHaeCon2.2015-07-07 cd /hive/data/genomes/ce11/bed/lastzHaeCon2.2015-07-07 cat << '_EOF_' > DEF # ce11 vs haeCon2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis remanei haeCon2 SEQ2_DIR=/hive/data/genomes/haeCon2/haeCon2.2bit SEQ2_LEN=/hive/data/genomes/haeCon2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzHaeCon2.2015-07-07 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 20m35.223s cat fb.ce11.chainHaeCon2Link.txt # 8961368 bases of 100286401 (8.936%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 haeCon2) > rbest.log 2>&1 & # real 0m45.145s # and for the swap: mkdir /hive/data/genomes/haeCon2/bed/blastz.ce11.swap cd /hive/data/genomes/haeCon2/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzHaeCon2.2015-07-07/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m2.810s cat fb.haeCon2.chainCe11Link.txt # 11782596 bases of 346001353 (3.405%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 ce11) \ > rbest.log 2>&1 # real 1m27.137s ######################################################################### # LASTZ Caenorhabditis tropicalis/caeSp111 - (DONE - 2015-07-07 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaeSp111.2015-07-07 cd /hive/data/genomes/ce11/bed/lastzCaeSp111.2015-07-07 cat << '_EOF_' > DEF # ce11 vs caeSp111 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis tropicalis caeSp111 SEQ2_DIR=/hive/data/genomes/caeSp111/caeSp111.2bit SEQ2_LEN=/hive/data/genomes/caeSp111/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaeSp111.2015-07-07 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 9m34.458s cat fb.ce11.chainCaeSp111Link.txt # 37978854 bases of 100286401 (37.870%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caeSp111) > rbest.log 2>&1 & # real 1m50.903s # and for the swap: mkdir /hive/data/genomes/caeSp111/bed/blastz.ce11.swap cd /hive/data/genomes/caeSp111/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaeSp111.2015-07-07/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m36.576s cat fb.caeSp111.chainCe11Link.txt # 36230284 bases of 76497192 (47.362%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp111 ce11) \ > rbest.log 2>&1 # real 1m52.882s ######################################################################### # LASTZ Brugia malayi/bruMal2 - (DONE - 2015-07-08 - Hiram) # incorrect date name on this directory, it is actually 07-08 # rerun with wolbachia in bruMal2 2015-08-11 mkdir /hive/data/genomes/ce11/bed/lastzBruMal2.2015-08-11 cd /hive/data/genomes/ce11/bed/lastzBruMal2.2015-08-11 cat << '_EOF_' > DEF # ce11 vs bruMal2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Brugia malayi bruMal2 SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzBruMal2.2015-08-11 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 16m9.123s cat fb.ce11.chainBruMal2Link.txt # 5079517 bases of 100286401 (5.065%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 bruMal2) > rbest.log 2>&1 & # real 0m32.617s # and for the swap: mkdir /hive/data/genomes/bruMal2/bed/blastz.ce11.swap cd /hive/data/genomes/bruMal2/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzBruMal2.2015-08-11/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m30.341s cat fb.bruMal2.chainCe11Link.txt # 4826613 bases of 87424120 (5.521%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 ce11) \ > rbest.log 2>&1 # real 0m35.554s ######################################################################### # LASTZ Caenorhabditis sp5 ju800/caeSp51 - (DONE - 2015-07-08 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzCaeSp51.2015-07-08 cd /hive/data/genomes/ce11/bed/lastzCaeSp51.2015-07-08 cat << '_EOF_' > DEF # ce11 vs caeSp51 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Caenorhabditis sp5 ju800 caeSp51 SEQ2_DIR=/hive/data/genomes/caeSp51/caeSp51.2bit SEQ2_LEN=/hive/data/genomes/caeSp51/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzCaeSp51.2015-07-08 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 15m45.540s cat fb.ce11.chainCaeSp51Link.txt # 40447272 bases of 100286401 (40.332%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 caeSp51) > rbest.log 2>&1 & # real 1m32.172s # and for the swap: mkdir /hive/data/genomes/caeSp51/bed/blastz.ce11.swap cd /hive/data/genomes/caeSp51/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzCaeSp51.2015-07-08/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 5m1.154s cat fb.caeSp51.chainCe11Link.txt # 41416178 bases of 130562982 (31.721%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` caeSp51 ce11) \ > rbest.log 2>&1 # real 2m24.577s ######################################################################### # LASTZ Strongyloides ratti/strRat2 - (DONE - 2015-07-09 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzStrRat2.2015-07-09 cd /hive/data/genomes/ce11/bed/lastzStrRat2.2015-07-09 cat << '_EOF_' > DEF # ce11 vs strRat2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Strongyloides ratti strRat2 SEQ2_DIR=/hive/data/genomes/strRat2/strRat2.2bit SEQ2_LEN=/hive/data/genomes/strRat2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzStrRat2.2015-07-09 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 6m56.113s cat fb.ce11.chainStrRat2Link.txt # 5685737 bases of 100286401 (5.669%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 strRat2) > rbest.log 2>&1 & # real 0m40.891s # and for the swap: mkdir /hive/data/genomes/strRat2/bed/blastz.ce11.swap cd /hive/data/genomes/strRat2/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzStrRat2.2015-07-09/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m33.814s cat fb.strRat2.chainCe11Link.txt # 5112630 bases of 43150242 (11.848%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat2 ce11) \ > rbest.log 2>&1 # real 6m38.814s ######################################################################### # LASTZ Strongyloides ratti/strRat1 - (DONE - 2015-07-09 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzStrRat1.2015-07-09 cd /hive/data/genomes/ce11/bed/lastzStrRat1.2015-07-09 cat << '_EOF_' > DEF # ce11 vs strRat1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Strongyloides ratti strRat1 SEQ2_DIR=/hive/data/genomes/strRat1/strRat1.2bit SEQ2_LEN=/hive/data/genomes/strRat1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzStrRat1.2015-07-09 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 7m12.063s cat fb.ce11.chainStrRat1Link.txt # 5240485 bases of 100286401 (5.226%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 strRat1) > rbest.log 2>&1 & # real 0m33.050s # and for the swap: mkdir /hive/data/genomes/strRat1/bed/blastz.ce11.swap cd /hive/data/genomes/strRat1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzStrRat1.2015-07-09/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m58.800s cat fb.strRat1.chainCe11Link.txt # 5068899 bases of 52634366 (9.630%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat1 ce11) \ > rbest.log 2>&1 # real 4m42.820s ######################################################################### # LASTZ Bursaphelenchus xylophilus/burXyl1 - (DONE - 2015-07-09 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzBurXyl1.2015-07-09 cd /hive/data/genomes/ce11/bed/lastzBurXyl1.2015-07-09 cat << '_EOF_' > DEF # ce11 vs burXyl1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Bursaphelenchus xylophilus burXyl1 SEQ2_DIR=/hive/data/genomes/burXyl1/burXyl1.2bit SEQ2_LEN=/hive/data/genomes/burXyl1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzBurXyl1.2015-07-09 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 10m8.319s cat fb.ce11.chainBurXyl1Link.txt # 6308717 bases of 100286401 (6.291%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 burXyl1) > rbest.log 2>&1 & # real 0m35.024s # and for the swap: mkdir /hive/data/genomes/burXyl1/bed/blastz.ce11.swap cd /hive/data/genomes/burXyl1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzBurXyl1.2015-07-09/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m57.394s cat fb.burXyl1.chainCe11Link.txt # 6062162 bases of 73100506 (8.293%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 ce11) \ > rbest.log 2>&1 # real 0m38.169s ######################################################################### # LASTZ Onchocerca volvulus/oncVol1 - (DONE - 2015-08-10 - Hiram) # run first time 2015-07-09 without wolbachia in oncVol1 # rerun with wolbachia in oncVol1 2015-08-10 mkdir /hive/data/genomes/ce11/bed/lastzOncVol1.2015-08-10 cd /hive/data/genomes/ce11/bed/lastzOncVol1.2015-08-10 cat << '_EOF_' > DEF # ce11 vs oncVol1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Onchocerca volvulus oncVol1 SEQ2_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit SEQ2_LEN=/hive/data/genomes/oncVol1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzOncVol1.2015-08-10 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 6m19.199s cat fb.ce11.chainOncVol1Link.txt # 5207855 bases of 100286401 (5.193%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 oncVol1) > rbest.log 2>&1 & # real 0m47.202s # and for the swap: mkdir /hive/data/genomes/oncVol1/bed/blastz.ce11.swap cd /hive/data/genomes/oncVol1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzOncVol1.2015-08-10/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m48.137s cat fb.oncVol1.chainCe11Link.txt # 4803154 bases of 94327777 (5.092%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 ce11) \ > rbest.log 2>&1 # real 0m46.013s ######################################################################### # LASTZ Loa loa/loaLoa1/eye worm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzLoaLoa1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzLoaLoa1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs loaLoa1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Loa loa/eye worm loaLoa1 SEQ2_DIR=/hive/data/genomes/loaLoa1/loaLoa1.2bit SEQ2_LEN=/hive/data/genomes/loaLoa1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzLoaLoa1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 36m9.828s cat fb.ce11.chainLoaLoa1Link.txt # 5070900 bases of 100286401 (5.056%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 loaLoa1) > rbest.log 2>&1 & # real 0m53.872s # and for the swap: mkdir /hive/data/genomes/loaLoa1/bed/blastz.ce11.swap cd /hive/data/genomes/loaLoa1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzLoaLoa1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m59.293s cat fb.loaLoa1.chainCe11Link.txt # 4616591 bases of 87533141 (5.274%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 ce11) \ > rbest.log 2>&1 # real 0m39.512s ######################################################################### # LASTZ Ancylostoma ceylanicum/ancCey1/hookworm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzAncCey1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzAncCey1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs ancCey1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Ancylostoma ceylanicum/hookworm ancCey1 SEQ2_DIR=/hive/data/genomes/ancCey1/ancCey1.2bit SEQ2_LEN=/hive/data/genomes/ancCey1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzAncCey1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 30m30.162s cat fb.ce11.chainAncCey1Link.txt # 9764266 bases of 100286401 (9.736%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 ancCey1) > rbest.log 2>&1 & # real 0m45.818s # and for the swap: mkdir /hive/data/genomes/ancCey1/bed/blastz.ce11.swap cd /hive/data/genomes/ancCey1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzAncCey1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m22.649s cat fb.ancCey1.chainCe11Link.txt # 9740545 bases of 300914990 (3.237%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 ce11) \ > rbest.log 2>&1 # real 0m56.069s ######################################################################### # LASTZ Trichuris suis/triSui1/whipworm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzTriSui1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzTriSui1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs triSui1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Trichuris suis/whipworm triSui1 SEQ2_DIR=/hive/data/genomes/triSui1/triSui1.2bit SEQ2_LEN=/hive/data/genomes/triSui1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzTriSui1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 17m56.424s cat fb.ce11.chainTriSui1Link.txt # 2925422 bases of 100286401 (2.917%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 triSui1) > rbest.log 2>&1 & # real 0m23.479s # and for the swap: mkdir /hive/data/genomes/triSui1/bed/blastz.ce11.swap cd /hive/data/genomes/triSui1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzTriSui1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m46.282s cat fb.triSui1.chainCe11Link.txt # 2667549 bases of 71825323 (3.714%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 ce11) \ > rbest.log 2>&1 # real 0m24.047s ######################################################################### # LASTZ Trichinella spiralis/triSpi1 - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzTriSpi1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzTriSpi1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs triSpi1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Trichinella spiralis triSpi1 SEQ2_DIR=/hive/data/genomes/triSpi1/triSpi1.2bit SEQ2_LEN=/hive/data/genomes/triSpi1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzTriSpi1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 36m27.819s cat fb.ce11.chainTriSpi1Link.txt # 2856166 bases of 100286401 (2.848%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 triSpi1) > rbest.log 2>&1 & # real 0m28.110s # and for the swap: mkdir /hive/data/genomes/triSpi1/bed/blastz.ce11.swap cd /hive/data/genomes/triSpi1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzTriSpi1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m45.506s cat fb.triSpi1.chainCe11Link.txt # 2739585 bases of 58558192 (4.678%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 ce11) \ > rbest.log 2>&1 # real 0m25.677s ######################################################################### # LASTZ Pristionchus exspectatus/priExs1 - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzPriExs1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzPriExs1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs priExs1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Pristionchus exspectatus priExs1 SEQ2_DIR=/hive/data/genomes/priExs1/priExs1.2bit SEQ2_LEN=/hive/data/genomes/priExs1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzPriExs1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 41m4.486s cat fb.ce11.chainPriExs1Link.txt # 6239735 bases of 100286401 (6.222%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 priExs1) > rbest.log 2>&1 & # real 0m37.199s # and for the swap: mkdir /hive/data/genomes/priExs1/bed/blastz.ce11.swap cd /hive/data/genomes/priExs1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzPriExs1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m6.611s cat fb.priExs1.chainCe11Link.txt # 7213135 bases of 166917800 (4.321%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 ce11) \ > rbest.log 2>&1 # real 0m49.363s ######################################################################### # LASTZ Dirofilaria immitis/dirImm1/dog heartworm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzDirImm1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzDirImm1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs dirImm1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Dirofilaria immitis/dog heartworm dirImm1 SEQ2_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit SEQ2_LEN=/hive/data/genomes/dirImm1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzDirImm1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 50m17.230s cat fb.ce11.chainDirImm1Link.txt # 5019106 bases of 100286401 (5.005%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 dirImm1) > rbest.log 2>&1 & # real 0m30.527s # and for the swap: mkdir /hive/data/genomes/dirImm1/bed/blastz.ce11.swap cd /hive/data/genomes/dirImm1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzDirImm1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m4.937s cat fb.dirImm1.chainCe11Link.txt # 4648391 bases of 84923352 (5.474%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 ce11) \ > rbest.log 2>&1 # real 0m40.636s ######################################################################### # LASTZ Ascaris suum/ascSuu1/pig roundworm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzAscSuu1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzAscSuu1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs ascSuu1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Ascaris suum/pig roundworm ascSuu1 SEQ2_DIR=/hive/data/genomes/ascSuu1/ascSuu1.2bit SEQ2_LEN=/hive/data/genomes/ascSuu1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzAscSuu1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 47m30.635s cat fb.ce11.chainAscSuu1Link.txt # 5737990 bases of 100286401 (5.722%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 ascSuu1) > rbest.log 2>&1 & # real 0m35.701s # and for the swap: mkdir /hive/data/genomes/ascSuu1/bed/blastz.ce11.swap cd /hive/data/genomes/ascSuu1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzAscSuu1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m5.353s cat fb.ascSuu1.chainCe11Link.txt # 5839616 bases of 262604320 (2.224%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 ce11) \ > rbest.log 2>&1 # real 0m47.468s ######################################################################### # LASTZ Heterorhabditis bacteriophora/hetBac1/ - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzHetBac1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzHetBac1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs hetBac1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Heterorhabditis bacteriophora hetBac1 SEQ2_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ2_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzHetBac1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 16m29.397s cat fb.ce11.chainHetBac1Link.txt # 10516501 bases of 100286401 (10.486%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 hetBac1) > rbest.log 2>&1 & # real 0m41.981s # and for the swap: mkdir /hive/data/genomes/hetBac1/bed/blastz.ce11.swap cd /hive/data/genomes/hetBac1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzHetBac1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m5.754s cat fb.hetBac1.chainCe11Link.txt # 10082123 bases of 74374900 (13.556%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hetBac1 ce11) \ > rbest.log 2>&1 # real 0m47.745s ######################################################################### # LASTZ Necator americanus/necAme1/hookworm - (DONE - 2015-07-23 - Hiram) mkdir /hive/data/genomes/ce11/bed/lastzNecAme1.2015-07-23 cd /hive/data/genomes/ce11/bed/lastzNecAme1.2015-07-23 cat << '_EOF_' > DEF # ce11 vs necAme1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET: elegans ce11 SEQ1_DIR=/hive/data/genomes/ce11/ce11.2bit SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_CHUNK=1000000 SEQ1_LAP=10000 # QUERY: Necator americanus necAme1/hookworm SEQ2_DIR=/hive/data/genomes/necAme1/necAme1.2bit SEQ2_LEN=/hive/data/genomes/necAme1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=50 SEQ2_LAP=0 BASE=/hive/data/genomes/ce11/bed/lastzNecAme1.2015-07-23 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -smallClusterHub=ku -syntenicNet) > do.log 2>&1 # real 37m25.778s cat fb.ce11.chainNecAme1Link.txt # 8927298 bases of 100286401 (8.902%) in intersection time (doRecipBest.pl -buildDir=`pwd` ce11 necAme1) > rbest.log 2>&1 & # real 0m40.993s # and for the swap: mkdir /hive/data/genomes/necAme1/bed/blastz.ce11.swap cd /hive/data/genomes/necAme1/bed/blastz.ce11.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/ce11/bed/lastzNecAme1.2015-07-23/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m16.620s cat fb.necAme1.chainCe11Link.txt # 8566890 bases of 208187215 (4.115%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 ce11) \ > rbest.log 2>&1 # real 0m58.661s ######################################################################### # LASTZ self ce11 vs. ce11 - (DONE - 2015-09-14 - Hiram) # need nib files to run this with lineage specific repeats mkdir -p /hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/nibs cd /hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/nibs cut -f1 ../../../chrom.sizes | while read C do twoBitToFa -seq=${C} ../../../ce11.2bit stdout \ | faToNib -softMask stdin ${C}.nib echo ${C} 1>&2 done # verify all sequence is here faSize *.fa # 100286401 bases (0 N's 100286401 real 87628173 upper 12658228 lower) in 7 sequences in 7 files head -1 ../../../faSize.ce11.2bit.txt # 100286401 bases (0 N's 100286401 real 87628173 upper 12658228 lower) in 7 sequences in 1 files # construct 'lineage specific repeats' which for this self business # happens to be all the repeats found in ce11. They will be excluded # during the alignment. mkdir /hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/lineageSpecificRepeats cd /hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/lineageSpecificRepeats cut -f1 ../../../chrom.sizes | while read C do head -3 ../../repeatMasker/ce11.sorted.fa.out > ${C}.out.spec perl -ne '/ '${C}' / && print' ../../repeatMasker/ce11.sorted.fa.out \ >> ${C}.out.spec echo ${C} 1>&2 done # verify we have everything here correctly: sort -u ../../repeatMasker/ce11.sorted.fa.out | sum # 01618 10225 sort -u *.out.spec | sum # 01618 10225 cd /hive/data/genomes/ce11/bed/lastzSelf.2015-09-14 cat << '_EOF_' > DEF # ce11 vs ce11 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=254 BLASTZ_ABRIDGE_REPEATS=1 # TARGET: elegans ce11 - 20,000,000 chunk will accomodate entire single chroms SEQ1_DIR=/hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/nibs SEQ1_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ1_SMSK=/hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/lineageSpecificRepeats SEQ1_CHUNK=2000000 SEQ1_LAP=10000 # QUERY: elegans ce11 SEQ2_DIR=/hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/nibs SEQ2_LEN=/hive/data/genomes/ce11/chrom.sizes SEQ2_SMSK=/hive/data/genomes/ce11/bed/lastzSelf.2015-09-14/lineageSpecificRepeats SEQ2_CHUNK=2000000 SEQ2_LAP=10000 BASE=/hive/data/genomes/ce11/bed/lastzSelf.2015-09-14 TMPDIR=/dev/shm '_EOF_' # << happy emacs time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku -smallClusterHub=ku \ -chainMinScore=10000 -chainLinearGap=medium) > do.out 2>&1 # real 170m43.852s featureBits ce11 chainSelfLink > fb.ce11.chainSelfLink.txt 2>&1 # 25553508 bases of 100286401 (25.481%) in intersection #########################################################################